1.1 --- a/molwind-chemical/pom.xml Thu Oct 15 17:28:16 2009 +0200
1.2 +++ b/molwind-chemical/pom.xml Thu Oct 29 11:19:09 2009 +0100
1.3 @@ -38,11 +38,32 @@
1.4 <dependency>
1.5 <groupId>org.molwind</groupId>
1.6 <artifactId>molwind-core</artifactId>
1.7 + <version>1.0-SNAPSHOT</version>
1.8 </dependency>
1.9 <dependency>
1.10 <groupId>org.openscience.cdk</groupId>
1.11 <artifactId>cdk</artifactId>
1.12 </dependency>
1.13 + <dependency>
1.14 + <groupId>net.sf.jung</groupId>
1.15 + <artifactId>jung-api</artifactId>
1.16 + <version>2.0</version>
1.17 + </dependency>
1.18 + <dependency>
1.19 + <groupId>net.sf.jung</groupId>
1.20 + <artifactId>jung-io</artifactId>
1.21 + <version>2.0</version>
1.22 + </dependency>
1.23 + <dependency>
1.24 + <groupId>net.sf.jung</groupId>
1.25 + <artifactId>jung-visualization</artifactId>
1.26 + <version>2.0</version>
1.27 + </dependency>
1.28 + <dependency>
1.29 + <groupId>net.sf.jung</groupId>
1.30 + <artifactId>jung-graph-impl</artifactId>
1.31 + <version>2.0</version>
1.32 + </dependency>
1.33 </dependencies>
1.34
1.35 <parent>
1.36 @@ -55,7 +76,31 @@
1.37
1.38
1.39 <!-- Build Settings -->
1.40 -
1.41 +<profiles>
1.42 + <profile>
1.43 + <id>graph</id>
1.44 + <build>
1.45 + <defaultGoal>test</defaultGoal>
1.46 + <plugins>
1.47 + <plugin>
1.48 + <groupId>org.codehaus.mojo</groupId>
1.49 + <artifactId>exec-maven-plugin</artifactId>
1.50 + <executions>
1.51 + <execution>
1.52 + <phase>test</phase>
1.53 + <goals>
1.54 + <goal>java</goal>
1.55 + </goals>
1.56 + <configuration>
1.57 + <mainClass>org.molwind.chemical.io.GraphMain2</mainClass>
1.58 + </configuration>
1.59 + </execution>
1.60 + </executions>
1.61 + </plugin>
1.62 + </plugins>
1.63 + </build>
1.64 + </profile>
1.65 + </profiles>
1.66
1.67
1.68
1.69 @@ -79,4 +124,4 @@
1.70
1.71
1.72
1.73 -</project>
1.74 \ No newline at end of file
1.75 +</project>
2.1 --- a/molwind-chemical/src/main/java/org/molwind/chemical/io/SDFileIterator.java Thu Oct 15 17:28:16 2009 +0200
2.2 +++ b/molwind-chemical/src/main/java/org/molwind/chemical/io/SDFileIterator.java Thu Oct 29 11:19:09 2009 +0100
2.3 @@ -47,11 +47,12 @@
2.4 private ArrayList<File> files;
2.5 private Iterator fileIterator;
2.6 private Iterator entityIterator;
2.7 - private IteratingMDLReader sdfReader;
2.8 + private IteratingMDLReader sdfReader=null;
2.9 private RelationshipResolver relationshipResolver;
2.10 private ChemicalEntity currentEntity;
2.11 private ChemicalEntity lastEntity;
2.12 private EntityGraph compounds;
2.13 +
2.14
2.15 /**
2.16 * Creates a new chemical entity iterator based on the underlying SD files
2.17 @@ -64,8 +65,12 @@
2.18 */
2.19 public SDFileIterator(final File[] theFiles,
2.20 final RelationshipResolver resolver) {
2.21 - files = (ArrayList<File>) Arrays.asList(theFiles);
2.22 - fileIterator = null;
2.23 + files = new ArrayList<File>();
2.24 + for(File f:theFiles){
2.25 + files.add(f);
2.26 + }
2.27 +
2.28 + fileIterator = null;
2.29 entityIterator = null;
2.30 sdfReader = null;
2.31 relationshipResolver = resolver;
2.32 @@ -73,18 +78,35 @@
2.33 lastEntity = null;
2.34 compounds = null;
2.35 }
2.36 +
2.37 +
2.38 +
2.39 +
2.40 +
2.41 +
2.42 +
2.43 +
2.44 +
2.45
2.46
2.47 private ChemicalEntity readNext()
2.48 throws IOException {
2.49 +
2.50 +
2.51 if (sdfReader == null || !sdfReader.hasNext()) {
2.52 +
2.53 +
2.54 +
2.55 +
2.56 if (fileIterator == null) {
2.57 fileIterator = files.iterator();
2.58 }
2.59 if (sdfReader != null) {
2.60 - sdfReader.close();
2.61 + sdfReader.close();
2.62 + return null;
2.63 }
2.64 if (!fileIterator.hasNext()) {
2.65 +
2.66 return null;
2.67 }
2.68
2.69 @@ -92,38 +114,79 @@
2.70 FileReader fileReader = new FileReader(file);
2.71 sdfReader = new IteratingMDLReader(fileReader,
2.72 DefaultChemObjectBuilder.getInstance());
2.73 +
2.74 + if (!sdfReader.hasNext()) {
2.75 +
2.76 + sdfReader.close();
2.77
2.78 - if (!sdfReader.hasNext()) {
2.79 - sdfReader.close();
2.80 return null;
2.81 }
2.82 }
2.83
2.84 - IMolecule molecule = (IMolecule) sdfReader.next();
2.85 - ChemicalEntity chemicalEntity = new ChemicalEntity(molecule);
2.86 + IMolecule molecule = (IMolecule) sdfReader.next();
2.87 +
2.88 + ChemicalEntity chemicalEntity = new ChemicalEntity(molecule);
2.89 + if ((relationshipResolver != null)
2.90 + && (relationshipResolver instanceof Identity)) {
2.91 + chemicalEntity.setIdentity((Identity) relationshipResolver);
2.92 + }
2.93 +
2.94 + return chemicalEntity;
2.95 + }
2.96
2.97 - if ((relationshipResolver != null)
2.98 - && (relationshipResolver instanceof Identity)) {
2.99 - chemicalEntity.setIdentity((Identity) relationshipResolver);
2.100 - }
2.101
2.102 - return chemicalEntity;
2.103 +
2.104 +
2.105 + /**
2.106 + *
2.107 + *
2.108 + *
2.109 + *
2.110 + */
2.111 + public void setFileReader(File f)
2.112 + throws IOException{
2.113 + FileReader fileReader = new FileReader(f);
2.114 + sdfReader = new IteratingMDLReader(fileReader,DefaultChemObjectBuilder.getInstance());
2.115 +
2.116 + }
2.117 +
2.118 + /**
2.119 + *
2.120 + *
2.121 + *
2.122 + *
2.123 + *
2.124 + */
2.125 + public DefaultEntityGraph getGraph2()
2.126 + throws IOException{
2.127 +
2.128 + return (DefaultEntityGraph) getGraph();
2.129 }
2.130
2.131 private EntityGraph getGraph()
2.132 throws IOException {
2.133 +
2.134 if (compounds == null) {
2.135 +
2.136 +
2.137 ChemicalEntity currentEntity = null;
2.138 ChemicalEntity lastEntity = null;
2.139 -
2.140 + int i = 0;
2.141 while ((currentEntity = readNext()) != null) {
2.142 +
2.143 if ((relationshipResolver != null) && (lastEntity != null)) {
2.144 relationshipResolver.related(lastEntity, currentEntity);
2.145 }
2.146 +
2.147 lastEntity = currentEntity;
2.148 +
2.149 }
2.150 +
2.151 if (relationshipResolver != null) {
2.152 +
2.153 +
2.154 compounds = relationshipResolver.resolve();
2.155 +
2.156 } else {
2.157 compounds = new DefaultEntityGraph();
2.158 }
3.1 --- a/molwind-chemical/src/main/java/org/molwind/chemical/io/SDFileLocator.java Thu Oct 15 17:28:16 2009 +0200
3.2 +++ b/molwind-chemical/src/main/java/org/molwind/chemical/io/SDFileLocator.java Thu Oct 29 11:19:09 2009 +0100
3.3 @@ -264,9 +264,8 @@
3.4 private void iterateDirectory(String dPath,ArrayList<String> result)throws Exception
3.5 {
3.6
3.7 -
3.8 File file = new File(dPath);
3.9 -
3.10 +
3.11
3.12
3.13 File[] files = file.listFiles();
4.1 --- a/molwind-chemical/src/main/java/org/molwind/chemical/model/ChemicalEntity.java Thu Oct 15 17:28:16 2009 +0200
4.2 +++ b/molwind-chemical/src/main/java/org/molwind/chemical/model/ChemicalEntity.java Thu Oct 29 11:19:09 2009 +0100
4.3 @@ -48,7 +48,8 @@
4.4 private IMolecule molecule;
4.5 private Identity identity;
4.6 private MoleculeRenderer moleculeRenderer;
4.7 -
4.8 + private String id;
4.9 + private String parentId;
4.10 private static InChIGeneratorFactory inChIFactory;
4.11
4.12 /**
4.13 @@ -89,8 +90,7 @@
4.14 * the new Identity value
4.15 */
4.16 public void setIdentity(final Identity newIdentity) {
4.17 - this.identity = newIdentity;
4.18 - }
4.19 + this.identity = newIdentity; }
4.20
4.21 /**
4.22 * Adds a new relationship if it is not existing already.
4.23 @@ -267,7 +267,12 @@
4.24 * the value of the attribute
4.25 */
4.26 public String getAttribute(final String name) {
4.27 - // TODO Auto-generated method stub
4.28 + if(name=="ID")
4.29 + return this.id;
4.30 + if(name=="PARENT_ID")
4.31 + return this.parentId;
4.32 +
4.33 +
4.34 return null;
4.35 }
4.36
4.37 @@ -280,7 +285,12 @@
4.38 * the value of the attribute
4.39 */
4.40 public void setAttribute(final String name, final String value) {
4.41 - // TODO Auto-generated method stub
4.42 + if(name.equals("ID"))
4.43 + this.id=value;
4.44 +
4.45 + if(name.equals("PARENT_ID"))
4.46 + this.parentId=value;
4.47 +
4.48 }
4.49
4.50 }
5.1 --- a/molwind-chemical/src/main/java/org/molwind/chemical/model/SubstructureResolver.java Thu Oct 15 17:28:16 2009 +0200
5.2 +++ b/molwind-chemical/src/main/java/org/molwind/chemical/model/SubstructureResolver.java Thu Oct 29 11:19:09 2009 +0100
5.3 @@ -37,10 +37,13 @@
5.4 public class SubstructureResolver
5.5 implements RelationshipResolver, EntityGraphAnalyzer, Identity {
5.6
5.7 - private String parentName;
5.8 - private String idName;
5.9 +
5.10 +
5.11 private EntityGraph compounds;
5.12 private boolean analyzed;
5.13 +
5.14 + private String idName = "ID";
5.15 + private String parentName="PARENT_ID";
5.16
5.17 /**
5.18 * Creates a new Substructure resolver which uses the given attributes to
5.19 @@ -103,6 +106,7 @@
5.20 */
5.21 public boolean related(final WorldEntity entity1,
5.22 final WorldEntity entity2) {
5.23 +
5.24 if ((entity1 == null)
5.25 || (entity2 == null)
5.26 || !(entity1 instanceof ChemicalEntity)
5.27 @@ -112,14 +116,19 @@
5.28
5.29 ChemicalEntity chemicalEntity1 = (ChemicalEntity) entity1;
5.30 ChemicalEntity chemicalEntity2 = (ChemicalEntity) entity2;
5.31 -
5.32 String parentId1 = chemicalEntity1.getAttribute(parentName);
5.33 String id1 = getId(chemicalEntity1);
5.34 String parentId2 = chemicalEntity2.getAttribute(parentName);
5.35 String id2 = getId(chemicalEntity2);
5.36
5.37 - boolean related = false;
5.38
5.39 + /** System.out.println("ChemicalEntity 1: "+ chemicalEntity1.getAttribute(idName));
5.40 + * System.out.println("ChemicalEntity 2: "+ chemicalEntity1.getAttribute(idName));
5.41 + * System.out.println("ParentEntity 1: "+ chemicalEntity1.getAttribute(parentName));
5.42 + * System.out.println("ParentEntity 2: "+ chemicalEntity2.getAttribute(parentName));
5.43 + */
5.44 +
5.45 + boolean related = false;
5.46 if (parentId1 != null) {
5.47 if (parentId1.equals(id2)) {
5.48 return addRelation(chemicalEntity1, chemicalEntity2);
6.1 Binary file molwind-chemical/target/classes/org/molwind/chemical/io/SDFileIterator.class has changed
7.1 Binary file molwind-chemical/target/classes/org/molwind/chemical/io/SDFileLocator.class has changed
8.1 Binary file molwind-chemical/target/classes/org/molwind/chemical/model/ChemicalEntity.class has changed
9.1 Binary file molwind-chemical/target/classes/org/molwind/chemical/model/SubstructureResolver.class has changed
10.1 --- a/molwind-client/molwind-webservice/molwind-endpoint/target/generated/wsdl/org/molwind/webservice/jaxws/GetWorldNames.java Thu Oct 15 17:28:16 2009 +0200
10.2 +++ b/molwind-client/molwind-webservice/molwind-endpoint/target/generated/wsdl/org/molwind/webservice/jaxws/GetWorldNames.java Thu Oct 29 11:19:09 2009 +0100
10.3 @@ -8,7 +8,7 @@
10.4
10.5 /**
10.6 * This class was generated by the CXF 2.0.9
10.7 - * Thu Oct 15 17:27:16 CEST 2009
10.8 + * Wed Oct 28 17:11:36 CET 2009
10.9 * Generated source version: 2.0.9
10.10 *
10.11 */
11.1 --- a/molwind-client/molwind-webservice/molwind-endpoint/target/generated/wsdl/org/molwind/webservice/jaxws/GetWorldNamesResponse.java Thu Oct 15 17:28:16 2009 +0200
11.2 +++ b/molwind-client/molwind-webservice/molwind-endpoint/target/generated/wsdl/org/molwind/webservice/jaxws/GetWorldNamesResponse.java Thu Oct 29 11:19:09 2009 +0100
11.3 @@ -9,7 +9,7 @@
11.4
11.5 /**
11.6 * This class was generated by the CXF 2.0.9
11.7 - * Thu Oct 15 17:27:16 CEST 2009
11.8 + * Wed Oct 28 17:11:36 CET 2009
11.9 * Generated source version: 2.0.9
11.10 *
11.11 */
12.1 --- a/molwind-client/molwind-webservice/molwind-endpoint/target/generated/wsdl/org/molwind/webservice/jaxws/IOExceptionBean.java Thu Oct 15 17:28:16 2009 +0200
12.2 +++ b/molwind-client/molwind-webservice/molwind-endpoint/target/generated/wsdl/org/molwind/webservice/jaxws/IOExceptionBean.java Thu Oct 29 11:19:09 2009 +0100
12.3 @@ -8,7 +8,7 @@
12.4
12.5 /**
12.6 * This class was generated by the CXF 2.0.9
12.7 - * Thu Oct 15 17:27:19 CEST 2009
12.8 + * Wed Oct 28 17:11:39 CET 2009
12.9 * Generated source version: 2.0.9
12.10 *
12.11 */
13.1 --- a/molwind-client/molwind-webservice/molwind-endpoint/target/generated/wsdl/org/molwind/webservice/jaxws/JDOMExceptionBean.java Thu Oct 15 17:28:16 2009 +0200
13.2 +++ b/molwind-client/molwind-webservice/molwind-endpoint/target/generated/wsdl/org/molwind/webservice/jaxws/JDOMExceptionBean.java Thu Oct 29 11:19:09 2009 +0100
13.3 @@ -8,7 +8,7 @@
13.4
13.5 /**
13.6 * This class was generated by the CXF 2.0.9
13.7 - * Thu Oct 15 17:27:18 CEST 2009
13.8 + * Wed Oct 28 17:11:39 CET 2009
13.9 * Generated source version: 2.0.9
13.10 *
13.11 */
14.1 --- a/molwind-client/molwind-webservice/molwind-webclient/src/main/java/org/molwind/webservice/IMolwindWebservice.java Thu Oct 15 17:28:16 2009 +0200
14.2 +++ b/molwind-client/molwind-webservice/molwind-webclient/src/main/java/org/molwind/webservice/IMolwindWebservice.java Thu Oct 29 11:19:09 2009 +0100
14.3 @@ -9,7 +9,7 @@
14.4
14.5 /**
14.6 * This class was generated by Apache CXF 2.2.4
14.7 - * Thu Oct 15 17:27:34 CEST 2009
14.8 + * Wed Oct 28 17:12:07 CET 2009
14.9 * Generated source version: 2.2.4
14.10 *
14.11 */
15.1 --- a/molwind-client/molwind-webservice/molwind-webclient/src/main/java/org/molwind/webservice/IOException_Exception.java Thu Oct 15 17:28:16 2009 +0200
15.2 +++ b/molwind-client/molwind-webservice/molwind-webclient/src/main/java/org/molwind/webservice/IOException_Exception.java Thu Oct 29 11:19:09 2009 +0100
15.3 @@ -6,14 +6,14 @@
15.4
15.5 /**
15.6 * This class was generated by Apache CXF 2.2.4
15.7 - * Thu Oct 15 17:27:34 CEST 2009
15.8 + * Wed Oct 28 17:12:07 CET 2009
15.9 * Generated source version: 2.2.4
15.10 *
15.11 */
15.12
15.13 @WebFault(name = "IOException", targetNamespace = "http://webservice.molwind.org/")
15.14 public class IOException_Exception extends Exception {
15.15 - public static final long serialVersionUID = 20091015172734L;
15.16 + public static final long serialVersionUID = 20091028171207L;
15.17
15.18 private org.molwind.webservice.IOException ioException;
15.19
16.1 --- a/molwind-client/molwind-webservice/molwind-webclient/src/main/java/org/molwind/webservice/JDOMException_Exception.java Thu Oct 15 17:28:16 2009 +0200
16.2 +++ b/molwind-client/molwind-webservice/molwind-webclient/src/main/java/org/molwind/webservice/JDOMException_Exception.java Thu Oct 29 11:19:09 2009 +0100
16.3 @@ -6,14 +6,14 @@
16.4
16.5 /**
16.6 * This class was generated by Apache CXF 2.2.4
16.7 - * Thu Oct 15 17:27:34 CEST 2009
16.8 + * Wed Oct 28 17:12:07 CET 2009
16.9 * Generated source version: 2.2.4
16.10 *
16.11 */
16.12
16.13 @WebFault(name = "JDOMException", targetNamespace = "http://webservice.molwind.org/")
16.14 public class JDOMException_Exception extends Exception {
16.15 - public static final long serialVersionUID = 20091015172734L;
16.16 + public static final long serialVersionUID = 20091028171207L;
16.17
16.18 private org.molwind.webservice.JDOMException jdomException;
16.19
17.1 --- a/molwind-client/molwind-webservice/molwind-webclient/src/main/java/org/molwind/webservice/MolwindWebserviceService.java Thu Oct 15 17:28:16 2009 +0200
17.2 +++ b/molwind-client/molwind-webservice/molwind-webclient/src/main/java/org/molwind/webservice/MolwindWebserviceService.java Thu Oct 29 11:19:09 2009 +0100
17.3 @@ -15,7 +15,7 @@
17.4
17.5 /**
17.6 * This class was generated by Apache CXF 2.2.4
17.7 - * Thu Oct 15 17:27:34 CEST 2009
17.8 + * Wed Oct 28 17:12:07 CET 2009
17.9 * Generated source version: 2.2.4
17.10 *
17.11 */
18.1 Binary file molwind-client/molwind-webservice/molwind-webclient/target/classes/org/molwind/webservice/IOException_Exception.class has changed
19.1 Binary file molwind-client/molwind-webservice/molwind-webclient/target/classes/org/molwind/webservice/JDOMException_Exception.class has changed
20.1 --- a/molwind-core/pom.xml Thu Oct 15 17:28:16 2009 +0200
20.2 +++ b/molwind-core/pom.xml Thu Oct 29 11:19:09 2009 +0100
20.3 @@ -51,6 +51,11 @@
20.4 </dependency>
20.5 <dependency>
20.6 <groupId>net.sf.jung</groupId>
20.7 + <artifactId>jung-visualization</artifactId>
20.8 + <version>2.0</version>
20.9 + </dependency>
20.10 + <dependency>
20.11 + <groupId>net.sf.jung</groupId>
20.12 <artifactId>jung-graph-impl</artifactId>
20.13 <version>2.0</version>
20.14 </dependency>
20.15 @@ -75,6 +80,8 @@
20.16 </plugin>
20.17 </plugins>
20.18 </build>
20.19 +
20.20 +
20.21
20.22
20.23
20.24 @@ -96,6 +103,31 @@
20.25 <url>http://freehg.org/u/molwind/molwind</url>
20.26 </scm>
20.27
20.28 +<profiles>
20.29 + <profile>
20.30 + <id>graph</id>
20.31 + <build>
20.32 + <defaultGoal>test</defaultGoal>
20.33 + <plugins>
20.34 + <plugin>
20.35 + <groupId>org.codehaus.mojo</groupId>
20.36 + <artifactId>exec-maven-plugin</artifactId>
20.37 + <executions>
20.38 + <execution>
20.39 + <phase>test</phase>
20.40 + <goals>
20.41 + <goal>java</goal>
20.42 + </goals>
20.43 + <configuration>
20.44 + <mainClass>org.molwind.graph.Test</mainClass>
20.45 + </configuration>
20.46 + </execution>
20.47 + </executions>
20.48 + </plugin>
20.49 + </plugins>
20.50 + </build>
20.51 + </profile>
20.52 + </profiles>
20.53
20.54
20.55
21.1 --- a/molwind-core/src/main/java/org/molwind/graph/DefaultEntityGraph.java Thu Oct 15 17:28:16 2009 +0200
21.2 +++ b/molwind-core/src/main/java/org/molwind/graph/DefaultEntityGraph.java Thu Oct 29 11:19:09 2009 +0100
21.3 @@ -29,6 +29,18 @@
21.4
21.5 import edu.uci.ics.jung.graph.SparseGraph;
21.6 import edu.uci.ics.jung.io.GraphMLWriter;
21.7 +import edu.uci.ics.jung.graph.util.Pair;
21.8 +import edu.uci.ics.jung.graph.util.EdgeType;
21.9 +
21.10 +import edu.uci.ics.jung.algorithms.layout.Layout;
21.11 +import edu.uci.ics.jung.algorithms.layout.CircleLayout;
21.12 +
21.13 +import edu.uci.ics.jung.graph.Graph;
21.14 +import edu.uci.ics.jung.visualization.BasicVisualizationServer;
21.15 +
21.16 +import javax.swing.JFrame;
21.17 +import java.awt.Dimension;
21.18 +
21.19
21.20
21.21 /**
21.22 @@ -42,14 +54,17 @@
21.23 private SparseGraph graph;
21.24 private HashMap entities;
21.25
21.26 +
21.27 /**
21.28 * Creates a new (empty) graph of entities.
21.29 */
21.30 public DefaultEntityGraph() {
21.31 - graph = new SparseGraph();
21.32 + graph = new SparseGraph<EntityVertex,EntityEdge>();
21.33 entities = new HashMap();
21.34 }
21.35
21.36 +
21.37 +
21.38 /**
21.39 * Adds an entity i.e. vertex to graph. If the vertex id is existing
21.40 * already the vertex is replaced.
21.41 @@ -123,10 +138,11 @@
21.42 entities.put(vertexId2, vertex2);
21.43 graph.addVertex(vertex2);
21.44 }
21.45 + Pair<EntityVertex> endpoints = new Pair<EntityVertex>(vertex1,vertex2);
21.46
21.47 DefaultEntityEdge edge = new DefaultEntityEdge(vertex1, vertex2);
21.48 edge.setRelationship(relation);
21.49 - //TODO.....find solution for the new jung2 api graph.addEdge(edge);
21.50 + graph.addEdge(edge,endpoints,EdgeType.DIRECTED);
21.51 }
21.52
21.53 /**
21.54 @@ -137,7 +153,7 @@
21.55 */
21.56 public void analyze(final EntityGraphAnalyzer analyzer) {
21.57 Iterator it = entities.entrySet().iterator();
21.58 -
21.59 +
21.60 while (it.hasNext()) {
21.61 Map.Entry entry = (Map.Entry) it.next();
21.62 EntityVertex vertex = (EntityVertex) entry.getValue();
21.63 @@ -147,6 +163,8 @@
21.64 }
21.65 }
21.66 }
21.67 +
21.68 +
21.69
21.70 /**
21.71 * Returns an iterator over a set of elements.
21.72 @@ -174,4 +192,27 @@
21.73 }
21.74 return sw.toString();
21.75 }
21.76 +
21.77 +
21.78 + public void viewGraph(int size){
21.79 +
21.80 + Layout layout = new CircleLayout(graph);
21.81 + layout.setSize(new Dimension(size, size));
21.82 +
21.83 + BasicVisualizationServer vv = new BasicVisualizationServer(layout);
21.84 + vv.setPreferredSize(new Dimension(size, size)); //Sets the viewing area size
21.85 + JFrame frame = new JFrame("Simple Graph View");
21.86 + frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
21.87 + frame.getContentPane().add(vv);
21.88 + frame.pack();
21.89 + frame.setVisible(true);
21.90 +
21.91 + }
21.92 +
21.93 +
21.94 +
21.95 +
21.96 +
21.97 +
21.98 +
21.99 }
22.1 Binary file molwind-core/target/classes/org/molwind/graph/DefaultEntityGraph.class has changed
23.1 --- a/pom.xml Thu Oct 15 17:28:16 2009 +0200
23.2 +++ b/pom.xml Thu Oct 29 11:19:09 2009 +0100
23.3 @@ -91,7 +91,8 @@
23.4 <version>1.0.4</version>
23.5 <scope>system</scope>
23.6 <systemPath>/cdata/media/molwind/cdk-1.0.4.jar</systemPath>
23.7 - </dependency>
23.8 + </dependency>
23.9 +
23.10 <dependency>
23.11 <groupId>jdom</groupId>
23.12 <artifactId>jdom</artifactId>
23.13 @@ -107,6 +108,7 @@
23.14 <module>molwind-chemical</module>
23.15 <module>molwind-client</module>
23.16 </modules>
23.17 +
23.18
23.19 <properties>
23.20 <encoding>UTF-8</encoding>
23.21 @@ -146,7 +148,7 @@
23.22 <groupId>org.apache.maven.plugins</groupId>
23.23 <artifactId>maven-shade-plugin</artifactId>
23.24 <version>1.2</version>
23.25 - <executions>
23.26 + <!--<executions>
23.27 <execution>
23.28 <phase>package</phase>
23.29 <goals>
23.30 @@ -165,7 +167,7 @@
23.31 </artifactSet>
23.32 </configuration>
23.33 </execution>
23.34 - </executions>
23.35 + </executions> -->
23.36 </plugin>
23.37 <plugin>
23.38 <groupId>org.apache.maven.plugins</groupId>
23.39 @@ -277,7 +279,7 @@
23.40 </releases>
23.41 </pluginRepository>
23.42 </pluginRepositories>
23.43 -
23.44 +
23.45
23.46
23.47