refactoring

.github/workflows/ant.yml

@@ -9,9 +9,9 @@ jobs:
 
     steps:
     - uses: actions/checkout@v1
-    - name: Set up JDK 1.8
+    - name: Set up JDK 21
       uses: actions/setup-java@v1
       with:
-        java-version: 1.8
+        java-version: 21
     - name: Build with Ant
       run: ant -noinput -buildfile build.xml

src/graphtea/extensions/AlgorithmUtils.java

@@ -132,7 +132,7 @@ void clearVertexMarks(GraphModel g) {
     }
 
     /**
-     * returns the subtree rooted by subTreeRoot in the rooted tree tree with the root treeRoot
+     * returns the subtree rooted by subTreeRoot in the rooted tree with the root treeRoot
      * the vertices are ordered by their distances to subTreeRoot
      * the exact distance is placed in v.getProp().obj as an Integer, starting distance is 0 which is subTreeRoot
      */
@@ -144,6 +144,7 @@ ArrayList<Vertex> getSubTree(GraphModel tree, Vertex treeRoot, Vertex subTreeRoo
         clearVertexMarks(tree);
 
 //close the path to tree root
+        assert pathToRoot != null;
         for (Vertex vertex : pathToRoot) {
             vertex.setMark(true);
         }
@@ -351,7 +352,7 @@ public static double getAngle(GPoint p1, GPoint p2) {
     }
 
     /**
-     * locations v in a r-teta coordination
+     * locations v in an r-teta coordination
      */
     public static void setLocation(Vertex v, GPoint center, double radius, double ang) {
         v.setLocation(new GPoint(center.x + radius * Math.cos(ang), center.y + radius * Math.sin(ang)));
@@ -426,17 +427,17 @@ 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";
+                res.append(AlgorithmUtils.round(rv[i], 10)).append(" + ").append(AlgorithmUtils.round(iv[i], 10)).append("i");
             else
-                res += "" + AlgorithmUtils.round(rv[i],10);
+                res.append(AlgorithmUtils.round(rv[i], 10));
             if(i!=rv.length-1) {
-                res += ",";
+                res.append(",");
             }
         }
-        return res;
+        return res.toString();
     }
 
     /**
@@ -493,25 +494,25 @@ public static String getEigenValues(Matrix A) {
         EigenvalueDecomposition ed = A.eig();
         double[] rv = ed.getRealEigenvalues();
         double[] iv = ed.getImagEigenvalues();
-        String res = "";
+        StringBuilder res = new StringBuilder();
         Vector<Double> EigenValues = new Vector<>();
         for (int i = 0; i < rv.length; i++) {
             if (iv[i] != 0)
-                res +="" + AlgorithmUtils.round(rv[i],10) + " + " + AlgorithmUtils.round(iv[i],10) + "i";
+                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.size() > 0) {
-            res = "";
+        if(!EigenValues.isEmpty()) {
+            res = new StringBuilder();
             EigenValues.sort((aDouble, t1) -> -aDouble.compareTo(t1));
             for (int i = 0; i < EigenValues.size(); i++) {
-                res += EigenValues.get(i);
+                res.append(EigenValues.get(i));
                 if(i != EigenValues.size() - 1) {
-                    res+=",";
+                    res.append(",");
                 }
             }
         }
-        return res;
+        return res.toString();
     }
 
     // get kth minimum degree
@@ -541,7 +542,7 @@ public static double getDegreeSumOfVertex(GraphModel g, double alpha, Vertex v)
     public static double getDegreeSum(GraphModel g, double alpha) {
         int sum = 0;
         for(Vertex v: g) {
-            sum+=getDegreeSumOfVertex(g,alpha,v);
+            sum+= (int) getDegreeSumOfVertex(g,alpha,v);
         }
         return sum;
     }
@@ -677,7 +678,7 @@ public static Matrix getMaxDegreeAdjacencyMatrix (GraphModel g) {
     /**
      * Distance adjacency matrix
      * Distance Energy based on
-     * Gopalapillai Indulal,a Ivan Gutmanb and Vijayakumarc
+     * Gopalapillai Indulal,an Ivan Gutmanb and Vijayakumarc
      * ON DISTANCE ENERGY OF GRAPHS
      * MATCH Commun. Math. Comput. Chem. 60 (2008) 461-472.
      *
@@ -714,7 +715,7 @@ public static Matrix getLaplacian(Matrix A) {
         for (int i = 0; i < n; i++) {
             sum = 0;
             for (int j = 0; j < n; j++) {
-                sum += ATemp[j][i];
+                sum += (int) ATemp[j][i];
             }
             DTemp[i][i] = sum;
         }
@@ -781,7 +782,7 @@ public static Matrix getSignlessLaplacian(Matrix A) {
         for (int i = 0; i < n; i++) {
             sum = 0;
             for (int j = 0; j < n; j++) {
-                sum += ATemp[j][i];
+                sum += (int) ATemp[j][i];
             }
             DTemp[i][i] = sum;
         }

src/graphtea/extensions/G6Format.java

@@ -126,29 +126,29 @@ public static String graphToG6(GraphModel g) {
     }
 
     public static String createAdjMatrix (Matrix m){
-        String result="";
+        StringBuilder result= new StringBuilder();
 
         for (int i = 1, k = 1; k < m.getColumnDimension(); i++, k++) {
             for (int j = 0; j < i; j++) {
-                if (m.get(j,i) != 0) result += "1";
-                else result += "0";
+                if (m.get(j,i) != 0) result.append("1");
+                else result.append("0");
             }
         }
-        return result;
+        return result.toString();
     }
 
 
     public static String encodeGraph(int NoNodes, String adjmatrix) {
-        String rv = "";
+        StringBuilder rv = new StringBuilder();
         int[] nn = encodeN(NoNodes);
         int[] adj = encodeR(adjmatrix);
         int[] res = new int[nn.length + adj.length];
         System.arraycopy(nn, 0, res, 0, nn.length);
         System.arraycopy(adj, 0, res, nn.length, adj.length);
         for (int re : res) {
-            rv = rv + (char) re;
+            rv.append((char) re);
         }
-        return rv;
+        return rv.toString();
     }
 
     private static int[] encodeN(long i) {
@@ -189,16 +189,14 @@ private static int[] encodeR(String a) {
 
     private static String padR(String str) {
         int padwith = 6 - (str.length() % 6);
-        for (int i = 0; i < padwith; i++) {
-            str += "0";
-        }
+        str = str + "0".repeat(padwith);
         return str;
     }
 
     private static String padL(String str, int h) {
-        String retval = "";
+        StringBuilder retval = new StringBuilder();
         for (int i = 0; i < h - str.length(); i++) {
-            retval += "0";
+            retval.append("0");
         }
         return retval + str;
     }

src/graphtea/extensions/actions/ExtractSubGraph.java

@@ -31,7 +31,7 @@ public void action(GraphData graphData) {
 
         SubGraph sg = SubGraphRenderer.sgbck;
         HashMap<Integer,Integer> idid= new HashMap<>();
-        if(sg.vertices.size()!=0) {
+        if(!sg.vertices.isEmpty()) {
             for(Vertex v : sg.vertices) {
                 Vertex tmp = new Vertex();
                 tmp.setLabel(v.getLabel());

src/graphtea/extensions/actions/g6/G6CSVStringLoader.java

@@ -60,7 +60,7 @@ public void action(GraphData graphData) {
                 if (id == given_id)
                     g6 = line.substring(line.lastIndexOf(",") + 1).trim();
             }
-            if(!g6.equals("")) {
+            if(!g6.isEmpty()) {
                 GraphModel g = G6Format.stringToGraphModel(g6);
                 GPoint[] pp = PositionGenerators.circle(200, 400, 250, g.numOfVertices());
 

src/graphtea/extensions/algorithms/DAG.java

@@ -36,7 +36,7 @@ public static AbstractList<Vertex> doSort(GraphModel graph) {
                 v.setMark(true);
             }
 
-        while (alv.size() != 0) {
+        while (!alv.isEmpty()) {
             Vertex v = alv.remove(0);
             out.add(v);
 

src/graphtea/extensions/algorithms/EndomorphismAnimator.java

@@ -42,7 +42,6 @@ public void doAlgorithm() {
 
         boolean[] isThere = new boolean[mapSize];
         int numOfThere = 0;
-        for(int i=0;i < mapSize;i++) isThere[i]=false;
         for(int j=0;j < 100;j++) {
             if(numOfThere == mapSize) break;
             step(j+"th step");

src/graphtea/extensions/algorithms/GreedyColoring.java

@@ -1,16 +1,13 @@
 package graphtea.extensions.algorithms;
 
-import graphtea.graph.graph.Edge;
 import graphtea.graph.graph.GraphModel;
 import graphtea.graph.graph.Vertex;
 import graphtea.platform.core.BlackBoard;
 import graphtea.plugins.algorithmanimator.core.GraphAlgorithm;
 import graphtea.plugins.algorithmanimator.extension.AlgorithmExtension;
 import graphtea.plugins.main.core.actions.ResetGraph;
 
-import java.util.ArrayList;
 import java.util.Collections;
-import java.util.Iterator;
 import java.util.Vector;
 
 /**

src/graphtea/extensions/algorithms/IndSetProductColoring.java

@@ -131,7 +131,7 @@ public Vector<Vector<Integer>> setproduct(Vector<Vector<Integer>> set1,Vector<Ve
                         break;
                     }
                 }
-                if (!sameItem && tmp.size() != 0 && integers.size() != 0) {
+                if (!sameItem && !tmp.isEmpty() && !integers.isEmpty()) {
                     tmp.add(-1);
                     tmp.addAll(integers);
                 }

src/graphtea/extensions/algorithms/LloydKMeans.java

@@ -6,18 +6,18 @@
 import java.util.Arrays;
 
 /**
- * http://frodriguez.webs.com/Java%20Algo/kmeans.txt
- *
+ * <a href="http://frodriguez.webs.com/Java%20Algo/kmeans.txt">...</a>
+ * <p>
  * Lloyd's Algorithm - A greedy approximation to the kmeans clustering problem (NP-HARD), this is similar to
  *                     finding the centers of the voronoi cells of a tessellation that has the input points
  *                     distributed as evenly as possible throughout the cells.
- *
+ * <p>
  * Steps:
  * 		1) It guesses an initial location for the center of each cluster
  * 		2) It assigns each input point to one cluster (the one with the closest center)
  *			3) For each cluster, move its center to the centroid of all its assigned points.
  *			4) Repeat steps 2-3 until no change occurs.
- *
+ * <p>
  * Returns: An array of Clusters. If you need exactly k clusters you may have to run it several times since
  *          some clusters may die out during the algorithm, this shouldn't be a problem because this function
  *          usually runs very fast.
@@ -89,7 +89,7 @@ public static Cluster[] cluster(GPoint[] p, int k) {
 
 		// remove all empty clusters (due to bad initial placement)
 		for (int i = 0; i < ret.size(); i++)
-			if (ret.get(i).getMembers().size() == 0)
+			if (ret.get(i).getMembers().isEmpty())
 				ret.remove(i--);
 
 		return ret.toArray(new Cluster[0]); // the result may not have exactly k

src/graphtea/extensions/algorithms/TopologicalSort.java

@@ -31,7 +31,7 @@ public class TopologicalSort extends Algorithm implements AutomatedAlgorithm {
             if (graph.getInDegree(v) == 0)
                 alv.add(v);
 
-        while (alv.size() != 0) {
+        while (!alv.isEmpty()) {
             Vertex v = alv.remove(0);
             out.add(v);
 

src/graphtea/extensions/algorithms/shortestpath/DijkstraAlgorithm.java

@@ -14,7 +14,7 @@
 /**
  *  This method finds the shortest path from a vertex to all vertices
  *  of a graph.
- *
+ * <p>
  * Created by rostam on 06.03.15.
  * @author M. Ali Rostami
  */
@@ -25,11 +25,11 @@ public DijkstraAlgorithm(BlackBoard blackBoard) {
 
     /**
      * This method finds a reference array using Dijkstra algorithm
-     * from which, one can find
+     * from which one can find
      * the shortest paths of all vertices of a graph from an arbitrary
      * given vertex.
-     *
-     * graph  Graph object to be searched.
+     * <p>
+     * graph Graph object to be searched.
      * vertex The source of the paths.
      * Creates Vector of vertices that for each i, it has a reference to
      *         the vertex, before the vertex with ID number i in the shortest path

src/graphtea/extensions/algorithms/shortestpath/algs/Johnson.java

@@ -56,7 +56,6 @@ public int[][] ComputePaths(GraphModel g) {
         if (sp.computePaths(g, u) != null) {
             Vector<Vertex> pd = sp.computePaths(g, u);
             for (Vertex v : g) {
-
                 int dd = 0;
                 Edge h;
                 while (v != u) {

src/graphtea/extensions/algorithms/spanningtree/Prim.java

@@ -31,12 +31,6 @@ public class Prim extends Algorithm implements AutomatedAlgorithm {
      * Temporary reference to the graph the algorithm is going to run on it.
      */
     final GraphModel graph;
-    /**
-     * Reference to a GraphConverter object which is responsible for duplication
-     * of the graph elements, because graph edges and vertices are going to be
-     * copied to the newly created spanning tree.
-     */
-    private final EdgeVertexCopier<Vertex, Edge> gc;
     /**
      * Priority queue implemented as a binary heap to store edges, sorted according
      * to their weights.
@@ -73,7 +67,6 @@ public Prim(GraphModel graph,
         //	throw new NullPointerException();
 
         this.graph = graph;
-        this.gc = gc;
         this.ec = new DefaultEdgeComparator();
     }
 

src/graphtea/extensions/generators/BananaTreeGenerator.java

@@ -14,8 +14,8 @@
 
 /**
  * Author: Ali Rostami
- *
- * https://mathworld.wolfram.com/BananaTree.html
+ * <p><a href="
+ ">* <a href="https://mathworld.wolfram.com/Ba</a>nanaTree.html">...</a>
  */
 
 @CommandAttitude(name = "generate_banana_tree", abbreviation = "_g_banana", description = "generates a Banana graph")

src/graphtea/extensions/generators/CrownGraph.java

@@ -19,9 +19,8 @@
 
 /**
  * Author: Ali Rostami
+ * <a <a href="href="https://mathworld.wolfram.com/CrownGrap">...</a>h.html">...</a>
  *
- * https://mathworld.wolfram.com/CrownGraph.html
- * 
  */
 @CommandAttitude(name = "generate_crown", abbreviation = "_g_crown",
         description = "generates a Crown graph of order n")

src/graphtea/extensions/generators/ExampleChainGraph1.java

@@ -17,8 +17,6 @@
 import graphtea.plugins.graphgenerator.core.extension.GraphGeneratorExtension;
 
 import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
 
 /**
  * @author azin azadi

src/graphtea/extensions/generators/FlowerGraph.java

@@ -68,7 +68,7 @@ public GPoint[] getVertexPositions()
 		int w = 1000;
 		double mw = ((double)w)/2.0, qw = ((double)w)/4.0;
 		GPoint[] result = new GPoint[2*n+1];
-		result[2*n] = new GPoint(w/2, w/2);
+		result[2*n] = new GPoint((double) w /2, (double) w /2);
 		double ang = Math.PI*2.0/n;
 		double offset = 0.0;
 		if ((n % 2) == 0)

src/graphtea/extensions/generators/HelmGraph.java

@@ -72,7 +72,7 @@ public GPoint[] getVertexPositions() {
 		int w = 1000;
 		double mw = ((double) w) / 2.0, qw = ((double) w) / 4.0;
 		GPoint[] result = new GPoint[2 * n + 1];
-		result[2 * n] = new GPoint(w / 2, w / 2);
+		result[2 * n] = new GPoint((double) w / 2, (double) w / 2);
 		double ang = Math.PI * 2.0 / n;
 		double offset = 0.0;
 		if ((n % 2) == 0)
@@ -97,7 +97,7 @@ public GraphModel generateGraph() {
 
 	/**
 	 * generates a Helm Graph with given parameters
-	 *
+	 * <p>
 	 * A helm graph, denoted Hn is a graph obtained by attaching a single
 	 * edge and node to each node of the outer circuit of a wheel graph Wn.
 	 *