From: Ulrich B. <zzz...@us...> - 2004-07-24 18:43:32
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Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/graph In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv6454/src/org/openscience/cdk/graph Modified Files: BiconnectivityInspector.java MinimalPathIterator.java MoleculeGraphs.java Log Message: added JavaDoc & copyright to SSSRFinder related classes fixed the getConnectionMatrix() and addBonds() problems Index: BiconnectivityInspector.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/graph/BiconnectivityInspector.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- BiconnectivityInspector.java 23 Jul 2004 14:23:52 -0000 1.1 +++ BiconnectivityInspector.java 24 Jul 2004 18:42:50 -0000 1.2 @@ -1,3 +1,32 @@ +/* $RCSfile$ + * $Author$ + * $Date$ + * $Revision$ + * + * Copyright (C) 2004 The Chemistry Development Kit (CDK) project + * + * Contact: cdk...@li... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. + * + */ + package org.openscience.cdk.graph; import java.util.ArrayList; import java.util.HashMap; @@ -15,21 +44,29 @@ import org._3pq.jgrapht.graph.SimpleGraph; import org._3pq.jgrapht.graph.Subgraph; -/* - * Created on May 2, 2004 - * - */ - /** - * @author uli + * Finds the biconnected components of a graph. + * + * Two edges belong to the same biconnected component if and only if they are + * identical or both belong to a simple cycle. + * + * @author Ulrich Bauer <ba...@cs...> + * + * + * @cdk.module standard * + * @cdk.builddepends jgrapht-0.5.3.jar + * @cdk.depends jgrapht-0.5.3.jar */ - public class BiconnectivityInspector { List m_biconnectedSets; Map m_vertexToConnectedSet; private UndirectedGraph graph; + /** + * Creates a biconnectivity inspector for the specified undirected graph. + * @param g the specified graph + */ public BiconnectivityInspector(UndirectedGraph g) { @@ -164,10 +201,17 @@ return m_biconnectedSets; } + /** + * Returns a list of <code>Set</code>s, where each set contains all edge that are + * in the same biconnected component. All graph edges occur in exactly one set. + * @return a list of <code>Set</code>s, where each set contains all edge that are + * in the same biconnected component + */ public List biconnectedSets( ) { return lazyFindBiconnectedSets( ); } + /* public List hopcroftTarjanKnuthFindBiconnectedSets() { Map rank; Map parent; @@ -184,5 +228,5 @@ return m_biconnectedSets; } - + */ } Index: MinimalPathIterator.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/graph/MinimalPathIterator.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- MinimalPathIterator.java 23 Jul 2004 14:23:52 -0000 1.1 +++ MinimalPathIterator.java 24 Jul 2004 18:42:51 -0000 1.2 @@ -1,3 +1,32 @@ +/* $RCSfile$ + * $Author$ + * $Date$ + * $Revision$ + * + * Copyright (C) 2004 The Chemistry Development Kit (CDK) project + * + * Contact: cdk...@li... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. + * + */ + package org.openscience.cdk.graph; import java.util.ArrayList; import java.util.HashMap; @@ -16,13 +45,16 @@ import org._3pq.jgrapht.graph.SimpleGraph; import org._3pq.jgrapht.traverse.ClosestFirstIterator; -/* - * Created on May 11, 2004 - * - */ /** - * @author uli + * Iterates over all shortest paths between two vertices in an undirected, unweighted graph. + * + * @author Ulrich Bauer <ba...@cs...> + * + * + * @cdk.module standard * + * @cdk.builddepends jgrapht-0.5.3.jar + * @cdk.depends jgrapht-0.5.3.jar */ public class MinimalPathIterator implements Iterator { @@ -35,6 +67,12 @@ Object next; + /** + * Creates a minimal path iterator for the specified undirected graph. + * @param g the specified graph + * @param startVertex the start vertex for the paths + * @param targetVertex the target vertex for the paths + */ public MinimalPathIterator(SimpleGraph g, Object startVertex, Object targetVertex) { this.g = g; @@ -42,10 +80,10 @@ this.startVertex = startVertex; this.targetVertex = targetVertex; - createShortestPathTree(); + createShortestPathGraph(); } - private void createShortestPathTree() { + private void createShortestPathGraph() { shortestPathGraph = new DefaultDirectedGraph(); shortestPathGraph.addAllVertices(g.vertexSet()); Index: MoleculeGraphs.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/graph/MoleculeGraphs.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- MoleculeGraphs.java 23 Jul 2004 14:23:52 -0000 1.1 +++ MoleculeGraphs.java 24 Jul 2004 18:42:51 -0000 1.2 @@ -1,23 +1,60 @@ -package org.openscience.cdk.graph; -import java.util.Iterator; +/* $RCSfile$ + * $Author$ + * $Date$ + * $Revision$ + * + * Copyright (C) 2004 The Chemistry Development Kit (CDK) project + * + * Contact: cdk...@li... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * All we ask is that proper credit is given for our work, which includes + * - but is not limited to - adding the above copyright notice to the beginning + * of your source code files, and to any copyright notice that you may distribute + * with programs based on this work. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. + * + */ -import org._3pq.jgrapht.Graph; +package org.openscience.cdk.graph; import org._3pq.jgrapht.graph.SimpleGraph; import org.openscience.cdk.Atom; import org.openscience.cdk.Bond; import org.openscience.cdk.Molecule; -/* - * Created on May 22, 2004 - * - */ /** - * @author uli + * Utility class to create a molecule graph for use with jgrapht. + * + * @author Ulrich Bauer <ba...@cs...> + * + * + * @cdk.module standard * + * @cdk.builddepends jgrapht-0.5.3.jar + * @cdk.depends jgrapht-0.5.3.jar */ public class MoleculeGraphs { + // make class non-instantiable private MoleculeGraphs() {} + /** + * Creates a molecule graph for use with jgrapht. + * Bond orders are not respected. + * + * @param molecule the specified molecule + * @return a graph representing the molecule + */ static public SimpleGraph getMoleculeGraph(Molecule molecule) { SimpleGraph graph = new SimpleGraph(); for (int i=0; i<molecule.getAtomCount(); i++ ) { @@ -39,6 +76,7 @@ return graph; } + /* static public String asString(Graph molGraph) { StringBuffer buf = new StringBuffer(); buf.append("["); @@ -57,4 +95,5 @@ return "(" + buf.toString() + ", " + molGraph.edgeSet().toString( ) + ")"; } + */ } |