1.1 --- a/build.xml Fri Oct 02 13:43:53 2009 +0200
1.2 +++ b/build.xml Mon Oct 26 15:40:22 2009 +0100
1.3 @@ -3,9 +3,7 @@
1.4 Ant build script for BiNA Core
1.5 </description>
1.6
1.7 - <import file="../bina_platform/global.xml"/>
1.8 -
1.9 - <target name="init" depends="base_init">
1.10 + <target name="init">
1.11 <tstamp/>
1.12
1.13 <property name="plugin_name" value="BiNA Core"/>
1.14 @@ -18,8 +16,6 @@
1.15
1.16 <property name="platform_dir" value="../bina_platform/" />
1.17
1.18 - <property name="resources_path" value="org/bina/sif/resources/" />
1.19 -
1.20 <property name="api" value="doc/"/>
1.21
1.22 <property name="target_dir" value="plugin/"/>
1.23 @@ -33,7 +29,8 @@
1.24 <property name="bcp_jar" value="${platform_dir}plugins/org.bina.bcp/bcp.jar"/>
1.25 <property name="visualization_jar" value="${platform_dir}plugins/org.bina.visualization/visualization.jar"/>
1.26
1.27 - <property name="bina_jar" value="${platform_dir}${platform_jar}" />
1.28 + <property name="bina_jar" value="${platform_dir}BiNA.jar" />
1.29 +
1.30 <property name="classpath" value="${bina_jar}:${bnpp_model_jar}:${bcp_jar}:${visualization_jar}" />
1.31
1.32 </target>
2.1 --- a/src/org/bina/sif/PluginExtensions.java Fri Oct 02 13:43:53 2009 +0200
2.2 +++ b/src/org/bina/sif/PluginExtensions.java Mon Oct 26 15:40:22 2009 +0100
2.3 @@ -5,7 +5,6 @@
2.4
2.5 import javax.swing.ImageIcon;
2.6
2.7 -
2.8 import org.bina.bcp.controllers.io.Serializer;
2.9 import org.bina.bcp.datasource.importer.ImporterExtension;
2.10 import org.bina.platform.extensions.AbstractPlugin;
2.11 @@ -15,7 +14,9 @@
2.12 import org.bina.platform.gui.IconRepository;
2.13 import org.bina.sif.importer.SIFImporter;
2.14 import org.bina.sif.resources.Resources;
2.15 +import org.bina.sif.visualization.model.impl.basic.BasicSIFUIFactory;
2.16 import org.bina.sif.visualization.serialization.SIFSerializer;
2.17 +import org.bina.visualization.model.ui.basic.BasicUIFactory;
2.18
2.19
2.20 /**
2.21 @@ -43,6 +44,8 @@
2.22 boolean ret = true;
2.23 ret &= addExtension(pm, "org.bina.bcp.datasource.importer", new ImporterExtension("sif_importer", "Cytoscapes Standard Interaction Format (SIF)", new ImageIcon(Resources.class.getResource("sif/sif_format.png")), SIFImporter.class));
2.24 ret &= addExtension(pm, "org.bina.controllers.io", new DefaultExtension<Serializer>("serializer", "sif_serializer", "SIF Serializer", SIFSerializer.class));
2.25 +
2.26 + pm.getExtensionPoint("org.bina.visualization.model.ui.basic.factory").registerExtension(new DefaultExtension<BasicUIFactory>("uifactory", "basic_sif_uifactory", "Basic SIF UI Factory", BasicSIFUIFactory.class));
2.27 return true;
2.28 }
2.29
3.1 --- a/src/org/bina/sif/visualization/model/impl/SIFMappingModel.java Fri Oct 02 13:43:53 2009 +0200
3.2 +++ b/src/org/bina/sif/visualization/model/impl/SIFMappingModel.java Mon Oct 26 15:40:22 2009 +0100
3.3 @@ -5,25 +5,22 @@
3.4 import javax.swing.Icon;
3.5
3.6 import org.bina.bcp.controllers.DataNotVisualizableException;
3.7 -import org.bina.sif.model.SIFRelation;
3.8 import org.bina.sif.model.SIFModel;
3.9 import org.bina.sif.model.SIFObject;
3.10 +import org.bina.sif.model.SIFRelation;
3.11 import org.bina.visualization.StandardController;
3.12 -import org.bina.visualization.model.IComponent;
3.13 import org.bina.visualization.model.impl.MappingModelAdapter;
3.14 -import org.bina.visualization.model.regulation.IProteinComponent;
3.15 -import org.bina.visualization.model.regulation.impl.ProteinComplexComponent;
3.16 -import org.bina.visualization.model.regulation.impl.ProteinComponent;
3.17 -import org.bina.visualization.model.regulation.impl.RegulationMappingModelAdapter;
3.18 -import org.bina.visualization.model.regulation.impl.RegulativeEventComponent;
3.19 -import org.bina.visualization.model.ui.IEdgeComponentUI;
3.20 -import org.bina.visualization.model.ui.INodeComponentUI;
3.21 +import org.bina.visualization.model.regulatory.IProteinComponent;
3.22 +import org.bina.visualization.model.regulatory.impl.ProteinComplexComponent;
3.23 +import org.bina.visualization.model.regulatory.impl.ProteinComponent;
3.24 +import org.bina.visualization.model.regulatory.impl.RegulativeEventComponent;
3.25 +import org.bina.visualization.model.regulatory.impl.RegulatoryMappingModelAdapter;
3.26
3.27 import com.thoughtworks.xstream.XStream;
3.28
3.29
3.30
3.31 -public class SIFMappingModel extends RegulationMappingModelAdapter {
3.32 +public class SIFMappingModel extends RegulatoryMappingModelAdapter {
3.33
3.34 public static void configureStream(XStream stream) {
3.35 MappingModelAdapter.configureStream(stream);
3.36 @@ -36,13 +33,13 @@
3.37
3.38 private HashMap<IProteinComponent, SIFObject> comp_object = null;
3.39
3.40 - private HashMap<RegulativeEventComponent, SIFRelation> comp_interaction = null;
3.41 + private HashMap<RegulativeEventComponent, SIFRelation> comp_relation = null;
3.42
3.43 public SIFMappingModel(StandardController controller) {
3.44 super(controller, "sif_mapping_model", "SIF Mapping Model");
3.45
3.46 comp_object = new HashMap<IProteinComponent, SIFObject>();
3.47 - comp_interaction = new HashMap<RegulativeEventComponent, SIFRelation>();
3.48 + comp_relation = new HashMap<RegulativeEventComponent, SIFRelation>();
3.49
3.50 clear();
3.51 }
3.52 @@ -57,7 +54,7 @@
3.53 public synchronized void clear() {
3.54 super.clear();
3.55
3.56 - comp_interaction.clear();
3.57 + comp_relation.clear();
3.58 comp_object.clear();
3.59 }
3.60
3.61 @@ -96,27 +93,27 @@
3.62 @Override
3.63 public synchronized void update() {
3.64 // create proteins and complexes
3.65 - for (SIFRelation i : sifModel.getRelations()) {
3.66 - for (SIFObject o : i.getSources()) {
3.67 + for (SIFRelation r : sifModel.getRelations()) {
3.68 + for (SIFObject o : r.getSources()) {
3.69 createProtein(o);
3.70 }
3.71
3.72 - for (SIFObject o : i.getTargets()) {
3.73 + for (SIFObject o : r.getTargets()) {
3.74 createProtein(o);
3.75 }
3.76 }
3.77
3.78 - for (SIFRelation i : sifModel.getRelations()) {
3.79 - if (!registry.containsComponent(i.toString())) {
3.80 - RegulativeEventComponent regulation = createRegulation(this.rootComponent, i.toString());
3.81 - comp_interaction.put(regulation, i);
3.82 + for (SIFRelation r : sifModel.getRelations()) {
3.83 + if (!registry.containsComponent(r.toString())) {
3.84 + RegulativeEventComponent regulation = createRegulation(this.rootComponent, r.toString());
3.85 + comp_relation.put(regulation, r);
3.86
3.87 - for (SIFObject o : i.getSources()) {
3.88 + for (SIFObject o : r.getSources()) {
3.89 IProteinComponent pc = createProtein(o);
3.90 regulation.addEffector(pc);
3.91 }
3.92
3.93 - for (SIFObject o : i.getTargets()) {
3.94 + for (SIFObject o : r.getTargets()) {
3.95 IProteinComponent pc = createProtein(o);
3.96 regulation.addReceiver(pc);
3.97 }
3.98 @@ -126,18 +123,6 @@
3.99
3.100 }
3.101
3.102 - @Override
3.103 - public void initUI(IComponent comp) {
3.104 - if (comp instanceof ProteinComponent && comp.getUI() instanceof INodeComponentUI) {
3.105 - ((INodeComponentUI) comp.getUI()).setLabel(comp.getId());
3.106 - } else if (comp instanceof RegulativeEventComponent && comp.getUI() instanceof IEdgeComponentUI) {
3.107 - SIFRelation interaction = comp_interaction.get(comp);
3.108 - if (interaction != null && interaction.getValue() != null)
3.109 - ((IEdgeComponentUI) comp.getUI()).setLabel(interaction.getValue());
3.110 - }
3.111 -
3.112 -
3.113 - }
3.114
3.115 @Override
3.116 public int canVisualize(Object data) {
3.117 @@ -163,5 +148,9 @@
3.118 public String getSVGIcon() {
3.119 return null;
3.120 }
3.121 +
3.122 + public SIFRelation getRelation(RegulativeEventComponent comp) {
3.123 + return comp_relation.get(comp);
3.124 + }
3.125
3.126 }
4.1 --- a/src/org/bina/sif/visualization/serialization/SIFSerializer.java Fri Oct 02 13:43:53 2009 +0200
4.2 +++ b/src/org/bina/sif/visualization/serialization/SIFSerializer.java Mon Oct 26 15:40:22 2009 +0100
4.3 @@ -15,10 +15,10 @@
4.4 import org.bina.sif.visualization.model.impl.SIFMappingModel;
4.5 import org.bina.visualization.StandardController;
4.6 import org.bina.visualization.model.IComponent;
4.7 -import org.bina.visualization.model.regulation.IParticipantComponent;
4.8 -import org.bina.visualization.model.regulation.impl.ProteinComponent;
4.9 -import org.bina.visualization.model.regulation.impl.RegulationMappingModelAdapter;
4.10 -import org.bina.visualization.model.regulation.impl.RegulativeEventComponent;
4.11 +import org.bina.visualization.model.regulatory.IParticipantComponent;
4.12 +import org.bina.visualization.model.regulatory.impl.ProteinComponent;
4.13 +import org.bina.visualization.model.regulatory.impl.RegulatoryMappingModelAdapter;
4.14 +import org.bina.visualization.model.regulatory.impl.RegulativeEventComponent;
4.15
4.16 public class SIFSerializer extends Serializer {
4.17
4.18 @@ -57,8 +57,8 @@
4.19 SIFWriter w = new SIFWriter(sifMM.getModel());
4.20 w.setFile(file);
4.21 w.writeData(null);
4.22 - } else if (sc.getMappingModel() instanceof RegulationMappingModelAdapter) {
4.23 - SIFModel m = createModel((RegulationMappingModelAdapter) sc.getMappingModel());
4.24 + } else if (sc.getMappingModel() instanceof RegulatoryMappingModelAdapter) {
4.25 + SIFModel m = createModel((RegulatoryMappingModelAdapter) sc.getMappingModel());
4.26
4.27 SIFWriter w = new SIFWriter(m);
4.28 w.setFile(file);
4.29 @@ -71,13 +71,13 @@
4.30 public boolean canWrite(Controller<?> controller) {
4.31 if (controller instanceof StandardController) {
4.32 StandardController sc = (StandardController) controller;
4.33 - return sc.getMappingModel() instanceof RegulationMappingModelAdapter;
4.34 + return sc.getMappingModel() instanceof RegulatoryMappingModelAdapter;
4.35 }
4.36
4.37 return false;
4.38 }
4.39
4.40 - private SIFModel createModel(RegulationMappingModelAdapter mappingModel) {
4.41 + private SIFModel createModel(RegulatoryMappingModelAdapter mappingModel) {
4.42 SIFModel m = new SIFModel();
4.43
4.44 Set<IComponent> components = mappingModel.getRegistry().getComponents();