From cc7a8d17efb9ed33ff1453d6ae6779c6debf0bb5 Mon Sep 17 00:00:00 2001 From: brj1 Date: Fri, 23 Mar 2018 11:06:47 -0700 Subject: [PATCH 01/34] added Compartments; reworked xml structure a bit --- src/santa/simulator/Random.java | 4 + src/santa/simulator/Simulation.java | 210 ++- src/santa/simulator/SimulationEpoch.java | 116 +- src/santa/simulator/SimulatorParser.java | 1144 ++++++++++------- .../simulator/compartments/Compartment.java | 173 +++ .../compartments/CompartmentEpoch.java | 110 ++ .../simulator/compartments/Compartments.java | 109 ++ src/santa/simulator/genomes/BaseGenePool.java | 14 +- src/santa/simulator/genomes/BaseGenome.java | 25 +- .../simulator/genomes/CompactGenome.java | 9 + src/santa/simulator/genomes/Genome.java | 2 + src/santa/simulator/genomes/SimpleGenome.java | 9 + 12 files changed, 1220 insertions(+), 705 deletions(-) create mode 100644 src/santa/simulator/compartments/Compartment.java create mode 100644 src/santa/simulator/compartments/CompartmentEpoch.java create mode 100644 src/santa/simulator/compartments/Compartments.java diff --git a/src/santa/simulator/Random.java b/src/santa/simulator/Random.java index a9d1270..17666af 100644 --- a/src/santa/simulator/Random.java +++ b/src/santa/simulator/Random.java @@ -38,6 +38,10 @@ public static int[] nextPermutation(int i, int i1) { public static long nextPoisson(double v) { return randomData.nextPoisson(v); } + + public static int nextBinomial(int n, double p) { + return randomData.nextBinomial(n, p); + } public static Object[] nextSample(Collection collection, int i) { return randomData.nextSample(collection, i); diff --git a/src/santa/simulator/Simulation.java b/src/santa/simulator/Simulation.java index df90c6e..9a50a19 100644 --- a/src/santa/simulator/Simulation.java +++ b/src/santa/simulator/Simulation.java @@ -1,22 +1,11 @@ package santa.simulator; +import santa.simulator.compartments.CompartmentEpoch; import java.util.ArrayList; import java.util.List; import java.util.logging.Logger; - -import santa.simulator.genomes.GenePool; -import santa.simulator.genomes.GenomeDescription; -import santa.simulator.genomes.Sequence; -import santa.simulator.phylogeny.Phylogeny; -import santa.simulator.population.DynamicPopulation; -import santa.simulator.population.Population; -import santa.simulator.population.StaticPopulation; -import santa.simulator.samplers.SamplingSchedule; -import santa.simulator.selectors.DynamicSelector; -import santa.simulator.selectors.Selector; -import santa.simulator.selectors.SimpleRouletteWheelSelector; -import santa.simulator.selectors.BinarySearchSelector; - +import santa.simulator.compartments.Compartment; +import santa.simulator.compartments.Compartments; /** * @author Andrew Rambaut * @author Alexei Drummond @@ -24,104 +13,74 @@ */ public class Simulation { - private final int populationSize; - private final InoculumType inoculumType; - private final GenePool genePool; - private final List epochs; - private final Selector selector; - private final SamplingSchedule samplingSchedule; - - private final Population population; - - public enum InoculumType { - NONE, - CONSENSUS, - RANDOM, - ALL - }; - - //Default constructor (dynamic) - public Simulation ( - int populationSize, - InoculumType inoculumType, - GenePool genePool, - List epochs, - SamplingSchedule samplingSchedule) { - - this.populationSize = populationSize; - this.inoculumType = inoculumType; - this.epochs = epochs; - this.samplingSchedule = samplingSchedule; - this.genePool = genePool; - this.selector = new DynamicSelector(); - - population = new DynamicPopulation(genePool, selector, samplingSchedule.isSamplingTrees() ? new Phylogeny(populationSize) : null); - } - - //Default constructor (dynamic) - public Simulation ( - int populationSize, - DynamicSelector dynamicSelector, - InoculumType inoculumType, - GenePool genePool, - List epochs, - SamplingSchedule samplingSchedule) { - - this.populationSize = populationSize; - this.inoculumType = inoculumType; - this.epochs = epochs; - this.samplingSchedule = samplingSchedule; - this.genePool = genePool; - this.selector = dynamicSelector; - - population = new DynamicPopulation(genePool, selector, samplingSchedule.isSamplingTrees() ? new Phylogeny(populationSize) : null); + private List epochs; + private Compartments compartments; + private static Logger memlogger = Simulator.memlogger; + + public Simulation(Compartments compartments) { + this.compartments = compartments; + + //fix Epochs + this.epochs = new ArrayList<>(); + int compartmentEpochIndex = 0; + boolean cont = true; + + while (cont) { + int minGenerations = Integer.MAX_VALUE; + String epochName = ""; + + for (Compartment compartment: compartments) { + CompartmentEpoch currentCompartmentEpoch = compartment.getEpochs().get(compartmentEpochIndex); + epochName += currentCompartmentEpoch.getName(); + + if (minGenerations > currentCompartmentEpoch.getGenerationCount()) { + minGenerations = currentCompartmentEpoch.getGenerationCount(); + } + } + + for (Compartment compartment: compartments) { + List compartmentEpochs = compartment.getEpochs(); + CompartmentEpoch currentCompartmentEpoch = compartmentEpochs.get(compartmentEpochIndex); + + if (minGenerations < currentCompartmentEpoch.getGenerationCount()) { + compartmentEpochs.add(compartmentEpochIndex + 1, new CompartmentEpoch( + currentCompartmentEpoch.getName(), + currentCompartmentEpoch.getGenerationCount() - minGenerations, + currentCompartmentEpoch.getFitnessFunction(), + currentCompartmentEpoch.getMutator(), + currentCompartmentEpoch.getReplicator())); + } + + compartmentEpochs.set(compartmentEpochIndex, new CompartmentEpoch( + epochName, + minGenerations, + currentCompartmentEpoch.getFitnessFunction(), + currentCompartmentEpoch.getMutator(), + currentCompartmentEpoch.getReplicator())); + + if (compartmentEpochs.size() <= compartmentEpochIndex + 1) + cont = false; + } + + this.epochs.add(new SimulationEpoch(epochName, minGenerations)); + + /* + * TODO: + * Add check for duplicate epoch names + * Add check / deal with different overall epoch length + */ + + compartmentEpochIndex++; + } } - - //Constructor for static population - public Simulation ( - int populationSize, - InoculumType inoculumType, - GenePool genePool, - List epochs, - SamplingSchedule samplingSchedule, - String populationType){ - - this.populationSize = populationSize; - this.inoculumType = inoculumType; - this.epochs = epochs; - this.samplingSchedule = samplingSchedule; - this.genePool = genePool; - this.selector = new BinarySearchSelector(); -// this.selector = new SimpleRouletteWheelSelector(); - population = new StaticPopulation(populationSize, genePool, selector, samplingSchedule.isSamplingTrees() ? new Phylogeny(populationSize) : null); + - } public void run(int replicate, Logger logger) { - - samplingSchedule.initialize(replicate); - - EventLogger.setReplicate(replicate); - - logger.finer("Initializing population: " + populationSize + " viruses."); - - List inoculum = new ArrayList(); - if (inoculumType == InoculumType.CONSENSUS) { - inoculum.add(GenomeDescription.getConsensus()); - } else if (inoculumType == InoculumType.ALL) { - inoculum.addAll(GenomeDescription.getSequences()); - } else if (inoculumType == InoculumType.RANDOM) { - List sequences = GenomeDescription.getSequences(); - if (sequences.size() == 1) { - inoculum.add(sequences.get(0)); - } else { - inoculum.add(sequences.get(Random.nextInt(0, sequences.size() - 1))); - } - } else { // NONE - // do nothing - } - population.initialize(inoculum, populationSize); - + for (Compartment compartment: compartments) { + compartment.initalize(replicate, logger); + } + int generation = 1; int epochCount = 0; @@ -130,28 +89,29 @@ public void run(int replicate, Logger logger) { EventLogger.setEpoch(epochCount); generation = epoch.run(this, logger, generation); - if(population.getCurrentGeneration().size() == 0) { + + boolean allDead = true; + + for (Compartment compartment: compartments) { + if (!compartment.getPopulation().getCurrentGeneration().isEmpty()) { + allDead = false; + break; + } + } + + if (allDead) { System.err.println("Population crashed after "+generation+" generations."); return; } epochCount++; } - samplingSchedule.cleanUp(); - } - - public GenePool getGenePool() { - return genePool; - } - - public Population getPopulation() { - return population; - } - - public int getPopulationSize() { - return populationSize; + + for (Compartment compartment: compartments) { + compartment.cleanup(replicate, logger); + } } - - public SamplingSchedule getSamplingSchedule() { - return samplingSchedule; + + public Compartments getCompartments() { + return compartments; } } diff --git a/src/santa/simulator/SimulationEpoch.java b/src/santa/simulator/SimulationEpoch.java index 6c2699d..2f27e99 100644 --- a/src/santa/simulator/SimulationEpoch.java +++ b/src/santa/simulator/SimulationEpoch.java @@ -1,116 +1,66 @@ -/* - * Created on Mar 12, 2007 - * - * To change the template for this generated file go to - * Window>Preferences>Java>Code Generation>Code and Comments - */ package santa.simulator; -import santa.simulator.fitness.FitnessFunction; -import santa.simulator.genomes.GenePool; -import santa.simulator.mutators.Mutator; -import santa.simulator.population.Population; -import santa.simulator.replicators.Replicator; -import santa.simulator.samplers.SamplingSchedule; - +import java.util.ArrayList; import java.util.logging.Logger; - import static santa.simulator.Simulator.readableByteCount; import static santa.simulator.Simulator.usedMemory; +import santa.simulator.compartments.Compartment; +import santa.simulator.compartments.CompartmentEpoch; +import santa.simulator.compartments.Compartments; +/** + * + * @author Bradley R. Jones + */ public class SimulationEpoch { private String name; private int generationCount; - private FitnessFunction fitnessFunction; - private Mutator mutator; - private Replicator replicator; - private static Logger memlogger = Simulator.memlogger; - - public SimulationEpoch(String name, int generationCount, - FitnessFunction fitnessFunction, Mutator mutator, - Replicator replicator) { + private static Logger memlogger = Simulator.memlogger; + + public SimulationEpoch(String name, int generationCount) { this.name = name; this.generationCount = generationCount; - this.fitnessFunction = fitnessFunction; - this.mutator = mutator; - this.replicator = replicator; } - + public int run(Simulation simulation, Logger logger, int startGeneration) { System.err.println("Starting epoch: " + (name != null ? name : "(unnamed)")); - Population population = simulation.getPopulation(); - GenePool genePool = simulation.getGenePool(); - SamplingSchedule samplingSchedule = simulation.getSamplingSchedule(); + Compartments compartments = simulation.getCompartments(); + ArrayList compartmentEpochs = new ArrayList<>(); + + for (Compartment compartment: compartments) { + compartmentEpochs.add(compartment.getCurrentEpoch(name)); + } final int endGeneration = startGeneration + generationCount; - memlogger.fine("@start of Epoch Memory used = " + readableByteCount(usedMemory())); + memlogger.fine("@start of Epoch Memory used = " + readableByteCount(usedMemory())); for (int generation = startGeneration; generation < endGeneration; ++generation) { EventLogger.setEpoch(generation); - - fitnessFunction.updateGeneration(generation, population); - - if (generation == startGeneration) { - // adapt to this epoch, and the new generation - population.updateAllFitnesses(fitnessFunction); - - System.err.println("Initial population: fitness = " + population.getMeanFitness() + - ", distance = " + population.getMeanDistance() + - ", max freq = " + population.getMaxFrequency() + - ", genepool size = " + genePool.getUniqueGenomeCount() + - " (" + genePool.getUnusedGenomeCount() + " available)"); + + int i = 0; + int totalPopulation = 0; + for (Compartment compartment: compartments) { + totalPopulation += compartmentEpochs.get(i++).step(compartment, logger, startGeneration, generation); } - - population.selectNextGeneration(generation, replicator, mutator, fitnessFunction); - if(population.getCurrentGeneration().size() == 0) { + + if (totalPopulation == 0) { return generation; } + if (compartments.getNumCompartments() > 1) + compartments.genomeTransfer(generation); + if (generation % 100 == 0) { - if (population.getPhylogeny() != null) - population.getPhylogeny().pruneDeadLineages(); - - memlogger.finest("Generation "+ generation + - " used memory: " + readableByteCount(usedMemory())); - - System.err.print("Generation " + generation + ": fitness = " + population.getMeanFitness() + - ", distance = " + population.getMeanDistance() + - ", max freq = " + population.getMaxFrequency() + - ", genepool size = " + genePool.getUniqueGenomeCount() + - " (" + genePool.getUnusedGenomeCount() + " available)"); - if (population.getPhylogeny() != null) { - population.getPhylogeny().pruneDeadLineages(); - System.err.println(", phylogeny size = " + population.getPhylogeny().getSize() + - " (used = " + population.getPhylogeny().getLineageCount()+ ")" + - ", tmrca = " + population.getPhylogeny().getMRCA().getGeneration() ); - } else - System.err.println(); - } else { - logger.finest("Generation " + generation + ": fitness = " + population.getMeanFitness() + - ", distance = " + population.getMeanDistance() + - ", max freq = " + population.getMaxFrequency() + - ", genepool size= " + genePool.getUniqueGenomeCount() + - "(" + genePool.getUnusedGenomeCount() + " available)"); + memlogger.finest("Generation "+ generation + " used memory: " + readableByteCount(usedMemory())); } - - samplingSchedule.doSampling(generation, population); } return endGeneration; } - - public FitnessFunction getFitnessFunction() { - return fitnessFunction; - } - - public Mutator getMutator() { - return mutator; + + public String getName() { + return name; } - - public Replicator getReplicator() { - return replicator; - } - } diff --git a/src/santa/simulator/SimulatorParser.java b/src/santa/simulator/SimulatorParser.java index dc6a00f..56115b6 100644 --- a/src/santa/simulator/SimulatorParser.java +++ b/src/santa/simulator/SimulatorParser.java @@ -1,6 +1,7 @@ package santa.simulator; +import santa.simulator.compartments.CompartmentEpoch; import java.io.FileWriter; import java.io.IOException; import java.io.PrintWriter; @@ -17,6 +18,8 @@ import static java.nio.file.Paths.get; import org.jdom2.Element; +import santa.simulator.compartments.Compartment; +import santa.simulator.compartments.Compartments; import santa.simulator.fitness.AgeDependentFitnessFactor; import santa.simulator.fitness.BetaDistributedPurifyingFitnessModel; @@ -53,7 +56,6 @@ import santa.simulator.samplers.StatisticsSampler; import santa.simulator.samplers.TreeSampler; import santa.simulator.samplers.GenomeDescriptionSampler; -import santa.simulator.IndelModel; import santa.simulator.selectors.DynamicSelector; /** @@ -68,7 +70,10 @@ public class SimulatorParser { private final static String REPLICATE_COUNT = "replicates"; private final static String SIMULATION = "simulation"; - + + private final static String COMPARTMENT = "compartment"; + private final static String TRANSFER_RATES = "transferRates"; + private final static String EPOCH = "epoch"; private final static String NAME = "name"; private final static String GENERATION_COUNT = "generationCount"; @@ -193,7 +198,7 @@ public class SimulatorParser { /* * Object Cache methods */ - private Map objectIdMap = new HashMap(); + private Map objectIdMap = new HashMap<>(); private Object lookupObjectById(String id, Class expectedType) throws ParseException { @@ -290,12 +295,61 @@ Simulator parse(Element element) throws ParseException { return simulator; } - //Default populationType is dynamicPopulation but in the xml file static population could be selected - Simulation parseSimulation(Element element) throws ParseException { - - Simulation.InoculumType inoculumType = Simulation.InoculumType.NONE; - - int populationSize = -1; + Simulation parseSimulation(Element element) throws ParseException { + Compartments compartments = null; + ArrayList compartmentList = new ArrayList<>(); + + Element e = element.getChildren().get(0); + switch (e.getName()) { + case COMPARTMENT: + case TRANSFER_RATES: + break; + default: + double[] transferRates = {1}; + + compartmentList.add(parseCompartment(element)); + compartments = new Compartments(compartmentList, transferRates); + + break; + } + + if (compartments == null) { + double[] transferRates = null; + + for (Object o: element.getChildren()) { + e = (Element)element.getChildren().get(0); + switch (e.getName()) { + case COMPARTMENT: + compartmentList.add(parseCompartment(e)); + case TRANSFER_RATES: + transferRates = parseNumberList(e); + default: + throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + e.getName() + "> is unrecognized"); + } + } + + if (transferRates == null) { + throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + TRANSFER_RATES + "> is missing"); + } + + if (compartmentList.isEmpty()) { + throw new ParseException("Error parsing <" + SIMULATION + "> no <" + COMPARTMENT + "> found"); + } + + if (transferRates.length != compartmentList.size() * compartmentList.size()) { + throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + TRANSFER_RATES + "> should be size (" + compartmentList.size() * compartmentList.size() + "), but was (" + transferRates.length + ") instead"); + } + + compartments = new Compartments(compartmentList, transferRates); + } + + return new Simulation(compartments); + } + + //Default populationType is dynamicPopulation but in the xml file static population could be selected + Compartment parseCompartment(Element element) throws ParseException { + Compartment.InoculumType inoculumType = Compartment.InoculumType.NONE; + int populationSize = -1; boolean genomeDescription = false; for (Object o : element.getChildren()) { @@ -307,7 +361,7 @@ Simulation parseSimulation(Element element) throws ParseException { } if (!genomeDescription) { - throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + GENOME_DESCRIPTION + "> is missing"); + throw new ParseException("Error parsing <" + element.getName() + "> element: <" + GENOME_DESCRIPTION + "> is missing"); } for (Object o : element.getChildren()) { @@ -316,28 +370,37 @@ Simulation parseSimulation(Element element) throws ParseException { for (Object o1 : e.getChildren()) { Element e1 = (Element)o1; - if (e1.getName().equals(POPULATION_SIZE)) { - try { - populationSize = parseInteger(e1, 1, Integer.MAX_VALUE); - } catch (ParseException pe) { - throw new ParseException("Error parsing <" + POPULATION + "> element: " + pe.getMessage()); - } - } else if (e1.getName().equals(INOCULUM)) { - String v = e1.getTextNormalize(); - if (v.equals(INOCULUM_NONE)) { - inoculumType = Simulation.InoculumType.NONE; - } else if (v.equals(INOCULUM_CONSENSUS)) { - inoculumType = Simulation.InoculumType.CONSENSUS; - } else if (v.equals(INOCULUM_RANDOM)) { - inoculumType = Simulation.InoculumType.RANDOM; - } else if (v.equals(INOCULUM_ALL)) { - inoculumType = Simulation.InoculumType.ALL; - } else { - // do nothing - } - } else { - throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + e.getName() + "> is unrecognized"); - } + switch (e1.getName()) { + case POPULATION_SIZE: + try { + populationSize = parseInteger(e1, 1, Integer.MAX_VALUE); + } catch (ParseException pe) { + throw new ParseException("Error parsing <" + POPULATION + "> element: " + pe.getMessage()); + } + break; + case INOCULUM: + String v = e1.getTextNormalize(); + switch (v) { + case INOCULUM_NONE: + inoculumType = Compartment.InoculumType.NONE; + break; + case INOCULUM_CONSENSUS: + inoculumType = Compartment.InoculumType.CONSENSUS; + break; + case INOCULUM_RANDOM: + inoculumType = Compartment.InoculumType.RANDOM; + break; + case INOCULUM_ALL: + inoculumType = Compartment.InoculumType.ALL; + break; + // do nothing + default: + break; + } + break; + default: + throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e.getName() + "> is unrecognized"); + } } } else if (!e.getName().equals(GENOME_DESCRIPTION) && !e.getName().equals(GENE_POOL) && @@ -350,19 +413,20 @@ Simulation parseSimulation(Element element) throws ParseException { !e.getName().equals(POPULATION_TYPE) && !e.getName().equals(GROWTH_MODEL) && !e.getName().equals(RECOMBINATION_HOTSPOTS)) { - throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + e.getName() + "> is unrecognized"); + throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e.getName() + "> is unrecognized"); } } if (populationSize == -1) { - throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + POPULATION_SIZE + "> is missing"); + throw new ParseException("Error parsing <" + element.getName() + "> element: <" + POPULATION_SIZE + "> is missing"); } if (!GenomeDescription.isSet()) { - throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + GENOME_DESCRIPTION + "> is missing"); + throw new ParseException("Error parsing <" + element.getName() + "> element: <" + GENOME_DESCRIPTION + "> is missing"); } + String compartmentName = ""; SamplingSchedule samplingSchedule = null; GenePool genePool = null; @@ -373,59 +437,74 @@ Simulation parseSimulation(Element element) throws ParseException { String populationType = null; DynamicSelector dynamicSelector = null; - List recombinationHotSpots = new ArrayList(); + List recombinationHotSpots = new ArrayList<>(); for (Object o : element.getChildren()) { Element e = (Element)o; String name = e.getName(); - if (name.equals(GENE_POOL)) { - genePool = parseGenePool(e); - } else if (name.equals(SAMPLING_SCHEDULE)) { - samplingSchedule = parseSamplingSchedule(e); - } else if (name.equals(EVENT_LOGGER)) { - parseEventLogger(e); - } else if (name.equals(FITNESS_FUNCTION)) { - defaultFitnessFunction = parseFitnessFunction(e); - } else if (name.equals(MUTATOR)) { - defaultMutator = parseMutator(e); - } else if (name.equals(RECOMBINATION_HOTSPOTS)){ - recombinationHotSpots = parseRecombinationHotSpots(e); - GenomeDescription.setHotSpots(recombinationHotSpots); - } else if (name.equals(POPULATION_TYPE)){ - populationType = (String) e.getTextNormalize(); - } else if (name.equals(REPLICATOR)) { - defaultReplicator = parseReplicator(e); - } else if (name.equals(GROWTH_MODEL)) { - dynamicSelector = parseGrowthModel(e); - } + switch (name) { + case NAME: + compartmentName = (String)e.getTextNormalize(); + break; + case GENE_POOL: + genePool = parseGenePool(e); + break; + case SAMPLING_SCHEDULE: + samplingSchedule = parseSamplingSchedule(e); + break; + case EVENT_LOGGER: + parseEventLogger(e); + break; + case FITNESS_FUNCTION: + defaultFitnessFunction = parseFitnessFunction(e); + break; + case MUTATOR: + defaultMutator = parseMutator(e); + break; + case RECOMBINATION_HOTSPOTS: + recombinationHotSpots = parseRecombinationHotSpots(e); + GenomeDescription.setHotSpots(recombinationHotSpots); + break; + case POPULATION_TYPE: + populationType = (String)e.getTextNormalize(); + break; + case REPLICATOR: + defaultReplicator = parseReplicator(e); + break; + case GROWTH_MODEL: + dynamicSelector = parseGrowthModel(e); + break; + default: + break; + } } if (samplingSchedule == null) - throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + SAMPLING_SCHEDULE + "> is missing"); + throw new ParseException("Error parsing <" + element.getName() + "> element: <" + SAMPLING_SCHEDULE + "> is missing"); if (genePool == null) { genePool = new SimpleGenePool(); } if (defaultFitnessFunction == null) - throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + FITNESS_FUNCTION + "> is missing"); + throw new ParseException("Error parsing <" + element.getName() + "> element: <" + FITNESS_FUNCTION + "> is missing"); if (defaultMutator == null) - throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + MUTATOR + "> is missing"); + throw new ParseException("Error parsing <" + element.getName() + "> element: <" + MUTATOR + "> is missing"); if (defaultReplicator == null) - throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + REPLICATOR + "> is missing"); + throw new ParseException("Error parsing <" + element.getName() + "> element: <" + REPLICATOR + "> is missing"); if (populationType == null) { populationType = STATIC_POPULATION; } - List epochs = new ArrayList(); + List epochs = new ArrayList<>(); for (Object o : element.getChildren()) { Element e = (Element)o; if (e.getName().equals(EPOCH)) { - SimulationEpoch epoch = parseSimulationEpoch(e, + CompartmentEpoch epoch = parseSimulationEpoch(e, defaultFitnessFunction, defaultMutator, defaultReplicator); epochs.add(epoch); @@ -433,18 +512,20 @@ Simulation parseSimulation(Element element) throws ParseException { } if (epochs.isEmpty()) - throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + EPOCH + "> is missing"); + throw new ParseException("Error parsing <" + element.getName() + "> element: <" + EPOCH + "> is missing"); - if (populationType.equals(STATIC_POPULATION)) - return new Simulation(populationSize, inoculumType, genePool, epochs, samplingSchedule, populationType); - else if (populationType.equals(DYNAMIC_POPULATION)) { - if (dynamicSelector == null) { - return new Simulation(populationSize, inoculumType, genePool, epochs, samplingSchedule); - } else { - return new Simulation(populationSize, dynamicSelector, inoculumType, genePool, epochs, samplingSchedule); + switch (populationType) { + case STATIC_POPULATION: + return new Compartment(compartmentName, populationSize, inoculumType, genePool, epochs, samplingSchedule, populationType); + case DYNAMIC_POPULATION: + if (dynamicSelector == null) { + return new Compartment(compartmentName, populationSize, inoculumType, genePool, epochs, samplingSchedule); + } else { + return new Compartment(compartmentName, populationSize, dynamicSelector, inoculumType, genePool, epochs, samplingSchedule); + } + default: + throw new ParseException("unrecognized population type. should be either staticPopulation or dynamicPopulation."); } - } - else throw new ParseException("unrecognized population type. should be either staticPopulation or dynamicPopulation."); } @@ -453,13 +534,16 @@ DynamicSelector parseGrowthModel(Element element) throws ParseException { double carryingPopulation = -1; for (Object o : element.getChildren()) { Element e = (Element)o; - if (e.getName().equals(GROWTH_RATE)) { - growthRate = Double.parseDouble(e.getTextNormalize()); - } else if (e.getName().equals(CARRYING_POPULATION)) { - carryingPopulation = Double.parseDouble(e.getTextNormalize()); - } else { - throw new ParseException("Error parsing <" + GROWTH_MODEL + "> element: unknown XML element within " + GROWTH_MODEL); - } + switch (e.getName()) { + case GROWTH_RATE: + growthRate = Double.parseDouble(e.getTextNormalize()); + break; + case CARRYING_POPULATION: + carryingPopulation = Double.parseDouble(e.getTextNormalize()); + break; + default: + throw new ParseException("Error parsing <" + GROWTH_MODEL + "> element: unknown XML element within " + GROWTH_MODEL); + } } if (growthRate != -1 && carryingPopulation != -1) { @@ -470,7 +554,7 @@ DynamicSelector parseGrowthModel(Element element) throws ParseException { } - SimulationEpoch parseSimulationEpoch(Element element, + CompartmentEpoch parseSimulationEpoch(Element element, FitnessFunction fitnessFunction, Mutator mutator, Replicator replicator) throws ParseException { @@ -500,50 +584,60 @@ SimulationEpoch parseSimulationEpoch(Element element, for (Object o : element.getChildren()) { Element e = (Element)o; - if (e.getName().equals(FITNESS_FUNCTION)) { - fitnessFunction = parseFitnessFunction(e); - } else if (e.getName().equals(MUTATOR)) { - mutator = parseMutator(e); - } else if (e.getName().equals(REPLICATOR)) { - replicator = parseReplicator(e); - } + switch (e.getName()) { + case FITNESS_FUNCTION: + fitnessFunction = parseFitnessFunction(e); + break; + case MUTATOR: + mutator = parseMutator(e); + break; + case REPLICATOR: + replicator = parseReplicator(e); + break; + default: + break; + } } - return new SimulationEpoch(name, generationCount, fitnessFunction, mutator, replicator); + return new CompartmentEpoch(name, generationCount, fitnessFunction, mutator, replicator); } private void parseGenomeDescription(Element element) throws ParseException { int genomeLength = -1; - List features = new ArrayList(); + List features = new ArrayList<>(); List sequences = null; for (Object o : element.getChildren()) { Element e = (Element)o; - if (e.getName().equals(GENOME_LENGTH)) { - try { - genomeLength = parseInteger(e, 1, Integer.MAX_VALUE); - } catch (ParseException pe) { - throw new ParseException("Error parsing <" + GENOME_DESCRIPTION + "> element: " + pe.getMessage()); - } - } else if (e.getName().equals(FEATURE)) { - features.add(parseFeature(e)); - } else if (e.getName().equals(SEQUENCES)) { - if (e.getAttributeValue(FILENAME) != null) { - try { - // quick and dirty one-liner to read in a text file. - // http://jdevelopment.nl/java-7-oneliner-read-file-string/ - String text = new String(readAllBytes(get(e.getAttributeValue(FILENAME)))); - sequences = parseAlignment(text); - } catch (IOException eio) { - throw new ParseException("Error parsing <" + SEQUENCES + "> file attribute: Cannot open file " + eio.getMessage()); - } - } else { - sequences = parseAlignment(e.getTextTrim()); - } - } else { - throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e.getName() + "> is unrecognized"); - } + switch (e.getName()) { + case GENOME_LENGTH: + try { + genomeLength = parseInteger(e, 1, Integer.MAX_VALUE); + } catch (ParseException pe) { + throw new ParseException("Error parsing <" + GENOME_DESCRIPTION + "> element: " + pe.getMessage()); + } + break; + case FEATURE: + features.add(parseFeature(e)); + break; + case SEQUENCES: + if (e.getAttributeValue(FILENAME) != null) { + try { + // quick and dirty one-liner to read in a text file. + // http://jdevelopment.nl/java-7-oneliner-read-file-string/ + String text = new String(readAllBytes(get(e.getAttributeValue(FILENAME)))); + sequences = parseAlignment(text); + } catch (IOException eio) { + throw new ParseException("Error parsing <" + SEQUENCES + "> file attribute: Cannot open file " + eio.getMessage()); + } + } else { + sequences = parseAlignment(e.getTextTrim()); + } + break; + default: + throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e.getName() + "> is unrecognized"); + } } if (genomeLength == -1) { @@ -558,30 +652,37 @@ private Feature parseFeature(Element element) throws ParseException { String name = null; Feature.Type type = Feature.Type.NUCLEOTIDE; String sites = null; - List parts = new ArrayList(); + List parts = new ArrayList<>(); for (Object o : element.getChildren()) { Element e = (Element) o; - if (e.getName().equals(NAME)) { - name = e.getTextNormalize(); - } else if (e.getName().equals(TYPE)) { - if (e.getTextNormalize().equals(AMINO_ACID)) { - type = Feature.Type.AMINO_ACID; - } else if (e.getTextNormalize().equals(NUCLEOTIDE)) { - type = Feature.Type.NUCLEOTIDE; - } else { - String msg = String.format("Error parsing <%s> element: <%s> should be '%s' or '%s'", - element.getName(), e.getName(),NUCLEOTIDE, AMINO_ACID); - throw new ParseException(msg); - } - } else if (e.getName().equals(COORDINATES)) { - sites = e.getTextNormalize(); - parts = Arrays.asList(sites.split(",")); - } else { - throw new ParseException("Error parsing <" + element.getName() - + "> element: <" + e.getName() + "> is unrecognized"); - } + switch (e.getName()) { + case NAME: + name = e.getTextNormalize(); + break; + case TYPE: + switch (e.getTextNormalize()) { + case AMINO_ACID: + type = Feature.Type.AMINO_ACID; + break; + case NUCLEOTIDE: + type = Feature.Type.NUCLEOTIDE; + break; + default: + String msg = String.format("Error parsing <%s> element: <%s> should be '%s' or '%s'", + element.getName(), e.getName(),NUCLEOTIDE, AMINO_ACID); + throw new ParseException(msg); + } + break; + case COORDINATES: + sites = e.getTextNormalize(); + parts = Arrays.asList(sites.split(",")); + break; + default: + throw new ParseException("Error parsing <" + element.getName() + + "> element: <" + e.getName() + "> is unrecognized"); + } } Feature feature = new Feature(name, type); @@ -634,7 +735,7 @@ private RecombinationHotSpot parseRecombinationHotSpot(Element element) throws P } private List parseRecombinationHotSpots(Element element) throws ParseException{ - List recombinationHotSpots = new ArrayList(); + List recombinationHotSpots = new ArrayList<>(); for (Object o : element.getChildren()) { Element e = (Element) o; RecombinationHotSpot segment = null; @@ -647,30 +748,38 @@ private List parseRecombinationHotSpots(Element element) t } private FitnessFunction parseFitnessFunction(Element element) throws ParseException { - List components = new ArrayList(); + List components = new ArrayList<>(); for (Object o : element.getChildren()) { Element e = (Element) o; FitnessFactor factor = null; - if (e.getName().equals(NEUTRAL_MODEL_FITNESS_FUNCTION)) { - // don't need to add a factor to the product - } else if (e.getName().equals(PURIFYING_FITNESS_FUNCTION)) { - factor = parsePurifyingFitnessFunction(e); - } else if (e.getName().equals(EMPIRICAL_FITNESS_FUNCTION)) { - factor = parseEmpiricalFitnessFunction(e); - } else if (e.getName().equals(FREQUENCY_DEPENDENT_FITNESS_FUNCTION)) { - factor = parseFrequencyDependentFitnessFunction(e); - } else if (e.getName().equals(AGE_DEPENDENT_FITNESS_FUNCTION)) { - factor = parseAgeDependentFitnessFunction(e); - } else if (e.getName().equals(EXPOSURE_DEPENDENT_FITNESS_FUNCTION)) { - factor = parseExposureDependentFitnessFunction(e); - } else if (e.getName().equals(POPULATION_SIZE_DEPENDENT_FITNESS_FUNCTION)) { - factor = parsePopulationSizeDependentFitnessFunction(e); - } else { - throw new ParseException("Error parsing <" + element.getName() - + "> element: <" + e.getName() + "> is unrecognized"); - } + switch (e.getName()) { + // don't need to add a factor to the product + case NEUTRAL_MODEL_FITNESS_FUNCTION: + break; + case PURIFYING_FITNESS_FUNCTION: + factor = parsePurifyingFitnessFunction(e); + break; + case EMPIRICAL_FITNESS_FUNCTION: + factor = parseEmpiricalFitnessFunction(e); + break; + case FREQUENCY_DEPENDENT_FITNESS_FUNCTION: + factor = parseFrequencyDependentFitnessFunction(e); + break; + case AGE_DEPENDENT_FITNESS_FUNCTION: + factor = parseAgeDependentFitnessFunction(e); + break; + case EXPOSURE_DEPENDENT_FITNESS_FUNCTION: + factor = parseExposureDependentFitnessFunction(e); + break; + case POPULATION_SIZE_DEPENDENT_FITNESS_FUNCTION: + factor = parsePopulationSizeDependentFitnessFunction(e); + break; + default: + throw new ParseException("Error parsing <" + element.getName() + + "> element: <" + e.getName() + "> is unrecognized"); + } if (factor != null) { components.add(factor); @@ -981,9 +1090,9 @@ private FeatureAndSites parseFeatureAndSites(Element element) throws ParseExcept } } - if (sites == null || sites.size() == 0) { + if (sites == null || sites.isEmpty()) { // assume the full length of the feature - sites = new TreeSet(); + sites = new TreeSet<>(); for (int i = 0; i < feature.getLength(); i++) { sites.add(i); } @@ -1005,54 +1114,55 @@ private PurifyingFitnessModel parsePurifyingFitnessModel(Element element, Featur for (Object o:element.getChildren()) { Element e = (Element) o; - if (e.getName().equals(BETA_DISTIBUTED)) { - - // Carrasco et al (2007) J Virology 81:12979-12984 - double a = 1.151; - double b = 1.709; - double pLethal = 0.4; - - int alphabetSize = alphabet.getStateCount(); - int sites = factor.sites.size(); - - Element aChild = e.getChild("a"); - a = Double.parseDouble(aChild.getText()); - Element bChild = e.getChild("b"); - b = Double.parseDouble(bChild.getText()); - Element pChild = e.getChild("pLethal"); - pLethal = Double.parseDouble(pChild.getText()); - - return new BetaDistributedPurifyingFitnessModel(a,b, pLethal, alphabetSize, sites); - } - else if (e.getName().equals(VALUES)) { - double[] fitnesses; - try { - fitnesses = parseNumberList(e); - - // confirm that we parsed one fitness value for each possible state. - if (fitnesses.length != alphabet.getStateCount()) { - throw new ParseException("expected " + alphabet.getStateCount() +" fitnesses, got " + fitnesses.length); - } - } catch (ParseException e1) { - throw new ParseException("Error parsing <" + e.getName() + "> element: " + e1.getMessage()); - } - - return new PurifyingFitnessValuesModel(fitnesses); - } else if (e.getName().equals(MINIMUM_FITNESS)) { - try { - minimumFitness = parseDouble(e, 0, 1); - } catch (ParseException pe) { - throw new ParseException("Error parsing <" + e.getName() + "> element: " + pe.getMessage()); - } - } else if (e.getName().equals(LOW_FITNESS)) { - try { - lowFitness = parseDouble(e, 0, 1); - } catch (ParseException pe) { - throw new ParseException("Error parsing <" + e.getName() + "> element: " + pe.getMessage()); - } - } else { - throw new ParseException("Error parsing <" + e.getName() + "> element: <" + e.getName() + "> is unrecognized"); - } + switch (e.getName()) { + case BETA_DISTIBUTED: + // Carrasco et al (2007) J Virology 81:12979-12984 + double a = 1.151; + double b = 1.709; + double pLethal = 0.4; + + int alphabetSize = alphabet.getStateCount(); + int sites = factor.sites.size(); + + Element aChild = e.getChild("a"); + a = Double.parseDouble(aChild.getText()); + Element bChild = e.getChild("b"); + b = Double.parseDouble(bChild.getText()); + Element pChild = e.getChild("pLethal"); + pLethal = Double.parseDouble(pChild.getText()); + + return new BetaDistributedPurifyingFitnessModel(a,b, pLethal, alphabetSize, sites); + case VALUES: + double[] fitnesses; + try { + fitnesses = parseNumberList(e); + + // confirm that we parsed one fitness value for each possible state. + if (fitnesses.length != alphabet.getStateCount()) { + throw new ParseException("expected " + alphabet.getStateCount() +" fitnesses, got " + fitnesses.length); + } + } catch (ParseException e1) { + throw new ParseException("Error parsing <" + e.getName() + "> element: " + e1.getMessage()); + } + + return new PurifyingFitnessValuesModel(fitnesses); + case MINIMUM_FITNESS: + try { + minimumFitness = parseDouble(e, 0, 1); + } catch (ParseException pe) { + throw new ParseException("Error parsing <" + e.getName() + "> element: " + pe.getMessage()); + } + break; + case LOW_FITNESS: + try { + lowFitness = parseDouble(e, 0, 1); + } catch (ParseException pe) { + throw new ParseException("Error parsing <" + e.getName() + "> element: " + pe.getMessage()); + } + break; + default: + throw new ParseException("Error parsing <" + e.getName() + "> element: <" + e.getName() + "> is unrecognized"); + } } if (minimumFitness == -1 || lowFitness == -1) { throw new ParseException("Error parsing <" + element.getName() + "> element: expecting either a <" + VALUES @@ -1123,13 +1233,17 @@ private PurifyingFitnessRank parsePurifyingFitnessRank(Element element, FeatureA if (breakTiesElement == null) throw new ParseException("Error parsing <" + element.getName() + "> element: missing <" + BREAK_TIES + ">"); String breakTies = breakTiesElement.getTextNormalize(); - if (breakTies.equals(BREAK_TIES_RANDOM)) - breakTiesRandom = true; - else if (breakTies.equals(BREAK_TIES_ORDERED)) - breakTiesRandom = false; - else - throw new ParseException("Error parsing <" + BREAK_TIES + "> element: value must be one of '" - + BREAK_TIES_RANDOM + "' or '" + BREAK_TIES_ORDERED + "'"); + switch (breakTies) { + case BREAK_TIES_RANDOM: + breakTiesRandom = true; + break; + case BREAK_TIES_ORDERED: + breakTiesRandom = false; + break; + default: + throw new ParseException("Error parsing <" + BREAK_TIES + "> element: value must be one of '" + + BREAK_TIES_RANDOM + "' or '" + BREAK_TIES_ORDERED + "'"); + } for (Object o:element.getChildren()) { Element e = (Element) o; @@ -1137,30 +1251,35 @@ else if (breakTies.equals(BREAK_TIES_ORDERED)) if (e.getName().equals(ORDER)) { String v = e.getTextNormalize(); - if (v.equals(ORDER_OBSERVED_FREQUENCY)) { - order = OrderEnum.OBSERVED; - } else if (v.equals(ORDER_CHEMICAL)) { - order = OrderEnum.CLASSES; - orderSetClasses = parseProbableSetClasses(alphabet, CHEMICAL_CLASSES); - } else if (v.equals(ORDER_HYDROPATHY)) { - order = OrderEnum.CLASSES; - orderSetClasses = parseProbableSetClasses(alphabet, HYDROPATHY_CLASSES); - } else if (v.equals(ORDER_VOLUME)) { - order = OrderEnum.CLASSES; - orderSetClasses = parseProbableSetClasses(alphabet, VOLUME_CLASSES); - } else { - if (v.contains("|")) { - order = OrderEnum.CLASSES; - orderSetClasses = parseProbableSetClasses(alphabet, v); - } else { - order = OrderEnum.STATES; - stateOrder = new ArrayList(); - - for (int i = 0; i < v.length(); ++i) { - stateOrder.add(alphabet.parse(v.charAt(i))); - } - } - } + switch (v) { + case ORDER_OBSERVED_FREQUENCY: + order = OrderEnum.OBSERVED; + break; + case ORDER_CHEMICAL: + order = OrderEnum.CLASSES; + orderSetClasses = parseProbableSetClasses(alphabet, CHEMICAL_CLASSES); + break; + case ORDER_HYDROPATHY: + order = OrderEnum.CLASSES; + orderSetClasses = parseProbableSetClasses(alphabet, HYDROPATHY_CLASSES); + break; + case ORDER_VOLUME: + order = OrderEnum.CLASSES; + orderSetClasses = parseProbableSetClasses(alphabet, VOLUME_CLASSES); + break; + default: + if (v.contains("|")) { + order = OrderEnum.CLASSES; + orderSetClasses = parseProbableSetClasses(alphabet, v); + } else { + order = OrderEnum.STATES; + stateOrder = new ArrayList(); + + for (int i = 0; i < v.length(); ++i) { + stateOrder.add(alphabet.parse(v.charAt(i))); + } + } break; + } } else if (e.getName().equals(PROBABLE_SET)) { probableNumber = parseInteger(e, 1, alphabet.getStateCount()); } else if (!e.getName().equals(BREAK_TIES)) { @@ -1200,12 +1319,12 @@ else if (breakTies.equals(BREAK_TIES_ORDERED)) } private List> parseProbableSetClasses(SequenceAlphabet alphabet, String str) throws ParseException { - Set completeCheck = new HashSet(); - List> classes = new ArrayList>(); + Set completeCheck = new HashSet<>(); + List> classes = new ArrayList<>(); String[] sets = str.split("\\|"); for (String set : sets) { - Set stateSet = new HashSet(); + Set stateSet = new HashSet<>(); for (int i = 0; i < set.length(); i++) { byte symbol = alphabet.parse(set.charAt(i)); stateSet.add(symbol); @@ -1225,7 +1344,7 @@ private List> parseProbableSetClasses(SequenceAlphabet alphabet, Strin } private List parseAlignment(String text) throws ParseException { - List result = new ArrayList(); + List result = new ArrayList<>(); int firstLength = 0; String[] seqStrings; @@ -1288,7 +1407,7 @@ public double[] parseNumberList(Element element) throws ParseException { } private Set parseSites(Element element, Feature feature) throws ParseException { - Set result = new TreeSet(); + Set result = new TreeSet<>(); String sites = element.getTextNormalize(); String[] parts = sites.split(","); @@ -1335,7 +1454,7 @@ private void addSite(Set result, int j, Feature feature) throws ParseEx } private Mutator parseMutator(Element element) throws ParseException { - if (element.getChildren().size() == 0) { + if (element.getChildren().isEmpty()) { throw new ParseException("Error parsing <" + element.getName() + "> element: the element is empty"); } @@ -1354,38 +1473,46 @@ private Mutator parseMutator(Element element) throws ParseException { for (Object o : e.getChildren()) { Element e1 = (Element)o; try { - // this should really be a switch statement if we could use a modern java implementation... - if (e1.getName().equals(MUTATION_RATE)) { - mutationRate = parseDouble(e1, 0.0, Double.MAX_VALUE); - } else if (e1.getName().equals(TRANSITION_BIAS)) { - transitionBias = parseDouble(e1, 0.0, Double.MAX_VALUE); - } else if (e1.getName().equals(RATE_BIAS)) { - rateBiases = parseNumberList(e1); - if (rateBiases.length != 12) { - throw new ParseException("expected 12 rate biases, got " + rateBiases.length); - } - } else if (e1.getName().equals(INSERT_PROB)) { - // http://abacus.gene.ucl.ac.uk/software/indelible/manual/model.shtml#[indelmodel] - if (insertProb != -1.0) { - throw new ParseException("insertion probability is already set - see previous <" + INSERT_PROB + "> or <" + INDEL_PROB + ">."); - } - insertProb = parseDouble(e1, 0.0, 1.0); - } else if (e1.getName().equals(DELETE_PROB)) { - if (deleteProb != -1.0) { - throw new ParseException("deletion probability already set - see previous <" + DELETE_PROB + "> or <" + INDEL_PROB + ">."); - } - deleteProb = parseDouble(e1, 0.0, 1.0); - } else if (e1.getName().equals(INDEL_PROB)) { - if (insertProb != -1.0 || deleteProb != -1.0) { - throw new ParseException("insertion or deletion probability already set - see previous <" + DELETE_PROB + ">, <" + INSERT_PROB + ">, or <" + INDEL_PROB + ">."); - } - insertProb = parseDouble(e1, 0.0, 1.0); - deleteProb = insertProb; - } else if (e1.getName().equals(INDEL_MODEL)) { - indelModel = parseIndelModel(e1); - } else { - throw new ParseException("element is unrecognized"); - } + // this should really be a switch statement if we could use a modern java implementation... + switch (e1.getName()) { + case MUTATION_RATE: + mutationRate = parseDouble(e1, 0.0, Double.MAX_VALUE); + break; + case TRANSITION_BIAS: + transitionBias = parseDouble(e1, 0.0, Double.MAX_VALUE); + break; + case RATE_BIAS: + rateBiases = parseNumberList(e1); + if (rateBiases.length != 12) { + throw new ParseException("expected 12 rate biases, got " + rateBiases.length); + } + break; + case INSERT_PROB: + // http://abacus.gene.ucl.ac.uk/software/indelible/manual/model.shtml#[indelmodel] + if (insertProb != -1.0) { + throw new ParseException("insertion probability is already set - see previous <" + INSERT_PROB + "> or <" + INDEL_PROB + ">."); + } + insertProb = parseDouble(e1, 0.0, 1.0); + break; + case DELETE_PROB: + if (deleteProb != -1.0) { + throw new ParseException("deletion probability already set - see previous <" + DELETE_PROB + "> or <" + INDEL_PROB + ">."); + } + deleteProb = parseDouble(e1, 0.0, 1.0); + break; + case INDEL_PROB: + if (insertProb != -1.0 || deleteProb != -1.0) { + throw new ParseException("insertion or deletion probability already set - see previous <" + DELETE_PROB + ">, <" + INSERT_PROB + ">, or <" + INDEL_PROB + ">."); + } + insertProb = parseDouble(e1, 0.0, 1.0); + deleteProb = insertProb; + break; + case INDEL_MODEL: + indelModel = parseIndelModel(e1); + break; + default: + throw new ParseException("element is unrecognized"); + } } catch(ParseException pe) { throw new ParseException("element: <" + e1.getName() + ">: " + pe.getMessage()); @@ -1454,104 +1581,106 @@ private IndelModel parseIndelModel(Element element) throws ParseException { private Replicator parseReplicator(Element element) throws ParseException { - if (element.getChildren().size() == 0) { + if (element.getChildren().isEmpty()) { throw new ParseException("Error parsing <" + element.getName() + "> element: the element is empty"); } Element e = (Element)element.getChildren().get(0); - if (e.getName().equals(CLONAL_REPLICATOR)) { - return new ClonalReplicator(); - } else if (e.getName().equals(RECOMBINANT_REPLICATOR_WITH_HOTSPOTS)) { - double dualInfectionProbability = -1.0; - double recombinationProbability = -1.0; - - for (Object o : e.getChildren()) { - Element e1 = (Element)o; - if (e1.getName().equals(DUAL_INFECTION_PROBABILITY)) { - try { - dualInfectionProbability = parseDouble(e1, 0.0, 1.0); - } catch (ParseException pe) { - throw new ParseException("Error parsing <" + e.getName() + "> element: " + pe.getMessage()); - } - } else if (e1.getName().equals(RECOMBINATION_PROBABILITY)) { - try { - recombinationProbability = parseDouble(e1, 0.0, 1.0); - } catch (ParseException pe) { - throw new ParseException("Error parsing <" + e.getName() + "> element: " + pe.getMessage()); - } - } else { - throw new ParseException("Error parsing <" + e.getName() + "> element: <" + e1.getName() + "> is unrecognized"); - } - - } - if (dualInfectionProbability < 0.0) { - throw new ParseException("Error parsing <" + element.getName() + "> element: <" + DUAL_INFECTION_PROBABILITY + "> is missing"); - } - - if (recombinationProbability < 0.0) { - throw new ParseException("Error parsing <" + element.getName() + "> element: <" + RECOMBINATION_PROBABILITY + "> is missing"); - } - - return new RecombinantReplicatorWithHotSpots(dualInfectionProbability, recombinationProbability); - } - - else if (e.getName().equals(RECOMBINANT_REPLICATOR)) { - double dualInfectionProbability = -1.0; - double recombinationProbability = -1.0; - - for (Object o : e.getChildren()) { - Element e1 = (Element)o; - if (e1.getName().equals(DUAL_INFECTION_PROBABILITY)) { - try { - dualInfectionProbability = parseDouble(e1, 0.0, 1.0); - } catch (ParseException pe) { - throw new ParseException("Error parsing <" + e.getName() + "> element: " + pe.getMessage()); - } - } else if (e1.getName().equals(RECOMBINATION_PROBABILITY)) { - try { - recombinationProbability = parseDouble(e1, 0.0, 1.0); - } catch (ParseException pe) { - throw new ParseException("Error parsing <" + e.getName() + "> element: " + pe.getMessage()); - } - } else { - throw new ParseException("Error parsing <" + e.getName() + "> element: <" + e1.getName() + "> is unrecognized"); - } - - } - if (dualInfectionProbability < 0.0) { - throw new ParseException("Error parsing <" + element.getName() + "> element: <" + DUAL_INFECTION_PROBABILITY + "> is missing"); - } - - if (recombinationProbability < 0.0) { - throw new ParseException("Error parsing <" + element.getName() + "> element: <" + RECOMBINATION_PROBABILITY + "> is missing"); - } - - return new RecombinantReplicator(dualInfectionProbability, recombinationProbability); - } - - - else { - throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e.getName() + "> is unrecognized"); - } + switch (e.getName()) { + case CLONAL_REPLICATOR: + return new ClonalReplicator(); + case RECOMBINANT_REPLICATOR_WITH_HOTSPOTS: + { + double dualInfectionProbability = -1.0; + double recombinationProbability = -1.0; + + for (Object o : e.getChildren()) { + Element e1 = (Element)o; + if (e1.getName().equals(DUAL_INFECTION_PROBABILITY)) { + try { + dualInfectionProbability = parseDouble(e1, 0.0, 1.0); + } catch (ParseException pe) { + throw new ParseException("Error parsing <" + e.getName() + "> element: " + pe.getMessage()); + } + } else if (e1.getName().equals(RECOMBINATION_PROBABILITY)) { + try { + recombinationProbability = parseDouble(e1, 0.0, 1.0); + } catch (ParseException pe) { + throw new ParseException("Error parsing <" + e.getName() + "> element: " + pe.getMessage()); + } + } else { + throw new ParseException("Error parsing <" + e.getName() + "> element: <" + e1.getName() + "> is unrecognized"); + } + + } + if (dualInfectionProbability < 0.0) { + throw new ParseException("Error parsing <" + element.getName() + "> element: <" + DUAL_INFECTION_PROBABILITY + "> is missing"); + } + + if (recombinationProbability < 0.0) { + throw new ParseException("Error parsing <" + element.getName() + "> element: <" + RECOMBINATION_PROBABILITY + "> is missing"); + } + + return new RecombinantReplicatorWithHotSpots(dualInfectionProbability, recombinationProbability); + } + case RECOMBINANT_REPLICATOR: + { + double dualInfectionProbability = -1.0; + double recombinationProbability = -1.0; + + for (Object o : e.getChildren()) { + Element e1 = (Element)o; + switch (e1.getName()) { + case DUAL_INFECTION_PROBABILITY: + try { + dualInfectionProbability = parseDouble(e1, 0.0, 1.0); + } catch (ParseException pe) { + throw new ParseException("Error parsing <" + e.getName() + "> element: " + pe.getMessage()); + } break; + case RECOMBINATION_PROBABILITY: + try { + recombinationProbability = parseDouble(e1, 0.0, 1.0); + } catch (ParseException pe) { + throw new ParseException("Error parsing <" + e.getName() + "> element: " + pe.getMessage()); + } break; + default: + throw new ParseException("Error parsing <" + e.getName() + "> element: <" + e1.getName() + "> is unrecognized"); + } + + } + if (dualInfectionProbability < 0.0) { + throw new ParseException("Error parsing <" + element.getName() + "> element: <" + DUAL_INFECTION_PROBABILITY + "> is missing"); + } + + if (recombinationProbability < 0.0) { + throw new ParseException("Error parsing <" + element.getName() + "> element: <" + RECOMBINATION_PROBABILITY + "> is missing"); + } + + return new RecombinantReplicator(dualInfectionProbability, recombinationProbability); + } + default: + throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e.getName() + "> is unrecognized"); + } } private GenePool parseGenePool(Element element) throws ParseException { - if (element.getChildren().size() == 0) { + if (element.getChildren().isEmpty()) { throw new ParseException("Error parsing <" + element.getName() + "> element: the element is empty"); } Element e = (Element)element.getChildren().get(0); - if (e.getName().equals(SIMPLE_GENE_POOL)) { - // SimpleGenome/GenePool uses a simple format where the whole sequence is stored - return new SimpleGenePool(); - } else if (e.getName().equals(COMPACT_GENE_POOL)) { - // CompactGenome/GenePool uses a compact format where only changes are stored - return new CompactGenePool(); - } else { - throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e.getName() + "> is unrecognized"); - } + switch (e.getName()) { + case SIMPLE_GENE_POOL: + // SimpleGenome/GenePool uses a simple format where the whole sequence is stored + return new SimpleGenePool(); + case COMPACT_GENE_POOL: + // CompactGenome/GenePool uses a compact format where only changes are stored + return new CompactGenePool(); + default: + throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e.getName() + "> is unrecognized"); + } } @@ -1580,23 +1709,28 @@ private void parseSampler(Element element, SamplingSchedule samplingSchedule) th for (Object o : element.getChildren()) { Element e1 = (Element)o; - if (e1.getName().equals(AT_FREQUENCY)) { - try { - frequency = parseInteger(e1, 1, Integer.MAX_VALUE); - } catch (ParseException pe) { - throw new ParseException("Error parsing <" + element.getName() + "> element: " + pe.getMessage()); - } - } else if (e1.getName().equals(AT_GENERATION)) { - try { - generation = parseInteger(e1, 1, Integer.MAX_VALUE); - } catch (ParseException pe) { - throw new ParseException("Error parsing <" + element.getName() + "> element: " + pe.getMessage()); - } - } else if (e1.getName().equals(FILE_NAME)) { - fileName = e1.getTextNormalize(); - } else { - // skip over it - } + switch (e1.getName()) { + case AT_FREQUENCY: + try { + frequency = parseInteger(e1, 1, Integer.MAX_VALUE); + } catch (ParseException pe) { + throw new ParseException("Error parsing <" + element.getName() + "> element: " + pe.getMessage()); + } + break; + case AT_GENERATION: + try { + generation = parseInteger(e1, 1, Integer.MAX_VALUE); + } catch (ParseException pe) { + throw new ParseException("Error parsing <" + element.getName() + "> element: " + pe.getMessage()); + } + break; + case FILE_NAME: + fileName = e1.getTextNormalize(); + break; + // skip over it + default: + break; + } } @@ -1612,21 +1746,30 @@ private void parseSampler(Element element, SamplingSchedule samplingSchedule) th for (Object o : element.getChildren()) { Element e1 = (Element)o; - if (e1.getName().equals(ALIGNMENT)) { - sampler = parseAlignmentSampler(e1, samplingSchedule, fileName); - } else if (e1.getName().equals(GENOMEDESCRIPTION)) { - sampler = parseGenomeDescriptionSampler(e1, samplingSchedule, fileName); - } else if (e1.getName().equals(TREE)) { - sampler = parseTreeSampler(e1, samplingSchedule, fileName); - } else if (e1.getName().equals(ALLELE_FREQUENCY)) { - sampler = parseAlleleFrequencySampler(e1, samplingSchedule, fileName); - } else if (e1.getName().equals(STATISTICS)) { - sampler = parseStatisticsSampler(e1, samplingSchedule, fileName); - } else if (e1.getName().equals(AT_FREQUENCY) || e1.getName().equals(AT_GENERATION) || e1.getName().equals(FILE_NAME)) { - // skip over it - } else { - throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e1.getName() + "> is unrecognized"); - } + switch (e1.getName()) { + case ALIGNMENT: + sampler = parseAlignmentSampler(e1, samplingSchedule, fileName); + break; + case GENOMEDESCRIPTION: + sampler = parseGenomeDescriptionSampler(e1, samplingSchedule, fileName); + break; + case TREE: + sampler = parseTreeSampler(e1, samplingSchedule, fileName); + break; + case ALLELE_FREQUENCY: + sampler = parseAlleleFrequencySampler(e1, samplingSchedule, fileName); + break; + case STATISTICS: + sampler = parseStatisticsSampler(e1, samplingSchedule, fileName); + break; + // skip over it + case AT_FREQUENCY: + case AT_GENERATION: + case FILE_NAME: + break; + default: + throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e1.getName() + "> is unrecognized"); + } } @@ -1652,31 +1795,35 @@ private Sampler parseGenomeDescriptionSampler(Element element, SamplingSchedule for (Object o : element.getChildren()) { Element e1 = (Element)o; - if (e1.getName().equals(SAMPLE_SIZE)) { - try { - sampleSize = parseInteger(e1, 1, Integer.MAX_VALUE); - } catch (ParseException pe) { - throw new ParseException("Error parsing <" + element.getName() + "> element: " + pe.getMessage()); - } - } else if (e1.getName().equals(SCHEDULE)) { - String[] values = e1.getTextTrim().split("\\s+"); - schedule = new TreeMap(); - try { - for (int i = 0; i element: " - + e.getMessage()); - } - } else if (e1.getName().equals(LABEL)) { - label = e1.getTextNormalize(); - } else { - throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e1.getName() + "> is unrecognized"); - } + switch (e1.getName()) { + case SAMPLE_SIZE: + try { + sampleSize = parseInteger(e1, 1, Integer.MAX_VALUE); + } catch (ParseException pe) { + throw new ParseException("Error parsing <" + element.getName() + "> element: " + pe.getMessage()); + } + break; + case SCHEDULE: + String[] values = e1.getTextTrim().split("\\s+"); + schedule = new TreeMap<>(); + try { + for (int i = 0; i element: " + + e.getMessage()); + } + break; + case LABEL: + label = e1.getTextNormalize(); + break; + default: + throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e1.getName() + "> is unrecognized"); + } } @@ -1701,51 +1848,57 @@ private Sampler parseAlignmentSampler(Element element, SamplingSchedule sampling for (Object o : element.getChildren()) { Element e1 = (Element)o; - if (e1.getName().equals(SAMPLE_SIZE)) { - try { - sampleSize = parseInteger(e1, 1, Integer.MAX_VALUE); - } catch (ParseException pe) { - throw new ParseException("Error parsing <" + element.getName() + "> element: " + pe.getMessage()); - } - } else if (e1.getName().equals(SCHEDULE)) { - String[] values = e1.getTextTrim().split("\\s+"); - schedule = new TreeMap(); - try { - for (int i = 0; i element: " - + e.getMessage()); - } - } else if (e1.getName().equals(FORMAT)) { - String formatText = e1.getTextNormalize(); - if (formatText.equalsIgnoreCase("NEXUS")) { - format = AlignmentSampler.Format.NEXUS; - } else if (formatText.equalsIgnoreCase("FASTA")) { - format = AlignmentSampler.Format.FASTA; - } else if (formatText.equalsIgnoreCase("XML")) { - format = AlignmentSampler.Format.XML; - } else { - throw new ParseException("Error parsing <" + element.getName() + "> element: <" + FORMAT + "> value of " + formatText + " is unrecognized"); - } - } else if (e1.getName().equals(CONSENSUS)) { - String booleanText = e1.getTextNormalize(); - if (booleanText.equalsIgnoreCase("TRUE")) { - consensus = true; - } else if (booleanText.equalsIgnoreCase("FALSE")) { - consensus = false; - } else { - throw new ParseException("Error parsing <" + element.getName() + "> element: <" + CONSENSUS + "> value " + booleanText + " is unrecognized"); - } - } else if (e1.getName().equals(LABEL)) { - label = e1.getTextNormalize(); - } else { - throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e1.getName() + "> is unrecognized"); - } + switch (e1.getName()) { + case SAMPLE_SIZE: + try { + sampleSize = parseInteger(e1, 1, Integer.MAX_VALUE); + } catch (ParseException pe) { + throw new ParseException("Error parsing <" + element.getName() + "> element: " + pe.getMessage()); + } + break; + case SCHEDULE: + String[] values = e1.getTextTrim().split("\\s+"); + schedule = new TreeMap<>(); + try { + for (int i = 0; i element: " + + e.getMessage()); + } + break; + case FORMAT: + String formatText = e1.getTextNormalize(); + if (formatText.equalsIgnoreCase("NEXUS")) { + format = AlignmentSampler.Format.NEXUS; + } else if (formatText.equalsIgnoreCase("FASTA")) { + format = AlignmentSampler.Format.FASTA; + } else if (formatText.equalsIgnoreCase("XML")) { + format = AlignmentSampler.Format.XML; + } else { + throw new ParseException("Error parsing <" + element.getName() + "> element: <" + FORMAT + "> value of " + formatText + " is unrecognized"); + } + break; + case CONSENSUS: + String booleanText = e1.getTextNormalize(); + if (booleanText.equalsIgnoreCase("TRUE")) { + consensus = true; + } else if (booleanText.equalsIgnoreCase("FALSE")) { + consensus = false; + } else { + throw new ParseException("Error parsing <" + element.getName() + "> element: <" + CONSENSUS + "> value " + booleanText + " is unrecognized"); + } + break; + case LABEL: + label = e1.getTextNormalize(); + break; + default: + throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e1.getName() + "> is unrecognized"); + } } @@ -1766,40 +1919,45 @@ private Sampler parseTreeSampler(Element element, SamplingSchedule samplingSched for (Object o : element.getChildren()) { Element e1 = (Element)o; - if (e1.getName().equals(SAMPLE_SIZE)) { - try { - sampleSize = parseInteger(e1, 1, Integer.MAX_VALUE); - } catch (ParseException pe) { - throw new ParseException("Error parsing <" + element.getName() + "> element: " + pe.getMessage()); - } - } else if (e1.getName().equals(SCHEDULE)) { - String[] values = e1.getTextTrim().split("\\s+"); - schedule = new TreeMap(); - try { - for (int i = 0; i element: " - + e.getMessage()); - } - } else if (e1.getName().equals(FORMAT)) { - String formatText = e1.getTextNormalize(); - if (formatText.equalsIgnoreCase("NEXUS")) { - format = TreeSampler.Format.NEXUS; - } else if (formatText.equalsIgnoreCase("NEWICK")) { - format = TreeSampler.Format.NEWICK; - } else { - throw new ParseException("Error parsing <" + element.getName() + "> element: <" + FORMAT + "> value of " + formatText + " is unrecognized"); - } - } else if (e1.getName().equals(LABEL)) { - label = e1.getTextNormalize(); - } else { - throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e1.getName() + "> is unrecognized"); - } + switch (e1.getName()) { + case SAMPLE_SIZE: + try { + sampleSize = parseInteger(e1, 1, Integer.MAX_VALUE); + } catch (ParseException pe) { + throw new ParseException("Error parsing <" + element.getName() + "> element: " + pe.getMessage()); + } + break; + case SCHEDULE: + String[] values = e1.getTextTrim().split("\\s+"); + schedule = new TreeMap(); + try { + for (int i = 0; i element: " + + e.getMessage()); + } + break; + case FORMAT: + String formatText = e1.getTextNormalize(); + if (formatText.equalsIgnoreCase("NEXUS")) { + format = TreeSampler.Format.NEXUS; + } else if (formatText.equalsIgnoreCase("NEWICK")) { + format = TreeSampler.Format.NEWICK; + } else { + throw new ParseException("Error parsing <" + element.getName() + "> element: <" + FORMAT + "> value of " + formatText + " is unrecognized"); + } + break; + case LABEL: + label = e1.getTextNormalize(); + break; + default: + throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e1.getName() + "> is unrecognized"); + } } diff --git a/src/santa/simulator/compartments/Compartment.java b/src/santa/simulator/compartments/Compartment.java new file mode 100644 index 0000000..da28691 --- /dev/null +++ b/src/santa/simulator/compartments/Compartment.java @@ -0,0 +1,173 @@ +package santa.simulator.compartments; + +import java.util.ArrayList; +import java.util.List; +import java.util.logging.Logger; +import santa.simulator.EventLogger; +import santa.simulator.Random; +import santa.simulator.genomes.GenePool; +import santa.simulator.genomes.GenomeDescription; +import santa.simulator.genomes.Sequence; +import santa.simulator.phylogeny.Phylogeny; +import santa.simulator.population.DynamicPopulation; +import santa.simulator.population.Population; +import santa.simulator.population.StaticPopulation; +import santa.simulator.samplers.SamplingSchedule; +import santa.simulator.selectors.BinarySearchSelector; +import santa.simulator.selectors.DynamicSelector; +import santa.simulator.selectors.Selector; + +/** + * + * @author Bradley R. Jones + */ +public class Compartment { + private int populationSize; + private String name; + private Compartment.InoculumType inoculumType; + private GenePool genePool; + private List epochs; + private Selector selector; + private SamplingSchedule samplingSchedule; + private Population population; + + public enum InoculumType { + NONE, + CONSENSUS, + RANDOM, + ALL + }; + + //Default constructor (dynamic) + public Compartment ( + String name, + int populationSize, + InoculumType inoculumType, + GenePool genePool, + List epochs, + SamplingSchedule samplingSchedule) { + + this.name = name; + this.populationSize = populationSize; + this.inoculumType = inoculumType; + this.epochs = epochs; + this.samplingSchedule = samplingSchedule; + this.genePool = genePool; + this.selector = new DynamicSelector(); + + population = new DynamicPopulation(genePool, selector, samplingSchedule.isSamplingTrees() ? new Phylogeny(populationSize) : null); + } + + //Default constructor (dynamic) + public Compartment ( + String name, + int populationSize, + DynamicSelector dynamicSelector, + InoculumType inoculumType, + GenePool genePool, + List epochs, + SamplingSchedule samplingSchedule) { + + this.name = name; + this.populationSize = populationSize; + this.inoculumType = inoculumType; + this.epochs = epochs; + this.samplingSchedule = samplingSchedule; + this.genePool = genePool; + this.selector = dynamicSelector; + + population = new DynamicPopulation(genePool, selector, samplingSchedule.isSamplingTrees() ? new Phylogeny(populationSize) : null); + } + + //Constructor for static population + public Compartment ( + String name, + int populationSize, + InoculumType inoculumType, + GenePool genePool, + List epochs, + SamplingSchedule samplingSchedule, + String populationType){ + + this.name = name; + this.populationSize = populationSize; + this.inoculumType = inoculumType; + this.epochs = epochs; + this.samplingSchedule = samplingSchedule; + this.genePool = genePool; + this.selector = new BinarySearchSelector(); +// this.selector = new SimpleRouletteWheelSelector(); + population = new StaticPopulation(populationSize, genePool, selector, samplingSchedule.isSamplingTrees() ? new Phylogeny(populationSize) : null); + + } + + public void initalize(int replicate, Logger logger) { + samplingSchedule.initialize(replicate); + + EventLogger.setReplicate(replicate); + + logger.finer("Initializing population: " + populationSize + " viruses."); + + List inoculum = new ArrayList<>(); + if (null == inoculumType) { // NONE + // do nothing + } else switch (inoculumType) { + case CONSENSUS: + inoculum.add(GenomeDescription.getConsensus()); + break; + case ALL: + inoculum.addAll(GenomeDescription.getSequences()); + break; + case RANDOM: + List sequences = GenomeDescription.getSequences(); + if (sequences.size() == 1) { + inoculum.add(sequences.get(0)); + } else { + inoculum.add(sequences.get(Random.nextInt(0, sequences.size() - 1))); + } + break; + default: + break; + } + population.initialize(inoculum, populationSize); + } + + public void cleanup(int replicate, Logger logger) { + samplingSchedule.cleanUp(); + } + + public CompartmentEpoch getCurrentEpoch(String name) { + int index; + + for (index = 0; index < epochs.size(); index++) { + if (epochs.get(index).getName().equals(name)) + break; + } + + return epochs.get(index); + } + + public GenePool getGenePool() { + return genePool; + } + + public Population getPopulation() { + return population; + } + + public int getPopulationSize() { + return populationSize; + } + + public SamplingSchedule getSamplingSchedule() { + return samplingSchedule; + } + + public String getName() { + return name; + } + + public List getEpochs() { + return epochs; + } +} diff --git a/src/santa/simulator/compartments/CompartmentEpoch.java b/src/santa/simulator/compartments/CompartmentEpoch.java new file mode 100644 index 0000000..031ee4a --- /dev/null +++ b/src/santa/simulator/compartments/CompartmentEpoch.java @@ -0,0 +1,110 @@ + +package santa.simulator.compartments; + + +import java.util.logging.Logger; +import santa.simulator.fitness.FitnessFunction; +import santa.simulator.genomes.GenePool; +import santa.simulator.mutators.Mutator; +import santa.simulator.population.Population; +import santa.simulator.replicators.Replicator; +import santa.simulator.samplers.SamplingSchedule; + +/* + * @author Bradley R. Jones +*/ +public class CompartmentEpoch { + private String name; + private int generationCount; + private FitnessFunction fitnessFunction; + private Mutator mutator; + private Replicator replicator; + + public CompartmentEpoch(String name, int generationCount, + FitnessFunction fitnessFunction, Mutator mutator, + Replicator replicator) { + this.name = name; + this.generationCount = generationCount; + this.fitnessFunction = fitnessFunction; + this.mutator = mutator; + this.replicator = replicator; + } + + public int step(Compartment compartment, Logger logger, int startGeneration, int generation) { + Population population = compartment.getPopulation(); + GenePool genePool = compartment.getGenePool(); + SamplingSchedule samplingSchedule = compartment.getSamplingSchedule(); + + if (population.getCurrentGeneration().isEmpty()) + return 0; + + fitnessFunction.updateGeneration(generation, population); + + if (generation == startGeneration) { + // adapt to this epoch, and the new generation + population.updateAllFitnesses(fitnessFunction); + + System.err.println("Initial population: compartment = " + compartment.getName() + + ", fitness = " + population.getMeanFitness() + + ", distance = " + population.getMeanDistance() + + ", max freq = " + population.getMaxFrequency() + + ", genepool size = " + genePool.getUniqueGenomeCount() + + " (" + genePool.getUnusedGenomeCount() + " available)"); + } + + population.selectNextGeneration(generation, replicator, mutator, fitnessFunction); + + if (population.getCurrentGeneration().isEmpty()) + return 0; + + if (generation % 100 == 0) { + if (population.getPhylogeny() != null) + population.getPhylogeny().pruneDeadLineages(); + + System.err.print("Generation " + generation + ": compartment = " + compartment.getName() + + ", fitness = " + population.getMeanFitness() + + ", distance = " + population.getMeanDistance() + + ", max freq = " + population.getMaxFrequency() + + ", genepool size = " + genePool.getUniqueGenomeCount() + + " (" + genePool.getUnusedGenomeCount() + " available)"); + if (population.getPhylogeny() != null) { + population.getPhylogeny().pruneDeadLineages(); + System.err.println(", phylogeny size = " + population.getPhylogeny().getSize() + + " (used = " + population.getPhylogeny().getLineageCount()+ ")" + + ", tmrca = " + population.getPhylogeny().getMRCA().getGeneration() ); + } else + System.err.println(); + } else { + logger.finest("Generation " + generation + ": compartment = " + compartment.getName() + + " fitness = " + population.getMeanFitness() + + ", distance = " + population.getMeanDistance() + + ", max freq = " + population.getMaxFrequency() + + ", genepool size= " + genePool.getUniqueGenomeCount() + + "(" + genePool.getUnusedGenomeCount() + " available)"); + } + + samplingSchedule.doSampling(generation, population); + + return population.getPopulationSize(); + } + + public FitnessFunction getFitnessFunction() { + return fitnessFunction; + } + + public Mutator getMutator() { + return mutator; + } + + public Replicator getReplicator() { + return replicator; + } + + public int getGenerationCount() { + return generationCount; + } + + public String getName() { + return name; + } +} diff --git a/src/santa/simulator/compartments/Compartments.java b/src/santa/simulator/compartments/Compartments.java new file mode 100644 index 0000000..06fa0c1 --- /dev/null +++ b/src/santa/simulator/compartments/Compartments.java @@ -0,0 +1,109 @@ +/* + * To change this license header, choose License Headers in Project Properties. + * To change this template file, choose Tools | Templates + * and open the template in the editor. + */ +package santa.simulator.compartments; + +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; +import santa.simulator.Random; +import santa.simulator.genomes.GenePool; +import santa.simulator.genomes.Genome; +import santa.simulator.population.Population; + +/** + * + * @author Bradley R. Jones + */ +public class Compartments implements Iterable { + private double[][] transferProbs; + private List compartments; + private int numCompartments; + + public Compartments(List compartments, double[] transferRates) { + this.compartments = compartments; + this.numCompartments = compartments.size(); + this.transferProbs = new double[this.numCompartments][this.numCompartments]; + + double[] sum = new double[this.numCompartments]; + for (int i = 0; i < transferRates.length; i++) { + sum[i / this.numCompartments] += transferRates[i]; + } + for (int i = 0; i < transferRates.length; i++) { + this.transferProbs[i / this.numCompartments][i % this.numCompartments] = transferRates[i] / sum[i / this.numCompartments]; + } + } + + public void genomeTransfer(int generation) { + ArrayList< ArrayList > allGenomesToAdd = new ArrayList(numCompartments); + ArrayList< ArrayList > allGenomes = new ArrayList<>(numCompartments); + + for (int i = 0; i < numCompartments; i++) { + allGenomesToAdd.add(new ArrayList<>()); + } + + for (int i = 0; i < numCompartments; i++) { + Compartment migrator = compartments.get(i); + Population population = migrator.getPopulation(); + GenePool migratorGenePool = migrator.getGenePool(); + ArrayList genomes = new ArrayList<>(); + allGenomes.set(i, genomes); + for (Genome genome: migratorGenePool.getGenomes()) { + genomes.add(genome.copy()); + } + + for (int j = 0; j < numCompartments; j++) { + ArrayList genomesToAdd = allGenomesToAdd.get(j); + + if (i != j) { + for (Genome genome: genomes) { + if (transferProbs[i][j] > 0) { + int n = genome.getFrequency(); + int numMigrating = Random.nextBinomial(n, transferProbs[i][j]); + Genome migratingGenome = genome.copy(); + + genome.setFrequency(n - numMigrating); + migratingGenome.setFrequency(numMigrating); + + genomesToAdd.add(migratingGenome); + } + } + } + } + } + + for (int i = 0; i < numCompartments; i++) { + ArrayList genomes = allGenomes.get(i); + GenePool compartmentGenePool = compartments.get(i).getGenePool(); + List compartmentGenomes = compartmentGenePool.getGenomes(); + for (int j = 0; j < genomes.size(); j++) { + Genome compartmentGenome = compartmentGenomes.get(j); + + compartmentGenome.setFrequency(genomes.get(j).getFrequency()); + + if (compartmentGenome.getFrequency() <= 0) { + compartmentGenome.setFrequency(1); + compartmentGenePool.killGenome(compartmentGenome); + } + } + + for (Genome genome: allGenomesToAdd.get(i)) { + Genome newGenome = compartmentGenePool.createGenome(genome.getSequence(), genome.getDescription()); + + newGenome.setFrequency(genome.getFrequency()); + compartmentGenomes.add(newGenome); + } + } + } + + public int getNumCompartments() { + return numCompartments; + } + + @Override + public Iterator iterator() { + return compartments.iterator(); + } +} diff --git a/src/santa/simulator/genomes/BaseGenePool.java b/src/santa/simulator/genomes/BaseGenePool.java index e164d9e..1289bf1 100644 --- a/src/santa/simulator/genomes/BaseGenePool.java +++ b/src/santa/simulator/genomes/BaseGenePool.java @@ -12,9 +12,10 @@ public abstract class BaseGenePool implements GenePool { protected int uniqueGenomeCount = 0; protected final int[][] stateFrequencies; - protected final LinkedList genomes = new LinkedList(); - protected final LinkedList unusedGenomes = new LinkedList(); + protected final LinkedList genomes = new LinkedList<>(); + protected final LinkedList unusedGenomes = new LinkedList<>(); + @Override public LinkedList getGenomes() { return genomes; } @@ -26,6 +27,7 @@ public BaseGenePool() { stateFrequencies = new int[GenomeDescription.root.getGenomeLength()][4]; } + @Override public void initialize() { unusedGenomes.clear(); //unusedGenomes.addAll(genomes); @@ -34,6 +36,7 @@ public void initialize() { } + @Override public Genome createGenome(Sequence sequence, GenomeDescription gd) { Genome newGenome = createGenome(sequence); newGenome.setDescription(gd); @@ -42,6 +45,7 @@ public Genome createGenome(Sequence sequence, GenomeDescription gd) { } + @Override public int[][] getStateFrequencies() { calculateStateFrequencies(); return stateFrequencies; @@ -71,6 +75,7 @@ private boolean uniformPool() { * frequencies. * **/ + @Override public int[][] getStateFrequencies(Feature feature, Set sites) { int[][] freqs = new int[sites.size()][feature.getAlphabet().getStateCount()]; @@ -110,6 +115,7 @@ public int[][] getStateFrequencies(Feature feature, Set sites) { * meaningful consensus without first aligning the sequences. **/ + @Override public Sequence getConsensusSequence() { /* * Fail if all genomes do not have the same GenomeDescription. @@ -154,6 +160,7 @@ private void calculateStateFrequencies() { } } + @Override public void updateAllFitnesses(FitnessFunction fitnessFunction) { for (Genome genome : genomes) { fitnessFunction.computeLogFitness(genome); @@ -166,6 +173,7 @@ public void updateAllFitnesses(FitnessFunction fitnessFunction) { * @param genome2 another genome * @return the hamming distance */ + @Override public int hammingDistance(Genome genome1, Genome genome2) { return hammingDistance(genome1.getSequence(), genome2.getSequence()); } @@ -180,10 +188,12 @@ public int hammingDistance(Sequence sequence1, Sequence sequence2) { return distance; } + @Override public int getUniqueGenomeCount() { return uniqueGenomeCount; } + @Override public int getUnusedGenomeCount() { return unusedGenomes.size(); } diff --git a/src/santa/simulator/genomes/BaseGenome.java b/src/santa/simulator/genomes/BaseGenome.java index 2e1584b..f8ff998 100644 --- a/src/santa/simulator/genomes/BaseGenome.java +++ b/src/santa/simulator/genomes/BaseGenome.java @@ -16,16 +16,19 @@ public BaseGenome() { this.descriptor = GenomeDescription.root; } + @Override public void setDescription(GenomeDescription gd) { this.descriptor = gd; assert(this.descriptor.getGenomeLength() == getLength()); } // REMIND - do we still need this? + @Override public GenomeDescription getDescription() { return descriptor; } + @Override public int getTotalMutationCount() { return totalMutationCount; } @@ -38,22 +41,27 @@ protected void incrementTotalMutationCount() { totalMutationCount++; } + @Override public int getFrequency() { return frequency; } + @Override public void setFrequency(int frequency) { this.frequency = frequency; } + @Override public void incrementFrequency() { frequency++; } + @Override public double getLogFitness() { return logFitness; } + @Override public void setLogFitness(double logFitness) { if (logFitness != this.logFitness) { this.logFitness = logFitness; @@ -61,6 +69,7 @@ public void setLogFitness(double logFitness) { } } + @Override public double getFitness() { if (!fitnessKnown) { fitness = Math.exp(logFitness); @@ -69,10 +78,12 @@ public double getFitness() { return fitness; } + @Override public FitnessFunction.FitnessGenomeCache getFitnessCache() { return fitnessCache; } + @Override public void setFitnessCache(FitnessFunction.FitnessGenomeCache fitnessCache) { this.fitnessCache = fitnessCache; } @@ -82,6 +93,7 @@ public void setFitnessCache(FitnessFunction.FitnessGenomeCache fitnessCache) { * * @return byte array of nucleotides (encoded as integer states) **/ + @Override public byte[] getNucleotides(Feature feature) { byte[] nucleotides = null; Feature f = descriptor.getFeature(feature.getName()); @@ -99,6 +111,7 @@ public byte[] getNucleotides(Feature feature) { } + @Override public byte[] getStates(Feature feature) { Sequence seq = new SimpleSequence(getNucleotides(feature)); return seq.getStates(feature.getAlphabet()); @@ -122,10 +135,11 @@ public byte[] getStates(Feature feature) { * information. Other fitness functions ignore the data computed * here. * - * @param feature Feature object over which the changes should be computed. + * @param featureByName Feature object over which the changes should be computed. * @param mutations set of mutations that are inducing changes. * @return list of objects **/ + @Override public List getChanges(Feature featureByName, SortedSet mutations) { List changes = new ArrayList(); @@ -226,11 +240,11 @@ public List getChanges(Feature featureByName, SortedSet m } + @Override public int binomialDeviate(double mutationRate) { return descriptor.binomialDeviate(mutationRate); } - /** * Reference to an GenomeDescription. It is through the * decription that one can obtain Feature coordinates and SiteMaps @@ -251,4 +265,11 @@ public int binomialDeviate(double mutationRate) { private int totalMutationCount = 0; FitnessFunction.FitnessGenomeCache fitnessCache; + + public void baseCopy(BaseGenome g) { + g.descriptor = this.descriptor; + + g.frequency = this.frequency; + g.totalMutationCount = this.totalMutationCount; + } } diff --git a/src/santa/simulator/genomes/CompactGenome.java b/src/santa/simulator/genomes/CompactGenome.java index 6d0a216..2ae0310 100644 --- a/src/santa/simulator/genomes/CompactGenome.java +++ b/src/santa/simulator/genomes/CompactGenome.java @@ -174,4 +174,13 @@ static void setMasterSequence(Sequence masterSequence) { private static Sequence masterSequence = null; + @Override + public Genome copy() { + CompactGenome g = new CompactGenome(); + + this.baseCopy(g); + g.applyMutations(this.mutations); + + return g; + } } diff --git a/src/santa/simulator/genomes/Genome.java b/src/santa/simulator/genomes/Genome.java index 9810f5b..1e98bb9 100644 --- a/src/santa/simulator/genomes/Genome.java +++ b/src/santa/simulator/genomes/Genome.java @@ -56,5 +56,7 @@ public interface Genome { GenomeDescription getDescription(); void setDescription(GenomeDescription gd); + + Genome copy(); } diff --git a/src/santa/simulator/genomes/SimpleGenome.java b/src/santa/simulator/genomes/SimpleGenome.java index 02ad2f6..29db8c7 100644 --- a/src/santa/simulator/genomes/SimpleGenome.java +++ b/src/santa/simulator/genomes/SimpleGenome.java @@ -134,6 +134,15 @@ public boolean delete(int position, int count) { public boolean insert(int position, SimpleSequence seq) { return sequence.insertSequence(position, seq); } + + public Genome copy() { + SimpleGenome g = new SimpleGenome(); + + this.baseCopy(g); + g.sequence = new SimpleSequence(this.sequence); + + return g; + } // private members From 7c501f267803392ee680566b645a0e12a63fe100 Mon Sep 17 00:00:00 2001 From: brj1 Date: Fri, 23 Mar 2018 14:37:01 -0700 Subject: [PATCH 02/34] added noFitness fitness factor --- src/santa/simulator/SimulatorParser.java | 9 ++++++ .../simulator/compartments/Compartments.java | 8 ++--- .../simulator/fitness/NoFitnessFactor.java | 32 +++++++++++++++++++ 3 files changed, 45 insertions(+), 4 deletions(-) create mode 100644 src/santa/simulator/fitness/NoFitnessFactor.java diff --git a/src/santa/simulator/SimulatorParser.java b/src/santa/simulator/SimulatorParser.java index 56115b6..5bc260d 100644 --- a/src/santa/simulator/SimulatorParser.java +++ b/src/santa/simulator/SimulatorParser.java @@ -27,6 +27,7 @@ import santa.simulator.fitness.FitnessFactor; import santa.simulator.fitness.FitnessFunction; import santa.simulator.fitness.FrequencyDependentFitnessFactor; +import santa.simulator.fitness.NoFitnessFactor; import santa.simulator.fitness.PopulationSizeDependentFitnessFactor; import santa.simulator.fitness.PurifyingFitnessFactor; import santa.simulator.fitness.PurifyingFitnessModel; @@ -148,6 +149,7 @@ public class SimulatorParser { private final static String EMPIRICAL_FITNESS_FUNCTION = "empiricalFitness"; private final static String POPULATION_SIZE_DEPENDENT_FITNESS_FUNCTION = "populationSizeDependentFitness"; private final static String MAX_POP_SIZE = "maxPopulationSize"; + private final static String NO_FITNESS_FUNCTION = "noFitness"; private final static String MUTATOR = "mutator"; private final static String REPLICATOR = "replicator"; @@ -776,6 +778,9 @@ private FitnessFunction parseFitnessFunction(Element element) throws ParseExcept case POPULATION_SIZE_DEPENDENT_FITNESS_FUNCTION: factor = parsePopulationSizeDependentFitnessFunction(e); break; + case NO_FITNESS_FUNCTION: + factor = parseNoFitnessFunction(e); + break; default: throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e.getName() + "> is unrecognized"); @@ -905,6 +910,10 @@ private FitnessFactor parsePopulationSizeDependentFitnessFunction(Element elemen return new PopulationSizeDependentFitnessFactor((int) maxPopSize, declineRate, factor.feature, factor.sites); } + + private FitnessFactor parseNoFitnessFunction(Element element) throws ParseException { + return new NoFitnessFactor(); + } /** * @param element diff --git a/src/santa/simulator/compartments/Compartments.java b/src/santa/simulator/compartments/Compartments.java index 06fa0c1..fa2e387 100644 --- a/src/santa/simulator/compartments/Compartments.java +++ b/src/santa/simulator/compartments/Compartments.java @@ -28,11 +28,11 @@ public Compartments(List compartments, double[] transferRates) { this.transferProbs = new double[this.numCompartments][this.numCompartments]; double[] sum = new double[this.numCompartments]; +// for (int i = 0; i < transferRates.length; i++) { +// sum[i / this.numCompartments] += transferRates[i]; +// } for (int i = 0; i < transferRates.length; i++) { - sum[i / this.numCompartments] += transferRates[i]; - } - for (int i = 0; i < transferRates.length; i++) { - this.transferProbs[i / this.numCompartments][i % this.numCompartments] = transferRates[i] / sum[i / this.numCompartments]; + this.transferProbs[i / this.numCompartments][i % this.numCompartments] = transferRates[i]; } } diff --git a/src/santa/simulator/fitness/NoFitnessFactor.java b/src/santa/simulator/fitness/NoFitnessFactor.java new file mode 100644 index 0000000..eb1610e --- /dev/null +++ b/src/santa/simulator/fitness/NoFitnessFactor.java @@ -0,0 +1,32 @@ +/* + * To change this license header, choose License Headers in Project Properties. + * To change this template file, choose Tools | Templates + * and open the template in the editor. + */ +package santa.simulator.fitness; + +import java.util.Set; +import santa.simulator.genomes.Feature; +import santa.simulator.genomes.StateChange; + +/** + * + * @author Bradley R. Jones + */ +public class NoFitnessFactor extends AbstractFitnessFactor { + + public NoFitnessFactor() { + super(null, null); + } + + @Override + public double computeLogFitness(byte[] states) { + return Double.NEGATIVE_INFINITY; + } + + @Override + public double getLogFitnessChange(StateChange change) { + return 0; + } + +} From 686f8125364c09e77a3ef19e2abae71693f084f7 Mon Sep 17 00:00:00 2001 From: brj1 Date: Fri, 23 Mar 2018 15:19:15 -0700 Subject: [PATCH 03/34] removed NoFitessFactor; added exponential and logitstic populatins toXML --- src/santa/simulator/SimulatorParser.java | 36 ++++++++++++++----- .../simulator/compartments/Compartment.java | 23 ++++++++++-- .../simulator/fitness/NoFitnessFactor.java | 32 ----------------- 3 files changed, 47 insertions(+), 44 deletions(-) delete mode 100644 src/santa/simulator/fitness/NoFitnessFactor.java diff --git a/src/santa/simulator/SimulatorParser.java b/src/santa/simulator/SimulatorParser.java index 5bc260d..2d8379e 100644 --- a/src/santa/simulator/SimulatorParser.java +++ b/src/santa/simulator/SimulatorParser.java @@ -27,7 +27,7 @@ import santa.simulator.fitness.FitnessFactor; import santa.simulator.fitness.FitnessFunction; import santa.simulator.fitness.FrequencyDependentFitnessFactor; -import santa.simulator.fitness.NoFitnessFactor; +//import santa.simulator.fitness.NoFitnessFactor; import santa.simulator.fitness.PopulationSizeDependentFitnessFactor; import santa.simulator.fitness.PurifyingFitnessFactor; import santa.simulator.fitness.PurifyingFitnessModel; @@ -84,6 +84,8 @@ public class SimulatorParser { private final static String POPULATION_TYPE = "populationType"; private final static String STATIC_POPULATION = "staticPopulation"; private final static String DYNAMIC_POPULATION = "dynamicPopulation"; + private final static String MAX_POPULATION_SIZE = "maxPopulationSize"; + private final static String RECOMBINATION_HOTSPOTS = "recombinationHotSpots"; private final static String RECOMBINATION_HOTSPOT = "recombinationHotSpot"; @@ -149,7 +151,7 @@ public class SimulatorParser { private final static String EMPIRICAL_FITNESS_FUNCTION = "empiricalFitness"; private final static String POPULATION_SIZE_DEPENDENT_FITNESS_FUNCTION = "populationSizeDependentFitness"; private final static String MAX_POP_SIZE = "maxPopulationSize"; - private final static String NO_FITNESS_FUNCTION = "noFitness"; +// private final static String NO_FITNESS_FUNCTION = "noFitness"; private final static String MUTATOR = "mutator"; private final static String REPLICATOR = "replicator"; @@ -352,6 +354,8 @@ Simulation parseSimulation(Element element) throws ParseException { Compartment parseCompartment(Element element) throws ParseException { Compartment.InoculumType inoculumType = Compartment.InoculumType.NONE; int populationSize = -1; + int maxPopulationSize = -1; + double growthRate = -1; boolean genomeDescription = false; for (Object o : element.getChildren()) { @@ -380,6 +384,20 @@ Compartment parseCompartment(Element element) throws ParseException { throw new ParseException("Error parsing <" + POPULATION + "> element: " + pe.getMessage()); } break; + case MAX_POPULATION_SIZE: + try { + maxPopulationSize = parseInteger(e1, 1, Integer.MAX_VALUE); + } catch (ParseException pe) { + throw new ParseException("Error parsing <" + POPULATION + "> element: " + pe.getMessage()); + } + break; + case GROWTH_RATE: + try { + growthRate = parseDouble(e1, 0, Double.MAX_VALUE); + } catch (ParseException pe) { + throw new ParseException("Error parsing <" + POPULATION + "> element: " + pe.getMessage()); + } + break; case INOCULUM: String v = e1.getTextNormalize(); switch (v) { @@ -518,7 +536,7 @@ Compartment parseCompartment(Element element) throws ParseException { switch (populationType) { case STATIC_POPULATION: - return new Compartment(compartmentName, populationSize, inoculumType, genePool, epochs, samplingSchedule, populationType); + return new Compartment(compartmentName, populationSize, inoculumType, genePool, epochs, samplingSchedule, populationType, growthRate, maxPopulationSize); case DYNAMIC_POPULATION: if (dynamicSelector == null) { return new Compartment(compartmentName, populationSize, inoculumType, genePool, epochs, samplingSchedule); @@ -778,9 +796,9 @@ private FitnessFunction parseFitnessFunction(Element element) throws ParseExcept case POPULATION_SIZE_DEPENDENT_FITNESS_FUNCTION: factor = parsePopulationSizeDependentFitnessFunction(e); break; - case NO_FITNESS_FUNCTION: - factor = parseNoFitnessFunction(e); - break; +// case NO_FITNESS_FUNCTION: +// factor = parseNoFitnessFunction(e); +// break; default: throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e.getName() + "> is unrecognized"); @@ -911,9 +929,9 @@ private FitnessFactor parsePopulationSizeDependentFitnessFunction(Element elemen return new PopulationSizeDependentFitnessFactor((int) maxPopSize, declineRate, factor.feature, factor.sites); } - private FitnessFactor parseNoFitnessFunction(Element element) throws ParseException { - return new NoFitnessFactor(); - } +// private FitnessFactor parseNoFitnessFunction(Element element) throws ParseException { +// return new NoFitnessFactor(); +// } /** * @param element diff --git a/src/santa/simulator/compartments/Compartment.java b/src/santa/simulator/compartments/Compartment.java index da28691..cb762fd 100644 --- a/src/santa/simulator/compartments/Compartment.java +++ b/src/santa/simulator/compartments/Compartment.java @@ -10,6 +10,8 @@ import santa.simulator.genomes.Sequence; import santa.simulator.phylogeny.Phylogeny; import santa.simulator.population.DynamicPopulation; +import santa.simulator.population.ExponentialPopulation; +import santa.simulator.population.LogisticPopulation; import santa.simulator.population.Population; import santa.simulator.population.StaticPopulation; import santa.simulator.samplers.SamplingSchedule; @@ -87,7 +89,9 @@ public Compartment ( GenePool genePool, List epochs, SamplingSchedule samplingSchedule, - String populationType){ + String populationType, + double growthRate, + int maxPopulationSize){ this.name = name; this.populationSize = populationSize; @@ -97,7 +101,18 @@ public Compartment ( this.genePool = genePool; this.selector = new BinarySearchSelector(); // this.selector = new SimpleRouletteWheelSelector(); - population = new StaticPopulation(populationSize, genePool, selector, samplingSchedule.isSamplingTrees() ? new Phylogeny(populationSize) : null); + switch (populationType) { + case "exponential": + population = new ExponentialPopulation(populationSize, growthRate, genePool, selector, samplingSchedule.isSamplingTrees() ? new Phylogeny(populationSize) : null); + break; + case "logistic": + population = new LogisticPopulation(populationSize, (int)growthRate, maxPopulationSize, genePool, selector, samplingSchedule.isSamplingTrees() ? new Phylogeny(populationSize) : null); + break; + default: + population = new StaticPopulation(populationSize, genePool, selector, samplingSchedule.isSamplingTrees() ? new Phylogeny(populationSize) : null); + break; + } + } @@ -129,7 +144,7 @@ public void initalize(int replicate, Logger logger) { default: break; } - population.initialize(inoculum, populationSize); + population.initialize(inoculum, getPopulationSize()); } public void cleanup(int replicate, Logger logger) { @@ -156,6 +171,8 @@ public Population getPopulation() { } public int getPopulationSize() { + populationSize = population.getPopulationSize(); + return populationSize; } diff --git a/src/santa/simulator/fitness/NoFitnessFactor.java b/src/santa/simulator/fitness/NoFitnessFactor.java deleted file mode 100644 index eb1610e..0000000 --- a/src/santa/simulator/fitness/NoFitnessFactor.java +++ /dev/null @@ -1,32 +0,0 @@ -/* - * To change this license header, choose License Headers in Project Properties. - * To change this template file, choose Tools | Templates - * and open the template in the editor. - */ -package santa.simulator.fitness; - -import java.util.Set; -import santa.simulator.genomes.Feature; -import santa.simulator.genomes.StateChange; - -/** - * - * @author Bradley R. Jones - */ -public class NoFitnessFactor extends AbstractFitnessFactor { - - public NoFitnessFactor() { - super(null, null); - } - - @Override - public double computeLogFitness(byte[] states) { - return Double.NEGATIVE_INFINITY; - } - - @Override - public double getLogFitnessChange(StateChange change) { - return 0; - } - -} From b16adfad1acbb5b1ec38c5ffa97e9feb462fdc60 Mon Sep 17 00:00:00 2001 From: brj1 Date: Fri, 23 Mar 2018 15:25:17 -0700 Subject: [PATCH 04/34] fixed introduced bug --- src/santa/simulator/compartments/Compartment.java | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/santa/simulator/compartments/Compartment.java b/src/santa/simulator/compartments/Compartment.java index cb762fd..2e84b66 100644 --- a/src/santa/simulator/compartments/Compartment.java +++ b/src/santa/simulator/compartments/Compartment.java @@ -144,7 +144,7 @@ public void initalize(int replicate, Logger logger) { default: break; } - population.initialize(inoculum, getPopulationSize()); + population.initialize(inoculum, populationSize); } public void cleanup(int replicate, Logger logger) { @@ -171,8 +171,6 @@ public Population getPopulation() { } public int getPopulationSize() { - populationSize = population.getPopulationSize(); - return populationSize; } From ee51fd0724fa4e83ef7781cef3877b694518ad72 Mon Sep 17 00:00:00 2001 From: brj1 Date: Mon, 26 Mar 2018 13:07:39 -0700 Subject: [PATCH 05/34] fixed authors --- src/santa/simulator/SimulationEpoch.java | 1 + src/santa/simulator/SimulatorParser.java | 1 + src/santa/simulator/compartments/CompartmentEpoch.java | 1 + 3 files changed, 3 insertions(+) diff --git a/src/santa/simulator/SimulationEpoch.java b/src/santa/simulator/SimulationEpoch.java index 2f27e99..4ea86e1 100644 --- a/src/santa/simulator/SimulationEpoch.java +++ b/src/santa/simulator/SimulationEpoch.java @@ -10,6 +10,7 @@ /** * + * @author Andrew Rambaut * @author Bradley R. Jones */ public class SimulationEpoch { diff --git a/src/santa/simulator/SimulatorParser.java b/src/santa/simulator/SimulatorParser.java index 2d8379e..b74b607 100644 --- a/src/santa/simulator/SimulatorParser.java +++ b/src/santa/simulator/SimulatorParser.java @@ -62,6 +62,7 @@ /** * @author Andrew Rambaut * @author Alexei Drummond + * @author Bradley R. Jones * @version $Id: SimulatorParser.java,v 1.19 2006/07/19 14:35:32 kdforc0 Exp $ */ public class SimulatorParser { diff --git a/src/santa/simulator/compartments/CompartmentEpoch.java b/src/santa/simulator/compartments/CompartmentEpoch.java index 031ee4a..0c11198 100644 --- a/src/santa/simulator/compartments/CompartmentEpoch.java +++ b/src/santa/simulator/compartments/CompartmentEpoch.java @@ -11,6 +11,7 @@ import santa.simulator.samplers.SamplingSchedule; /* + * @author Andrew Rambaut * @author Bradley R. Jones */ public class CompartmentEpoch { From 501c106b9a9c719912b062b8591f2c56cd48b008 Mon Sep 17 00:00:00 2001 From: brj1 Date: Mon, 26 Mar 2018 13:09:12 -0700 Subject: [PATCH 06/34] fixed authors --- src/santa/simulator/Simulation.java | 1 + 1 file changed, 1 insertion(+) diff --git a/src/santa/simulator/Simulation.java b/src/santa/simulator/Simulation.java index 9a50a19..2845509 100644 --- a/src/santa/simulator/Simulation.java +++ b/src/santa/simulator/Simulation.java @@ -9,6 +9,7 @@ /** * @author Andrew Rambaut * @author Alexei Drummond + * @author Bradley R. Jones * @version $Id: Simulation.java,v 1.11 2006/07/19 12:53:05 kdforc0 Exp $ */ public class Simulation { From 9d739306bfe1ad340b90e6178cef6c83f3ff18e3 Mon Sep 17 00:00:00 2001 From: brj1 Date: Tue, 27 Mar 2018 11:22:17 -0700 Subject: [PATCH 07/34] fixed Virus/Genome transfer --- examples/HIV-1_latent.xml | 191 ++++++++++++++++++ src/santa/simulator/SimulatorMain.java | 2 +- src/santa/simulator/SimulatorParser.java | 51 +++-- .../simulator/compartments/Compartment.java | 4 +- .../simulator/compartments/Compartments.java | 62 +++--- 5 files changed, 253 insertions(+), 57 deletions(-) create mode 100644 examples/HIV-1_latent.xml diff --git a/examples/HIV-1_latent.xml b/examples/HIV-1_latent.xml new file mode 100644 index 0000000..019f3ae --- /dev/null +++ b/examples/HIV-1_latent.xml @@ -0,0 +1,191 @@ + + 1 + + 0 3.5e-6 0.001 0 + + + 9719 + + TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA + + + PR + aminoAcid + + 2253-2549 + + + RT + aminoAcid + 2550-4229 + + + IN + aminoAcid + 4230-5096 + + + + + plasma + + dynamicPopulation + + + 1000 + all + + + + + PR + 1-99 + 0.005 + 50000 + + + RT + 1 + + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 1.20 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + + + + + + + 2.5E-5 + + 0.42 2.49 0.29 + 1.73 0.23 4.73 + 6.99 0.20 0.60 + 1.02 2.56 0.88 + + + + + + + 0.05 + 0.001 + + + + + active + 1080 + + + + treatment + 1080 + + + + PR + 1-99 + 1 + 1 + + + + + + 2.5E-5 + + 0.42 2.49 0.29 + 1.73 0.23 4.73 + 6.99 0.20 0.60 + 1.02 2.56 0.88 + + + + + + + 0.05 + 0.001 + + + + + + + 216 + alignment_%r.fasta + + 10 + FASTA + + + + + + + + latent_reservoir + + dynamicPopulation + + + 0 + all + + + + + + + 0 + + 0.42 2.49 0.29 + 1.73 0.23 4.73 + 6.99 0.20 0.60 + 1.02 2.56 0.88 + + + + + + + + + + epoch + 2160 + + + + + 2160 + alignment_latent.fasta + + 20 + FASTA + + + + + + + diff --git a/src/santa/simulator/SimulatorMain.java b/src/santa/simulator/SimulatorMain.java index ee6db7b..ea14e20 100644 --- a/src/santa/simulator/SimulatorMain.java +++ b/src/santa/simulator/SimulatorMain.java @@ -21,7 +21,7 @@ public static void main(String[] args) { Simulator simulator; if (args.length > 0) { - simulator = simulatorFactory(args); + simulator = simulatorFactory(args); Logger.getLogger("santa.simulator").addHandler(new ConsoleHandler()); diff --git a/src/santa/simulator/SimulatorParser.java b/src/santa/simulator/SimulatorParser.java index b74b607..09dab59 100644 --- a/src/santa/simulator/SimulatorParser.java +++ b/src/santa/simulator/SimulatorParser.java @@ -85,6 +85,8 @@ public class SimulatorParser { private final static String POPULATION_TYPE = "populationType"; private final static String STATIC_POPULATION = "staticPopulation"; private final static String DYNAMIC_POPULATION = "dynamicPopulation"; + private final static String EXPONENTIAL_POPULATION = "exponentialPopulation"; + private final static String LOGISTIC_POPULATION = "logisticPopulation"; private final static String MAX_POPULATION_SIZE = "maxPopulationSize"; @@ -304,12 +306,24 @@ Simulation parseSimulation(Element element) throws ParseException { Compartments compartments = null; ArrayList compartmentList = new ArrayList<>(); + boolean genomeDescription = false; + for (Object o : element.getChildren()) { + Element e1 = (Element)o; + if (e1.getName().equals(GENOME_DESCRIPTION)) { + parseGenomeDescription(e1); + genomeDescription = true; + } + } + + if (!genomeDescription) { + throw new ParseException("Error parsing <" + element.getName() + "> element: <" + GENOME_DESCRIPTION + "> is missing"); + } + Element e = element.getChildren().get(0); switch (e.getName()) { - case COMPARTMENT: case TRANSFER_RATES: break; - default: + default: double[] transferRates = {1}; compartmentList.add(parseCompartment(element)); @@ -322,12 +336,16 @@ Simulation parseSimulation(Element element) throws ParseException { double[] transferRates = null; for (Object o: element.getChildren()) { - e = (Element)element.getChildren().get(0); + e = (Element)o; switch (e.getName()) { case COMPARTMENT: compartmentList.add(parseCompartment(e)); + break; case TRANSFER_RATES: transferRates = parseNumberList(e); + break; + case GENOME_DESCRIPTION: + break; default: throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + e.getName() + "> is unrecognized"); } @@ -358,20 +376,7 @@ Compartment parseCompartment(Element element) throws ParseException { int maxPopulationSize = -1; double growthRate = -1; - boolean genomeDescription = false; - for (Object o : element.getChildren()) { - Element e = (Element)o; - if (e.getName().equals(GENOME_DESCRIPTION)) { - parseGenomeDescription(e); - genomeDescription = true; - } - } - - if (!genomeDescription) { - throw new ParseException("Error parsing <" + element.getName() + "> element: <" + GENOME_DESCRIPTION + "> is missing"); - } - - for (Object o : element.getChildren()) { + for (Object o : element.getChildren()) { Element e = (Element)o; if (e.getName().equals(POPULATION)) { @@ -380,7 +385,7 @@ Compartment parseCompartment(Element element) throws ParseException { switch (e1.getName()) { case POPULATION_SIZE: try { - populationSize = parseInteger(e1, 1, Integer.MAX_VALUE); + populationSize = parseInteger(e1, 0, Integer.MAX_VALUE); } catch (ParseException pe) { throw new ParseException("Error parsing <" + POPULATION + "> element: " + pe.getMessage()); } @@ -420,11 +425,10 @@ Compartment parseCompartment(Element element) throws ParseException { } break; default: - throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e.getName() + "> is unrecognized"); + throw new ParseException("Error parsing <" + e.getName() + "> element: <" + e1.getName() + "> is unrecognized"); } } - } else if (!e.getName().equals(GENOME_DESCRIPTION) && - !e.getName().equals(GENE_POOL) && + } else if ( !e.getName().equals(GENE_POOL) && !e.getName().equals(FITNESS_FUNCTION) && !e.getName().equals(MUTATOR) && !e.getName().equals(REPLICATOR) && @@ -433,7 +437,8 @@ Compartment parseCompartment(Element element) throws ParseException { !e.getName().equals(EPOCH) && !e.getName().equals(POPULATION_TYPE) && !e.getName().equals(GROWTH_MODEL) && - !e.getName().equals(RECOMBINATION_HOTSPOTS)) { + !e.getName().equals(RECOMBINATION_HOTSPOTS) && + !e.getName().equals(NAME)) { throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e.getName() + "> is unrecognized"); } } @@ -537,6 +542,8 @@ Compartment parseCompartment(Element element) throws ParseException { switch (populationType) { case STATIC_POPULATION: + case EXPONENTIAL_POPULATION: + case LOGISTIC_POPULATION: return new Compartment(compartmentName, populationSize, inoculumType, genePool, epochs, samplingSchedule, populationType, growthRate, maxPopulationSize); case DYNAMIC_POPULATION: if (dynamicSelector == null) { diff --git a/src/santa/simulator/compartments/Compartment.java b/src/santa/simulator/compartments/Compartment.java index 2e84b66..518be9f 100644 --- a/src/santa/simulator/compartments/Compartment.java +++ b/src/santa/simulator/compartments/Compartment.java @@ -102,10 +102,10 @@ public Compartment ( this.selector = new BinarySearchSelector(); // this.selector = new SimpleRouletteWheelSelector(); switch (populationType) { - case "exponential": + case "exponentialPopulation": population = new ExponentialPopulation(populationSize, growthRate, genePool, selector, samplingSchedule.isSamplingTrees() ? new Phylogeny(populationSize) : null); break; - case "logistic": + case "logisticPopulation": population = new LogisticPopulation(populationSize, (int)growthRate, maxPopulationSize, genePool, selector, samplingSchedule.isSamplingTrees() ? new Phylogeny(populationSize) : null); break; default: diff --git a/src/santa/simulator/compartments/Compartments.java b/src/santa/simulator/compartments/Compartments.java index fa2e387..40b2d86 100644 --- a/src/santa/simulator/compartments/Compartments.java +++ b/src/santa/simulator/compartments/Compartments.java @@ -9,6 +9,7 @@ import java.util.Iterator; import java.util.List; import santa.simulator.Random; +import santa.simulator.Virus; import santa.simulator.genomes.GenePool; import santa.simulator.genomes.Genome; import santa.simulator.population.Population; @@ -36,38 +37,42 @@ public Compartments(List compartments, double[] transferRates) { } } - public void genomeTransfer(int generation) { + public void genomeTransfer(int generation) { + if (numCompartments > 1) { ArrayList< ArrayList > allGenomesToAdd = new ArrayList(numCompartments); - ArrayList< ArrayList > allGenomes = new ArrayList<>(numCompartments); + ArrayList< ArrayList > allVirusesToAdd = new ArrayList(numCompartments); for (int i = 0; i < numCompartments; i++) { allGenomesToAdd.add(new ArrayList<>()); + allVirusesToAdd.add(new ArrayList<>()); } for (int i = 0; i < numCompartments; i++) { Compartment migrator = compartments.get(i); - Population population = migrator.getPopulation(); - GenePool migratorGenePool = migrator.getGenePool(); - ArrayList genomes = new ArrayList<>(); - allGenomes.set(i, genomes); - for (Genome genome: migratorGenePool.getGenomes()) { - genomes.add(genome.copy()); - } + List viruses = migrator.getPopulation().getCurrentGeneration(); + GenePool genePool = migrator.getGenePool(); for (int j = 0; j < numCompartments; j++) { - ArrayList genomesToAdd = allGenomesToAdd.get(j); - if (i != j) { - for (Genome genome: genomes) { + ArrayList genomesToAdd = allGenomesToAdd.get(j); + ArrayList virusesToAdd = allVirusesToAdd.get(j); + + for (int k =0; k < viruses.size(); k++) { if (transferProbs[i][j] > 0) { - int n = genome.getFrequency(); - int numMigrating = Random.nextBinomial(n, transferProbs[i][j]); - Genome migratingGenome = genome.copy(); - - genome.setFrequency(n - numMigrating); - migratingGenome.setFrequency(numMigrating); - - genomesToAdd.add(migratingGenome); + boolean transfer = Random.nextUniform(0, 1) <= transferProbs[i][j]; + + if (transfer) { + Virus virus = viruses.get(k); + Genome genome = virus.getGenome(); + Genome migratingGenome = genome.copy(); + + virus.setGenome(migratingGenome); + virusesToAdd.add(virus); + viruses.remove(k); + + genePool.killGenome(genome); + genomesToAdd.add(migratingGenome); + } } } } @@ -75,19 +80,9 @@ public void genomeTransfer(int generation) { } for (int i = 0; i < numCompartments; i++) { - ArrayList genomes = allGenomes.get(i); GenePool compartmentGenePool = compartments.get(i).getGenePool(); - List compartmentGenomes = compartmentGenePool.getGenomes(); - for (int j = 0; j < genomes.size(); j++) { - Genome compartmentGenome = compartmentGenomes.get(j); - - compartmentGenome.setFrequency(genomes.get(j).getFrequency()); - - if (compartmentGenome.getFrequency() <= 0) { - compartmentGenome.setFrequency(1); - compartmentGenePool.killGenome(compartmentGenome); - } - } + List compartmentGenomes = compartmentGenePool.getGenomes(); + List viruses = compartments.get(i).getPopulation().getCurrentGeneration(); for (Genome genome: allGenomesToAdd.get(i)) { Genome newGenome = compartmentGenePool.createGenome(genome.getSequence(), genome.getDescription()); @@ -95,6 +90,9 @@ public void genomeTransfer(int generation) { newGenome.setFrequency(genome.getFrequency()); compartmentGenomes.add(newGenome); } + + viruses.addAll(allVirusesToAdd.get(i)); + } } } From 1c9d50ff77f45b180cc12dac636044d1d3c50a42 Mon Sep 17 00:00:00 2001 From: brj1 Date: Tue, 27 Mar 2018 14:43:12 -0700 Subject: [PATCH 08/34] updates --- examples/HIV-1_latent.xml | 58 +++++++++---------- .../simulator/compartments/Compartments.java | 4 +- 2 files changed, 28 insertions(+), 34 deletions(-) diff --git a/examples/HIV-1_latent.xml b/examples/HIV-1_latent.xml index 019f3ae..158ae57 100644 --- a/examples/HIV-1_latent.xml +++ b/examples/HIV-1_latent.xml @@ -33,7 +33,7 @@ dynamicPopulation - 1000 + 10000 all @@ -45,9 +45,9 @@ 50000 - RT - 1 - + RT + 1 + 0.01 0.01 0.01 @@ -68,8 +68,8 @@ 0.01 0.01 0.01 - - + + @@ -100,39 +100,35 @@ treatment 1080 - +` - PR - 1-99 - 1 - 1 - - + 1 + 1 + + - - - 2.5E-5 - - 0.42 2.49 0.29 - 1.73 0.23 4.73 - 6.99 0.20 0.60 - 1.02 2.56 0.88 - - - + + + 2.5E-5 + + 0.42 2.49 0.29 + 1.73 0.23 4.73 + 6.99 0.20 0.60 + 1.02 2.56 0.88 + + + - - - 0.05 - 0.001 - - + + + + 216 - alignment_%r.fasta + alignment_plasma.fasta 10 FASTA diff --git a/src/santa/simulator/compartments/Compartments.java b/src/santa/simulator/compartments/Compartments.java index 40b2d86..335ea5a 100644 --- a/src/santa/simulator/compartments/Compartments.java +++ b/src/santa/simulator/compartments/Compartments.java @@ -29,9 +29,7 @@ public Compartments(List compartments, double[] transferRates) { this.transferProbs = new double[this.numCompartments][this.numCompartments]; double[] sum = new double[this.numCompartments]; -// for (int i = 0; i < transferRates.length; i++) { -// sum[i / this.numCompartments] += transferRates[i]; -// } + for (int i = 0; i < transferRates.length; i++) { this.transferProbs[i / this.numCompartments][i % this.numCompartments] = transferRates[i]; } From e1df7a4dce931112b6391b749262a9193d6574f2 Mon Sep 17 00:00:00 2001 From: brj1 Date: Fri, 23 Mar 2018 14:37:01 -0700 Subject: [PATCH 09/34] readd NoFitnessFactor --- src/santa/simulator/SimulatorParser.java | 18 +++++------ .../simulator/compartments/Compartments.java | 2 +- .../simulator/fitness/NoFitnessFactor.java | 32 +++++++++++++++++++ 3 files changed, 42 insertions(+), 10 deletions(-) create mode 100644 src/santa/simulator/fitness/NoFitnessFactor.java diff --git a/src/santa/simulator/SimulatorParser.java b/src/santa/simulator/SimulatorParser.java index 09dab59..e08ae52 100644 --- a/src/santa/simulator/SimulatorParser.java +++ b/src/santa/simulator/SimulatorParser.java @@ -27,7 +27,7 @@ import santa.simulator.fitness.FitnessFactor; import santa.simulator.fitness.FitnessFunction; import santa.simulator.fitness.FrequencyDependentFitnessFactor; -//import santa.simulator.fitness.NoFitnessFactor; +import santa.simulator.fitness.NoFitnessFactor; import santa.simulator.fitness.PopulationSizeDependentFitnessFactor; import santa.simulator.fitness.PurifyingFitnessFactor; import santa.simulator.fitness.PurifyingFitnessModel; @@ -154,7 +154,7 @@ public class SimulatorParser { private final static String EMPIRICAL_FITNESS_FUNCTION = "empiricalFitness"; private final static String POPULATION_SIZE_DEPENDENT_FITNESS_FUNCTION = "populationSizeDependentFitness"; private final static String MAX_POP_SIZE = "maxPopulationSize"; -// private final static String NO_FITNESS_FUNCTION = "noFitness"; + private final static String NO_FITNESS_FUNCTION = "noFitness"; private final static String MUTATOR = "mutator"; private final static String REPLICATOR = "replicator"; @@ -804,9 +804,9 @@ private FitnessFunction parseFitnessFunction(Element element) throws ParseExcept case POPULATION_SIZE_DEPENDENT_FITNESS_FUNCTION: factor = parsePopulationSizeDependentFitnessFunction(e); break; -// case NO_FITNESS_FUNCTION: -// factor = parseNoFitnessFunction(e); -// break; + case NO_FITNESS_FUNCTION: + factor = parseNoFitnessFunction(e); + break; default: throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e.getName() + "> is unrecognized"); @@ -936,10 +936,10 @@ private FitnessFactor parsePopulationSizeDependentFitnessFunction(Element elemen return new PopulationSizeDependentFitnessFactor((int) maxPopSize, declineRate, factor.feature, factor.sites); } - -// private FitnessFactor parseNoFitnessFunction(Element element) throws ParseException { -// return new NoFitnessFactor(); -// } + + private FitnessFactor parseNoFitnessFunction(Element element) throws ParseException { + return new NoFitnessFactor(); + } /** * @param element diff --git a/src/santa/simulator/compartments/Compartments.java b/src/santa/simulator/compartments/Compartments.java index 335ea5a..98903df 100644 --- a/src/santa/simulator/compartments/Compartments.java +++ b/src/santa/simulator/compartments/Compartments.java @@ -29,7 +29,7 @@ public Compartments(List compartments, double[] transferRates) { this.transferProbs = new double[this.numCompartments][this.numCompartments]; double[] sum = new double[this.numCompartments]; - + for (int i = 0; i < transferRates.length; i++) { this.transferProbs[i / this.numCompartments][i % this.numCompartments] = transferRates[i]; } diff --git a/src/santa/simulator/fitness/NoFitnessFactor.java b/src/santa/simulator/fitness/NoFitnessFactor.java new file mode 100644 index 0000000..eb1610e --- /dev/null +++ b/src/santa/simulator/fitness/NoFitnessFactor.java @@ -0,0 +1,32 @@ +/* + * To change this license header, choose License Headers in Project Properties. + * To change this template file, choose Tools | Templates + * and open the template in the editor. + */ +package santa.simulator.fitness; + +import java.util.Set; +import santa.simulator.genomes.Feature; +import santa.simulator.genomes.StateChange; + +/** + * + * @author Bradley R. Jones + */ +public class NoFitnessFactor extends AbstractFitnessFactor { + + public NoFitnessFactor() { + super(null, null); + } + + @Override + public double computeLogFitness(byte[] states) { + return Double.NEGATIVE_INFINITY; + } + + @Override + public double getLogFitnessChange(StateChange change) { + return 0; + } + +} From 604f8fe3277a7050a5b79e43f7a9e2032f902e5c Mon Sep 17 00:00:00 2001 From: brj1 Date: Wed, 28 Mar 2018 12:26:03 -0700 Subject: [PATCH 10/34] fixed Genome copy bug --- examples/HIV-1_latent.xml | 39 +++++++------------ src/santa/simulator/SimulationEpoch.java | 2 +- .../compartments/CompartmentEpoch.java | 12 ++++-- .../simulator/compartments/Compartments.java | 19 ++++++--- src/santa/simulator/genomes/BaseGenome.java | 7 ---- .../simulator/genomes/CompactGenome.java | 3 +- src/santa/simulator/genomes/SimpleGenome.java | 7 ++-- 7 files changed, 42 insertions(+), 47 deletions(-) diff --git a/examples/HIV-1_latent.xml b/examples/HIV-1_latent.xml index 158ae57..ec43e29 100644 --- a/examples/HIV-1_latent.xml +++ b/examples/HIV-1_latent.xml @@ -2,7 +2,7 @@ xsi:noNamespaceSchemaLocation="santa.xsd"> 1 - 0 3.5e-6 0.001 0 + 0 0.00001 0.00001 0 9719 @@ -28,14 +28,19 @@ - plasma + plasma dynamicPopulation - 10000 + 100 all + + + 1.1 + 100000 + @@ -101,28 +106,9 @@ 1080 ` - - 1 - 1 - + + - - - - 2.5E-5 - - 0.42 2.49 0.29 - 1.73 0.23 4.73 - 6.99 0.20 0.60 - 1.02 2.56 0.88 - - - - - - - - @@ -148,6 +134,11 @@ all + + 1.01 + 10000 + + diff --git a/src/santa/simulator/SimulationEpoch.java b/src/santa/simulator/SimulationEpoch.java index 4ea86e1..83e9c53 100644 --- a/src/santa/simulator/SimulationEpoch.java +++ b/src/santa/simulator/SimulationEpoch.java @@ -51,7 +51,7 @@ public int run(Simulation simulation, Logger logger, int startGeneration) { } if (compartments.getNumCompartments() > 1) - compartments.genomeTransfer(generation); + compartments.genomeTransfer(generation, compartmentEpochs); if (generation % 100 == 0) { memlogger.finest("Generation "+ generation + " used memory: " + readableByteCount(usedMemory())); diff --git a/src/santa/simulator/compartments/CompartmentEpoch.java b/src/santa/simulator/compartments/CompartmentEpoch.java index 0c11198..7927c85 100644 --- a/src/santa/simulator/compartments/CompartmentEpoch.java +++ b/src/santa/simulator/compartments/CompartmentEpoch.java @@ -45,7 +45,9 @@ public int step(Compartment compartment, Logger logger, int startGeneration, int // adapt to this epoch, and the new generation population.updateAllFitnesses(fitnessFunction); - System.err.println("Initial population: compartment = " + compartment.getName() + + System.err.println("Initial population:" + + " compartment = " + compartment.getName() + + ", population = " + population.getCurrentGeneration().size() + ", fitness = " + population.getMeanFitness() + ", distance = " + population.getMeanDistance() + ", max freq = " + population.getMaxFrequency() + @@ -62,7 +64,9 @@ public int step(Compartment compartment, Logger logger, int startGeneration, int if (population.getPhylogeny() != null) population.getPhylogeny().pruneDeadLineages(); - System.err.print("Generation " + generation + ": compartment = " + compartment.getName() + + System.err.print("Generation " + generation + + ": compartment = " + compartment.getName() + + ", population = " + population.getCurrentGeneration().size() + ", fitness = " + population.getMeanFitness() + ", distance = " + population.getMeanDistance() + ", max freq = " + population.getMaxFrequency() + @@ -76,7 +80,9 @@ public int step(Compartment compartment, Logger logger, int startGeneration, int } else System.err.println(); } else { - logger.finest("Generation " + generation + ": compartment = " + compartment.getName() + + logger.finest("Generation " + generation + + ": compartment = " + compartment.getName() + + ", population = " + population.getCurrentGeneration().size() + " fitness = " + population.getMeanFitness() + ", distance = " + population.getMeanDistance() + ", max freq = " + population.getMaxFrequency() + diff --git a/src/santa/simulator/compartments/Compartments.java b/src/santa/simulator/compartments/Compartments.java index 98903df..45c8694 100644 --- a/src/santa/simulator/compartments/Compartments.java +++ b/src/santa/simulator/compartments/Compartments.java @@ -8,11 +8,12 @@ import java.util.ArrayList; import java.util.Iterator; import java.util.List; +import java.util.TreeSet; import santa.simulator.Random; import santa.simulator.Virus; +import santa.simulator.fitness.FitnessFunction; import santa.simulator.genomes.GenePool; import santa.simulator.genomes.Genome; -import santa.simulator.population.Population; /** * @@ -35,10 +36,10 @@ public Compartments(List compartments, double[] transferRates) { } } - public void genomeTransfer(int generation) { + public void genomeTransfer(int generation, List currentEpochs) { if (numCompartments > 1) { - ArrayList< ArrayList > allGenomesToAdd = new ArrayList(numCompartments); - ArrayList< ArrayList > allVirusesToAdd = new ArrayList(numCompartments); + ArrayList< ArrayList > allGenomesToAdd = new ArrayList<>(numCompartments); + ArrayList< ArrayList > allVirusesToAdd = new ArrayList<>(numCompartments); for (int i = 0; i < numCompartments; i++) { allGenomesToAdd.add(new ArrayList<>()); @@ -63,12 +64,14 @@ public void genomeTransfer(int generation) { Virus virus = viruses.get(k); Genome genome = virus.getGenome(); Genome migratingGenome = genome.copy(); - + virus.setGenome(migratingGenome); virusesToAdd.add(virus); viruses.remove(k); + // fix this later to make less genomes genePool.killGenome(genome); + migratingGenome.setFrequency(1); genomesToAdd.add(migratingGenome); } } @@ -78,6 +81,7 @@ public void genomeTransfer(int generation) { } for (int i = 0; i < numCompartments; i++) { + FitnessFunction fitnessFunction = currentEpochs.get(i).getFitnessFunction(); GenePool compartmentGenePool = compartments.get(i).getGenePool(); List compartmentGenomes = compartmentGenePool.getGenomes(); List viruses = compartments.get(i).getPopulation().getCurrentGeneration(); @@ -85,7 +89,10 @@ public void genomeTransfer(int generation) { for (Genome genome: allGenomesToAdd.get(i)) { Genome newGenome = compartmentGenePool.createGenome(genome.getSequence(), genome.getDescription()); - newGenome.setFrequency(genome.getFrequency()); + for (int j = 0; j < genome.getFrequency(); j++) { + compartmentGenePool.duplicateGenome(newGenome, new TreeSet<>(), fitnessFunction); + } + compartmentGenomes.add(newGenome); } diff --git a/src/santa/simulator/genomes/BaseGenome.java b/src/santa/simulator/genomes/BaseGenome.java index f8ff998..cd6a188 100644 --- a/src/santa/simulator/genomes/BaseGenome.java +++ b/src/santa/simulator/genomes/BaseGenome.java @@ -265,11 +265,4 @@ public int binomialDeviate(double mutationRate) { private int totalMutationCount = 0; FitnessFunction.FitnessGenomeCache fitnessCache; - - public void baseCopy(BaseGenome g) { - g.descriptor = this.descriptor; - - g.frequency = this.frequency; - g.totalMutationCount = this.totalMutationCount; - } } diff --git a/src/santa/simulator/genomes/CompactGenome.java b/src/santa/simulator/genomes/CompactGenome.java index 2ae0310..db361ee 100644 --- a/src/santa/simulator/genomes/CompactGenome.java +++ b/src/santa/simulator/genomes/CompactGenome.java @@ -178,8 +178,7 @@ static void setMasterSequence(Sequence masterSequence) { public Genome copy() { CompactGenome g = new CompactGenome(); - this.baseCopy(g); - g.applyMutations(this.mutations); + g.duplicate(this); return g; } diff --git a/src/santa/simulator/genomes/SimpleGenome.java b/src/santa/simulator/genomes/SimpleGenome.java index 29db8c7..792d235 100644 --- a/src/santa/simulator/genomes/SimpleGenome.java +++ b/src/santa/simulator/genomes/SimpleGenome.java @@ -11,7 +11,7 @@ public SimpleGenome() { public void duplicate(SimpleGenome source) { this.sequence = new SimpleSequence(source.sequence); - this.fitnessCache = source.fitnessCache.clone(); + this.fitnessCache = source.fitnessCache.clone(); this.descriptor = source.descriptor; setLogFitness(source.getLogFitness()); assert(this.descriptor.getGenomeLength() == this.sequence.getLength()); @@ -137,9 +137,8 @@ public boolean insert(int position, SimpleSequence seq) { public Genome copy() { SimpleGenome g = new SimpleGenome(); - - this.baseCopy(g); - g.sequence = new SimpleSequence(this.sequence); + + g.duplicate(this); return g; } From 3bf92f0bc9c94abf8cff9716b19465eb356540ba Mon Sep 17 00:00:00 2001 From: brj1 Date: Wed, 28 Mar 2018 16:18:47 -0700 Subject: [PATCH 11/34] fixed bugs --- src/santa/simulator/SimulatorParser.java | 4 +++- src/santa/simulator/fitness/NoFitnessFactor.java | 4 ++-- src/santa/simulator/mutators/AbstractMutator.java | 5 ++++- 3 files changed, 9 insertions(+), 4 deletions(-) diff --git a/src/santa/simulator/SimulatorParser.java b/src/santa/simulator/SimulatorParser.java index e08ae52..c68f246 100644 --- a/src/santa/simulator/SimulatorParser.java +++ b/src/santa/simulator/SimulatorParser.java @@ -938,7 +938,9 @@ private FitnessFactor parsePopulationSizeDependentFitnessFunction(Element elemen } private FitnessFactor parseNoFitnessFunction(Element element) throws ParseException { - return new NoFitnessFactor(); + FeatureAndSites factor = parseFeatureAndSites(element); + + return new NoFitnessFactor(factor.feature, factor.sites); } /** diff --git a/src/santa/simulator/fitness/NoFitnessFactor.java b/src/santa/simulator/fitness/NoFitnessFactor.java index eb1610e..2604cc5 100644 --- a/src/santa/simulator/fitness/NoFitnessFactor.java +++ b/src/santa/simulator/fitness/NoFitnessFactor.java @@ -15,8 +15,8 @@ */ public class NoFitnessFactor extends AbstractFitnessFactor { - public NoFitnessFactor() { - super(null, null); + public NoFitnessFactor(Feature feature, Set sites) { + super(feature, sites); } @Override diff --git a/src/santa/simulator/mutators/AbstractMutator.java b/src/santa/simulator/mutators/AbstractMutator.java index 756fc6d..1e7fbcb 100644 --- a/src/santa/simulator/mutators/AbstractMutator.java +++ b/src/santa/simulator/mutators/AbstractMutator.java @@ -23,7 +23,10 @@ public SortedSet mutate(Genome genome) { // iterate. This would avoid the sort at the end. SortedSet mutations = new TreeSet(); - int mutationCount = genome.binomialDeviate(mutationRate); + int mutationCount = 0; + + if (mutationRate > 0) + genome.binomialDeviate(mutationRate); // We expect only a few mutations per genome. Therefore, simply check // by looping over the already generated mutations to avoid duplicates hits. From ac66840e3a0d2bf0a1201a2076a0fb0c4ee34d3d Mon Sep 17 00:00:00 2001 From: brj1 Date: Thu, 12 Apr 2018 11:50:18 -0700 Subject: [PATCH 12/34] updated HIV-latent.xml --- examples/HIV-1_latent.xml | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/examples/HIV-1_latent.xml b/examples/HIV-1_latent.xml index ec43e29..7c2a436 100644 --- a/examples/HIV-1_latent.xml +++ b/examples/HIV-1_latent.xml @@ -2,7 +2,7 @@ xsi:noNamespaceSchemaLocation="santa.xsd"> 1 - 0 0.00001 0.00001 0 + 0 0.001 1e-7 0 9719 @@ -143,12 +143,11 @@ - 0 + 0.0 - 0.42 2.49 0.29 - 1.73 0.23 4.73 - 6.99 0.20 0.60 - 1.02 2.56 0.88 + 0 0 0 0 + 0 0 0 0 + 0 0 0 0 From 60597ac1e6ac1f036ff9d52465c4e109b811ffa5 Mon Sep 17 00:00:00 2001 From: brj1 Date: Fri, 13 Apr 2018 11:00:14 -0700 Subject: [PATCH 13/34] merged and built --- src/santa/simulator/SimulatorParser.java | 11 ++-- .../simulator/compartments/Compartment.java | 65 ++----------------- .../replicators/RecombinantReplicator.java | 1 - 3 files changed, 12 insertions(+), 65 deletions(-) diff --git a/src/santa/simulator/SimulatorParser.java b/src/santa/simulator/SimulatorParser.java index 0f31d4a..9ca7b7a 100644 --- a/src/santa/simulator/SimulatorParser.java +++ b/src/santa/simulator/SimulatorParser.java @@ -545,14 +545,17 @@ Compartment parseCompartment(Element element) throws ParseException { if (epochs.isEmpty()) throw new ParseException("Error parsing <" + element.getName() + "> element: <" + EPOCH + "> is missing"); + Selector selector; + PopulationGrowth growth; + switch (populationType) { case STATIC_POPULATION: - Selector selector = new BinarySearchSelector(); - PopulationGrowth growth = new StaticPopulationGrowth(populationSize); + selector = new BinarySearchSelector(); + growth = new StaticPopulationGrowth(populationSize); return new Compartment(compartmentName, populationSize, selector, growth, inoculumType, genePool, epochs, samplingSchedule); case DYNAMIC_POPULATION: - PopulationGrowth growth = new DynamicPopulationGrowth(); - Selector selector = null; + growth = new DynamicPopulationGrowth(); + selector = null; if (dynamicSelector == null) { selector = new DynamicSelector(); diff --git a/src/santa/simulator/compartments/Compartment.java b/src/santa/simulator/compartments/Compartment.java index 755d936..198645c 100644 --- a/src/santa/simulator/compartments/Compartment.java +++ b/src/santa/simulator/compartments/Compartment.java @@ -10,9 +10,8 @@ import santa.simulator.genomes.Sequence; import santa.simulator.phylogeny.Phylogeny; import santa.simulator.population.Population; +import santa.simulator.population.PopulationGrowth; import santa.simulator.samplers.SamplingSchedule; -import santa.simulator.selectors.BinarySearchSelector; -import santa.simulator.selectors.DynamicSelector; import santa.simulator.selectors.Selector; /** @@ -40,6 +39,8 @@ public enum InoculumType { public Compartment ( String name, int populationSize, + Selector selector, + PopulationGrowth growth, InoculumType inoculumType, GenePool genePool, List epochs, @@ -51,65 +52,9 @@ public Compartment ( this.epochs = epochs; this.samplingSchedule = samplingSchedule; this.genePool = genePool; - this.selector = new DynamicSelector(); - - population = new DynamicPopulation(genePool, selector, samplingSchedule.isSamplingTrees() ? new Phylogeny(populationSize) : null); - } - - //Default constructor (dynamic) - public Compartment ( - String name, - int populationSize, - DynamicSelector dynamicSelector, - InoculumType inoculumType, - GenePool genePool, - List epochs, - SamplingSchedule samplingSchedule) { - - this.name = name; - this.populationSize = populationSize; - this.inoculumType = inoculumType; - this.epochs = epochs; - this.samplingSchedule = samplingSchedule; - this.genePool = genePool; - this.selector = dynamicSelector; - - population = new DynamicPopulation(genePool, selector, samplingSchedule.isSamplingTrees() ? new Phylogeny(populationSize) : null); - } - - //Constructor for static population - public Compartment ( - String name, - int populationSize, - InoculumType inoculumType, - GenePool genePool, - List epochs, - SamplingSchedule samplingSchedule, - String populationType, - double growthRate, - int maxPopulationSize){ - - this.name = name; - this.populationSize = populationSize; - this.inoculumType = inoculumType; - this.epochs = epochs; - this.samplingSchedule = samplingSchedule; - this.genePool = genePool; - this.selector = new BinarySearchSelector(); -// this.selector = new SimpleRouletteWheelSelector(); - switch (populationType) { - case "exponentialPopulation": - population = new ExponentialPopulation(populationSize, growthRate, genePool, selector, samplingSchedule.isSamplingTrees() ? new Phylogeny(populationSize) : null); - break; - case "logisticPopulation": - population = new LogisticPopulation(populationSize, (int)growthRate, maxPopulationSize, genePool, selector, samplingSchedule.isSamplingTrees() ? new Phylogeny(populationSize) : null); - break; - default: - population = new StaticPopulation(populationSize, genePool, selector, samplingSchedule.isSamplingTrees() ? new Phylogeny(populationSize) : null); - break; - } - + this.selector = selector; + population = new Population(genePool, selector, growth, samplingSchedule.isSamplingTrees() ? new Phylogeny(populationSize) : null); } public void initalize(int replicate, Logger logger) { diff --git a/src/santa/simulator/replicators/RecombinantReplicator.java b/src/santa/simulator/replicators/RecombinantReplicator.java index b253a53..ff78f7e 100644 --- a/src/santa/simulator/replicators/RecombinantReplicator.java +++ b/src/santa/simulator/replicators/RecombinantReplicator.java @@ -1,7 +1,6 @@ package santa.simulator.replicators; import java.util.Arrays; -import java.util.Comparator; import java.util.SortedSet; import java.util.TreeSet; import java.util.List; From 2e2195838665a1385ae8b17a9af760edc4ad39e1 Mon Sep 17 00:00:00 2001 From: brj1 Date: Mon, 23 Apr 2018 15:31:46 -0700 Subject: [PATCH 14/34] added clonal expansion --- examples/HIV-1_latent.xml | 13 ++++---- src/santa/simulator/SimulatorParser.java | 19 ++++++++--- .../simulator/mutators/AbstractMutator.java | 2 +- .../selectors/ClonalExpansionSelector.java | 33 +++++++++++++++++++ 4 files changed, 56 insertions(+), 11 deletions(-) create mode 100644 src/santa/simulator/selectors/ClonalExpansionSelector.java diff --git a/examples/HIV-1_latent.xml b/examples/HIV-1_latent.xml index 7c2a436..ea2eee6 100644 --- a/examples/HIV-1_latent.xml +++ b/examples/HIV-1_latent.xml @@ -2,7 +2,7 @@ xsi:noNamespaceSchemaLocation="santa.xsd"> 1 - 0 0.001 1e-7 0 + 0 0.001 1e-8 0 9719 @@ -103,7 +103,7 @@ treatment - 1080 + 540 ` @@ -135,8 +135,9 @@ - 1.01 + 1.001 10000 + @@ -158,15 +159,15 @@ epoch - 2160 + 1620 - 2160 + 1620 alignment_latent.fasta - 20 + 1000 FASTA diff --git a/src/santa/simulator/SimulatorParser.java b/src/santa/simulator/SimulatorParser.java index 9ca7b7a..2db57d1 100644 --- a/src/santa/simulator/SimulatorParser.java +++ b/src/santa/simulator/SimulatorParser.java @@ -61,6 +61,7 @@ import santa.simulator.samplers.TreeSampler; import santa.simulator.samplers.GenomeDescriptionSampler; import santa.simulator.selectors.BinarySearchSelector; +import santa.simulator.selectors.ClonalExpansionSelector; import santa.simulator.selectors.DynamicSelector; import santa.simulator.selectors.Selector; @@ -106,6 +107,7 @@ public class SimulatorParser { private final static String INOCULUM_ALL = "all"; private final static String GROWTH_MODEL = "growthModel"; + private final static String CLONAL_EXPANSION = "clonalExpansion"; private final static String GROWTH_RATE = "growthRate"; private final static String CARRYING_POPULATION = "carryingPopulation"; @@ -443,7 +445,8 @@ Compartment parseCompartment(Element element) throws ParseException { !e.getName().equals(POPULATION_TYPE) && !e.getName().equals(GROWTH_MODEL) && !e.getName().equals(RECOMBINATION_HOTSPOTS) && - !e.getName().equals(NAME)) { + !e.getName().equals(NAME) && + !e.getName().equals(GENOME_DESCRIPTION)) { throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e.getName() + "> is unrecognized"); } } @@ -466,7 +469,7 @@ Compartment parseCompartment(Element element) throws ParseException { Replicator defaultReplicator = null; String populationType = null; - DynamicSelector dynamicSelector = null; + Selector dynamicSelector = null; List recombinationHotSpots = new ArrayList<>(); @@ -569,9 +572,10 @@ Compartment parseCompartment(Element element) throws ParseException { } } - DynamicSelector parseGrowthModel(Element element) throws ParseException { + Selector parseGrowthModel(Element element) throws ParseException { double growthRate = -1; double carryingPopulation = -1; + boolean clonal = false; for (Object o : element.getChildren()) { Element e = (Element)o; switch (e.getName()) { @@ -581,13 +585,20 @@ DynamicSelector parseGrowthModel(Element element) throws ParseException { case CARRYING_POPULATION: carryingPopulation = Double.parseDouble(e.getTextNormalize()); break; + case CLONAL_EXPANSION: + clonal = true; + break; default: throw new ParseException("Error parsing <" + GROWTH_MODEL + "> element: unknown XML element within " + GROWTH_MODEL); } } if (growthRate != -1 && carryingPopulation != -1) { - return new DynamicSelector(growthRate, carryingPopulation); + if (clonal) { + return new ClonalExpansionSelector(growthRate, carryingPopulation); + } else { + return new DynamicSelector(growthRate, carryingPopulation); + } } else { return null; } diff --git a/src/santa/simulator/mutators/AbstractMutator.java b/src/santa/simulator/mutators/AbstractMutator.java index 1e7fbcb..64fb292 100644 --- a/src/santa/simulator/mutators/AbstractMutator.java +++ b/src/santa/simulator/mutators/AbstractMutator.java @@ -26,7 +26,7 @@ public SortedSet mutate(Genome genome) { int mutationCount = 0; if (mutationRate > 0) - genome.binomialDeviate(mutationRate); + mutationCount = genome.binomialDeviate(mutationRate); // We expect only a few mutations per genome. Therefore, simply check // by looping over the already generated mutations to avoid duplicates hits. diff --git a/src/santa/simulator/selectors/ClonalExpansionSelector.java b/src/santa/simulator/selectors/ClonalExpansionSelector.java new file mode 100644 index 0000000..2e2e00e --- /dev/null +++ b/src/santa/simulator/selectors/ClonalExpansionSelector.java @@ -0,0 +1,33 @@ +package santa.simulator.selectors; + +import java.util.Collections; +import java.util.List; +import santa.simulator.Random; +import santa.simulator.Virus; + +/** + * + * @author Bradley R. Jones + */ +public class ClonalExpansionSelector implements Selector { + private double growthRate; + private double carryingPopulation; + + public ClonalExpansionSelector(double growthRate, double carryingPopulation) { + this.growthRate = growthRate; + this.carryingPopulation = carryingPopulation; + } + + public void selectParents(List currentGeneration, List selectedParents, int sampleSize) { + for(int i = 0; i < currentGeneration.size(); ++i) { + double fitness = currentGeneration.get(i).getFitness(); + + double splitProb = Math.max(fitness * (1 - growthRate) * (1-selectedParents.size()/carryingPopulation),Double.MIN_VALUE); + long nbChildren = fitness == 0 ? 0 : Random.nextBinomial(1, splitProb) + 1; + for(long n = 0; n < nbChildren * sampleSize; ++n) { + selectedParents.add(i); + } + } + Collections.shuffle(selectedParents); + } +} From 0344975c115391fe9cdb66a6d9d7f4e60f1fb79f Mon Sep 17 00:00:00 2001 From: brj1 Date: Tue, 24 Apr 2018 13:27:05 -0700 Subject: [PATCH 15/34] added clonalexapansiongrowth --- examples/HIV-1_latent.xml | 10 +++++----- .../simulator/selectors/ClonalExpansionSelector.java | 3 ++- src/santa/simulator/selectors/DynamicSelector.java | 1 + 3 files changed, 8 insertions(+), 6 deletions(-) diff --git a/examples/HIV-1_latent.xml b/examples/HIV-1_latent.xml index ea2eee6..ba14039 100644 --- a/examples/HIV-1_latent.xml +++ b/examples/HIV-1_latent.xml @@ -2,7 +2,7 @@ xsi:noNamespaceSchemaLocation="santa.xsd"> 1 - 0 0.001 1e-8 0 + 0 3.5e-6 0.001 0 9719 @@ -38,7 +38,7 @@ - 1.1 + 1000 100000 @@ -105,7 +105,7 @@ treatment 540 -` + @@ -135,8 +135,8 @@ - 1.001 - 10000 + 1.0001 + 1000 diff --git a/src/santa/simulator/selectors/ClonalExpansionSelector.java b/src/santa/simulator/selectors/ClonalExpansionSelector.java index 2e2e00e..49dc0b8 100644 --- a/src/santa/simulator/selectors/ClonalExpansionSelector.java +++ b/src/santa/simulator/selectors/ClonalExpansionSelector.java @@ -19,10 +19,11 @@ public ClonalExpansionSelector(double growthRate, double carryingPopulation) { } public void selectParents(List currentGeneration, List selectedParents, int sampleSize) { + Collections.shuffle(currentGeneration); for(int i = 0; i < currentGeneration.size(); ++i) { double fitness = currentGeneration.get(i).getFitness(); - double splitProb = Math.max(fitness * (1 - growthRate) * (1-selectedParents.size()/carryingPopulation),Double.MIN_VALUE); + double splitProb = Math.max(fitness * (1 - growthRate) * (1-(selectedParents.size() + currentGeneration.size())/carryingPopulation),Double.MIN_VALUE); long nbChildren = fitness == 0 ? 0 : Random.nextBinomial(1, splitProb) + 1; for(long n = 0; n < nbChildren * sampleSize; ++n) { selectedParents.add(i); diff --git a/src/santa/simulator/selectors/DynamicSelector.java b/src/santa/simulator/selectors/DynamicSelector.java index 7647e54..dfe37e6 100644 --- a/src/santa/simulator/selectors/DynamicSelector.java +++ b/src/santa/simulator/selectors/DynamicSelector.java @@ -25,6 +25,7 @@ public DynamicSelector(double growthRate, double carryingPopulation) { } public void selectParents(List currentGeneration, List selectedParents, int nbOfParents) { + Collections.shuffle(currentGeneration); for(int i = 0; i < currentGeneration.size(); ++i) { double fitness = currentGeneration.get(i).getFitness(); //Abbas: The below formulation of logistic growth was implemented by Gertjan From b885db198b81c28c8f1bb591ac5e97e616ef5c26 Mon Sep 17 00:00:00 2001 From: brj1 Date: Thu, 26 Apr 2018 11:27:34 -0700 Subject: [PATCH 16/34] fixing bugs in virus transfer --- examples/HIV-1_latent.xml | 13 +++--- src/santa/simulator/SimulatorParser.java | 23 ++++++----- .../simulator/compartments/Compartments.java | 41 +++++++++---------- .../selectors/ClonalExpansionSelector.java | 25 +++++++---- 4 files changed, 55 insertions(+), 47 deletions(-) diff --git a/examples/HIV-1_latent.xml b/examples/HIV-1_latent.xml index ba14039..bbfbb1e 100644 --- a/examples/HIV-1_latent.xml +++ b/examples/HIV-1_latent.xml @@ -33,13 +33,13 @@ dynamicPopulation - 100 + 15000 all - 1000 - 100000 + 5 + 30000 @@ -130,14 +130,13 @@ dynamicPopulation - 0 + 100 all - 1.0001 - 1000 - + 0.003 + 0.003 diff --git a/src/santa/simulator/SimulatorParser.java b/src/santa/simulator/SimulatorParser.java index 2db57d1..9cc4f3a 100644 --- a/src/santa/simulator/SimulatorParser.java +++ b/src/santa/simulator/SimulatorParser.java @@ -107,9 +107,10 @@ public class SimulatorParser { private final static String INOCULUM_ALL = "all"; private final static String GROWTH_MODEL = "growthModel"; - private final static String CLONAL_EXPANSION = "clonalExpansion"; - private final static String GROWTH_RATE = "growthRate"; + private final static String GROWTH_RATE = "growthRate"; private final static String CARRYING_POPULATION = "carryingPopulation"; + private final static String SPLIT_PROBABILITY = "split"; + private final static String DEATH_PROBABILITY = "death"; private final static String GENOME_DESCRIPTION = "genome"; private final static String GENOME_LENGTH = "length"; @@ -575,7 +576,8 @@ Compartment parseCompartment(Element element) throws ParseException { Selector parseGrowthModel(Element element) throws ParseException { double growthRate = -1; double carryingPopulation = -1; - boolean clonal = false; + double split = -1; + double death = -1; for (Object o : element.getChildren()) { Element e = (Element)o; switch (e.getName()) { @@ -585,8 +587,11 @@ Selector parseGrowthModel(Element element) throws ParseException { case CARRYING_POPULATION: carryingPopulation = Double.parseDouble(e.getTextNormalize()); break; - case CLONAL_EXPANSION: - clonal = true; + case SPLIT_PROBABILITY: + split = Double.parseDouble(e.getTextNormalize()); + break; + case DEATH_PROBABILITY: + death = Double.parseDouble(e.getTextNormalize()); break; default: throw new ParseException("Error parsing <" + GROWTH_MODEL + "> element: unknown XML element within " + GROWTH_MODEL); @@ -594,11 +599,9 @@ Selector parseGrowthModel(Element element) throws ParseException { } if (growthRate != -1 && carryingPopulation != -1) { - if (clonal) { - return new ClonalExpansionSelector(growthRate, carryingPopulation); - } else { - return new DynamicSelector(growthRate, carryingPopulation); - } + return new DynamicSelector(growthRate, carryingPopulation); + } else if (split != -1 && death != -1) { + return new ClonalExpansionSelector(split, death); } else { return null; } diff --git a/src/santa/simulator/compartments/Compartments.java b/src/santa/simulator/compartments/Compartments.java index 45c8694..9acb20f 100644 --- a/src/santa/simulator/compartments/Compartments.java +++ b/src/santa/simulator/compartments/Compartments.java @@ -38,11 +38,9 @@ public Compartments(List compartments, double[] transferRates) { public void genomeTransfer(int generation, List currentEpochs) { if (numCompartments > 1) { - ArrayList< ArrayList > allGenomesToAdd = new ArrayList<>(numCompartments); ArrayList< ArrayList > allVirusesToAdd = new ArrayList<>(numCompartments); for (int i = 0; i < numCompartments; i++) { - allGenomesToAdd.add(new ArrayList<>()); allVirusesToAdd.add(new ArrayList<>()); } @@ -53,26 +51,22 @@ public void genomeTransfer(int generation, List currentEpochs) for (int j = 0; j < numCompartments; j++) { if (i != j) { - ArrayList genomesToAdd = allGenomesToAdd.get(j); ArrayList virusesToAdd = allVirusesToAdd.get(j); - for (int k =0; k < viruses.size(); k++) { + for (int k = 0; k < viruses.size();) { if (transferProbs[i][j] > 0) { boolean transfer = Random.nextUniform(0, 1) <= transferProbs[i][j]; if (transfer) { Virus virus = viruses.get(k); Genome genome = virus.getGenome(); - Genome migratingGenome = genome.copy(); - - virus.setGenome(migratingGenome); + virusesToAdd.add(virus); viruses.remove(k); - // fix this later to make less genomes genePool.killGenome(genome); - migratingGenome.setFrequency(1); - genomesToAdd.add(migratingGenome); + } else { + k++; } } } @@ -81,22 +75,25 @@ public void genomeTransfer(int generation, List currentEpochs) } for (int i = 0; i < numCompartments; i++) { - FitnessFunction fitnessFunction = currentEpochs.get(i).getFitnessFunction(); - GenePool compartmentGenePool = compartments.get(i).getGenePool(); - List compartmentGenomes = compartmentGenePool.getGenomes(); - List viruses = compartments.get(i).getPopulation().getCurrentGeneration(); + List virusesToAdd = allVirusesToAdd.get(i); + + if (!virusesToAdd.isEmpty()) { + FitnessFunction fitnessFunction = currentEpochs.get(i).getFitnessFunction(); + GenePool compartmentGenePool = compartments.get(i).getGenePool(); + List viruses = compartments.get(i).getPopulation().getCurrentGeneration(); - for (Genome genome: allGenomesToAdd.get(i)) { - Genome newGenome = compartmentGenePool.createGenome(genome.getSequence(), genome.getDescription()); - - for (int j = 0; j < genome.getFrequency(); j++) { + // fix later to remove create less genomes + for (Virus v: virusesToAdd) { + Genome genome = v.getGenome(); + Genome newGenome = compartmentGenePool.createGenome(genome.getSequence(), genome.getDescription()); + + v.setGenome(newGenome); + compartmentGenePool.duplicateGenome(newGenome, new TreeSet<>(), fitnessFunction); } - - compartmentGenomes.add(newGenome); - } - viruses.addAll(allVirusesToAdd.get(i)); + viruses.addAll(virusesToAdd); + } } } } diff --git a/src/santa/simulator/selectors/ClonalExpansionSelector.java b/src/santa/simulator/selectors/ClonalExpansionSelector.java index 49dc0b8..6c55135 100644 --- a/src/santa/simulator/selectors/ClonalExpansionSelector.java +++ b/src/santa/simulator/selectors/ClonalExpansionSelector.java @@ -10,21 +10,30 @@ * @author Bradley R. Jones */ public class ClonalExpansionSelector implements Selector { - private double growthRate; - private double carryingPopulation; + private double splitProbability; + private double deathProbability; + private double persistProbability; - public ClonalExpansionSelector(double growthRate, double carryingPopulation) { - this.growthRate = growthRate; - this.carryingPopulation = carryingPopulation; + public ClonalExpansionSelector(double splitProbability, double deathProbability) { + this.splitProbability = splitProbability; + this.deathProbability = deathProbability; + this.persistProbability = 1 - deathProbability; } public void selectParents(List currentGeneration, List selectedParents, int sampleSize) { - Collections.shuffle(currentGeneration); for(int i = 0; i < currentGeneration.size(); ++i) { double fitness = currentGeneration.get(i).getFitness(); + int nbChildren = 0; + + double draw = Random.nextUniform(0, 1); + if (draw < persistProbability * fitness) { + if (draw < splitProbability * fitness) { + nbChildren = 2; + } else { + nbChildren = 1; + } + } - double splitProb = Math.max(fitness * (1 - growthRate) * (1-(selectedParents.size() + currentGeneration.size())/carryingPopulation),Double.MIN_VALUE); - long nbChildren = fitness == 0 ? 0 : Random.nextBinomial(1, splitProb) + 1; for(long n = 0; n < nbChildren * sampleSize; ++n) { selectedParents.add(i); } From 5d29507c4df7bd0598825133eced418a2add662f Mon Sep 17 00:00:00 2001 From: brj1 Date: Thu, 9 Aug 2018 13:50:00 -0700 Subject: [PATCH 17/34] changed genome transfer to class --- src/santa/simulator/SimulatorParser.java | 71 +++++++------- .../simulator/compartments/Compartments.java | 72 +------------- .../compartments/MatrixTransfer.java | 96 +++++++++++++++++++ .../simulator/compartments/Transfer.java | 16 ++++ 4 files changed, 150 insertions(+), 105 deletions(-) create mode 100644 src/santa/simulator/compartments/MatrixTransfer.java create mode 100644 src/santa/simulator/compartments/Transfer.java diff --git a/src/santa/simulator/SimulatorParser.java b/src/santa/simulator/SimulatorParser.java index 9cc4f3a..2c7ccd1 100644 --- a/src/santa/simulator/SimulatorParser.java +++ b/src/santa/simulator/SimulatorParser.java @@ -20,6 +20,7 @@ import org.jdom2.Element; import santa.simulator.compartments.Compartment; import santa.simulator.compartments.Compartments; +import santa.simulator.compartments.MatrixTransfer; import santa.simulator.fitness.AgeDependentFitnessFactor; import santa.simulator.fitness.BetaDistributedPurifyingFitnessModel; @@ -327,52 +328,48 @@ Simulation parseSimulation(Element element) throws ParseException { throw new ParseException("Error parsing <" + element.getName() + "> element: <" + GENOME_DESCRIPTION + "> is missing"); } + double[] transferRates = null; + Element e = element.getChildren().get(0); switch (e.getName()) { case TRANSFER_RATES: + for (Object o: element.getChildren()) { + Element e2 = (Element)o; + switch (e2.getName()) { + case COMPARTMENT: + compartmentList.add(parseCompartment(e2)); + break; + case TRANSFER_RATES: + transferRates = parseNumberList(e2); + break; + case GENOME_DESCRIPTION: + break; + default: + throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + e.getName() + "> is unrecognized"); + } + } + + if (transferRates == null) { + throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + TRANSFER_RATES + "> is missing"); + } + + if (compartmentList.isEmpty()) { + throw new ParseException("Error parsing <" + SIMULATION + "> no <" + COMPARTMENT + "> found"); + } + + if (transferRates.length != compartmentList.size() * compartmentList.size()) { + throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + TRANSFER_RATES + "> should be size (" + compartmentList.size() * compartmentList.size() + "), but was (" + transferRates.length + ") instead"); + } break; default: - double[] transferRates = {1}; - - compartmentList.add(parseCompartment(element)); - compartments = new Compartments(compartmentList, transferRates); + transferRates = new double[1]; + transferRates[1] = 1; + compartmentList.add(parseCompartment(element)); break; } - if (compartments == null) { - double[] transferRates = null; - - for (Object o: element.getChildren()) { - e = (Element)o; - switch (e.getName()) { - case COMPARTMENT: - compartmentList.add(parseCompartment(e)); - break; - case TRANSFER_RATES: - transferRates = parseNumberList(e); - break; - case GENOME_DESCRIPTION: - break; - default: - throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + e.getName() + "> is unrecognized"); - } - } - - if (transferRates == null) { - throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + TRANSFER_RATES + "> is missing"); - } - - if (compartmentList.isEmpty()) { - throw new ParseException("Error parsing <" + SIMULATION + "> no <" + COMPARTMENT + "> found"); - } - - if (transferRates.length != compartmentList.size() * compartmentList.size()) { - throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + TRANSFER_RATES + "> should be size (" + compartmentList.size() * compartmentList.size() + "), but was (" + transferRates.length + ") instead"); - } - - compartments = new Compartments(compartmentList, transferRates); - } + compartments = new Compartments(compartmentList, new MatrixTransfer(transferRates, compartmentList.size())); return new Simulation(compartments); } diff --git a/src/santa/simulator/compartments/Compartments.java b/src/santa/simulator/compartments/Compartments.java index 9acb20f..6e12faa 100644 --- a/src/santa/simulator/compartments/Compartments.java +++ b/src/santa/simulator/compartments/Compartments.java @@ -20,82 +20,18 @@ * @author Bradley R. Jones */ public class Compartments implements Iterable { - private double[][] transferProbs; + private Transfer transfer; private List compartments; private int numCompartments; - public Compartments(List compartments, double[] transferRates) { + public Compartments(List compartments, Transfer transfer) { this.compartments = compartments; this.numCompartments = compartments.size(); - this.transferProbs = new double[this.numCompartments][this.numCompartments]; - - double[] sum = new double[this.numCompartments]; - - for (int i = 0; i < transferRates.length; i++) { - this.transferProbs[i / this.numCompartments][i % this.numCompartments] = transferRates[i]; - } + this.transfer = transfer; } public void genomeTransfer(int generation, List currentEpochs) { - if (numCompartments > 1) { - ArrayList< ArrayList > allVirusesToAdd = new ArrayList<>(numCompartments); - - for (int i = 0; i < numCompartments; i++) { - allVirusesToAdd.add(new ArrayList<>()); - } - - for (int i = 0; i < numCompartments; i++) { - Compartment migrator = compartments.get(i); - List viruses = migrator.getPopulation().getCurrentGeneration(); - GenePool genePool = migrator.getGenePool(); - - for (int j = 0; j < numCompartments; j++) { - if (i != j) { - ArrayList virusesToAdd = allVirusesToAdd.get(j); - - for (int k = 0; k < viruses.size();) { - if (transferProbs[i][j] > 0) { - boolean transfer = Random.nextUniform(0, 1) <= transferProbs[i][j]; - - if (transfer) { - Virus virus = viruses.get(k); - Genome genome = virus.getGenome(); - - virusesToAdd.add(virus); - viruses.remove(k); - - genePool.killGenome(genome); - } else { - k++; - } - } - } - } - } - } - - for (int i = 0; i < numCompartments; i++) { - List virusesToAdd = allVirusesToAdd.get(i); - - if (!virusesToAdd.isEmpty()) { - FitnessFunction fitnessFunction = currentEpochs.get(i).getFitnessFunction(); - GenePool compartmentGenePool = compartments.get(i).getGenePool(); - List viruses = compartments.get(i).getPopulation().getCurrentGeneration(); - - // fix later to remove create less genomes - for (Virus v: virusesToAdd) { - Genome genome = v.getGenome(); - Genome newGenome = compartmentGenePool.createGenome(genome.getSequence(), genome.getDescription()); - - v.setGenome(newGenome); - - compartmentGenePool.duplicateGenome(newGenome, new TreeSet<>(), fitnessFunction); - } - - viruses.addAll(virusesToAdd); - } - } - } + transfer.genomeTransfer(compartments, generation, currentEpochs); } public int getNumCompartments() { diff --git a/src/santa/simulator/compartments/MatrixTransfer.java b/src/santa/simulator/compartments/MatrixTransfer.java new file mode 100644 index 0000000..b81660f --- /dev/null +++ b/src/santa/simulator/compartments/MatrixTransfer.java @@ -0,0 +1,96 @@ +/* + * To change this license header, choose License Headers in Project Properties. + * To change this template file, choose Tools | Templates + * and open the template in the editor. + */ +package santa.simulator.compartments; + +import java.util.ArrayList; +import java.util.List; +import java.util.TreeSet; +import santa.simulator.Random; +import santa.simulator.Virus; +import santa.simulator.fitness.FitnessFunction; +import santa.simulator.genomes.GenePool; +import santa.simulator.genomes.Genome; +import santa.simulator.genomes.Mutation; + +/** + * + * @author Bradley R. Jones + */ +public class MatrixTransfer implements Transfer { + private double[][] transferProbs; + private int numCompartments; + + public MatrixTransfer(double [] transferRates, int numCompartment) { + this.numCompartments = numCompartments; + this.transferProbs = new double[this.numCompartments][this.numCompartments]; + + for (int i = 0; i < transferRates.length; i++) { + this.transferProbs[i / this.numCompartments][i % this.numCompartments] = transferRates[i]; + } + } + + public void genomeTransfer(List compartments, int generation, List currentEpochs) { + if (numCompartments > 1) { + ArrayList< ArrayList > allVirusesToAdd = new ArrayList<>(numCompartments); + + for (int i = 0; i < numCompartments; i++) { + allVirusesToAdd.add(new ArrayList()); + } + + for (int i = 0; i < numCompartments; i++) { + Compartment migrator = compartments.get(i); + List viruses = migrator.getPopulation().getCurrentGeneration(); + GenePool genePool = migrator.getGenePool(); + + for (int j = 0; j < numCompartments; j++) { + if (i != j) { + ArrayList virusesToAdd = allVirusesToAdd.get(j); + + for (int k = 0; k < viruses.size();) { + if (transferProbs[i][j] > 0) { + boolean transfer = Random.nextUniform(0, 1) <= transferProbs[i][j]; + + if (transfer) { + Virus virus = viruses.get(k); + Genome genome = virus.getGenome(); + + virusesToAdd.add(virus); + viruses.remove(k); + + genePool.killGenome(genome); + } else { + k++; + } + } + } + } + } + } + + for (int i = 0; i < numCompartments; i++) { + List virusesToAdd = allVirusesToAdd.get(i); + + if (!virusesToAdd.isEmpty()) { + FitnessFunction fitnessFunction = currentEpochs.get(i).getFitnessFunction(); + GenePool compartmentGenePool = compartments.get(i).getGenePool(); + List viruses = compartments.get(i).getPopulation().getCurrentGeneration(); + + // fix later to remove create less genomes + for (Virus v: virusesToAdd) { + Genome genome = v.getGenome(); + Genome newGenome = compartmentGenePool.createGenome(genome.getSequence(), genome.getDescription()); + + v.setGenome(newGenome); + + compartmentGenePool.duplicateGenome(newGenome, new TreeSet(), fitnessFunction); + } + + viruses.addAll(virusesToAdd); + } + } + } + } +} diff --git a/src/santa/simulator/compartments/Transfer.java b/src/santa/simulator/compartments/Transfer.java new file mode 100644 index 0000000..dc952ad --- /dev/null +++ b/src/santa/simulator/compartments/Transfer.java @@ -0,0 +1,16 @@ +/* + * To change this license header, choose License Headers in Project Properties. + * To change this template file, choose Tools | Templates + * and open the template in the editor. + */ +package santa.simulator.compartments; + +import java.util.List; + +/** + * + * @author Bradley R. Jones + */ +public interface Transfer { + void genomeTransfer(List compartments, int generation, List currentEpochs); +} From cd3404ebbe4c1b7113bd6af05c6d589dbe9d9b4e Mon Sep 17 00:00:00 2001 From: brj1 Date: Fri, 10 Aug 2018 11:38:24 -0700 Subject: [PATCH 18/34] fixed bugs --- src/santa/simulator/SimulatorParser.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/santa/simulator/SimulatorParser.java b/src/santa/simulator/SimulatorParser.java index 2c7ccd1..7d659f8 100644 --- a/src/santa/simulator/SimulatorParser.java +++ b/src/santa/simulator/SimulatorParser.java @@ -363,7 +363,7 @@ Simulation parseSimulation(Element element) throws ParseException { break; default: transferRates = new double[1]; - transferRates[1] = 1; + transferRates[0] = 1; compartmentList.add(parseCompartment(element)); break; From cf572f899eab676fb6a9762c0bbce54e3e82347f Mon Sep 17 00:00:00 2001 From: brj1 Date: Fri, 10 Aug 2018 11:38:45 -0700 Subject: [PATCH 19/34] fixed bugs --- src/santa/simulator/compartments/MatrixTransfer.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/santa/simulator/compartments/MatrixTransfer.java b/src/santa/simulator/compartments/MatrixTransfer.java index b81660f..449be16 100644 --- a/src/santa/simulator/compartments/MatrixTransfer.java +++ b/src/santa/simulator/compartments/MatrixTransfer.java @@ -23,7 +23,7 @@ public class MatrixTransfer implements Transfer { private double[][] transferProbs; private int numCompartments; - public MatrixTransfer(double [] transferRates, int numCompartment) { + public MatrixTransfer(double [] transferRates, int numCompartments) { this.numCompartments = numCompartments; this.transferProbs = new double[this.numCompartments][this.numCompartments]; @@ -64,6 +64,8 @@ public void genomeTransfer(List compartments, int generation, List< } else { k++; } + } else { + k++; } } } From d68a18d72df2847cd06b7770383cb137484e9138 Mon Sep 17 00:00:00 2001 From: brj1 Date: Fri, 10 Aug 2018 11:47:53 -0700 Subject: [PATCH 20/34] optimized AbstractSiteFitnessFactor by getting it to only look at the sites it cares about --- src/santa/simulator/fitness/AbstractSiteFitnessFactor.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/santa/simulator/fitness/AbstractSiteFitnessFactor.java b/src/santa/simulator/fitness/AbstractSiteFitnessFactor.java index 96eca48..60273c8 100644 --- a/src/santa/simulator/fitness/AbstractSiteFitnessFactor.java +++ b/src/santa/simulator/fitness/AbstractSiteFitnessFactor.java @@ -35,7 +35,7 @@ public double computeLogFitness(byte[] sequence) { if (this.logFitness.length != sequence.length) { logFitness = Double.NEGATIVE_INFINITY; } else { - for (int site = 0; site < this.logFitness.length; site++) { + for (int site: getSites()) { logFitness += this.logFitness[site][sequence[site]]; if (logFitness == Double.NEGATIVE_INFINITY) { break; From 5cb157576d243fbe60aef70afc1ac8aac3d4be0d Mon Sep 17 00:00:00 2001 From: brj1 Date: Mon, 13 Aug 2018 11:42:36 -0700 Subject: [PATCH 21/34] fixed bug introduced by last change --- src/santa/simulator/fitness/AbstractSiteFitnessFactor.java | 1 + 1 file changed, 1 insertion(+) diff --git a/src/santa/simulator/fitness/AbstractSiteFitnessFactor.java b/src/santa/simulator/fitness/AbstractSiteFitnessFactor.java index 60273c8..2cf99e0 100644 --- a/src/santa/simulator/fitness/AbstractSiteFitnessFactor.java +++ b/src/santa/simulator/fitness/AbstractSiteFitnessFactor.java @@ -59,6 +59,7 @@ public double getLogFitnessChange(StateChange change) { double fit = 0; // neutral fitness double[] logFitnessPosition = null; try { + if (getSites().contains(change.position)) logFitnessPosition = logFitness[change.position]; } catch(IndexOutOfBoundsException e) { // catch IndexOutOfBoundsException b/c insertions may have From fc5bc63fee007fec2f7fca66bc34ea967e8054e7 Mon Sep 17 00:00:00 2001 From: brj1 Date: Tue, 4 Sep 2018 14:02:18 -0700 Subject: [PATCH 22/34] added recording of compartment tranfers --- examples/HIV-1_VIL.xml | 1228 +++++++++++++++++ examples/HIV-1_latent.xml | 1062 +++++++++++++- src/santa/simulator/Virus.java | 12 + .../compartments/MatrixTransfer.java | 56 +- .../simulator/samplers/AlignmentSampler.java | 21 +- 5 files changed, 2317 insertions(+), 62 deletions(-) create mode 100644 examples/HIV-1_VIL.xml diff --git a/examples/HIV-1_VIL.xml b/examples/HIV-1_VIL.xml new file mode 100644 index 0000000..29b4891 --- /dev/null +++ b/examples/HIV-1_VIL.xml @@ -0,0 +1,1228 @@ + + 1 + + 0 1 0 0.9999965 0 3.5e-6 0.001 0 0.999 + + + 9719 + + TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATA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alignment_latent.fasta + + 50 + FASTA + + + + + + + diff --git a/examples/HIV-1_latent.xml b/examples/HIV-1_latent.xml index bbfbb1e..c7c891f 100644 --- a/examples/HIV-1_latent.xml +++ b/examples/HIV-1_latent.xml @@ -2,13 +2,18 @@ xsi:noNamespaceSchemaLocation="santa.xsd"> 1 - 0 3.5e-6 0.001 0 + 0 0.0001 0.001 0 - + 9719 - TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA + TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA + + gag + aminoAcid + 790-2289 + PR aminoAcid @@ -23,24 +28,17 @@ IN aminoAcid - 4230-5096 + 4230-5093 + + + NEF + aminoAcid + 8797-9414 plasma - - dynamicPopulation - - - 15000 - all - - - - 5 - 30000 - @@ -57,7 +55,7 @@ 0.01 0.01 0.01 - 0.01 + 0.01 0.01 0.01 0.01 @@ -75,8 +73,1020 @@ 0.01 + + + gag + 1-500 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + gag + 1 + + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 1.20 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + + + + + gag + 26 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.01 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + gag + 65 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 0.99 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + gag + 81 + + 0.99 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + gag + 104 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.01 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + gag + 268 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.02 + 1.00 + 1.00 + 0.98 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + gag + 331 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 0.98 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.02 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + gag + 390 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.01 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + gag + 479 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.01 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + RT + 1-560 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + RT + 200 + + 0.98 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + RT + 275 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.02 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + RT + 454 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.02 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 0.98 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + RT + 461 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.02 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 0.98 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + RT + 466 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 0.98 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + RT + 468 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.02 + 1.00 + 1.00 + 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1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.02 + 1.00 + 1.00 + 1.00 + + + + + NEF + 194 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.02 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 0.98 + 1.00 + 1.00 + + + dynamicPopulation + + + 10000 + all + + + + 5 + 100000 + + 2.5E-5 @@ -98,12 +1108,12 @@ active - 1080 + 1400 treatment - 540 + 1400 @@ -113,12 +1123,12 @@ - 216 + 140 alignment_plasma.fasta 10 FASTA - + @@ -130,7 +1140,7 @@ dynamicPopulation - 100 + 0 all @@ -158,17 +1168,17 @@ epoch - 1620 + 2800 - 1620 + 2800 alignment_latent.fasta - 1000 + 50 FASTA - + diff --git a/src/santa/simulator/Virus.java b/src/santa/simulator/Virus.java index 424b7c4..c35b34f 100644 --- a/src/santa/simulator/Virus.java +++ b/src/santa/simulator/Virus.java @@ -16,6 +16,8 @@ public Virus() { public Virus(Genome genome, Virus parent) { this.genome = genome; this.parent = parent; + if (parent != null) + this.age = parent.age; } public Genome getGenome() { @@ -34,12 +36,17 @@ public double getFitness() { return genome.getFitness(); } + public int getAge() { + return age; + } + public void setGenome(Genome genome) { this.genome = genome; } public void setParent(Virus parent) { this.parent = parent; + setAge(parent.age); } public int getOffspringCount() { @@ -49,9 +56,14 @@ public int getOffspringCount() { public void setOffspringCount(int offspringCount) { this.offspringCount = offspringCount; } + + public void setAge(int age) { + this.age = age; + } private Genome genome = null; private Virus parent = null; private int offspringCount = 0; + private int age = 0; } diff --git a/src/santa/simulator/compartments/MatrixTransfer.java b/src/santa/simulator/compartments/MatrixTransfer.java index 449be16..b5452a2 100644 --- a/src/santa/simulator/compartments/MatrixTransfer.java +++ b/src/santa/simulator/compartments/MatrixTransfer.java @@ -40,45 +40,46 @@ public void genomeTransfer(List compartments, int generation, List< allVirusesToAdd.add(new ArrayList()); } - for (int i = 0; i < numCompartments; i++) { - Compartment migrator = compartments.get(i); + for (int compartmentFromID = 0; compartmentFromID < numCompartments; compartmentFromID++) { + Compartment migrator = compartments.get(compartmentFromID); List viruses = migrator.getPopulation().getCurrentGeneration(); GenePool genePool = migrator.getGenePool(); - for (int j = 0; j < numCompartments; j++) { - if (i != j) { - ArrayList virusesToAdd = allVirusesToAdd.get(j); - - for (int k = 0; k < viruses.size();) { - if (transferProbs[i][j] > 0) { - boolean transfer = Random.nextUniform(0, 1) <= transferProbs[i][j]; + for (int virusID = 0; virusID < viruses.size(); virusID++) { + double transfer = Random.nextUniform(0, 1); + + for (int compartmentToID = 0; compartmentToID < numCompartments; compartmentToID++) { + if (transfer < transferProbs[compartmentFromID][compartmentToID]) { + if (compartmentFromID != compartmentToID) { + ArrayList virusesToAdd = allVirusesToAdd.get(compartmentToID); + Virus virus = viruses.get(virusID); + Genome genome = virus.getGenome(); - if (transfer) { - Virus virus = viruses.get(k); - Genome genome = virus.getGenome(); - - virusesToAdd.add(virus); - viruses.remove(k); - - genePool.killGenome(genome); - } else { - k++; - } - } else { - k++; + // record compartment entry + virus.setAge(generation); + + virusesToAdd.add(virus); + viruses.remove(virusID); + genePool.killGenome(genome); + + virusID--; } + + break; + } else { + transfer -= transferProbs[compartmentFromID][compartmentToID]; } } } } - for (int i = 0; i < numCompartments; i++) { - List virusesToAdd = allVirusesToAdd.get(i); + for (int compartmentToID = 0; compartmentToID < numCompartments; compartmentToID++) { + List virusesToAdd = allVirusesToAdd.get(compartmentToID); if (!virusesToAdd.isEmpty()) { - FitnessFunction fitnessFunction = currentEpochs.get(i).getFitnessFunction(); - GenePool compartmentGenePool = compartments.get(i).getGenePool(); - List viruses = compartments.get(i).getPopulation().getCurrentGeneration(); + FitnessFunction fitnessFunction = currentEpochs.get(compartmentToID).getFitnessFunction(); + GenePool compartmentGenePool = compartments.get(compartmentToID).getGenePool(); + List viruses = compartments.get(compartmentToID).getPopulation().getCurrentGeneration(); // fix later to remove create less genomes for (Virus v: virusesToAdd) { @@ -86,7 +87,6 @@ public void genomeTransfer(List compartments, int generation, List< Genome newGenome = compartmentGenePool.createGenome(genome.getSequence(), genome.getDescription()); v.setGenome(newGenome); - compartmentGenePool.duplicateGenome(newGenome, new TreeSet(), fitnessFunction); } diff --git a/src/santa/simulator/samplers/AlignmentSampler.java b/src/santa/simulator/samplers/AlignmentSampler.java index bc7e984..e7888d6 100644 --- a/src/santa/simulator/samplers/AlignmentSampler.java +++ b/src/santa/simulator/samplers/AlignmentSampler.java @@ -44,7 +44,7 @@ public enum Format { * @param consensus write the consensus sequence of the sample rather than writing the sample ? * @param schedule amount of sequences to sample at irregular intervals * @param format format - * @param label label with possible %g, %s and %t variables + * @param label label with possible %g, %s, %t and %a variables * @param fileName name of the file to write the samples */ public AlignmentSampler(Feature feature, Set sites, int sampleSize, boolean consensus, @@ -69,7 +69,7 @@ public AlignmentSampler(Feature feature, Set sites, int sampleSize, boo public void initialize(int replicate) { this.replicate = replicate; - String fName = substituteVariables(fileName, 0, 0); + String fName = substituteVariables(fileName, 0, 0, null); try { destination = new PrintStream(fName); @@ -96,10 +96,15 @@ public void initialize(int replicate) { } } - private String substituteVariables(String name, int generation, int seq) { + private String substituteVariables(String name, int generation, int seq, Virus virus) { String result = name.replaceAll("%r", String.valueOf(replicate+1)); result = result.replaceAll("%g", String.valueOf(generation)); result = result.replaceAll("%s", String.valueOf(seq)); + + // generation when lineage entered its compartment + if (virus != null) + result = result.replaceAll("%a", String.valueOf(virus.getAge())); + return result; } @@ -165,14 +170,14 @@ protected Virus[] getSample(int generation, Population population) { private void writeNexusFormat(int generation, Virus[] sample) { if (consensus) { - String l = substituteVariables(label, generation, 0); + String l = substituteVariables(label, generation, 0, null); destination.print(l + "\t"); destination.println(computeConsensus(sample)); } else { int i = 1; for (Virus virus : sample) { - String l = substituteVariables(label, generation, i); + String l = substituteVariables(label, generation, i, virus); destination.print(l + "\t"); @@ -230,7 +235,7 @@ private String computeConsensus(Virus[] sample) { private void writeFastaFormat(int generation, Virus[] sample) { if (consensus) { - String l = substituteVariables(label, generation, 0); + String l = substituteVariables(label, generation, 0, null); destination.println(">" + l); destination.println(computeConsensus(sample)); @@ -238,7 +243,7 @@ private void writeFastaFormat(int generation, Virus[] sample) { int i = 1; for (Virus virus : sample) { - String l = substituteVariables(label, generation, i); + String l = substituteVariables(label, generation, i, virus); destination.println(">" + l); destination.println(virus.getGenome().getSequence().getNucleotides()); @@ -254,7 +259,7 @@ private void writeXMLFormat(int generation, Virus[] sample) { destination.println(""); int i = 1; for (Virus virus : sample) { - String l = substituteVariables(label, generation, i); + String l = substituteVariables(label, generation, i, virus); destination.println("\t"); destination.println("\t\t" + virus.getGenome().getSequence().getNucleotides()); destination.println("\t"); From 6f81fe56540ee94c63f4babeeb10a39027e237ba Mon Sep 17 00:00:00 2001 From: brj1 Date: Wed, 12 Sep 2018 11:14:47 -0700 Subject: [PATCH 23/34] added citation to fitness --- examples/HIV-1_latent.xml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/examples/HIV-1_latent.xml b/examples/HIV-1_latent.xml index c7c891f..f2f584c 100644 --- a/examples/HIV-1_latent.xml +++ b/examples/HIV-1_latent.xml @@ -74,6 +74,8 @@ + + gag 1-500 @@ -1078,7 +1080,7 @@ dynamicPopulation - 10000 + 100 all @@ -1089,7 +1091,7 @@ - 2.5E-5 + 9.3E-5 0.42 2.49 0.29 1.73 0.23 4.73 From eb39e35e04e5bb9b056c3f619dcfb5134eb91b19 Mon Sep 17 00:00:00 2001 From: brj1 Date: Wed, 24 Oct 2018 11:11:13 -0700 Subject: [PATCH 24/34] reworked transfer to make it modular; aded new exzample files --- examples/HIV-1_VIL.xml | 6 +- examples/HIV-1_multipat.xml | 1327 +++++++++++++++++ examples/HIV-1_nef_lifecycle.xml | 472 ++++++ src/santa/simulator/SimulatorParser.java | 134 +- .../simulator/compartments/Compartments.java | 12 - .../simulator/compartments/DoubleProb.java | 19 + .../simulator/compartments/FitnessProb.java | 24 + .../compartments/MatrixTransfer.java | 131 +- .../simulator/compartments/TimedTransfer.java | 107 ++ .../simulator/compartments/Transfer.java | 5 - .../simulator/compartments/TransferProb.java | 11 + .../simulator/selectors/DynamicSelector.java | 1 + 12 files changed, 2151 insertions(+), 98 deletions(-) create mode 100644 examples/HIV-1_multipat.xml create mode 100644 examples/HIV-1_nef_lifecycle.xml create mode 100644 src/santa/simulator/compartments/DoubleProb.java create mode 100644 src/santa/simulator/compartments/FitnessProb.java create mode 100644 src/santa/simulator/compartments/TimedTransfer.java create mode 100644 src/santa/simulator/compartments/TransferProb.java diff --git a/examples/HIV-1_VIL.xml b/examples/HIV-1_VIL.xml index 29b4891..860f72c 100644 --- a/examples/HIV-1_VIL.xml +++ b/examples/HIV-1_VIL.xml @@ -2,7 +2,11 @@ xsi:noNamespaceSchemaLocation="santa.xsd"> 1 - 0 1 0 0.9999965 0 3.5e-6 0.001 0 0.999 + 0 1 0 0 0 1 + + + + 0 0 9719 diff --git a/examples/HIV-1_multipat.xml b/examples/HIV-1_multipat.xml new file mode 100644 index 0000000..c4d4bd7 --- /dev/null +++ b/examples/HIV-1_multipat.xml @@ -0,0 +1,1327 @@ + + 1 + + + pat1 + pat2 + 500 + 100 + + + pat2 + pat3 + 1000 + 100 + + + + 9719 + + TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATA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+ 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + NEF + 93 + + 1.00 + 1.00 + 1.00 + 0.99 + 1.00 + 1.00 + 1.00 + 1.00 + 1.01 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + NEF + 94 + + 1.00 + 1.00 + 1.00 + 1.02 + 1.00 + 1.00 + 1.00 + 1.00 + 0.98 + 1.00 + 1.02 + 1.02 + 1.00 + 1.02 + 1.00 + 1.00 + 1.98 + 1.00 + 1.00 + 1.00 + + + + + NEF + 101 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.02 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 0.98 + 1.00 + 1.00 + + + + + NEF + 104 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.01 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + NEF + 105 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 0.98 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.02 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + NEF + 170 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.01 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + NEF + 192 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.02 + 1.00 + 1.00 + 1.00 + + + + + NEF + 194 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.02 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 0.98 + 1.00 + 1.00 + + + + + dynamicPopulation + + + 0 + all + + + + 5 + 100000 + + + + + 2.5E-5 + + 0.42 2.49 0.29 + 1.73 0.23 4.73 + 6.99 0.20 0.60 + 1.02 2.56 0.88 + + + + + + + 0.05 + 0.001 + + + + + active + 2000 + + + + + 200 + alignment_pat3.fasta + + 10 + FASTA + + + + + + + + diff --git a/examples/HIV-1_nef_lifecycle.xml b/examples/HIV-1_nef_lifecycle.xml new file mode 100644 index 0000000..ad5edd5 --- /dev/null +++ b/examples/HIV-1_nef_lifecycle.xml @@ -0,0 +1,472 @@ + + 1 + + 0 1 0 0 0 1 + + + + NEF + 10 + + 0.99 + 0.99 + 0.99 + 0.99 + 0.99 + 0.99 + 0.99 + 0.99 + 0.99 + 0.99 + 0.99 + 0.99 + 0.99 + 0.99 + 0.99 + 0.99 + 0.99 + 0.999 + 0.99 + 0.99 + + + + + NEF + 47 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 0.001 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + NEF + 68 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 0.10 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + NEF + 100 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 0.01 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + 0 0 + + + 618 + + ATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGC + + + NEF + aminoAcid + 1-618 + + + + + plasma + + + + + NEF + 1-206 + 0.005 + 1000 + + + + NEF + 1-206 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + NEF + 1 + + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 1.20 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + 0.01 + + + + + dynamicPopulation + + + 15000 + all + + + + 0.003 + 0.0033 + + + + + 0.0 + + 0 0 0 0 + 0 0 0 0 + 0 0 0 0 + + + + + + + + + + active + 1522 + + + + treatment + 1522 + + + + + + + + + epoch + 3044 + + + + + 152 + alignment_plasma.fasta + + 10 + FASTA + + + + + + + + rt + + dynamicPopulation + + + 15000 + all + + + + 0.003 + 0.0033 + + + + + + NEF + 10 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.10 + 1.00 + 1.00 + + + + + NEF + 47 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.01 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + NEF + 131 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 0.50 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + NEF + 181 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.01 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.10 + 1.00 + 1.00 + + + + + + + 0.05 + 0.001 + + + + + + 2.5E-5 + + 0.42 2.49 0.29 + 1.73 0.23 4.73 + 6.99 0.20 0.60 + 1.02 2.56 0.88 + + + + + + active + 1522 + + + + treatment + 1522 + + + + + + + + + + + + + dna + + dynamicPopulation + + + 15000 + all + + + + 0.003 + 0.0028 + + + + + + + 0.0 + + 0 0 0 0 + 0 0 0 0 + 0 0 0 0 + + + + + + + + + + epoch + 3044 + + + + + 3044 + dna.fasta + + 50 + FASTA + + + + + + + diff --git a/src/santa/simulator/SimulatorParser.java b/src/santa/simulator/SimulatorParser.java index 7d659f8..3ac9e31 100644 --- a/src/santa/simulator/SimulatorParser.java +++ b/src/santa/simulator/SimulatorParser.java @@ -20,7 +20,11 @@ import org.jdom2.Element; import santa.simulator.compartments.Compartment; import santa.simulator.compartments.Compartments; +import santa.simulator.compartments.DoubleProb; +import santa.simulator.compartments.FitnessProb; import santa.simulator.compartments.MatrixTransfer; +import santa.simulator.compartments.TimedTransfer; +import santa.simulator.compartments.TransferProb; import santa.simulator.fitness.AgeDependentFitnessFactor; import santa.simulator.fitness.BetaDistributedPurifyingFitnessModel; @@ -83,6 +87,14 @@ public class SimulatorParser { private final static String COMPARTMENT = "compartment"; private final static String TRANSFER_RATES = "transferRates"; + private final static String FITNESS_TRANSFER = "transferFitness"; + + private final static String TIMED_TRANSFER = "timedTransfer"; + private final static String TO_COMPARTMENT = "toCompartment"; + private final static String FROM_COMPARTMENT = "fromCompartment"; + private final static String TRANSFER_GENERATION = "generation"; + private final static String TRANSFER_AMOUNT = "amountToTransfer"; + private final static String EPOCH = "epoch"; private final static String NAME = "name"; private final static String GENERATION_COUNT = "generationCount"; @@ -328,11 +340,14 @@ Simulation parseSimulation(Element element) throws ParseException { throw new ParseException("Error parsing <" + element.getName() + "> element: <" + GENOME_DESCRIPTION + "> is missing"); } - double[] transferRates = null; + ArrayList transferRates = new ArrayList<>(); + ArrayList transferEvents = new ArrayList<>(); Element e = element.getChildren().get(0); switch (e.getName()) { case TRANSFER_RATES: + case TIMED_TRANSFER: + case FITNESS_TRANSFER: for (Object o: element.getChildren()) { Element e2 = (Element)o; switch (e2.getName()) { @@ -340,16 +355,37 @@ Simulation parseSimulation(Element element) throws ParseException { compartmentList.add(parseCompartment(e2)); break; case TRANSFER_RATES: - transferRates = parseNumberList(e2); + double[] parsedRates = parseNumberList(e2); + + for (int i = 0; i < parsedRates.length; i++) { + transferRates.add(new DoubleProb(parsedRates[i])); + } + + break; + case FITNESS_TRANSFER: + for (Object o3: e2.getChildren()) { + Element e3 = (Element)o3; + + if (e3.getName().equals(FITNESS_FUNCTION)) { + FitnessFunction fitness = parseFitnessFunction(e3); + + transferRates.add(new FitnessProb(fitness)); + } else { + throw new ParseException("Error parsing <" + FITNESS_TRANSFER + "> element: <" + e3.getName() + "> is unrecognized"); + } + } + break; + case TIMED_TRANSFER: + transferEvents.add(parseTransferEvent(e2)); break; case GENOME_DESCRIPTION: break; default: - throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + e.getName() + "> is unrecognized"); + throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + e2.getName() + "> is unrecognized"); } } - if (transferRates == null) { + if (transferRates.isEmpty() && transferEvents.isEmpty()) { throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + TRANSFER_RATES + "> is missing"); } @@ -357,19 +393,45 @@ Simulation parseSimulation(Element element) throws ParseException { throw new ParseException("Error parsing <" + SIMULATION + "> no <" + COMPARTMENT + "> found"); } - if (transferRates.length != compartmentList.size() * compartmentList.size()) { - throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + TRANSFER_RATES + "> should be size (" + compartmentList.size() * compartmentList.size() + "), but was (" + transferRates.length + ") instead"); + if (transferRates.isEmpty() && transferRates.size() != compartmentList.size() * compartmentList.size()) { + throw new ParseException( + "Error parsing <" + + SIMULATION + + "> element: <" + + TRANSFER_RATES + + "> should be size (" + + compartmentList.size() * compartmentList.size() + + "), but was (" + + transferRates.size() + + ") instead" + ); } - break; - default: - transferRates = new double[1]; - transferRates[0] = 1; + + break; + default: + transferRates.add(new DoubleProb(1)); compartmentList.add(parseCompartment(element)); break; } - compartments = new Compartments(compartmentList, new MatrixTransfer(transferRates, compartmentList.size())); + if (!transferEvents.isEmpty()) { + ArrayList compartmentNames = new ArrayList<>(); + + for (Compartment compartment: compartmentList) { + compartmentNames.add(compartment.getName()); + } + + for (TimedTransfer.TransferEvent event: transferEvents) { + if (!event.findCompartmentIndices(compartmentNames)) { + throw new ParseException("Compartment not found for timedTransfer"); + } + } + + compartments = new Compartments(compartmentList, new TimedTransfer(transferEvents)); + } else { + compartments = new Compartments(compartmentList, new MatrixTransfer(transferRates, compartmentList.size())); + } return new Simulation(compartments); } @@ -382,9 +444,8 @@ Compartment parseCompartment(Element element) throws ParseException { double growthRate = -1; for (Object o : element.getChildren()) { - Element e = (Element)o; - if (e.getName().equals(POPULATION)) { - + Element e = (Element)o; + if (e.getName().equals(POPULATION)) { for (Object o1 : e.getChildren()) { Element e1 = (Element)o1; switch (e1.getName()) { @@ -603,6 +664,51 @@ Selector parseGrowthModel(Element element) throws ParseException { return null; } + } + + TimedTransfer.TransferEvent parseTransferEvent(Element element) throws ParseException { + String toCompartment = null; + String fromCompartment = null; + int generation = -1; + int amountToTransfer = -1; + + for (Object o : element.getChildren()) { + Element e = (Element)o; + switch (e.getName()){ + case TO_COMPARTMENT: + toCompartment = e.getTextNormalize(); + break; + case FROM_COMPARTMENT: + fromCompartment = e.getTextNormalize(); + break; + case TRANSFER_GENERATION: + generation = Integer.parseInt(e.getTextNormalize()); + break; + case TRANSFER_AMOUNT: + amountToTransfer = Integer.parseInt(e.getTextNormalize()); + break; + default: + throw new ParseException("Error parsing <" + TIMED_TRANSFER + "> element: unknown XML element within " + TIMED_TRANSFER); + } + } + + if (toCompartment == null) { + throw new ParseException("Error parsing <" + TIMED_TRANSFER + "> element: " + TO_COMPARTMENT + " was not found"); + } + + if (fromCompartment == null) { + throw new ParseException("Error parsing <" + TIMED_TRANSFER + "> element: " + FROM_COMPARTMENT + " was not found"); + } + + if (generation < 0) { + throw new ParseException("Error parsing <" + TIMED_TRANSFER + "> element: " + TRANSFER_GENERATION + " is negative or was not found"); + } + + if (amountToTransfer < 0) { + throw new ParseException("Error parsing <" + TIMED_TRANSFER + "> element: " + TRANSFER_AMOUNT + " is negative or was not found"); + } + + return new TimedTransfer.TransferEvent(toCompartment, fromCompartment, generation, amountToTransfer); } CompartmentEpoch parseSimulationEpoch(Element element, diff --git a/src/santa/simulator/compartments/Compartments.java b/src/santa/simulator/compartments/Compartments.java index 6e12faa..3065e3e 100644 --- a/src/santa/simulator/compartments/Compartments.java +++ b/src/santa/simulator/compartments/Compartments.java @@ -1,19 +1,7 @@ -/* - * To change this license header, choose License Headers in Project Properties. - * To change this template file, choose Tools | Templates - * and open the template in the editor. - */ package santa.simulator.compartments; -import java.util.ArrayList; import java.util.Iterator; import java.util.List; -import java.util.TreeSet; -import santa.simulator.Random; -import santa.simulator.Virus; -import santa.simulator.fitness.FitnessFunction; -import santa.simulator.genomes.GenePool; -import santa.simulator.genomes.Genome; /** * diff --git a/src/santa/simulator/compartments/DoubleProb.java b/src/santa/simulator/compartments/DoubleProb.java new file mode 100644 index 0000000..f2aca2c --- /dev/null +++ b/src/santa/simulator/compartments/DoubleProb.java @@ -0,0 +1,19 @@ +package santa.simulator.compartments; + +import santa.simulator.Virus; + +/** + * + * @author Bradley R. Jones + */ +public class DoubleProb implements TransferProb { + private double transferRate; + + public DoubleProb(double transferRate) { + this.transferRate = transferRate; + } + + public double getProb(Virus virus, int generation) { + return transferRate; + } +} diff --git a/src/santa/simulator/compartments/FitnessProb.java b/src/santa/simulator/compartments/FitnessProb.java new file mode 100644 index 0000000..f28f887 --- /dev/null +++ b/src/santa/simulator/compartments/FitnessProb.java @@ -0,0 +1,24 @@ +package santa.simulator.compartments; + +import santa.simulator.Virus; +import santa.simulator.fitness.FitnessFunction; +import santa.simulator.genomes.Genome; + +/** + * + * @author Bradley R. Jones + */ +public class FitnessProb implements TransferProb { + public FitnessFunction fitness; + + public FitnessProb(FitnessFunction fitness) { + this.fitness = fitness; + } + + public double getProb(Virus virus, int generation) { + Genome genome = virus.getGenome().copy(); + fitness.computeLogFitness(genome); + + return genome.getFitness(); + } +} diff --git a/src/santa/simulator/compartments/MatrixTransfer.java b/src/santa/simulator/compartments/MatrixTransfer.java index b5452a2..2418f71 100644 --- a/src/santa/simulator/compartments/MatrixTransfer.java +++ b/src/santa/simulator/compartments/MatrixTransfer.java @@ -1,8 +1,3 @@ -/* - * To change this license header, choose License Headers in Project Properties. - * To change this template file, choose Tools | Templates - * and open the template in the editor. - */ package santa.simulator.compartments; import java.util.ArrayList; @@ -20,79 +15,83 @@ * @author Bradley R. Jones */ public class MatrixTransfer implements Transfer { - private double[][] transferProbs; + + private TransferProb[][] transferProbs; private int numCompartments; - - public MatrixTransfer(double [] transferRates, int numCompartments) { + + public MatrixTransfer(List transferRates, int numCompartments) { this.numCompartments = numCompartments; - this.transferProbs = new double[this.numCompartments][this.numCompartments]; - - for (int i = 0; i < transferRates.length; i++) { - this.transferProbs[i / this.numCompartments][i % this.numCompartments] = transferRates[i]; + this.transferProbs = new TransferProb[this.numCompartments][this.numCompartments]; + + for (int i = 0; i < transferRates.size(); i++) { + this.transferProbs[i / this.numCompartments][i % this.numCompartments] = transferRates.get(i); } } - + + @Override public void genomeTransfer(List compartments, int generation, List currentEpochs) { if (numCompartments > 1) { - ArrayList< ArrayList > allVirusesToAdd = new ArrayList<>(numCompartments); - - for (int i = 0; i < numCompartments; i++) { - allVirusesToAdd.add(new ArrayList()); - } - - for (int compartmentFromID = 0; compartmentFromID < numCompartments; compartmentFromID++) { - Compartment migrator = compartments.get(compartmentFromID); - List viruses = migrator.getPopulation().getCurrentGeneration(); - GenePool genePool = migrator.getGenePool(); - - for (int virusID = 0; virusID < viruses.size(); virusID++) { - double transfer = Random.nextUniform(0, 1); - - for (int compartmentToID = 0; compartmentToID < numCompartments; compartmentToID++) { - if (transfer < transferProbs[compartmentFromID][compartmentToID]) { - if (compartmentFromID != compartmentToID) { - ArrayList virusesToAdd = allVirusesToAdd.get(compartmentToID); - Virus virus = viruses.get(virusID); - Genome genome = virus.getGenome(); - - // record compartment entry - virus.setAge(generation); - - virusesToAdd.add(virus); - viruses.remove(virusID); - genePool.killGenome(genome); - - virusID--; - } + ArrayList< ArrayList> allVirusesToAdd = new ArrayList<>(numCompartments); + + for (int i = 0; i < numCompartments; i++) { + allVirusesToAdd.add(new ArrayList()); + } + + for (int compartmentFromID = 0; compartmentFromID < numCompartments; compartmentFromID++) { + Compartment migrator = compartments.get(compartmentFromID); + List viruses = migrator.getPopulation().getCurrentGeneration(); + GenePool genePool = migrator.getGenePool(); + + for (int virusID = 0; virusID < viruses.size(); virusID++) { + double transfer = Random.nextUniform(0, 1); + Virus virus = viruses.get(virusID); + + for (int compartmentToID = 0; compartmentToID < numCompartments; compartmentToID++) { + double prob = transferProbs[compartmentFromID][compartmentToID].getProb(virus, generation); - break; - } else { - transfer -= transferProbs[compartmentFromID][compartmentToID]; + if (transfer < prob) { + if (compartmentFromID != compartmentToID) { + ArrayList virusesToAdd = allVirusesToAdd.get(compartmentToID); + Genome genome = virus.getGenome(); + + // record compartment entry + virus.setAge(generation); + + virusesToAdd.add(virus); + viruses.remove(virusID); + genePool.killGenome(genome); + + virusID--; + } + + break; + } else { + transfer -= prob; + } } } } - } - - for (int compartmentToID = 0; compartmentToID < numCompartments; compartmentToID++) { - List virusesToAdd = allVirusesToAdd.get(compartmentToID); - - if (!virusesToAdd.isEmpty()) { - FitnessFunction fitnessFunction = currentEpochs.get(compartmentToID).getFitnessFunction(); - GenePool compartmentGenePool = compartments.get(compartmentToID).getGenePool(); - List viruses = compartments.get(compartmentToID).getPopulation().getCurrentGeneration(); - - // fix later to remove create less genomes - for (Virus v: virusesToAdd) { - Genome genome = v.getGenome(); - Genome newGenome = compartmentGenePool.createGenome(genome.getSequence(), genome.getDescription()); - - v.setGenome(newGenome); - compartmentGenePool.duplicateGenome(newGenome, new TreeSet(), fitnessFunction); + + for (int compartmentToID = 0; compartmentToID < numCompartments; compartmentToID++) { + List virusesToAdd = allVirusesToAdd.get(compartmentToID); + + if (!virusesToAdd.isEmpty()) { + FitnessFunction fitnessFunction = currentEpochs.get(compartmentToID).getFitnessFunction(); + GenePool compartmentGenePool = compartments.get(compartmentToID).getGenePool(); + List viruses = compartments.get(compartmentToID).getPopulation().getCurrentGeneration(); + + // fix later to remove create less genomes + for (Virus v : virusesToAdd) { + Genome genome = v.getGenome(); + Genome newGenome = compartmentGenePool.createGenome(genome.getSequence(), genome.getDescription()); + + v.setGenome(newGenome); + compartmentGenePool.duplicateGenome(newGenome, new TreeSet(), fitnessFunction); + } + + viruses.addAll(virusesToAdd); } - - viruses.addAll(virusesToAdd); } } - } } } diff --git a/src/santa/simulator/compartments/TimedTransfer.java b/src/santa/simulator/compartments/TimedTransfer.java new file mode 100644 index 0000000..e90d800 --- /dev/null +++ b/src/santa/simulator/compartments/TimedTransfer.java @@ -0,0 +1,107 @@ +package santa.simulator.compartments; + +import java.util.List; +import java.util.TreeSet; +import santa.simulator.Random; +import santa.simulator.Virus; +import santa.simulator.fitness.FitnessFunction; +import santa.simulator.genomes.GenePool; +import santa.simulator.genomes.Genome; +import santa.simulator.genomes.Mutation; + +/** + * + * @author Bradley R. Jones + */ +public class TimedTransfer implements Transfer { + private List transferEvents; + private int currentIndex = 0; + + public TimedTransfer(List transferEvents) { + this.transferEvents = transferEvents; + + // sort in order of generation + transferEvents.sort(null); + } + + public void genomeTransfer(List compartments, int generation, List currentEpochs) { + TransferEvent nextEvent = null; + + if (currentIndex < transferEvents.size()) + nextEvent = transferEvents.get(currentIndex); + + while (nextEvent != null && nextEvent.getGeneration() == generation) { + Compartment fromCompartment = compartments.get(nextEvent.getFromCompartmentIndex()); + Compartment toCompartment = compartments.get(nextEvent.getToCompartmentIndex()); + List fromViruses = fromCompartment.getPopulation().getCurrentGeneration(); + List toViruses = toCompartment.getPopulation().getCurrentGeneration(); + GenePool toGenePool = fromCompartment.getGenePool(); + GenePool fromGenePool = toCompartment.getGenePool(); + FitnessFunction fitness = currentEpochs.get(nextEvent.getToCompartmentIndex()).getFitnessFunction(); + + Object[] virusesToTransfer = Random.nextSample(fromViruses, nextEvent.getAmountToTransfer()); + + for (Object o: virusesToTransfer) { + Virus virus = (Virus)o; + Genome genome = virus.getGenome(); + + fromViruses.remove(virus); + fromGenePool.killGenome(genome); + + virus.setAge(generation); + Genome newGenome = toGenePool.createGenome(genome.getSequence(), genome.getDescription()); + virus.setGenome(newGenome); + fromGenePool.duplicateGenome(newGenome, new TreeSet(), fitness); + toViruses.add(virus); + } + + if (++currentIndex < transferEvents.size()) + nextEvent = transferEvents.get(currentIndex); + else + nextEvent = null; + } + } + + public static class TransferEvent implements Comparable { + private String fromCompartment; + private String toCompartment; + private int fromCompartmentIndex; + private int toCompartmentIndex; + private int generation; + private int amountToTransfer; + + public TransferEvent(String fromCompartment, String toCompartment, int generation, int amountToTransfer) { + this.fromCompartment = fromCompartment; + this.toCompartment = toCompartment; + this.generation = generation; + this.amountToTransfer = amountToTransfer; + } + + public boolean findCompartmentIndices(List compartmentNames) { + fromCompartmentIndex = compartmentNames.indexOf(fromCompartment); + toCompartmentIndex = compartmentNames.indexOf(toCompartment); + + return fromCompartmentIndex != -1 && toCompartmentIndex != -1; + } + + public int getFromCompartmentIndex() { + return fromCompartmentIndex; + } + + public int getToCompartmentIndex() { + return toCompartmentIndex; + } + + public int getGeneration() { + return generation; + } + + public int getAmountToTransfer() { + return amountToTransfer; + } + + public int compareTo(TransferEvent event) { + return Integer.compare(this.generation, event.generation); + } + } +} diff --git a/src/santa/simulator/compartments/Transfer.java b/src/santa/simulator/compartments/Transfer.java index dc952ad..f58cca8 100644 --- a/src/santa/simulator/compartments/Transfer.java +++ b/src/santa/simulator/compartments/Transfer.java @@ -1,8 +1,3 @@ -/* - * To change this license header, choose License Headers in Project Properties. - * To change this template file, choose Tools | Templates - * and open the template in the editor. - */ package santa.simulator.compartments; import java.util.List; diff --git a/src/santa/simulator/compartments/TransferProb.java b/src/santa/simulator/compartments/TransferProb.java new file mode 100644 index 0000000..560855f --- /dev/null +++ b/src/santa/simulator/compartments/TransferProb.java @@ -0,0 +1,11 @@ +package santa.simulator.compartments; + +import santa.simulator.Virus; + +/** + * + * @author Bradley R. Jones + */ +public interface TransferProb { + public double getProb(Virus virus, int generation); +} \ No newline at end of file diff --git a/src/santa/simulator/selectors/DynamicSelector.java b/src/santa/simulator/selectors/DynamicSelector.java index dfe37e6..3c5c0db 100644 --- a/src/santa/simulator/selectors/DynamicSelector.java +++ b/src/santa/simulator/selectors/DynamicSelector.java @@ -33,6 +33,7 @@ public void selectParents(List currentGeneration, List selectedP //A slightly different formulation is introduced according to: https://www.maa.org/press/periodicals/loci/joma/logistic-growth-model-background-logistic-modeling //expectedProgenyCount = Math.max(fitness * (1 + growthRate*(1-selectedParents.size()/carryingPopulation)),Double.MIN_VALUE); expectedProgenyCount = Math.max(fitness * growthRate*(1-selectedParents.size()/carryingPopulation),Double.MIN_VALUE); + long nbChildren = fitness == 0 ? 0 : Random.nextPoisson(expectedProgenyCount); for(long n = 0; n < nbChildren * nbOfParents; ++n) { selectedParents.add(i); From c73331c23541a17b3fa596743eaa69ab4dca81f0 Mon Sep 17 00:00:00 2001 From: brj1 Date: Mon, 3 Dec 2018 10:29:25 -0800 Subject: [PATCH 25/34] small change to latent example --- examples/HIV-1_latent.xml | 35 +---------------------------------- 1 file changed, 1 insertion(+), 34 deletions(-) diff --git a/examples/HIV-1_latent.xml b/examples/HIV-1_latent.xml index f2f584c..a65cd95 100644 --- a/examples/HIV-1_latent.xml +++ b/examples/HIV-1_latent.xml @@ -41,40 +41,7 @@ plasma - - PR - 1-99 - 0.005 - 50000 - - - RT - 1 - - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 1.20 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - - - - + gag From 6fa5856a16fe96e545f1688eb7f57a28ebe97d53 Mon Sep 17 00:00:00 2001 From: brj1 Date: Mon, 10 Dec 2018 14:42:24 -0800 Subject: [PATCH 26/34] fixed bug with low fitnesses calling nextPoission --- src/santa/simulator/selectors/DynamicSelector.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/santa/simulator/selectors/DynamicSelector.java b/src/santa/simulator/selectors/DynamicSelector.java index 3c5c0db..97f3f22 100644 --- a/src/santa/simulator/selectors/DynamicSelector.java +++ b/src/santa/simulator/selectors/DynamicSelector.java @@ -32,9 +32,9 @@ public void selectParents(List currentGeneration, List selectedP //It was noticed that for slower growth rates, the simulator overshoots the carrying size. //A slightly different formulation is introduced according to: https://www.maa.org/press/periodicals/loci/joma/logistic-growth-model-background-logistic-modeling //expectedProgenyCount = Math.max(fitness * (1 + growthRate*(1-selectedParents.size()/carryingPopulation)),Double.MIN_VALUE); - expectedProgenyCount = Math.max(fitness * growthRate*(1-selectedParents.size()/carryingPopulation),Double.MIN_VALUE); + expectedProgenyCount = fitness * growthRate*(1-selectedParents.size()/carryingPopulation); - long nbChildren = fitness == 0 ? 0 : Random.nextPoisson(expectedProgenyCount); + long nbChildren = fitness == 0 || expectedProgenyCount <= Double.MIN_VALUE ? 0 : Random.nextPoisson(expectedProgenyCount); for(long n = 0; n < nbChildren * nbOfParents; ++n) { selectedParents.add(i); } From 5f97f3bbac3407065b50a1af6cfdac9b06e2061b Mon Sep 17 00:00:00 2001 From: brj1 Date: Wed, 28 Aug 2019 10:47:48 -0700 Subject: [PATCH 27/34] removed infinity from DynamicSelector; aligned randomness remove recursion testing edit edit removed randomness removed randomness i - 1 removed infinity --- src/santa/simulator/Random.java | 39 +++++++++++ .../compartments/CompartmentEpoch.java | 5 +- .../BetaDistributedPurifyingFitnessModel.java | 10 +-- .../fitness/PurifyingFitnessRank.java | 4 +- .../selectors/ClonalExpansionSelector.java | 2 +- .../simulator/selectors/DynamicSelector.java | 14 ++-- .../selectors/RouletteWheelSelector.java | 2 +- test/santa/simulator/RandomTest.java | 67 +++++++++++++++++++ 8 files changed, 128 insertions(+), 15 deletions(-) create mode 100644 test/santa/simulator/RandomTest.java diff --git a/src/santa/simulator/Random.java b/src/santa/simulator/Random.java index 17666af..60165dc 100644 --- a/src/santa/simulator/Random.java +++ b/src/santa/simulator/Random.java @@ -1,6 +1,10 @@ package santa.simulator; import java.util.Collection; +import java.util.List; +import java.util.Collections; +import java.util.ListIterator; +import java.util.RandomAccess; import org.apache.commons.math3.random.RandomDataGenerator; @@ -74,6 +78,41 @@ public static void shuffle(int[] numbers) { } } + // From java.util.Collections + public static void shuffle(List list) { + int size = list.size(); + if (size < 5000 || list instanceof RandomAccess) { + for (int i=size; i>1; i--) + Collections.swap(list, i-1, nextInt(0, i - 1)); + } else { + Object arr[] = list.toArray(); + + // Shuffle array + for (int i=size; i>1; i--) + swap(arr, i-1, nextInt(0, i - 1)); + + // Dump array back into list + // instead of using a raw type here, it's possible to capture + // the wildcard but it will require a call to a supplementary + // private method + ListIterator it = list.listIterator(); + for (int i=0; i createHistogram(SequenceAlphabet alphabet, boolean } if (breakTiesRandomly) - Collections.shuffle(counts); + Random.shuffle(counts); Collections.sort(counts); return counts; diff --git a/src/santa/simulator/selectors/ClonalExpansionSelector.java b/src/santa/simulator/selectors/ClonalExpansionSelector.java index 6c55135..d45f833 100644 --- a/src/santa/simulator/selectors/ClonalExpansionSelector.java +++ b/src/santa/simulator/selectors/ClonalExpansionSelector.java @@ -38,6 +38,6 @@ public void selectParents(List currentGeneration, List selectedP selectedParents.add(i); } } - Collections.shuffle(selectedParents); + Random.shuffle(selectedParents); } } diff --git a/src/santa/simulator/selectors/DynamicSelector.java b/src/santa/simulator/selectors/DynamicSelector.java index 97f3f22..040f303 100644 --- a/src/santa/simulator/selectors/DynamicSelector.java +++ b/src/santa/simulator/selectors/DynamicSelector.java @@ -25,21 +25,25 @@ public DynamicSelector(double growthRate, double carryingPopulation) { } public void selectParents(List currentGeneration, List selectedParents, int nbOfParents) { - Collections.shuffle(currentGeneration); + Random.shuffle(currentGeneration); for(int i = 0; i < currentGeneration.size(); ++i) { double fitness = currentGeneration.get(i).getFitness(); - //Abbas: The below formulation of logistic growth was implemented by Gertjan + + //Abbas: The below formulation of logistic growth was implemented by Gertjan //It was noticed that for slower growth rates, the simulator overshoots the carrying size. //A slightly different formulation is introduced according to: https://www.maa.org/press/periodicals/loci/joma/logistic-growth-model-background-logistic-modeling //expectedProgenyCount = Math.max(fitness * (1 + growthRate*(1-selectedParents.size()/carryingPopulation)),Double.MIN_VALUE); - expectedProgenyCount = fitness * growthRate*(1-selectedParents.size()/carryingPopulation); + expectedProgenyCount = fitness * growthRate * (1 - selectedParents.size() / carryingPopulation); - long nbChildren = fitness == 0 || expectedProgenyCount <= Double.MIN_VALUE ? 0 : Random.nextPoisson(expectedProgenyCount); + // Set to zero if infinite fitness is observed (this usually happens if zero fitness is changed to nonzero fitness) + long nbChildren = 0; + if (fitness > 0 && Double.isFinite(fitness) && expectedProgenyCount > Double.MIN_VALUE) + nbChildren = Random.nextPoisson(expectedProgenyCount); for(long n = 0; n < nbChildren * nbOfParents; ++n) { selectedParents.add(i); } } - Collections.shuffle(selectedParents); + Random.shuffle(selectedParents); } } diff --git a/src/santa/simulator/selectors/RouletteWheelSelector.java b/src/santa/simulator/selectors/RouletteWheelSelector.java index 5633313..c34148e 100644 --- a/src/santa/simulator/selectors/RouletteWheelSelector.java +++ b/src/santa/simulator/selectors/RouletteWheelSelector.java @@ -35,7 +35,7 @@ public void selectParents(List currentGeneration, List selectedP i++; } while (i < populationSize); - Collections.shuffle(selectedParents); + Random.shuffle(selectedParents); } private final void calculateCumulativeFitness(List currentGeneration) { diff --git a/test/santa/simulator/RandomTest.java b/test/santa/simulator/RandomTest.java new file mode 100644 index 0000000..615a9c0 --- /dev/null +++ b/test/santa/simulator/RandomTest.java @@ -0,0 +1,67 @@ +/* + * To change this license header, choose License Headers in Project Properties. + * To change this template file, choose Tools | Templates + * and open the template in the editor. + */ +package santa.simulator; + +import java.util.ArrayList; +import java.io.FileWriter; + +/** + * + * @author Bradley R. Jones + */ +public class RandomTest { + + private static final long SEED = 1989; + + public RandomTest() { + } + + // Not a real test + public ArrayList generatePoissons() { + Random.setSeed(SEED); + + final long count = 1000; + final double mean1 = 1.0; + final double mean2 = 100000.0; + final double mean3 = 0.1; + + ArrayList list = new ArrayList(); + + System.out.println("Mean: " + mean1); + for (long i = 0; i < count; i++) + list.add(Random.nextPoisson(mean1)); + System.out.println("Mean: " + mean2); + for (long i = 0; i < count; i++) + list.add(Random.nextPoisson(mean2)); + System.out.println("Mean: " + mean3); + for (long i = 0; i < count; i++) + list.add(Random.nextPoisson(mean3)); + + return list; + } + + public static void main(String[] args) { + try { + if (args.length > 0) { + String filename = args[0]; + FileWriter writer = new FileWriter(filename); + + RandomTest test = new RandomTest(); + ArrayList poissons = test.generatePoissons(); + + for (long value: poissons) { + writer.write("" + value + "\n"); + } + + writer.close(); + } else { + throw new Exception("Need to specify output filename."); + } + } catch (Exception e) { + System.out.println(e.getMessage()); + } + } +} From 05c31871ece2c1e28b5028cd6c1fc9089dec540a Mon Sep 17 00:00:00 2001 From: brj1 Date: Tue, 24 Sep 2019 15:08:37 -0700 Subject: [PATCH 28/34] add compartment tracking --- src/santa/simulator/Random.java | 1 + src/santa/simulator/Virus.java | 18 +++++++++++++++--- .../simulator/compartments/MatrixTransfer.java | 1 + .../simulator/compartments/TimedTransfer.java | 2 ++ .../simulator/samplers/AlignmentSampler.java | 15 ++++++++++++--- .../simulator/selectors/DynamicSelector.java | 2 +- 6 files changed, 32 insertions(+), 7 deletions(-) diff --git a/src/santa/simulator/Random.java b/src/santa/simulator/Random.java index 60165dc..7471469 100644 --- a/src/santa/simulator/Random.java +++ b/src/santa/simulator/Random.java @@ -79,6 +79,7 @@ public static void shuffle(int[] numbers) { } // From java.util.Collections + // Added so that all random calls go through this class public static void shuffle(List list) { int size = list.size(); if (size < 5000 || list instanceof RandomAccess) { diff --git a/src/santa/simulator/Virus.java b/src/santa/simulator/Virus.java index c35b34f..e32cef2 100644 --- a/src/santa/simulator/Virus.java +++ b/src/santa/simulator/Virus.java @@ -1,6 +1,8 @@ package santa.simulator; +import java.util.ArrayList; +import santa.simulator.compartments.Compartment; import santa.simulator.genomes.Genome; /** @@ -16,8 +18,10 @@ public Virus() { public Virus(Genome genome, Virus parent) { this.genome = genome; this.parent = parent; - if (parent != null) + if (parent != null) { this.age = parent.age; + this.lastCompartment = parent.lastCompartment; + } } public Genome getGenome() { @@ -40,6 +44,10 @@ public int getAge() { return age; } + public Compartment getLastCompartment() { + return lastCompartment; + } + public void setGenome(Genome genome) { this.genome = genome; } @@ -60,10 +68,14 @@ public void setOffspringCount(int offspringCount) { public void setAge(int age) { this.age = age; } - + + public void setLastCompartment(Compartment lastCompartment) { + this.lastCompartment = lastCompartment; + } + private Genome genome = null; private Virus parent = null; private int offspringCount = 0; private int age = 0; - + private Compartment lastCompartment = null; } diff --git a/src/santa/simulator/compartments/MatrixTransfer.java b/src/santa/simulator/compartments/MatrixTransfer.java index 2418f71..411556e 100644 --- a/src/santa/simulator/compartments/MatrixTransfer.java +++ b/src/santa/simulator/compartments/MatrixTransfer.java @@ -56,6 +56,7 @@ public void genomeTransfer(List compartments, int generation, List< // record compartment entry virus.setAge(generation); + virus.setLastCompartment(migrator); virusesToAdd.add(virus); viruses.remove(virusID); diff --git a/src/santa/simulator/compartments/TimedTransfer.java b/src/santa/simulator/compartments/TimedTransfer.java index e90d800..6bddb24 100644 --- a/src/santa/simulator/compartments/TimedTransfer.java +++ b/src/santa/simulator/compartments/TimedTransfer.java @@ -49,6 +49,8 @@ public void genomeTransfer(List compartments, int generation, List< fromGenePool.killGenome(genome); virus.setAge(generation); + virus.setLastCompartment(fromCompartment); + Genome newGenome = toGenePool.createGenome(genome.getSequence(), genome.getDescription()); virus.setGenome(newGenome); fromGenePool.duplicateGenome(newGenome, new TreeSet(), fitness); diff --git a/src/santa/simulator/samplers/AlignmentSampler.java b/src/santa/simulator/samplers/AlignmentSampler.java index e7888d6..32dd7c5 100644 --- a/src/santa/simulator/samplers/AlignmentSampler.java +++ b/src/santa/simulator/samplers/AlignmentSampler.java @@ -44,7 +44,7 @@ public enum Format { * @param consensus write the consensus sequence of the sample rather than writing the sample ? * @param schedule amount of sequences to sample at irregular intervals * @param format format - * @param label label with possible %g, %s, %t and %a variables + * @param label label with possible %g, %s, %r, %a and %c variables * @param fileName name of the file to write the samples */ public AlignmentSampler(Feature feature, Set sites, int sampleSize, boolean consensus, @@ -101,9 +101,18 @@ private String substituteVariables(String name, int generation, int seq, Virus v result = result.replaceAll("%g", String.valueOf(generation)); result = result.replaceAll("%s", String.valueOf(seq)); - // generation when lineage entered its compartment - if (virus != null) + if (virus != null) { + // generation when lineage entered its compartment result = result.replaceAll("%a", String.valueOf(virus.getAge())); + + // track last compartment + if (virus.getLastCompartment() != null) { + result = result.replace("%c", virus.getLastCompartment().getName()); + } + } + + result = result.replaceAll("%a", "NA"); + result = result.replaceAll("%c", "NA"); return result; } diff --git a/src/santa/simulator/selectors/DynamicSelector.java b/src/santa/simulator/selectors/DynamicSelector.java index 040f303..a4ec651 100644 --- a/src/santa/simulator/selectors/DynamicSelector.java +++ b/src/santa/simulator/selectors/DynamicSelector.java @@ -1,6 +1,5 @@ package santa.simulator.selectors; -import java.util.Collections; import java.util.List; import santa.simulator.Random; @@ -24,6 +23,7 @@ public DynamicSelector(double growthRate, double carryingPopulation) { this.carryingPopulation = carryingPopulation; } + @Override public void selectParents(List currentGeneration, List selectedParents, int nbOfParents) { Random.shuffle(currentGeneration); for(int i = 0; i < currentGeneration.size(); ++i) { From 65ec2c4fde0f832aa38543ae27f6d288921c8f6e Mon Sep 17 00:00:00 2001 From: brj1 Date: Tue, 17 Dec 2019 11:12:39 -0800 Subject: [PATCH 29/34] add and update HIV-1 latent example XMLs --- examples/HIV-1_latent.xml | 397 ++++++++- examples/HIV-1_latent_sim2.xml | 1527 ++++++++++++++++++++++++++++++++ 2 files changed, 1910 insertions(+), 14 deletions(-) create mode 100644 examples/HIV-1_latent_sim2.xml diff --git a/examples/HIV-1_latent.xml b/examples/HIV-1_latent.xml index a65cd95..b2e5ba1 100644 --- a/examples/HIV-1_latent.xml +++ b/examples/HIV-1_latent.xml @@ -2,7 +2,10 @@ xsi:noNamespaceSchemaLocation="santa.xsd"> 1 - 0 0.0001 0.001 0 + + 0 0.0001 0.00135 0 9719 @@ -41,7 +44,11 @@ plasma - + gag @@ -151,6 +158,60 @@ + + gag + 76 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.02 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 0.99 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + gag + 79 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.02 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 0.98 + + + gag 81 @@ -286,6 +347,60 @@ + + gag + 439 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.01 + 1.00 + 1.00 + 0.99 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + gag + 470 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.01 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + gag 479 @@ -393,7 +508,34 @@ 1.00 - + + + RT + 288 + + 1.02 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + RT 454 @@ -495,7 +637,7 @@ 1.00 1.00 0.98 - 1.10 + 1.01 1.00 1.00 1.00 @@ -555,6 +697,60 @@ 1.00 + + + IN + 91 + + 1.01 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + IN + 119 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 0.99 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + IN @@ -630,7 +826,7 @@ 1.00 1.00 1.00 - 1.01 + 0.99 1.00 1.00 1.00 @@ -691,12 +887,11 @@ - NEF 18 - 1.10 + 1.01 1.00 1.00 0.99 @@ -719,6 +914,60 @@ + + NEF + 18 + + 1.01 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + NEF + 23 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 0.99 + 1.00 + 1.00 + + + NEF 40 @@ -874,7 +1123,34 @@ 1.02 1.00 1.00 - 1.98 + 1.01 + 1.00 + 1.00 + 1.00 + + + + + NEF + 94 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 0.99 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 1.00 1.00 1.00 @@ -989,6 +1265,60 @@ + + NEF + 182 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.01 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + NEF + 188 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 0.99 + 1.00 + 1.00 + 1.00 + + + NEF 192 @@ -1009,7 +1339,7 @@ 1.00 1.00 1.00 - 1.02 + 1.01 1.00 1.00 1.00 @@ -1058,7 +1388,8 @@ - 9.3E-5 + + 9.3E-5 0.42 2.49 0.29 1.73 0.23 4.73 @@ -1075,9 +1406,10 @@ + active - 1400 + 1400 @@ -1113,6 +1445,7 @@ all + # possible proliferation from doi:10.1002/eji.200323763 but death rate is too high 0.003 0.003 @@ -1141,13 +1474,49 @@ + + 1680 + alignment_latent_1680.fasta + + 10 + FASTA + + + + + 1960 + alignment_latent_1960.fasta + + 10 + FASTA + + + + + 2240 + alignment_latent_2240.fasta + + 10 + FASTA + + + + + 2520 + alignment_latent_2520.fasta + + 10 + FASTA + + + 2800 - alignment_latent.fasta + alignment_latent_2800.fasta - 50 + 10 FASTA - + diff --git a/examples/HIV-1_latent_sim2.xml b/examples/HIV-1_latent_sim2.xml new file mode 100644 index 0000000..84b8432 --- /dev/null +++ b/examples/HIV-1_latent_sim2.xml @@ -0,0 +1,1527 @@ + + 1 + + + 0 0.0001 0.00135 0 + + + 9719 + + TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA 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+ 1.00 + 1.00 + 1.00 + 1.00 + 1.02 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 0.98 + 1.00 + 1.00 + + + + + dynamicPopulation + + + 100 + all + + + + 5 + 100000 + + + + + + 9.3E-5 + + 0.42 2.49 0.29 + 1.73 0.23 4.73 + 6.99 0.20 0.60 + 1.02 2.56 0.88 + + + + + + + 0.05 + 0.001 + + + + + + active + 560 + + + + treatment + 140 + + + + + + + + + + 19 + alignment_active_19.fasta + + 10 + FASTA + + + + + + 140 + alignment_active_140.fasta + + 10 + FASTA + + + + + + 560 + alignment_active_560.fasta + + 10 + FASTA + + + + + + + + latent_reservoir + + dynamicPopulation + + + 0 + all + + + # possible proliferation from doi:10.1002/eji.200323763 but death rate is too high + + 0.003 + 0.003 + + + + + + + 0.0 + + 0 0 0 0 + 0 0 0 0 + 0 0 0 0 + + + + + + + + + + epoch + 700 + + + + + 560 + alignment_latent_560.fasta + + 10 + FASTA + + + + + 630 + alignment_latent_630.fasta + + 10 + FASTA + + + + + 700 + alignment_latent_700.fasta + + 10 + FASTA + + + + + + + From f0ec849cac13370c7e81898cc1e47198882a1578 Mon Sep 17 00:00:00 2001 From: brad Date: Tue, 14 Apr 2020 12:13:54 -0700 Subject: [PATCH 30/34] updated example XMLs --- examples/HIV-1_VIL.xml | 1232 --------------- ...HIV-1_latent.xml => HIV-1_latent_sim1.xml} | 5 +- examples/HIV-1_latent_sim2.xml | 5 +- examples/HIV-1_multipat.xml | 1327 ----------------- examples/HIV-1_nef_lifecycle.xml | 472 ------ 5 files changed, 2 insertions(+), 3039 deletions(-) delete mode 100644 examples/HIV-1_VIL.xml rename examples/{HIV-1_latent.xml => HIV-1_latent_sim1.xml} (99%) delete mode 100644 examples/HIV-1_multipat.xml delete mode 100644 examples/HIV-1_nef_lifecycle.xml diff --git a/examples/HIV-1_VIL.xml b/examples/HIV-1_VIL.xml deleted file mode 100644 index 860f72c..0000000 --- a/examples/HIV-1_VIL.xml +++ /dev/null @@ -1,1232 +0,0 @@ - - 1 - - 0 1 0 0 0 1 - - - - 0 0 - - - 9719 - - TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA - - - gag - aminoAcid - 790-2289 - - - PR - aminoAcid - - 2253-2549 - - - RT - aminoAcid - 2550-4229 - - - IN - aminoAcid - 4230-5093 - - - NEF - aminoAcid - 8797-9414 - - - - - plasma - - - - PR - 1-99 - 0.005 - 50000 - - - RT - 1 - - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 1.20 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - - - - - gag - 1-500 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 1 - - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 1.20 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - - - - - gag - 26 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 65 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 81 - - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 104 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 268 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 331 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 390 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 479 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - RT - 1-560 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - RT - 200 - - 0.98 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - RT - 275 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - RT - 454 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - RT - 461 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - RT - 466 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - RT - 468 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 0.98 - 1.10 - 1.00 - 1.00 - 1.00 - - - - - RT - 469 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - IN - 1-288 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - IN - 138 - - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - IN - 173 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - IN - 218 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - - - - - NEF - 1-206 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 1 - - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 1.20 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - - - - - - NEF - 18 - - 1.10 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 40 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 83 - - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 87 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 91 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 93 - - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 94 - - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.02 - 1.02 - 1.00 - 1.02 - 1.00 - 1.00 - 1.98 - 1.00 - 1.00 - 1.00 - - - - - NEF - 101 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - - - - - NEF - 104 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 105 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 170 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 192 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - - - - - NEF - 194 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - - - - - dynamicPopulation - - - 15000 - all - - - - 4 - 0 - - - - - 0.0 - - 0 0 0 0 - 0 0 0 0 - 0 0 0 0 - - - - - - - - - - epoch - 3044 - - - - - - - - infected - - dynamicPopulation - - - 65000 - all - - - - 0 - 0.95 - - - - - - - 0.05 - 0.001 - - - - - - 2.5E-5 - - 0.42 2.49 0.29 - 1.73 0.23 4.73 - 6.99 0.20 0.60 - 1.02 2.56 0.88 - - - - - - active - 1522 - - - - treatment - 1522 - - - - - - - - - - 152 - alignment_plasma.fasta - - 10 - FASTA - - - - - - - - latent_reservoir - - dynamicPopulation - - - 0 - all - - - - 0 - 0.004 - - - - - - - 0.0 - - 0 0 0 0 - 0 0 0 0 - 0 0 0 0 - - - - - - - - - - epoch - 3044 - - - - - 3044 - alignment_latent.fasta - - 50 - FASTA - - - - - - - diff --git a/examples/HIV-1_latent.xml b/examples/HIV-1_latent_sim1.xml similarity index 99% rename from examples/HIV-1_latent.xml rename to examples/HIV-1_latent_sim1.xml index b2e5ba1..c745097 100644 --- a/examples/HIV-1_latent.xml +++ b/examples/HIV-1_latent_sim1.xml @@ -1400,10 +1400,7 @@ - - 0.05 - 0.001 - + diff --git a/examples/HIV-1_latent_sim2.xml b/examples/HIV-1_latent_sim2.xml index 84b8432..6bb78ab 100644 --- a/examples/HIV-1_latent_sim2.xml +++ b/examples/HIV-1_latent_sim2.xml @@ -1400,10 +1400,7 @@ - - 0.05 - 0.001 - + diff --git a/examples/HIV-1_multipat.xml b/examples/HIV-1_multipat.xml deleted file mode 100644 index c4d4bd7..0000000 --- a/examples/HIV-1_multipat.xml +++ /dev/null @@ -1,1327 +0,0 @@ - - 1 - - - pat1 - pat2 - 500 - 100 - - - pat2 - pat3 - 1000 - 100 - - - - 9719 - - TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA - - - gag - aminoAcid - 790-2289 - - - PR - aminoAcid - - 2253-2549 - - - RT - aminoAcid - 2550-4229 - - - IN - aminoAcid - 4230-5093 - - - NEF - aminoAcid - 8797-9414 - - - - - pat1 - - - - - NEF - 1-206 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 1 - - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 1.20 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - - - - - - NEF - 18 - - 1.10 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 40 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 83 - - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 87 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 91 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 93 - - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 94 - - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.02 - 1.02 - 1.00 - 1.02 - 1.00 - 1.00 - 1.98 - 1.00 - 1.00 - 1.00 - - - - - NEF - 101 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - - - - - NEF - 104 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 105 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 170 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 192 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - - - - - NEF - 194 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - - - - - dynamicPopulation - - - 100 - all - - - - 5 - 100000 - - - - - 2.5E-5 - - 0.42 2.49 0.29 - 1.73 0.23 4.73 - 6.99 0.20 0.60 - 1.02 2.56 0.88 - - - - - - - 0.05 - 0.001 - - - - - active - 2000 - - - - - 200 - alignment_pat1.fasta - - 10 - FASTA - - - - - - - - pat2 - - - - - NEF - 1-206 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 1 - - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 1.20 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - - - - - - NEF - 9 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 46 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 53 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 85 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 0.99 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 98 - - 1.00 - 1.00 - 0.99 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 150 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 151 - - 1.00 - 1.00 - 1.02 - 0.98 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 152 - - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 153 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - - - - - dynamicPopulation - - - 0 - all - - - - 5 - 100000 - - - - - 2.5E-5 - - 0.42 2.49 0.29 - 1.73 0.23 4.73 - 6.99 0.20 0.60 - 1.02 2.56 0.88 - - - - - - - 0.05 - 0.001 - - - - - active - 2000 - - - - - 200 - alignment_pat2.fasta - - 10 - FASTA - - - - - - - - pat3 - - - - - NEF - 1-206 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 1 - - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 1.20 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - - - - - - NEF - 18 - - 1.10 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 40 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 83 - - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 87 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 91 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 93 - - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 94 - - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.02 - 1.02 - 1.00 - 1.02 - 1.00 - 1.00 - 1.98 - 1.00 - 1.00 - 1.00 - - - - - NEF - 101 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - - - - - NEF - 104 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 105 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 170 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 192 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - - - - - NEF - 194 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - - - - - dynamicPopulation - - - 0 - all - - - - 5 - 100000 - - - - - 2.5E-5 - - 0.42 2.49 0.29 - 1.73 0.23 4.73 - 6.99 0.20 0.60 - 1.02 2.56 0.88 - - - - - - - 0.05 - 0.001 - - - - - active - 2000 - - - - - 200 - alignment_pat3.fasta - - 10 - FASTA - - - - - - - - diff --git a/examples/HIV-1_nef_lifecycle.xml b/examples/HIV-1_nef_lifecycle.xml deleted file mode 100644 index ad5edd5..0000000 --- a/examples/HIV-1_nef_lifecycle.xml +++ /dev/null @@ -1,472 +0,0 @@ - - 1 - - 0 1 0 0 0 1 - - - - NEF - 10 - - 0.99 - 0.99 - 0.99 - 0.99 - 0.99 - 0.99 - 0.99 - 0.99 - 0.99 - 0.99 - 0.99 - 0.99 - 0.99 - 0.99 - 0.99 - 0.99 - 0.99 - 0.999 - 0.99 - 0.99 - - - - - NEF - 47 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.001 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 68 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.10 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 100 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - 0 0 - - - 618 - - ATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGC - - - NEF - aminoAcid - 1-618 - - - - - plasma - - - - - NEF - 1-206 - 0.005 - 1000 - - - - NEF - 1-206 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 1 - - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 1.20 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - - - - - dynamicPopulation - - - 15000 - all - - - - 0.003 - 0.0033 - - - - - 0.0 - - 0 0 0 0 - 0 0 0 0 - 0 0 0 0 - - - - - - - - - - active - 1522 - - - - treatment - 1522 - - - - - - - - - epoch - 3044 - - - - - 152 - alignment_plasma.fasta - - 10 - FASTA - - - - - - - - rt - - dynamicPopulation - - - 15000 - all - - - - 0.003 - 0.0033 - - - - - - NEF - 10 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.10 - 1.00 - 1.00 - - - - - NEF - 47 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 131 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.50 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 181 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.10 - 1.00 - 1.00 - - - - - - - 0.05 - 0.001 - - - - - - 2.5E-5 - - 0.42 2.49 0.29 - 1.73 0.23 4.73 - 6.99 0.20 0.60 - 1.02 2.56 0.88 - - - - - - active - 1522 - - - - treatment - 1522 - - - - - - - - - - - - - dna - - dynamicPopulation - - - 15000 - all - - - - 0.003 - 0.0028 - - - - - - - 0.0 - - 0 0 0 0 - 0 0 0 0 - 0 0 0 0 - - - - - - - - - - epoch - 3044 - - - - - 3044 - dna.fasta - - 50 - FASTA - - - - - - - From c576aaef43fc8a8b49bfa8451a7552f8abd92259 Mon Sep 17 00:00:00 2001 From: brad Date: Wed, 17 Jun 2020 12:57:56 -0700 Subject: [PATCH 31/34] changed SimulationEpoch to use List of Epochs instead of matrching by name --- src/santa/simulator/Simulation.java | 26 +++++++---------- src/santa/simulator/SimulationEpoch.java | 29 ++++++++++++------- src/santa/simulator/SimulatorParser.java | 1 - .../simulator/compartments/Compartment.java | 11 ------- .../compartments/CompartmentEpoch.java | 4 +++ 5 files changed, 32 insertions(+), 39 deletions(-) diff --git a/src/santa/simulator/Simulation.java b/src/santa/simulator/Simulation.java index 773c29d..4579b8f 100644 --- a/src/santa/simulator/Simulation.java +++ b/src/santa/simulator/Simulation.java @@ -10,7 +10,6 @@ /** * @author Andrew Rambaut * @author Alexei Drummond - * @author Bradley R. Jones * @version $Id: Simulation.java,v 1.11 2006/07/19 12:53:05 kdforc0 Exp $ */ public class Simulation { @@ -22,18 +21,18 @@ public class Simulation { public Simulation(Compartments compartments) { this.compartments = compartments; - //fix Epochs + // split CompartmentEpochs so that they have the same time slices this.epochs = new ArrayList<>(); int compartmentEpochIndex = 0; boolean cont = true; - while (cont) { + while (cont) { int minGenerations = Integer.MAX_VALUE; - String epochName = ""; + ArrayList compartmentEpochs = new ArrayList(); for (Compartment compartment: compartments) { CompartmentEpoch currentCompartmentEpoch = compartment.getEpochs().get(compartmentEpochIndex); - epochName += currentCompartmentEpoch.getName(); + compartmentEpochs.add(currentCompartmentEpoch); if (minGenerations > currentCompartmentEpoch.getGenerationCount()) { minGenerations = currentCompartmentEpoch.getGenerationCount(); @@ -41,11 +40,11 @@ public Simulation(Compartments compartments) { } for (Compartment compartment: compartments) { - List compartmentEpochs = compartment.getEpochs(); - CompartmentEpoch currentCompartmentEpoch = compartmentEpochs.get(compartmentEpochIndex); + List compartmentsEpochs = compartment.getEpochs(); + CompartmentEpoch currentCompartmentEpoch = compartmentsEpochs.get(compartmentEpochIndex); if (minGenerations < currentCompartmentEpoch.getGenerationCount()) { - compartmentEpochs.add(compartmentEpochIndex + 1, new CompartmentEpoch( + compartmentsEpochs.add(compartmentEpochIndex + 1, new CompartmentEpoch( currentCompartmentEpoch.getName(), currentCompartmentEpoch.getGenerationCount() - minGenerations, currentCompartmentEpoch.getFitnessFunction(), @@ -53,18 +52,13 @@ public Simulation(Compartments compartments) { currentCompartmentEpoch.getReplicator())); } - compartmentEpochs.set(compartmentEpochIndex, new CompartmentEpoch( - epochName, - minGenerations, - currentCompartmentEpoch.getFitnessFunction(), - currentCompartmentEpoch.getMutator(), - currentCompartmentEpoch.getReplicator())); + currentCompartmentEpoch.setGenerationCount(minGenerations); - if (compartmentEpochs.size() <= compartmentEpochIndex + 1) + if (compartmentsEpochs.size() <= compartmentEpochIndex + 1) cont = false; } - this.epochs.add(new SimulationEpoch(epochName, minGenerations)); + this.epochs.add(new SimulationEpoch(compartmentEpochs, minGenerations)); /* * TODO: diff --git a/src/santa/simulator/SimulationEpoch.java b/src/santa/simulator/SimulationEpoch.java index 83e9c53..b04e574 100644 --- a/src/santa/simulator/SimulationEpoch.java +++ b/src/santa/simulator/SimulationEpoch.java @@ -7,34 +7,41 @@ import santa.simulator.compartments.Compartment; import santa.simulator.compartments.CompartmentEpoch; import santa.simulator.compartments.Compartments; +import java.util.List; /** * * @author Andrew Rambaut - * @author Bradley R. Jones */ public class SimulationEpoch { - private String name; private int generationCount; + private List compartmentEpochs; + private String name; private static Logger memlogger = Simulator.memlogger; - public SimulationEpoch(String name, int generationCount) { - this.name = name; + public SimulationEpoch(List epochs, int generationCount) { + this.compartmentEpochs = epochs; this.generationCount = generationCount; + + this.name = null; + + for (CompartmentEpoch epoch: compartmentEpochs) { + if (name == null) { + epoch.getName(); + } else { + this.name += ", " + epoch.getName(); + } + + } } public int run(Simulation simulation, Logger logger, int startGeneration) { - System.err.println("Starting epoch: " + (name != null ? name : "(unnamed)")); - Compartments compartments = simulation.getCompartments(); - ArrayList compartmentEpochs = new ArrayList<>(); - - for (Compartment compartment: compartments) { - compartmentEpochs.add(compartment.getCurrentEpoch(name)); - } final int endGeneration = startGeneration + generationCount; + System.err.println("Starting epochs: " + name); + memlogger.fine("@start of Epoch Memory used = " + readableByteCount(usedMemory())); for (int generation = startGeneration; generation < endGeneration; ++generation) { diff --git a/src/santa/simulator/SimulatorParser.java b/src/santa/simulator/SimulatorParser.java index 3ac9e31..44e8bc6 100644 --- a/src/santa/simulator/SimulatorParser.java +++ b/src/santa/simulator/SimulatorParser.java @@ -73,7 +73,6 @@ /** * @author Andrew Rambaut * @author Alexei Drummond - * @author Bradley R. Jones * @version $Id: SimulatorParser.java,v 1.19 2006/07/19 14:35:32 kdforc0 Exp $ */ public class SimulatorParser { diff --git a/src/santa/simulator/compartments/Compartment.java b/src/santa/simulator/compartments/Compartment.java index 198645c..7bbced2 100644 --- a/src/santa/simulator/compartments/Compartment.java +++ b/src/santa/simulator/compartments/Compartment.java @@ -92,17 +92,6 @@ public void cleanup(int replicate, Logger logger) { samplingSchedule.cleanUp(); } - public CompartmentEpoch getCurrentEpoch(String name) { - int index; - - for (index = 0; index < epochs.size(); index++) { - if (epochs.get(index).getName().equals(name)) - break; - } - - return epochs.get(index); - } - public GenePool getGenePool() { return genePool; } diff --git a/src/santa/simulator/compartments/CompartmentEpoch.java b/src/santa/simulator/compartments/CompartmentEpoch.java index 5c791d6..7a80a41 100644 --- a/src/santa/simulator/compartments/CompartmentEpoch.java +++ b/src/santa/simulator/compartments/CompartmentEpoch.java @@ -115,4 +115,8 @@ public int getGenerationCount() { public String getName() { return name; } + + public void setGenerationCount(int generationCount) { + this.generationCount = generationCount; + } } From c68336340f387b8c301f3c39408aedb15b81502d Mon Sep 17 00:00:00 2001 From: Brad Jones Date: Tue, 3 Nov 2020 11:19:22 -0800 Subject: [PATCH 32/34] added example for within HIV-1 evolution including the latent reservoir --- examples/HIV-1_latent.xml | 947 ++++++++++++++++++++ examples/HIV-1_latent_sim1.xml | 1522 ------------------------------- examples/HIV-1_latent_sim2.xml | 1524 -------------------------------- 3 files changed, 947 insertions(+), 3046 deletions(-) create mode 100644 examples/HIV-1_latent.xml delete mode 100644 examples/HIV-1_latent_sim1.xml delete mode 100644 examples/HIV-1_latent_sim2.xml diff --git a/examples/HIV-1_latent.xml b/examples/HIV-1_latent.xml new file mode 100644 index 0000000..f9fd745 --- /dev/null +++ b/examples/HIV-1_latent.xml @@ -0,0 +1,947 @@ + + 1 + + + 0 0.0026 0.00108 0 + + + 9719 + + TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATA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dynamicPopulation + + + 10 + all + + + + + 50 + 100000 + + + + + + 9.3E-5 + + 0.42 2.49 0.29 + 1.73 0.23 4.73 + 6.99 0.20 0.60 + 1.02 2.56 0.88 + + + + + + + + + + + active + 1400 + + + + treatment + 1400 + + + + + + + + + + 140 + alignment_plasma.fasta + + 10 + FASTA + + + + + + + + latent_reservoir + + dynamicPopulation + + + 0 + all + + + + + 0.003 + 0.0056 + + + + + + + 0.0 + + 0 0 0 0 + 0 0 0 0 + 0 0 0 0 + + + + + + + + + + epoch + 2800 + + + + + 1680 + alignment_latent_1680.fasta + + 10 + FASTA + + + + + 1960 + alignment_latent_1960.fasta + + 10 + FASTA + + + + + 2240 + alignment_latent_2240.fasta + + 10 + FASTA + + + + + 2520 + alignment_latent_2520.fasta + + 10 + FASTA + + + + + 2800 + alignment_latent_2800.fasta + + 10 + FASTA + + + + + + + diff --git a/examples/HIV-1_latent_sim1.xml b/examples/HIV-1_latent_sim1.xml deleted file mode 100644 index c745097..0000000 --- a/examples/HIV-1_latent_sim1.xml +++ /dev/null @@ -1,1522 +0,0 @@ - - 1 - - - 0 0.0001 0.00135 0 - - - 9719 - - TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA - - - gag - aminoAcid - 790-2289 - - - PR - aminoAcid - - 2253-2549 - - - RT - aminoAcid - 2550-4229 - - - IN - aminoAcid - 4230-5093 - - - NEF - aminoAcid - 8797-9414 - - - - - plasma - - - - - - gag - 1-500 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 1 - - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 1.20 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - - - - - gag - 26 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 65 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 76 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 79 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - - - - - gag - 81 - - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 104 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 268 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 331 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 390 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 439 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 470 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 479 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - RT - 1-560 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - RT - 200 - - 0.98 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - RT - 275 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - RT - 288 - - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - RT - 454 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - RT - 461 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - RT - 466 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - RT - 468 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 0.98 - 1.01 - 1.00 - 1.00 - 1.00 - - - - - RT - 469 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - IN - 1-288 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - IN - 91 - - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - IN - 119 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - IN - 138 - - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - IN - 173 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - IN - 218 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - - - - - NEF - 1-206 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 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- - - - NEF - 87 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 91 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 93 - - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 94 - - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.02 - 1.02 - 1.00 - 1.02 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - - - - - NEF - 94 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 101 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - - - - - NEF - 104 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 105 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 170 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 182 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 188 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - - - - - NEF - 192 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - - - - - NEF - 194 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - - - - - dynamicPopulation - - - 100 - all - - - - 5 - 100000 - - - - - - 9.3E-5 - - 0.42 2.49 0.29 - 1.73 0.23 4.73 - 6.99 0.20 0.60 - 1.02 2.56 0.88 - - - - - - - - - - - active - 1400 - - - - treatment - 1400 - - - - - - - - - - 140 - alignment_plasma.fasta - - 10 - FASTA - - - - - - - - latent_reservoir - - dynamicPopulation - - - 0 - all - - - # possible proliferation from doi:10.1002/eji.200323763 but death rate is too high - - 0.003 - 0.003 - - - - - - - 0.0 - - 0 0 0 0 - 0 0 0 0 - 0 0 0 0 - - - - - - - - - - epoch - 2800 - - - - - 1680 - alignment_latent_1680.fasta - - 10 - FASTA - - - - - 1960 - alignment_latent_1960.fasta - - 10 - FASTA - - - - - 2240 - alignment_latent_2240.fasta - - 10 - FASTA - - - - - 2520 - alignment_latent_2520.fasta - - 10 - FASTA - - - - - 2800 - alignment_latent_2800.fasta - - 10 - FASTA - - - - - - - diff --git a/examples/HIV-1_latent_sim2.xml b/examples/HIV-1_latent_sim2.xml deleted file mode 100644 index 6bb78ab..0000000 --- a/examples/HIV-1_latent_sim2.xml +++ /dev/null @@ -1,1524 +0,0 @@ - - 1 - - - 0 0.0001 0.00135 0 - - - 9719 - - TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA - - - gag - aminoAcid - 790-2289 - - - PR - aminoAcid - - 2253-2549 - - - RT - aminoAcid - 2550-4229 - - - IN - aminoAcid - 4230-5093 - - - NEF - aminoAcid - 8797-9414 - - - - - plasma - - - - - - gag - 1-500 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 1 - - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 1.20 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - - - - - gag - 26 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 65 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 76 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 79 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - - - - - gag - 81 - - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 104 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 268 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 331 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 390 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 439 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 470 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - gag - 479 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - RT - 1-560 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - RT - 200 - - 0.98 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - RT - 275 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - RT - 288 - - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - RT - 454 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - RT - 461 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - RT - 466 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - RT - 468 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 0.98 - 1.01 - 1.00 - 1.00 - 1.00 - - - - - RT - 469 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - IN - 1-288 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - IN - 91 - - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - IN - 119 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - IN - 138 - - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - IN - 173 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - IN - 218 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - - - - - NEF - 1-206 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 1 - - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 1.20 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - 0.01 - - - - - NEF - 18 - - 1.01 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 18 - - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 23 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - - - - - NEF - 40 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 83 - - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 87 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 91 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 93 - - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 94 - - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.02 - 1.02 - 1.00 - 1.02 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - - - - - NEF - 94 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 101 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - - - - - NEF - 104 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 105 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 170 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 182 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - - - - - NEF - 188 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.99 - 1.00 - 1.00 - 1.00 - - - - - NEF - 192 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.01 - 1.00 - 1.00 - 1.00 - - - - - NEF - 194 - - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.02 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 1.00 - 0.98 - 1.00 - 1.00 - - - - - dynamicPopulation - - - 100 - all - - - - 5 - 100000 - - - - - - 9.3E-5 - - 0.42 2.49 0.29 - 1.73 0.23 4.73 - 6.99 0.20 0.60 - 1.02 2.56 0.88 - - - - - - - - - - - active - 560 - - - - treatment - 140 - - - - - - - - - - 19 - alignment_active_19.fasta - - 10 - FASTA - - - - - - 140 - alignment_active_140.fasta - - 10 - FASTA - - - - - - 560 - alignment_active_560.fasta - - 10 - FASTA - - - - - - - - latent_reservoir - - dynamicPopulation - - - 0 - all - - - # possible proliferation from doi:10.1002/eji.200323763 but death rate is too high - - 0.003 - 0.003 - - - - - - - 0.0 - - 0 0 0 0 - 0 0 0 0 - 0 0 0 0 - - - - - - - - - - epoch - 700 - - - - - 560 - alignment_latent_560.fasta - - 10 - FASTA - - - - - 630 - alignment_latent_630.fasta - - 10 - FASTA - - - - - 700 - alignment_latent_700.fasta - - 10 - FASTA - - - - - - - From dbce312c93db81a5f62347551608ed97d6042d61 Mon Sep 17 00:00:00 2001 From: Brad Jones Date: Wed, 25 Jan 2023 16:28:16 -0800 Subject: [PATCH 33/34] fix bug where fitness of transferred genomes would be not calculated --- src/santa/simulator/compartments/MatrixTransfer.java | 1 + src/santa/simulator/compartments/TimedTransfer.java | 1 + 2 files changed, 2 insertions(+) diff --git a/src/santa/simulator/compartments/MatrixTransfer.java b/src/santa/simulator/compartments/MatrixTransfer.java index 411556e..fd2ec9e 100644 --- a/src/santa/simulator/compartments/MatrixTransfer.java +++ b/src/santa/simulator/compartments/MatrixTransfer.java @@ -87,6 +87,7 @@ public void genomeTransfer(List compartments, int generation, List< Genome newGenome = compartmentGenePool.createGenome(genome.getSequence(), genome.getDescription()); v.setGenome(newGenome); + fitnessFunction.computeLogFitness(newGenome); compartmentGenePool.duplicateGenome(newGenome, new TreeSet(), fitnessFunction); } diff --git a/src/santa/simulator/compartments/TimedTransfer.java b/src/santa/simulator/compartments/TimedTransfer.java index 6bddb24..84a517d 100644 --- a/src/santa/simulator/compartments/TimedTransfer.java +++ b/src/santa/simulator/compartments/TimedTransfer.java @@ -53,6 +53,7 @@ public void genomeTransfer(List compartments, int generation, List< Genome newGenome = toGenePool.createGenome(genome.getSequence(), genome.getDescription()); virus.setGenome(newGenome); + fitness.computeLogFitness(newGenome); fromGenePool.duplicateGenome(newGenome, new TreeSet(), fitness); toViruses.add(virus); } From a5bd594525d524121b7e6e212c05e18d9f6aa906 Mon Sep 17 00:00:00 2001 From: Brad Jones Date: Wed, 23 Aug 2023 14:16:12 -0700 Subject: [PATCH 34/34] added varying models from Virus Evol paper --- examples/HIV_models/HIV-1_C.xml | 515 +++++ examples/HIV_models/activegrowth_high.xml | 947 +++++++++ examples/HIV_models/activegrowth_low.xml | 947 +++++++++ examples/HIV_models/fitness_hla.xml | 2114 ++++++++++++++++++++ examples/HIV_models/fitness_none.xml | 237 +++ examples/HIV_models/indel.xml | 242 +++ examples/HIV_models/latencydeath_high.xml | 947 +++++++++ examples/HIV_models/latencydeath_low.xml | 947 +++++++++ examples/HIV_models/latencygrowth_high.xml | 947 +++++++++ examples/HIV_models/latencygrowth_low.xml | 947 +++++++++ examples/HIV_models/latencyrate_high.xml | 947 +++++++++ examples/HIV_models/latencyrate_low.xml | 947 +++++++++ examples/HIV_models/mutrate_high.xml | 947 +++++++++ examples/HIV_models/mutrate_low.xml | 947 +++++++++ examples/HIV_models/reactivation_high.xml | 947 +++++++++ examples/HIV_models/reactivation_low.xml | 947 +++++++++ examples/HIV_models/recomb.xml | 951 +++++++++ examples/HIV_models/size_1.xml | 947 +++++++++ examples/HIV_models/size_100.xml | 947 +++++++++ 19 files changed, 17317 insertions(+) create mode 100755 examples/HIV_models/HIV-1_C.xml create mode 100755 examples/HIV_models/activegrowth_high.xml create mode 100755 examples/HIV_models/activegrowth_low.xml create mode 100755 examples/HIV_models/fitness_hla.xml create mode 100755 examples/HIV_models/fitness_none.xml create mode 100755 examples/HIV_models/indel.xml create mode 100755 examples/HIV_models/latencydeath_high.xml create mode 100755 examples/HIV_models/latencydeath_low.xml create mode 100755 examples/HIV_models/latencygrowth_high.xml create mode 100755 examples/HIV_models/latencygrowth_low.xml create mode 100755 examples/HIV_models/latencyrate_high.xml create mode 100755 examples/HIV_models/latencyrate_low.xml create mode 100755 examples/HIV_models/mutrate_high.xml create mode 100755 examples/HIV_models/mutrate_low.xml create mode 100755 examples/HIV_models/reactivation_high.xml create mode 100755 examples/HIV_models/reactivation_low.xml create mode 100755 examples/HIV_models/recomb.xml create mode 100755 examples/HIV_models/size_1.xml create mode 100755 examples/HIV_models/size_100.xml diff --git a/examples/HIV_models/HIV-1_C.xml b/examples/HIV_models/HIV-1_C.xml new file mode 100755 index 0000000..3f5178c --- /dev/null +++ b/examples/HIV_models/HIV-1_C.xml @@ -0,0 +1,515 @@ + + 1 + + + 0 0.0026 0.00108 0 + + + 9705 + + CTGGAAGGGTTAATTTACTCCAAGAAAAGGCAAGACATCCTTGATTTGTGGGTTTATAACACACAAGGCTTCTTTCCTGATTGGCAAAACTACACACCGGGACCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTTCAAGCTAGTACCAGTTGACCCAAGGGAAGTAGAAGAAGCCAACGAAGGAGAAAACAACTGTCTGCTACACCCTATGAGCCAACATGGAATGGATGATGATCACAGAGAAGTATTAAAGTGGAAGTTTGACAGTCAACTAGCACACAAACACATGGCCCGCGAGCTACATCCGGAGTTTTACAAAGACTGCTGACACAAAAGGGACTTTCCGCTGGGACTTTCCACTTGGGCGTTCCAGGAGGTGGGGTCTGGGCGGGACCGGGGAGTGGCCAGCCCTCAGATGCTGCATATAAGCAGCTGCTTTTCGCCTGTACTGGGTCTCTCTAGGTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTGCCTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTCTAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCATTTTGGTTGCGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACTTGAAAGCGAAAGTAAGACCAGAGGAGATCTCTCGACGCAGGACTCGGCTTGCTGAAGTGCACTCGGCAAGAGGCGAGAGCGGCGACTGGTGAGTACGCCAATTTTATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAATATTAAGAGGGGGAAAATTAGATAAATGGGAAAAAATTAGGTTAAGGCCAGGGGGAAAGAAAAAATATCAGCTAAAACACCTAGTATGGGCAAGCAGGGAGCTGGAAAAATTTGCACTTAACCCTGACCTTTTAGAAACATCAGAAGGCTGTAAACAAATAATAAGACAGCTACACCCAGCTCTCCAGACAGGAACAGAGGAACTCAAATCACTATATAACACAGTAGCAACTCTCTATTGTGTACATAAAAATATAGATGTGCGAGACACCAAGGAGGCCTTAGACAGGATAGAGGAGGAACAAAACAAATGTCAGCAAAAAACACAGCAGGCAGCAGCGGCTGACGGACAGGTCAGTCGAAATTTTCCTATAGTACAGAATCTTCAAGGGCAAATGGTACACCAGCCCTTATCACCTAGAACTTTGAATGCTTGGGTAAAAGTAGTAGAGGAGAAGGGTTTCAACCCAGAGGTAATACCCATGTTTACAGCATTATCAGAAGGAGCCACCCCACAAGATATGAACACTATGTTAAATACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACCATCAATGAGGAGGCTGCAGAGTGGGATAGATTACATCCAGTACAGGCAGGGCCTGTTGCACCAGGCCAAATAAGGGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGCATGGATGACAAGTAACCCACCTGTTCCAGTGGGAGACATCTATAAAAGATGGATAATTCTGGGGTTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAAACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGATCGGTTCTTTAAAACTTTAAGGGCTGAACAGGCTACACAAGATGTAAAAAATTGGATGACAGACACCCTGTTGGTCCAAAATGCGAACCCAGATTGCAAGACCATTTTAAGAGCACTAGGACCAGGGGCTACATTAGAGGAAATGATGACAGCATGTCAAGGAGTGGGAGGACCTAGCCACAAAGCAAGAGTGTTAGCCGAGGCAATGAGCCAAACAAACACAAACATACTGATGCAGAGAAGCAATTTCAAAGGCACTAGAAGAATTGTTAAATGTTTCAACTGTGGCAAGGAAGGGCACATAGCCAAAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGACTGTACAGAAAGGCAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCCACAAGGGGAGGCCAGGGAATTTCCTTCAGAACAGGCCAGAGCCAACAGCCCCACCACTAGAACCAACAGCCCCACCAGCAGAGAGCTCCACCCCCGCTCTGAAGCAGGAGCAGAAAGACAGGGAACCCTCAATTTCCCTCAAATCACTCTTTGGCAACGACCCCTTGTCACAATAAGAGTAGGGGGACAAATAAAGGAGGCTCTATTAGACACAGGAGCAGATGACACAGTATTAGAAGAATTAAGTTTGCCAGGAAAATGGAAACCAAAAATGATAGGAGGAATTGGAGGATTTATCAAAGTAAGACAGTATGATCAAATATCTATAGAAATTTGTGGAAAAAAGGCTATAGGTACAGTATTGGTAGGACCTACACCTGTCAACATAATTGGAAGAAACATGTTGACTCAGCTTGGATGCACCCTAAATTTTCCAATTAGTCCCATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAGGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAACAGCAATTTGTGAAGAAATGGAAAAGGAAGGAAAAATTACAAAAATTGGGCCTGAAAACCCATATAACACTCCAGTATTTGCCATTAAAAAGAAGGACAGTACAAAGTGGAGAAAATTAGTAGATTTCAGGGAACTTAATAAAAGGACTCAAGACTTTTGGGAAGTTCAATTAGGAATACCACACCCAGCAGGGTTAAAAAAGAAAAAATCAGTGACAGTACTGGATGTGGGGGATGCATATTTTTCAGTTCCTTTAGATAAAGATTTCAGGAAATATACTGCATTCACCATACCTAGTATAAACAATGAAACACCAGGAATTAGATATCAATATAATGTGCTTCCACAAGGATGGAAAGGATCACCAGCAATATTCCAGAGTAGCATGACAAAAATCTTAGAGCCCTTTAGAGCAAAAAACCCAGAAATAGTCATCTATCAATATATGGATGACTTATATGTAGGGTCTGACTTAGAAATAGGGCAACATAGAGCAAAAATAGAGGAGTTAAGAAAACACCTATTGAAATGGGGATTTACCACACCAGACAAGAAACATCAGAAGGAGCCCCCATTTCTTTGGATGGGGTATGAACTCCATCCTGACAAATGGACAGTACAGTCTATACAGCTACCGGAAAAGGACAGCTGGACTGTCAATGATATACAGAAGTTAGTGGGAAAATTAAACTGGGCAAGTCAGATTTACCCAGGAATTAAAGTAAAGCAAATGTGTAAACTCCTTAGGGGAGCCAAAGCACTAACAGATGTAGTACCACTGACTGAAGAAGCAGAATTAGAATTGGCAGAGAACAGGGAAATTCTAAAAGAACCAGTACATGGAGTATATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAACAGGGAGATGACCAGTGGACATATCAAATTTACCAAGAACCATTCAAAAATCTAAAAACAGGAAAATATGCAAAACAGAGAACTGCCCACACAAATGATGTAAAACAATTAACTGAGGCAGTGCAGAAAATATGCATGGAAAGCATAGTAATATGGGGGAAGATTCCTAAGTTTAGACTACCCATCCAAAAGGAAACATGGGAGACATGGTGGACAGACTACTGGCAAGCCACCTGGATTCCTGAGTGGGAATTTATTAATACCCCTCCCCTAGTAAAATTATGGTATCAGCTGGAGAAGGAACCCATAGCAGGGGCAGAAACTTTCTATGTAGATGGAGCAGCTAATAGGGAAACTAAAAAGGGAAAAGCAGGTTATGTTACTGACAGAGGAAGGCAGAAAGTTGTTTCTCTAACTGGAACAACAAATCAAAAGACTGAGTTACAAGCAATTCAGCTAGCTTTGCAAGACTCAGGATCAGAAGTAAATATAGTAACAGACTCACAGTATGCATTAGGAATCATTCAAGCACAACCAGATAAGAGTGAATCAGAGTTAGTCAATCAAATAATAGAACAGCTAATAAAAAAGGAAAGAATCTACCTGTCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTAAGTAGTGGAATCAGGAAAGTACTGTTTCTAGATGGAATAGATAAAGCTCAAGAAGACCATGAAAGATATCACAGCAATTGGAGAGCGATGGCTAGCGAGTTTAATCTGCCACCCATAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGGGAAGCCATACATGGACAAGTAGACTGTAGTCCAGGGGTATGGCAACTAGATTGTACACACTTAGAAGGGAAAATCATCCTGGTAGCAGTCCATGTAGCCAGTGGATACATAGAAGCAGAAGTCATCCCAACAGAAACAGGACAAGAAACAGCATACTATATACTAAAATTAGCAGGAAGATGGCCAGTCAAAGTAATACATACAGACAATGGCCCTAATTTTACCAGTGCTGCAGTTAAGGCAGCCTGTTGGTGGGCAGGTATCCAACAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAGGGAGTAGTGGAATCCATGAATAAAGAATTAAAGAAAATCATAGGGCAAGTAAGAGATCAAGCTGAGCACCTTAAGACAGCAGTACAAATGGCAGTGTTCATTCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACACTGCAGGGGAAAGAATAATAGACATAATAGCAACAGACATACAAACTAAGCAATTACAAAAACAAATTATAAAAATTCAAAATTTTCGGGTTTATTACAGAGACAGCAGAGATCCAATTTGGAAAGGACCAGCCAAACTACTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAACAGTGACATAAAGGTAGTACCAAGAAGGAAAGCAAAGATTATTAAGGACTATGGAAAACAGATGGCAGGTGCTGATTGTGTGGCAGGTAGACAGGATGAAGATTAGAACATGGAATAGTCTAGTAAAGCACCATATGTATGTTTCAAGGAGAGCTGATGGATGGTTTTACAGACATCACTATGAAAGCAGACATCCAAAAATAAGTTCAGAAGTACACATCCCATTAGGGGATGCTAGATTAGTAATAAAAACATATTGGGGTTTGCAGACAGGAGAAAGAGCTTGGCATTTGGGTCATGGAGTCTCCATAGAATGGAGACTGAAAAGATATAGCACACAAGTAGACCCTGACCTGGCAGATCAACTAATTCATATGCATTATTTTGATTGTTTTGCAGACTCTGCCATAAGACAAGCCATACTAGGACACGTAGTTAGCCCTAGGTGTGACTATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTGACAGCATTGATAAAGCCAAAAAAGATAAAGCCACCTCTGCCTAGTGTTAGCAAGTTAGTAGAGGATAAATGGAACAAGCCCCAGAAGACCAGGGGCCGCAGAGGGAACCATACAATGAATGGACACTAGAGCTTCTAGAGGAACTCAAGCAGGAAGCTGTCAGACACTTTCCTAGGCCATGGCTTCACAGTTTAGGACAACATATCTATGAAACCTATGGGGACACTTGGACGGGAGTTGAAGCCATAATAAGAATTCTGCAACAACTGTTGTTTGTTCATTTCAGAATTGGGTGCCAGCATAGCAGAATAGGCATTATACGACAGAGAAGAGCAAGAAATGGAGCCAATAGATCCTAAACTAGAGCCCTGGAATCATCCAGGAAGCCAGCCTAAGACTGCTTGTAATAAGTGCTATTGTAAAAAATGTAGCTATCATTGTCTAGTTTGCTTTCAGACAAAAGGCTTAGGCATTTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGCGCTCCTCCAAGCAGTAAGGATCATCAAAATCCTCTACCAAAGCAGTAAGTATATGTAATGTTAGACTTAGTAGCAAGAGTAGATTATAGAATAGGAGTAGGAGCATTAATAGTAGCACTAATCATAGCAATAGTTGTGTGGATCCTAGCATATATAGAATATAAAAGGTGGTTAAAACAAAAGAAAATAGACTGGTTAATTAAAAGAATTAGGGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAGGGGGATACAGAGGAATTATCAACAATGGTGGATATGGAGCATCTTGGCCTTTTGGATGTTAATGGTTAGTGTGAGGGGAAACTTGTGGGTTACAGTCTATTATGGGGTACCTGTGTGGAAAGAAGCAAAAACTACTCTATTCTGTGCATCAGATGCTAAAGCATATGACAAGGAAGTGCATAATGTCTGGGCTACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAATAAAATTGGAAAATGTAACAGAAAATTTTAATATGTGGAAAAATGATATGGTGGATCAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTGAAGTTGACCCCACTTTGTGTCACTTTAAACTGTAGTCATAATATTACGGTTAATGGTACCATGGGAAATGGTACCAGGGGAAATGATAGTACGATTGGGAAAATGGGAGATGAAATGACAAATTGCTCTTTCAATGCAACCACAGAAATAAAAGATAAGAAAAAGCTAGAATATGCACTTTTTTATAAACTTGATGTAGTAACACTTGAGGAAAACTCCAGTGAGTACAGATTAATAAATTGTAATACCTCAGTAGTTACACAAGCCTGTCCAAAGGTTTCGTTTCACCCAATTCCTATACATTATTGTGCTCCTGCTGGTTATGCGATTCTAAAGTGTAATAATAAGACATTCAATGGAACAGGACCATGCAATAAGATCAGCACTGTACAGTGTACACATGGGATCAAGCCAGTGGTATCTACTCAACTACTGTTAAATGGTAGTCTAGCAGAAAAAGAGATAATAGTTAGATCTGAAAATATACAGGACAATGTCAAAACAATCATAGTACATCTTAATGAATCTGTGAAAATTGAGTGTACAAGGCCCGGCAATAATACAAGAAAAAGTGTGAGGATAGGACCAGGACAAACATTCTTTGCAACAGGAGACATAATAGGAGATATAAGACAAGCATACTGTACCATTAATGGGACTCAATGGAATGACACTTTAAATAGGGTAAGAGAAACATTACAAAGGCACTTCCCTAATAAAACAATAAAATTTAGACCACACTCAGGAGGGGACTTAGAAATTACAACACATAGCTTTAATTGTAGAGGAGAGTTTTTCTATTGCAATACATCAAAAATATTTGATAGTGACAATGCAAACAAAACTTCAGGAAATATCACACTCCCATGCAAAATAAAACAAATCATAAACATGTGGCAGGGGGTAGGAAGAGCAATGTATGCCCCTCCCATTGCAGGAAACATAACATGTACATCAAATATCACAGGACTACTATTGACACGTGATGGAGGCAATGTTACAAATGACACAGAGATATTCAGACCTGGAGGAGGAAATATGAGGGACAATTGGAGAAGTGAATTATACAAATATAAAGTGGTAGAAATTAAGCCATTAGGGATAGCACCCACCAAGGCAAAAAGGCGAGTGGTGGAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTGTATTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCGTCAATAGCGCTGACGGTACAGGCCAGACAATTGTTGTCTGGTATAGTGCAACAGCAAAACAATTTGCTGAGAGCTATAGAGGCGCAACAGCATATGTTGCAACTCACGGTCTGGGGCATTAAACAGCTCCAGGCAAGAGTCCTGGCTATAGAAAGATACCTAGAGGATCAACAGCTCCTAGGGATTTGGGGCTGCTCTGGAAAACTCATCTGCACCACTGCCGTGCCTTGGAACAATAGTTGGAGTAATAAATCTCAAGATGATATTTGGGGCAATATGACCTGGATGCAATGGGACAGAGAAATTAGCAATTACACAGACACAATATACAGGTTGCTTGAAGACTCGCAAATCCAGCAGGAAAAGAATGAAAAGGATTTACTAGCATTGGACAGTTGGCAAAATTTGTGGAATTGGTTTAACATAACAAAATGGCTGTGGTATATAAAAATATTCATAATGATAGTAGGAGGCTTAATAGGTTTAAGAATAATTTTTGCTGTACTATCTATAGTAAATAGAGTTAGGCAGGGATACTCACCTTTGTCGTTTCAGACCCTTATCCCAAACCAGAGGGAACCCGACAGGCTCGGAAGAATCGAAGAAGAAGGTGGAGAGCCAGACAGAAACAGATCCATTCGATTGGTGAACGGATTCTTAGCTCTTACCTGGGACGACCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGATTGAGAGACTTCATATTGGTGACAGTGAGAGTGGTGGAACTTCTGGGACGCAGCAGCTTCAGGGGACTACAGAGGGGGTGGGAAGCCCTTAAGTATCTGGGAAGCCTTGTGCAGTATTGGGGTCTAGAGCTAAAAAAGAGTGCTATTAGTTTGCTTGATACCACAGCAATAGCAGTAGCTGAAGGAACAGATAGGATTATAGAATTCCTACAGAGAATTTGTAGAGCTATCTACCATATACCTAGAAGAATAAGACAGGGCTTTGAAGCAGCTTTGCAATAAAATGGGGGGCAAGTGGTCAAAAAGCAGTATAGTTGGATGGCCTAATGTAAGGGAAAGAATAAGGCGAACTGATCCAGCAGCAGAGGGAGTAGGAGCAGCATCTCGAGACTTAGAGAGACATGGGGCACTTACTACCAGCAACACAGTCAGCAACAATGCTGCATGTGCCTGGCTGGAAGCACAAGAAGAGGAAAAAGAAGTAGGCTTTCCAGTCAGACCTCAAGTGCCTTTAAGACCAATGACTTATAAAGGAGCATTCGATCTCAGCTTCTTTTTAAAAGAAAAGGGGGGACTGGAAGGGTTAATTTACTCCAAGAAAAGGCAAGACATCCTTGATTTGTGGGTTTATAACACACAAGGCTTCTTTCCTGATTGGCAAAACTACACACCGGGACCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTTCAAGCTAGTACCAGTTGACCCAAGGGAAGTAGAAGAAGCCAACGAAGGAGAAAACAACTGTCTGCTACACCCTATGAGCCAACATGGAATGGATGATGATCACAGAGAAGTATTAAAGTGGAAGTTTGACAGTCAACTAGCACACAAACACATGGCCCGCGAGCTACATCCGGAGTTTTACAAAGACTGCTGACACAAAAGGGACTTTCCGCTGGGACTTTCCACTTGGGCGTTCCAGGAGGTGGGGTCTGGGCGGGACCGGGGAGTGGCCAGCCCTCAGATGCTGCATATAAGCAGCTGCTTTTCGCCTGTACTGGGTCTCTCTAGGTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTGCCTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTCTAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCATTTTGGTTGCGTGGAAAATCTCTAGCA + + + + gag + aminoAcid + 792-2270 + + + + pol + aminoAcid + 2072-5074 + + + + vif + aminoAcid + 5022-5597 + + + + vpu + aminoAcid + 6039-6293 + + + + env + aminoAcid + 6217-8775 + + + + NEF + aminoAcid + 8780-9400 + + + + + plasma + + + + + + gag + 1-492 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + gag + 1 + + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 1.00 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + + + + + pol + 1-1000 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + vif + 1-191 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + vif + 1 + + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 1.00 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + + + + + vpu + 1-84 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + vpu + 1 + + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 1.00 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + + + + + env + 1-852 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + env + 1 + + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 1.00 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + + + + + NEF + 1-206 + + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + 1.00 + + + + + NEF + 1 + + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 1.00 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + 0.001 + + + + + dynamicPopulation + + + 10 + all + + + + + 50 + 100000 + + + + + + 9.3E-5 + + 0.42 2.49 0.29 + 1.73 0.23 4.73 + 6.99 0.20 0.60 + 1.02 2.56 0.88 + + + + + + + + + + + active + 1400 + + + + treatment + 1400 + + + + + + + + + + 140 + alignment_plasma.fasta + + 10 + FASTA + + + + + + + + latent_reservoir + + dynamicPopulation + + + 0 + all + + + + + 0.003 + 0.0056 + + + + + + + 0.0 + + 0 0 0 0 + 0 0 0 0 + 0 0 0 0 + + + + + + + + + + epoch + 2800 + + + + + 1680 + alignment_latent_1680.fasta + + 10 + FASTA + + + + + 1960 + alignment_latent_1960.fasta + + 10 + FASTA + + + + + 2240 + alignment_latent_2240.fasta + + 10 + FASTA + + + + + 2520 + alignment_latent_2520.fasta + + 10 + FASTA + + + + + 2800 + alignment_latent_2800.fasta + + 10 + FASTA + + + + + + + diff --git a/examples/HIV_models/activegrowth_high.xml b/examples/HIV_models/activegrowth_high.xml new file mode 100755 index 0000000..50620f0 --- /dev/null +++ b/examples/HIV_models/activegrowth_high.xml @@ -0,0 +1,947 @@ + + 1 + + + 0 0.0026 0.00108 0 + + + 9719 + + TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATA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0.0026 0.00108 0 + + + 9719 + + TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATA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+ 9719 + + TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATA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0.42 2.49 0.29 + 1.73 0.23 4.73 + 6.99 0.20 0.60 + 1.02 2.56 0.88 + + + + + + + + + + + active + 1400 + + + + treatment + 1400 + + + + + + + + + + 140 + alignment_plasma.fasta + + 10 + FASTA + + + + + + + + latent_reservoir + + dynamicPopulation + + + 0 + all + + + + + 0.003 + 0.0056 + + + + + + + 0.0 + + 0 0 0 0 + 0 0 0 0 + 0 0 0 0 + + + + + + + + + + epoch + 2800 + + + + + 1680 + alignment_latent_1680.fasta + + 10 + FASTA + + + + + 1960 + alignment_latent_1960.fasta + + 10 + FASTA + + + + + 2240 + alignment_latent_2240.fasta + + 10 + FASTA + + + + + 2520 + alignment_latent_2520.fasta + + 10 + FASTA + + + + + 2800 + alignment_latent_2800.fasta + + 10 + FASTA + + + + + + + diff --git a/examples/HIV_models/fitness_none.xml b/examples/HIV_models/fitness_none.xml new file mode 100755 index 0000000..8ae10ec --- /dev/null +++ b/examples/HIV_models/fitness_none.xml @@ -0,0 +1,237 @@ + + 1 + + + 0 0.0026 0.00108 0 + + + 9719 + + TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAATGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA + + + + gag + aminoAcid + 790-2289 + + + + pol + aminoAcid + 2085-5093 + + + + PR + aminoAcid + 2253-2549 + + + RT + aminoAcid + 2550-4229 + + + IN + aminoAcid + 4230-5093 + + + + vif + aminoAcid + 5041-5616 + + + + vpr + aminoAcid + 5559-5847 + + + + vpu + aminoAcid + 6062-6307 + + + + env + aminoAcid + 6225-8792 + + + + NEF + aminoAcid + 8797-9414 + + + + + plasma + + + + + dynamicPopulation + + + 10 + all + + + + + 50 + 100000 + + + + + + 9.3E-5 + + 0.42 2.49 0.29 + 1.73 0.23 4.73 + 6.99 0.20 0.60 + 1.02 2.56 0.88 + + + + + + + + + + + active + 1400 + + + + treatment + 1400 + + + + + + + + + + 140 + alignment_plasma.fasta + + 10 + FASTA + + + + + + + + latent_reservoir + + dynamicPopulation + + + 0 + all + + + + + 0.003 + 0.0056 + + + + + + + 0.0 + + 0 0 0 0 + 0 0 0 0 + 0 0 0 0 + + + + + + + + + + epoch + 2800 + + + + + 1680 + alignment_latent_1680.fasta + + 10 + FASTA + + + + + 1960 + alignment_latent_1960.fasta + + 10 + FASTA + + + + + 2240 + alignment_latent_2240.fasta + + 10 + FASTA + + + + + 2520 + alignment_latent_2520.fasta + + 10 + FASTA + + + + + 2800 + alignment_latent_2800.fasta + + 10 + FASTA + + + + + + + diff --git a/examples/HIV_models/indel.xml b/examples/HIV_models/indel.xml new file mode 100755 index 0000000..d9875e9 --- /dev/null +++ b/examples/HIV_models/indel.xml @@ -0,0 +1,242 @@ + + 1 + + + 0 0.0026 0.00108 0 + + + 9719 + + TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAATGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA + + + + gag + aminoAcid + 790-2289 + + + + pol + aminoAcid + 2085-5093 + + + + PR + aminoAcid + 2253-2549 + + + RT + aminoAcid + 2550-4229 + + + IN + aminoAcid + 4230-5093 + + + + vif + aminoAcid + 5041-5616 + + + + vpr + aminoAcid + 5559-5847 + + + + vpu + aminoAcid + 6062-6307 + + + + env + aminoAcid + 6225-8792 + + + + NEF + aminoAcid + 8797-9414 + + + + + plasma + + + + + dynamicPopulation + + + 10 + all + + + + + 50 + 100000 + + + + + + 9.3E-5 + + 0.42 2.49 0.29 + 1.73 0.23 4.73 + 6.99 0.20 0.60 + 1.02 2.56 0.88 + + + + 0.08 1 + 6E-4 + 6E-4 + + + + + + + + + + active + 1400 + + + + treatment + 1400 + + + + + + + + + + 140 + alignment_plasma.fasta + + 10 + FASTA + + + + + + + + latent_reservoir + + dynamicPopulation + + + 0 + all + + + + + 0.003 + 0.0056 + + + + + + + 0.0 + + 0 0 0 0 + 0 0 0 0 + 0 0 0 0 + + + + + + + + + + epoch + 2800 + + + + + 1680 + alignment_latent_1680.fasta + + 10 + FASTA + + + + + 1960 + alignment_latent_1960.fasta + + 10 + FASTA + + + + + 2240 + alignment_latent_2240.fasta + + 10 + FASTA + + + + + 2520 + alignment_latent_2520.fasta + + 10 + FASTA + + + + + 2800 + alignment_latent_2800.fasta + + 10 + FASTA + + + + + + + diff --git a/examples/HIV_models/latencydeath_high.xml b/examples/HIV_models/latencydeath_high.xml new file mode 100755 index 0000000..34f93b6 --- /dev/null +++ b/examples/HIV_models/latencydeath_high.xml @@ -0,0 +1,947 @@ + + 1 + + + 0 0.0026 0.00108 0 + + + 9719 + + TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAATGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA 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0.00108 0 + + + 9719 + + TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATA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0.0026 0.00108 0 + + + 9719 + + TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATA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0.0026 0.00108 0 + + + 9719 + + TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATA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0.00108 0 + + + 9719 + + TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATA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0.00108 0 + + + 9719 + + TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATA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+ + 9719 + + TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATA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+ 9719 + + TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATA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0.0026 0.00216 0 + + + 9719 + + TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATA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0.00054 0 + + + 9719 + + TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATA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TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATA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