Java17 upgrade

.github/workflows/ant.yml

@@ -10,10 +10,10 @@ jobs:
     steps:
     - uses: actions/checkout@v4
 
-    - name: Set up JDK 11
+    - name: Set up JDK 17
       uses: actions/setup-java@v4
       with:
-        java-version: '11'
+        java-version: '17'
         distribution: 'temurin'
 
     - name: Download JUnit 5 dependencies

build.xml

@@ -48,7 +48,7 @@
     <target name="test" depends="compile" description="Compile and run JUnit 5 tests">
         <mkdir dir="${basedir}/build/test-classes"/>
         <javac srcdir="${basedir}/test" destdir="${basedir}/build/test-classes"
-               source="11" target="11" includeantruntime="false">
+               source="17" target="17" includeantruntime="false">
             <classpath>
                 <path refid="project.lib"/>
                 <pathelement location="${basedir}/build"/>
@@ -129,7 +129,7 @@
           target: compile
          ================================= -->
     <target name="compile" depends="depends" description="--> The ant build file of GraphTea Project.">
-        <javac srcdir="${src.dir}" destdir="${build.dir}" source="11" target="11" includeantruntime="false">
+        <javac srcdir="${src.dir}" destdir="${build.dir}" source="17" target="17" includeantruntime="false">
             <classpath>
                 <path refid="project.lib"/>
             </classpath>

src/graphtea/extensions/AlgorithmUtils.java

@@ -50,9 +50,11 @@ public static void resetVertexMarks(GraphModel g) {
     public static boolean isConnected(GraphModel g) {
         ArrayList<Integer> vs = new ArrayList<>();
         int[] parent = new int[g.getVerticesCount()];
-        for(int i=0;i < g.getVerticesCount();i++) parent[i] = -1;
+        for (int i = 0; i < g.getVerticesCount(); i++) {
+            parent[i] = -1;
+        }
         dfs(g, 0, vs, parent);
-        return Arrays.stream(vs.toArray()).distinct().toArray().length == g.getVerticesCount();
+        return vs.stream().distinct().count() == g.getVerticesCount();
     }
 
     /**
@@ -428,17 +430,19 @@ public static String getEigenValues(GraphModel g) {
         EigenvalueDecomposition ed = A.eig();
         double[] rv = ed.getRealEigenvalues();
         double[] iv = ed.getImagEigenvalues();
-        String res = "";
+        StringBuilder res = new StringBuilder();
         for (int i = 0; i < rv.length; i++) {
-            if (iv[i] != 0)
-                res +="" + AlgorithmUtils.round(rv[i],10) + " + " + AlgorithmUtils.round(iv[i],10) + "i";
-            else
-                res += "" + AlgorithmUtils.round(rv[i],10);
-            if(i!=rv.length-1) {
-                res += ",";
+            if (iv[i] != 0) {
+                res.append(AlgorithmUtils.round(rv[i], 10)).append(" + ")
+                   .append(AlgorithmUtils.round(iv[i], 10)).append("i");
+            } else {
+                res.append(AlgorithmUtils.round(rv[i], 10));
+            }
+            if (i != rv.length - 1) {
+                res.append(",");
             }
         }
-        return res;
+        return res.toString();
     }
 
     /**
@@ -485,6 +489,35 @@ public static double sumOfEigenValues(Matrix A) {
         return sum;
     }
 
+    /**
+     * Returns the all-pairs shortest-path distance matrix for {@code g} (unweighted).
+     * Convenience wrapper around {@link FloydWarshall} to avoid the two-liner boilerplate
+     * that appears throughout the codebase.
+     *
+     * @param g the graph
+     * @return distance matrix d where d[i][j] is the shortest path length from vertex i to vertex j
+     */
+    public static int[][] getAllPairsDistances(GraphModel g) {
+        return new FloydWarshall().getAllPairsShortestPathWithoutWeight(g);
+    }
+
+    /**
+     * Computes the spectral energy of a matrix: sum of |eigenvalue - shift| over all real eigenvalues.
+     * Use shift = 0 for plain energy (e.g. Distance Energy, Transmission Energy).
+     *
+     * @param A     the matrix whose eigenvalues to sum
+     * @param shift subtracted from each eigenvalue before taking the absolute value
+     * @return spectral energy
+     */
+    public static double spectralEnergy(Matrix A, double shift) {
+        double[] rv = A.eig().getRealEigenvalues();
+        double sum = 0;
+        for (double v : rv) {
+            sum += Math.abs(v - shift);
+        }
+        return sum;
+    }
+
     /**
      * Computes the eigen values
      *
@@ -495,25 +528,27 @@ public static String getEigenValues(Matrix A) {
         EigenvalueDecomposition ed = A.eig();
         double[] rv = ed.getRealEigenvalues();
         double[] iv = ed.getImagEigenvalues();
-        String res = "";
-        List<Double> EigenValues = new ArrayList<>();
+        StringBuilder res = new StringBuilder();
+        List<Double> eigenValues = new ArrayList<>();
         for (int i = 0; i < rv.length; i++) {
-            if (iv[i] != 0)
-                res +="" + AlgorithmUtils.round(rv[i],10) + " + " + AlgorithmUtils.round(iv[i],10) + "i";
-            else
-                EigenValues.add(AlgorithmUtils.round(rv[i],10));
-        }
-        if(EigenValues.size() > 0) {
-            res = "";
-            EigenValues.sort((aDouble, t1) -> -aDouble.compareTo(t1));
-            for (int i = 0; i < EigenValues.size(); i++) {
-                res += EigenValues.get(i);
-                if(i != EigenValues.size() - 1) {
-                    res+=",";
+            if (iv[i] != 0) {
+                res.append(AlgorithmUtils.round(rv[i], 10)).append(" + ")
+                   .append(AlgorithmUtils.round(iv[i], 10)).append("i");
+            } else {
+                eigenValues.add(AlgorithmUtils.round(rv[i], 10));
+            }
+        }
+        if (!eigenValues.isEmpty()) {
+            res = new StringBuilder();
+            eigenValues.sort((a, b) -> -a.compareTo(b));
+            for (int i = 0; i < eigenValues.size(); i++) {
+                res.append(eigenValues.get(i));
+                if (i != eigenValues.size() - 1) {
+                    res.append(",");
                 }
             }
         }
-        return res;
+        return res.toString();
     }
 
     // get kth minimum degree
@@ -682,8 +717,7 @@ public static Matrix getMaxDegreeAdjacencyMatrix (GraphModel g) {
      * @return the maximum degree adjacency matrix
      */
     public static Matrix getDistanceAdjacencyMatrix (GraphModel g) {
-        FloydWarshall fw = new FloydWarshall();
-        int[][] dist = fw.getAllPairsShortestPathWithoutWeight(g);
+        int[][] dist = getAllPairsDistances(g);
         Matrix adj = g.getAdjacencyMatrix();
         for(int i=0;i < adj.getColumnDimension();i++) {
             for(int j=0;j < adj.getRowDimension();j++) {
@@ -808,9 +842,8 @@ public static GPoint normalize(GPoint vector) {
     }
 
     public static Matrix getDistanceLaplacianMatrix (GraphModel g) {
-        FloydWarshall fw = new FloydWarshall();
         int sum;
-        int[][] dist = fw.getAllPairsShortestPathWithoutWeight(g);
+        int[][] dist = getAllPairsDistances(g);
         Matrix adj = g.getAdjacencyMatrix();
         for(int i=0;i < adj.getColumnDimension();i++) {
             sum=0;
@@ -825,9 +858,8 @@ public static Matrix getDistanceLaplacianMatrix (GraphModel g) {
     }
 
     public static Matrix getDistanceSignlessLaplacianMatrix (GraphModel g) {
-        FloydWarshall fw = new FloydWarshall();
         double sum;
-        int [][] dist = fw.getAllPairsShortestPathWithoutWeight(g);
+        int[][] dist = getAllPairsDistances(g);
         Matrix adj = g.getAdjacencyMatrix();
         for(int i=0;i < adj.getColumnDimension();i++) {
             sum=0;
@@ -844,9 +876,8 @@ public static Matrix getDistanceSignlessLaplacianMatrix (GraphModel g) {
     }
 
     public static Matrix getDiagonalTransMatrix (GraphModel g) {
-        FloydWarshall fw = new FloydWarshall();
         int sum;
-        int[][] dist = fw.getAllPairsShortestPathWithoutWeight(g);
+        int[][] dist = getAllPairsDistances(g);
         Matrix adj = g.getAdjacencyMatrix();
         for(int i=0;i < adj.getColumnDimension();i++) {
             sum=0;
@@ -861,9 +892,8 @@ public static Matrix getDiagonalTransMatrix (GraphModel g) {
     }
 
     public static Matrix getAverageTransMatrix (GraphModel g) {
-        FloydWarshall fw = new FloydWarshall();
-        int sum; sum=0;
-        int[][] dist = fw.getAllPairsShortestPathWithoutWeight(g);
+        int sum = 0;
+        int[][] dist = getAllPairsDistances(g);
         Matrix adj = g.getAdjacencyMatrix();
         for(int i=0;i < adj.getColumnDimension();i++) {
             for(int j=0;j < adj.getRowDimension();j++) {

src/graphtea/extensions/actions/EdgeSemitotalGraph.java

@@ -5,107 +5,17 @@
 
 package graphtea.extensions.actions;
 
-import graphtea.graph.graph.Edge;
-import graphtea.graph.graph.GPoint;
-import graphtea.graph.graph.GraphModel;
-import graphtea.graph.graph.Vertex;
-import graphtea.platform.parameter.Parameter;
-import graphtea.platform.parameter.Parametrizable;
-import graphtea.plugins.main.GraphData;
-import graphtea.plugins.main.extension.GraphActionExtension;
-
-
 /**
- * Creates a line graph from the current graph and shows it in a new tab
- *
  * @author Mohammad Ali Rostami
  * @author Azin Azadi
  */
-public class EdgeSemitotalGraph implements GraphActionExtension, Parametrizable {
-    @Parameter
-    public int k = 2;
-
-    public void action(GraphData graphData) {
-
-        GraphModel g1 = graphData.getGraph();
-        GraphModel g2 = new GraphModel(false);
-        g2.setIsEdgesCurved(true);
-
-        for(Vertex v : g1.getVertexArray()) {
-            Vertex tmp = new Vertex();
-            tmp.setLocation(v.getLocation());
-            g2.addVertex(tmp);
-        }
-
-        for(Edge e : g1.getEdges()) {
-            GPoint v1 = e.source.getLocation();
-            GPoint v2 = e.target.getLocation();
-            double dis = v1.distance(v2);
-            GPoint v3 = GPoint.sub(v2, v1);
-            v3 = GPoint.div(v3, k+1);
-
-            Vertex src = g2.getVertex(e.source.getId());
-            for (int i = 0; i < k; i++) {
-                Vertex tmp = new Vertex();
-                tmp.getProp().obj=e;
-                GPoint v4 = new GPoint(v3);
-                v4.multiply(i + 1);
-                v4.add(v1);
-                tmp.setLocation(v4);
-                g2.addVertex(tmp);
-                g2.addEdge(new Edge(src,tmp));
-                src=tmp;
-            }
-            g2.addEdge(new Edge(src, g2.getVertex(e.target.getId())));
-        }
-
-        for(Vertex v1 : g2.getVertexArray()) {
-            for (Vertex v2 : g2.getVertexArray()) {
-                if(v1.getProp().obj!=null) {
-                    if (v2.getProp().obj != null) {
-                        Edge e1 = (Edge) v1.getProp().obj;
-                        Edge e2 = (Edge) v2.getProp().obj;
-                        if(edgeConnects(e1,e2)) {
-                            Edge ee = new Edge(v1,v2);
-                            GPoint vector =
-                                    GPoint.sub(v1.getLocation(),v2.getLocation());
-                            vector= GPoint.div(vector,vector.norm());
-                            GPoint ppVec = new GPoint(-vector.y,vector.x);
-                            ppVec.multiply(30.0);
-                            ee.setCurveControlPoint(ppVec);
-                            g2.addEdge(ee);
-                        }
-                    }
-                }
-            }
-        }
-
-
-       graphData.core.showGraph(g2);
-    }
-
-    public boolean edgeConnects(Edge e1,Edge e2) {
-        if(e1.source.getId() == e2.source.getId()) return true;
-        if(e1.target.getId() == e2.source.getId()) return true;
-        if(e1.source.getId() == e2.target.getId()) return true;
-        return e1.target.getId() == e2.target.getId();
-    }
-
-    public String getName() {
-        return "Edge Semitotal Graph";
-    }
-
-    public String getDescription() {
-        return "Edge Semitotal Graph";
-    }
+public class EdgeSemitotalGraph extends SubdividedGraphBase {
+    @Override protected boolean markSubdivisionVertices() { return true; }
+    @Override protected boolean addSubdivisionVertexEdges() { return true; }
 
     @Override
-    public String checkParameters() {
-        return null;
-    }
+    public String getName() { return "Edge Semitotal Graph"; }
 
     @Override
-    public String getCategory() {
-        return "Transformations";
-    }
+    public String getDescription() { return "Edge Semitotal Graph"; }
 }