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add -savek option #18

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2 changes: 1 addition & 1 deletion candidateset.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -150,7 +150,7 @@ bool CandidateSet::update(string tree, double score) {
}

vector<double> CandidateSet::getBestScores(int numBestScore) {
if (numBestScore == 0)
if (numBestScore == 0 || numBestScore > size())
numBestScore = size();
vector<double> res;
for (reverse_iterator rit = rbegin(); rit != rend() && numBestScore > 0; rit++, numBestScore--) {
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2 changes: 1 addition & 1 deletion iqtree.cpp
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Expand Up @@ -1539,7 +1539,7 @@ string IQTree::optimizeModelParameters(bool printInfo) {
}

void IQTree::printBestScores(int numBestScore) {
vector<double> bestScores = candidateTrees.getBestScores(candidateTrees.popSize);
vector<double> bestScores = candidateTrees.getBestScores(numBestScore);
for (vector<double>::iterator it = bestScores.begin(); it != bestScores.end(); it++)
cout << (params->maximum_parsimony ? -(*it) : (*it)) << " ";
cout << endl;
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9 changes: 7 additions & 2 deletions phyloanalysis.cpp
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Expand Up @@ -1851,8 +1851,13 @@ void runTreeReconstruction(Params &params, string &original_model, IQTree &iqtre
if (iqtree.isSuperTree())
((PhyloSuperTree*) &iqtree)->mapTrees();
if (params.snni && params.min_iterations) {
cout << (params.maximum_parsimony ? "Scores" : "Log-likelihoods") << " of best " << params.popSize << " trees: " << endl;
iqtree.printBestScores(iqtree.candidateTrees.popSize);
if (params.savek == 0) {
cout << (params.maximum_parsimony ? "Scores" : "Log-likelihoods") << " of best " << params.popSize << " trees: " << endl;
iqtree.printBestScores(iqtree.candidateTrees.popSize);
} else {
cout << (params.maximum_parsimony ? "Scores" : "Log-likelihoods") << " of best " << params.savek << " trees: " << endl;
iqtree.printBestScores(params.savek);
}
}

/******** Performs final model parameters optimization ******************/
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10 changes: 10 additions & 0 deletions tools.cpp
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Expand Up @@ -805,6 +805,7 @@ void parseArg(int argc, char *argv[], Params &params) {
params.do_first_rell = false;
params.remove_dup_seq = false;
params.test_mode = false;
params.savek = 0;

#ifdef _OPENMP
params.num_threads = 0;
Expand Down Expand Up @@ -2263,6 +2264,15 @@ void parseArg(int argc, char *argv[], Params &params) {
assert(params.popSize < params.numParsTrees);
continue;
}
if (strcmp(argv[cnt], "-savek") == 0) {
cnt++;
if (cnt >= argc)
throw "Use -savek <number_of_saving_trees>";
params.savek = convert_int(argv[cnt]);
params.numParsTrees = max(params.savek, params.numParsTrees);
assert(params.savek > 0);
continue;
}
if (strcmp(argv[cnt], "-beststart") == 0) {
params.bestStart = true;
cnt++;
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5 changes: 5 additions & 0 deletions tools.h
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Expand Up @@ -1625,6 +1625,11 @@ struct Params {
*/
bool test_mode;

/**
* number of search trees saved
*/
int savek;

/*
* Diep:
* Use with -test_mode
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