Rename DGraph class

src/main/java/org/thegalactic/dgraph/DGraph.java → src/main/java/org/thegalactic/dgraph/ConcreteDGraph.java

@@ -1,7 +1,7 @@
 package org.thegalactic.dgraph;
 
 /*
- * DGraph.java
+ * ConcreteDGraph.java
  *
  * Copyright: 2010-2015 Karell Bertet, France
  * Copyright: 2015-2016 The Galactic Organization, France
@@ -33,17 +33,17 @@
  * that associates to each node a treeset of successors, defined by class
  * {@link Edge}; - a treemap of predecessors that associates to each node a
  * treeset of predecessors, defined by class {@link Edge}.
- *
- * This class provides methods implementing classical operation on a directed
- * graph:
- *
- * - sinks - wells - subgraph - reflexive closure and reduction - transitive
- * closure - strongly connected components - ...
- *
- * This class also provides a static method randomly generating a directed
- * graph.
- *
- * ![DGraph](DGraph.png)
+
+ This class provides methods implementing classical operation on a directed
+ graph:
+
+ - sinks - wells - subgraph - reflexive closure and reduction - transitive
+ closure - strongly connected components - ...
+
+ This class also provides a static method randomly generating a directed
+ graph.
+
+ ![ConcreteDGraph](ConcreteDGraph.png)
  *
  * @uml DGraph.png
  * !include resources/org/thegalactic/dgraph/DGraph.iuml
@@ -55,7 +55,7 @@
  * class DGraph #LightCyan
  * title DGraph UML graph
  */
-public class DGraph extends AbstractDGraph implements Cloneable {
+public class ConcreteDGraph extends AbstractDGraph implements Cloneable {
 
     /*
      * ------------- FIELDS ------------------
@@ -82,7 +82,7 @@ public class DGraph extends AbstractDGraph implements Cloneable {
     /**
      * Constructs a new directed graph with an empty set of node.
      */
-    public DGraph() {
+    public ConcreteDGraph() {
         this.nodes = new TreeSet<Node>();
         this.successors = new TreeMap<Node, SortedSet<Edge>>();
         this.predecessors = new TreeMap<Node, SortedSet<Edge>>();
@@ -96,7 +96,7 @@ public DGraph() {
      *
      * @param set the set of nodes
      */
-    public DGraph(final Set<Node> set) {
+    public ConcreteDGraph(final Set<Node> set) {
         this.nodes = new TreeSet<Node>(set);
         this.successors = new TreeMap<Node, SortedSet<Edge>>();
         for (Node node : this.nodes) {
@@ -113,7 +113,7 @@ public DGraph(final Set<Node> set) {
      *
      * @param graph the directed graph to be copied
      */
-    public DGraph(final DGraph graph) {
+    public ConcreteDGraph(final ConcreteDGraph graph) {
         this.nodes = new TreeSet<Node>(graph.nodes);
         this.successors = new TreeMap<Node, SortedSet<Edge>>();
         this.predecessors = new TreeMap<Node, SortedSet<Edge>>();
@@ -135,8 +135,8 @@ public DGraph(final DGraph graph) {
      * @throws java.lang.CloneNotSupportedException
      */
     @Override
-    public DGraph clone() throws CloneNotSupportedException {
-        return new DGraph(this);
+    public ConcreteDGraph clone() throws CloneNotSupportedException {
+        return new ConcreteDGraph(this);
     }
 
     /**
@@ -588,8 +588,8 @@ public List<Node> topologicalSort() {
      *
      * @todo implement a SubGraph class?
      */
-    public DGraph getSubgraphByNodes(final Set<Node> nodes) {
-        DGraph graph = new DGraph();
+    public ConcreteDGraph getSubgraphByNodes(final Set<Node> nodes) {
+        ConcreteDGraph graph = new ConcreteDGraph();
         // addition of nodes in the subgraph
         for (Node node : nodes) {
             if (this.containsNode(node)) {
@@ -618,8 +618,8 @@ public DGraph getSubgraphByNodes(final Set<Node> nodes) {
      *
      * @todo implement a SubGraph class?
      */
-    public DGraph getSubgraphByEdges(final Set<Edge> edges) {
-        DGraph graph = new DGraph();
+    public ConcreteDGraph getSubgraphByEdges(final Set<Edge> edges) {
+        ConcreteDGraph graph = new ConcreteDGraph();
         // addition of all nodes in the subgraph
         for (Node node : this.nodes) {
             graph.addNode(node);
@@ -736,7 +736,7 @@ public int transitiveClosure() {
      * its predecessor set, and its predecessor set by its successor set.
      */
     public void transpose() {
-        DGraph tmp = new DGraph(this);
+        ConcreteDGraph tmp = new ConcreteDGraph(this);
         for (Edge edge : tmp.getEdges()) {
             this.removeEdge(edge);
             this.addEdge(new Edge(edge.getTarget(), edge.getSource(), edge.getContent()));
@@ -756,11 +756,11 @@ public void transpose() {
     public DAGraph getStronglyConnectedComponent() {
         DAGraph cc = new DAGraph();
         // first depth first search
-        DGraph tmp = new DGraph(this);
+        ConcreteDGraph tmp = new ConcreteDGraph(this);
         tmp.transitiveClosure();
         ArrayList<Node> last = tmp.depthFirstSearch()[1];
         // transposition of the graph
-        DGraph transposedGraph = new DGraph(this);
+        ConcreteDGraph transposedGraph = new ConcreteDGraph(this);
         transposedGraph.transpose();
         // sort nodes according to the reverse last sort
         ArrayList<Node> sort = new ArrayList<Node>();
@@ -802,7 +802,7 @@ public DAGraph getStronglyConnectedComponent() {
      *
      * @return this for chaining
      */
-    protected DGraph setNodes(final TreeSet<Node> nodes) {
+    protected ConcreteDGraph setNodes(final TreeSet<Node> nodes) {
         this.nodes = nodes;
         return this;
     }
@@ -823,7 +823,7 @@ protected SortedMap<Node, SortedSet<Edge>> getSuccessors() {
      *
      * @return this for chaining
      */
-    protected DGraph setSuccessors(final TreeMap<Node, SortedSet<Edge>> successors) {
+    protected ConcreteDGraph setSuccessors(final TreeMap<Node, SortedSet<Edge>> successors) {
         this.successors = successors;
         return this;
     }
@@ -844,7 +844,7 @@ protected SortedMap<Node, SortedSet<Edge>> getPredecessors() {
      *
      * @return this for chaining
      */
-    protected DGraph setPredecessors(final TreeMap<Node, SortedSet<Edge>> predecessors) {
+    protected ConcreteDGraph setPredecessors(final TreeMap<Node, SortedSet<Edge>> predecessors) {
         this.predecessors = predecessors;
         return this;
     }
@@ -928,14 +928,14 @@ private class Edges extends AbstractSet<Edge> implements SortedSet<Edge> {
         /**
          * The underlying graph.
          */
-        private DGraph graph;
+        private ConcreteDGraph graph;
 
         /**
          * Get the underlying graph.
          *
          * @return the graph
          */
-        protected DGraph getGraph() {
+        protected ConcreteDGraph getGraph() {
             return graph;
         }
 
@@ -1022,9 +1022,9 @@ public boolean hasNext() {
         /**
          * Constructs a sorted set of the edges source a graph.
          *
-         * @param graph A DGraph
+         * @param graph A ConcreteDGraph
          */
-        Edges(DGraph graph) {
+        Edges(ConcreteDGraph graph) {
             this.graph = graph;
         }
 

src/main/java/org/thegalactic/dgraph/DAGraph.java

@@ -19,7 +19,7 @@
 
 /**
  * This class extends the representation of a directed graph given by class
- * {@link DGraph} for directed acyclic graph (DAG).
+ * {@link ConcreteDGraph} for directed acyclic graph (DAG).
  *
  * The main property of a directed acyclic graph is to be a partially ordered
  * set (poset) when transitively closed, and a Hasse diagram when transitively
@@ -54,7 +54,7 @@
  * class DAGraph #LightCyan
  * title DAGraph UML graph
  */
-public class DAGraph extends DGraph {
+public class DAGraph extends ConcreteDGraph {
 
     /*
      * ----------- STATIC GENERATION METHODS -------------
@@ -152,9 +152,9 @@ public DAGraph(final Set<Node> set) {
      * Acyclic property is checked for the specified DAG. When not verified,
      * this component is construct with the same set of nodes but with no edges.
      *
-     * @param graph the DGraph to be copied
+     * @param graph the ConcreteDGraph to be copied
      */
-    public DAGraph(final DGraph graph) {
+    public DAGraph(final ConcreteDGraph graph) {
         super(graph);
         if (this.isAcyclic()) {
             this.reflexiveReduction();
@@ -262,9 +262,9 @@ public DAGraph ideal(final Node node) {
      */
     @Override
     public DAGraph getSubgraphByNodes(final Set<Node> nodes) {
-        DGraph tmp = new DGraph(this);
+        ConcreteDGraph tmp = new ConcreteDGraph(this);
         tmp.transitiveClosure();
-        DGraph sub = tmp.getSubgraphByNodes(nodes);
+        ConcreteDGraph sub = tmp.getSubgraphByNodes(nodes);
         DAGraph sub2 = new DAGraph(sub);
         sub2.transitiveReduction();
         return sub2;
@@ -346,7 +346,7 @@ public int transitiveReduction() {
      * Computes the transitive closure of this component.
      *
      * This method overlaps the computation of the transitive closure for
-     * directed graph in class {@link DGraph} with an implementation of the
+     * directed graph in class {@link ConcreteDGraph} with an implementation of the
      * Goralcikova-Koubeck algorithm dedicated to acyclic directed graph. This
      * algorithm can also compute the transitive reduction of a directed acyclic
      * graph.

src/main/java/org/thegalactic/dgraph/DGraphFactory.java

@@ -31,8 +31,8 @@ public final class DGraphFactory {
      *
      * @return a random graph
      */
-    public DGraph random(final int size, final double threshold) {
-        final DGraph graph = new DGraph();
+    public ConcreteDGraph random(final int size, final double threshold) {
+        final ConcreteDGraph graph = new ConcreteDGraph();
         // addition of nodes
         for (int i = 1; i <= size; i++) {
             final Node node = new Node(i);
@@ -56,7 +56,7 @@ public DGraph random(final int size, final double threshold) {
      *
      * @return a random graph
      */
-    public DGraph random(final int size) {
+    public ConcreteDGraph random(final int size) {
         return this.random(size, 0.5);
     }
 

src/main/java/org/thegalactic/dgraph/io/DGraphIOFactory.java

@@ -11,12 +11,12 @@
  * This file is part of java-lattices.
  * You can redistribute it and/or modify it under the terms of the CeCILL-B license.
  */
-import org.thegalactic.dgraph.DGraph;
+import org.thegalactic.dgraph.ConcreteDGraph;
 
 /**
- * This class register readers and writers for the DGraph class.
- *
- * ![DGraphIOFactory](DGraphIOFactory.png)
+ * This class register readers and writers for the ConcreteDGraph class.
+
+ ![DGraphIOFactory](DGraphIOFactory.png)
  *
  * @uml DGraphIOFactory.png
  * !include resources/org/thegalactic/dgraph/io/DGraphIOFactory.iuml
@@ -26,7 +26,7 @@
  * class DGraphIOFactory #LightCyan
  * title DGraphIOFactory UML graph
  */
-public final class DGraphIOFactory extends org.thegalactic.io.IOFactory<DGraph> {
+public final class DGraphIOFactory extends org.thegalactic.io.IOFactory<ConcreteDGraph> {
 
     /**
      * The singleton instance.

src/main/java/org/thegalactic/dgraph/io/DGraphSerializerDot.java

@@ -14,7 +14,7 @@
 import java.io.BufferedWriter;
 import java.io.IOException;
 
-import org.thegalactic.dgraph.DGraph;
+import org.thegalactic.dgraph.ConcreteDGraph;
 import org.thegalactic.dgraph.Edge;
 import org.thegalactic.dgraph.Node;
 import org.thegalactic.io.Writer;
@@ -34,7 +34,7 @@
  * hide members show DGraphSerializerDot members class DGraphSerializerDot
  * #LightCyan title DGraphSerializerDot UML graph
  */
-public final class DGraphSerializerDot implements Writer<DGraph> {
+public final class DGraphSerializerDot implements Writer<ConcreteDGraph> {
 
     /**
      * The singleton instance.
@@ -72,7 +72,7 @@ private DGraphSerializerDot() {
      * @throws IOException When an IOException occurs
      */
     @Override
-    public void write(final DGraph graph, final BufferedWriter file) throws IOException {
+    public void write(final ConcreteDGraph graph, final BufferedWriter file) throws IOException {
         // Writing start of graph
         file.write("digraph G {");
         file.newLine();

src/main/java/org/thegalactic/lattice/ArrowRelation.java

@@ -16,7 +16,7 @@
 import java.util.TreeSet;
 
 import org.thegalactic.context.Context;
-import org.thegalactic.dgraph.DGraph;
+import org.thegalactic.dgraph.ConcreteDGraph;
 import org.thegalactic.dgraph.Edge;
 import org.thegalactic.dgraph.Node;
 import org.thegalactic.io.Filer;
@@ -52,7 +52,7 @@
  * class ArrowRelation #LightCyan
  * title ArrowRelation UML graph
  */
-public class ArrowRelation extends DGraph {
+public class ArrowRelation extends ConcreteDGraph {
 
     /**
      * Field used to encode up arrow relation.

src/main/java/org/thegalactic/lattice/BijectiveComponents.java

@@ -20,7 +20,7 @@
 import java.util.TreeSet;
 
 import org.thegalactic.context.Context;
-import org.thegalactic.dgraph.DGraph;
+import org.thegalactic.dgraph.ConcreteDGraph;
 import org.thegalactic.util.ComparableSet;
 
 /**
@@ -87,7 +87,7 @@ public class BijectiveComponents {
     /**
      * The dependency graph of the reduced lattice.
      */
-    private DGraph dependencyGraph = null;
+    private ConcreteDGraph dependencyGraph = null;
 
     /**
      * The minimal generators of the reduced lattice.
@@ -332,7 +332,7 @@ protected BijectiveComponents setReducedLattice(Lattice reducedLattice) {
      *
      * @return dependencyGraph dependency graph of this component
      */
-    public DGraph getDependencyGraph() {
+    public ConcreteDGraph getDependencyGraph() {
         if (dependencyGraph == null) {
             // FIXME: do we use getLattice or getReducedLattice ?
             dependencyGraph = this.getReducedLattice().getDependencyGraph();
@@ -347,7 +347,7 @@ public DGraph getDependencyGraph() {
      *
      * @return this for chaining
      */
-    protected BijectiveComponents setDependencyGraph(DGraph dependencyGraph) {
+    protected BijectiveComponents setDependencyGraph(ConcreteDGraph dependencyGraph) {
         this.dependencyGraph = dependencyGraph;
         return this;
     }

src/main/java/org/thegalactic/lattice/ClosureSystem.java

@@ -18,7 +18,7 @@
 import java.util.Vector;
 
 import org.thegalactic.dgraph.DAGraph;
-import org.thegalactic.dgraph.DGraph;
+import org.thegalactic.dgraph.ConcreteDGraph;
 import org.thegalactic.dgraph.Node;
 import org.thegalactic.util.ComparableSet;
 
@@ -208,7 +208,7 @@ public Concept nextClosure(Concept cl) {
      *
      * @return the precedence graph
      */
-    public DGraph precedenceGraph() {
+    public ConcreteDGraph precedenceGraph() {
         // compute a TreeMap of closures for each element of the component
         TreeMap<Comparable, TreeSet<Comparable>> closures = new TreeMap<Comparable, TreeSet<Comparable>>();
         for (Comparable x : this.getSet()) {
@@ -217,7 +217,7 @@ public DGraph precedenceGraph() {
             closures.put(x, this.closure(setX));
         }
         // nodes of the graph are elements
-        DGraph prec = new DGraph();
+        ConcreteDGraph prec = new ConcreteDGraph();
         TreeMap<Comparable, Node> nodeCreated = new TreeMap<Comparable, Node>();
         for (Comparable x : this.getSet()) {
             Node node = new Node(x);
@@ -253,7 +253,7 @@ public TreeMap<Object, TreeSet> getReducibleElements() {
         // Initialise a map Red of reducible attributes
         TreeMap<Object, TreeSet> red = new TreeMap();
         // Initialise the precedence graph G of the closure system
-        DGraph graph = this.precedenceGraph();
+        ConcreteDGraph graph = this.precedenceGraph();
         // First, compute each group of equivalent attributes
         // This group will be a strongly connected component on the graph.
         // Then, only one element of each group is skipped, others will be deleted.