Fixes #121. Post-Analysis edge width no longer uses an Equation.

Author: mikekucera

EnrichmentMapPlugin/.classpath

@@ -12,7 +12,7 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry excluding="**" including="**/*.java" kind="src" output="target/classes" path="src/main/resources">
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>

EnrichmentMapPlugin/pom.xml

@@ -99,11 +99,6 @@
 			<artifactId>group-api</artifactId>
 			<version>${cy3.version}</version>
 		</dependency>
-		<dependency>
-			<groupId>org.cytoscape</groupId>
-			<artifactId>equations-api</artifactId>
-			<version>${cy3.version}</version>
-		</dependency>
 
 		<!-- additional libraries -->
 		<dependency>

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/CyActivator.java

@@ -12,7 +12,7 @@
 import org.baderlab.csplugins.enrichmentmap.actions.LoadEnrichmentsPanelAction;
 import org.baderlab.csplugins.enrichmentmap.actions.LoadPostAnalysisPanelAction;
 import org.baderlab.csplugins.enrichmentmap.actions.ShowAboutPanelAction;
-import org.baderlab.csplugins.enrichmentmap.actions.ShowEdgeWidthPanelAction;
+import org.baderlab.csplugins.enrichmentmap.actions.ShowEdgeWidthDialogAction;
 import org.baderlab.csplugins.enrichmentmap.autoannotate.AutoAnnotationManager;
 import org.baderlab.csplugins.enrichmentmap.autoannotate.action.AutoAnnotationPanelAction;
 import org.baderlab.csplugins.enrichmentmap.autoannotate.action.DisplayOptionsPanelAction;
@@ -31,7 +31,6 @@
 import org.cytoscape.application.swing.CyAction;
 import org.cytoscape.application.swing.CySwingApplication;
 import org.cytoscape.command.CommandExecutorTaskFactory;
-import org.cytoscape.equations.EquationCompiler;
 import org.cytoscape.event.CyEventHelper;
 import org.cytoscape.group.CyGroupFactory;
 import org.cytoscape.group.CyGroupManager;
@@ -78,13 +77,8 @@ public class CyActivator extends AbstractCyActivator {
 	public void start(BundleContext bc) {
 
 		//fetch Cytoscape OSGi services that EM needs
-		//main service for dealing with the cytoscape application.  (used when putting in cytopanels...)
 		CySwingApplication cySwingApplicationRef = getService(bc,CySwingApplication.class);
-		
-		//open browser used by about, enrichment map panel,
 		OpenBrowser openBrowserRef = getService(bc, OpenBrowser.class);
-			
-		//get FileUtil
 		FileUtil fileUtil = getService(bc,FileUtil.class);
 		StreamUtil streamUtil = getService(bc, StreamUtil.class);
 		CyApplicationManager cyApplicationManagerRef = getService(bc,CyApplicationManager.class);
@@ -118,13 +112,12 @@ public void start(BundleContext bc) {
 		CommandExecutorTaskFactory commandExecutor = getService(bc, CommandExecutorTaskFactory.class);
 		//get the service registrar so we can register new services in different classes
 		CyServiceRegistrar registrar = getService(bc, CyServiceRegistrar.class);
-		EquationCompiler compilerServiceRef = getService(bc, EquationCompiler.class);
 
 
 		//create the Panels
 		BulkEMCreationPanel bulkEmPanel = new BulkEMCreationPanel(cySwingApplicationRef,fileUtil,registrar, sessionManager, streamUtil, cyApplicationManagerRef);		
 		EnrichmentMapInputPanel emPanel = new EnrichmentMapInputPanel(cyNetworkFactoryRef, cyApplicationManagerRef, cyNetworkManagerRef, cyNetworkViewManagerRef, tableFactory, tableManager, cyNetworkViewFactoryRef, visualMappingManagerRef, visualStyleFactoryRef,  continuousMappingFunctionFactoryRef,discreteMappingFunctionFactoryRef, passthroughMappingFunctionFactoryRef, dialogTaskManager, sessionManager, cySwingApplicationRef, openBrowserRef,fileUtil,streamUtil,registrar,layoutManager,mapTableToNetworkTable,bulkEmPanel);				
-		PostAnalysisPanel postEMPanel = new PostAnalysisPanel(cyApplicationManagerRef,cySwingApplicationRef, openBrowserRef,fileUtil,sessionManager, streamUtil,registrar, dialogTaskManager, syncTaskManager, eventHelper, compilerServiceRef, visualMappingManagerRef, visualStyleFactoryRef, continuousMappingFunctionFactoryRef, discreteMappingFunctionFactoryRef, passthroughMappingFunctionFactoryRef);		
+		PostAnalysisPanel postEMPanel = new PostAnalysisPanel(cyApplicationManagerRef,cySwingApplicationRef, openBrowserRef,fileUtil,sessionManager, streamUtil,registrar, dialogTaskManager, syncTaskManager, eventHelper, visualMappingManagerRef, visualStyleFactoryRef, continuousMappingFunctionFactoryRef, discreteMappingFunctionFactoryRef, passthroughMappingFunctionFactoryRef);		
 		//create two instances of the heatmap panel
 		HeatMapPanel heatMapPanel_node = new HeatMapPanel(true, cySwingApplicationRef, fileUtil, cyApplicationManagerRef, openBrowserRef,dialogTaskManager,streamUtil);
 		HeatMapPanel heatMapPanel_edge = new HeatMapPanel(false, cySwingApplicationRef, fileUtil, cyApplicationManagerRef, openBrowserRef,dialogTaskManager,streamUtil);
@@ -152,8 +145,6 @@ public void start(BundleContext bc) {
 		registerService(bc, autoAnnotationManager, ColumnDeletedListener.class, new Properties());
 		registerService(bc, autoAnnotationManager, ColumnNameChangedListener.class, new Properties());
 
-		WidthFunction widthFunction = new WidthFunction(cyNetworkManagerRef, continuousMappingFunctionFactoryRef, manager);
-		
 		//Create each Action within Enrichment map as a service
 		Map<String,String> serviceProperties;
 
@@ -195,7 +186,7 @@ public void start(BundleContext bc) {
 		serviceProperties = new HashMap<>();
 		serviceProperties.put("inMenuBar", "true");
 		serviceProperties.put("preferredMenu", "Apps.EnrichmentMap");
-		ShowEdgeWidthPanelAction edgeWidthPanelAction = new ShowEdgeWidthPanelAction(serviceProperties, cyApplicationManagerRef ,cyNetworkViewManagerRef, cySwingApplicationRef, manager, compilerServiceRef);
+		ShowEdgeWidthDialogAction edgeWidthPanelAction = new ShowEdgeWidthDialogAction(serviceProperties, cyApplicationManagerRef, continuousMappingFunctionFactoryRef, dialogTaskManager, cyNetworkViewManagerRef, cySwingApplicationRef);
 
 		//register the services
 		registerService(bc, LoadEnrichmentMapInputPanelAction, CyAction.class, new Properties());
@@ -229,7 +220,5 @@ public void start(BundleContext bc) {
 		tableColumnTaskFactoryProps.setProperty("tableTypes", "edge");
 		registerService(bc, tableColumnTaskFactory, TableColumnTaskFactory.class, tableColumnTaskFactoryProps);
 
-		// register width function (used in formulas/equations in the table browser)
-		compilerServiceRef.getParser().registerFunction(widthFunction);
 	}
 }

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/PostAnalysisVisualStyle.java

@@ -2,18 +2,11 @@
 
 import java.awt.Color;
 import java.awt.Paint;
-import java.util.HashMap;
-import java.util.Map;
 
 import org.baderlab.csplugins.enrichmentmap.task.BuildDiseaseSignatureTaskResult;
-import org.cytoscape.equations.Equation;
-import org.cytoscape.equations.EquationCompiler;
-import org.cytoscape.model.CyColumn;
 import org.cytoscape.model.CyEdge;
 import org.cytoscape.model.CyNetwork;
 import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyRow;
-import org.cytoscape.model.CyTable;
 import org.cytoscape.view.model.View;
 import org.cytoscape.view.presentation.property.BasicVisualLexicon;
 import org.cytoscape.view.presentation.property.LineTypeVisualProperty;
@@ -24,43 +17,31 @@
 import org.cytoscape.view.vizmap.VisualStyle;
 import org.cytoscape.view.vizmap.mappings.DiscreteMapping;
 import org.cytoscape.view.vizmap.mappings.PassthroughMapping;
+import org.cytoscape.work.TaskMonitor;
 
 public class PostAnalysisVisualStyle {
 
 	public static final String NAME = "Post_analysis_style";
 
-	public static final double DEFAULT_WIDTH_EM_LOWER = 1.0;
-	public static final double DEFAULT_WIDTH_EM_UPPER = 5.0;
-	public static final double DEFAULT_WIDTH_PA_LESS_THAN_100 = 8.0;
-	public static final double DEFAULT_WIDTH_PA_LESS_THAN_10 = 4.5;
-	public static final double DEFAULT_WIDTH_PA_GREATER = 1.0;
-	
-	
-	@SuppressWarnings("unused")
 	private final VisualMappingFunctionFactory vmfFactoryContinuous;
     private final VisualMappingFunctionFactory vmfFactoryDiscrete;
     private final VisualMappingFunctionFactory vmfFactoryPassthrough;
-    private final EquationCompiler equationCompiler;
 
 	private final EnrichmentMapVisualStyle delegateStyle;
 
-	// Column in edge table that holds the formula
-	public static final String EDGE_WIDTH_FORMULA_COLUMN = "Edge_width_formula";
-	// Column in network table that holds the edge parameters
-	public static final String EDGE_WIDTH_PARAMETERS_COLUMN = "EM_Edge_width_parameters";
-	
 	private static final Color PINK   = new Color(255,0,200);    
 	private static final Color YELLOW = new Color(255,255,0);
 
 
-	public PostAnalysisVisualStyle(EnrichmentMapParameters emParsms, EquationCompiler equationCompiler,
-			                       VisualMappingFunctionFactory vmfFactoryContinuous, VisualMappingFunctionFactory vmfFactoryDiscrete, VisualMappingFunctionFactory vmfFactoryPassthrough) {
+	public PostAnalysisVisualStyle(EnrichmentMapParameters emParsms,
+			                       VisualMappingFunctionFactory vmfFactoryContinuous, 
+			                       VisualMappingFunctionFactory vmfFactoryDiscrete, 
+			                       VisualMappingFunctionFactory vmfFactoryPassthrough) {
 
 		this.delegateStyle = new EnrichmentMapVisualStyle(emParsms, vmfFactoryContinuous, vmfFactoryDiscrete, vmfFactoryPassthrough);
 		this.vmfFactoryContinuous = vmfFactoryContinuous;
         this.vmfFactoryDiscrete = vmfFactoryDiscrete;
         this.vmfFactoryPassthrough = vmfFactoryPassthrough;   
-        this.equationCompiler = equationCompiler;
 	}
 
 	/**
@@ -74,16 +55,12 @@ public void createVisualStyle(VisualStyle vs, String prefix) {
 	/**
 	 * Sets node bypasses and edge equations.
 	 */
-	public void applyNetworkSpeficifProperties(BuildDiseaseSignatureTaskResult taskResult, String prefix) {
+	public void applyNetworkSpeficifProperties(BuildDiseaseSignatureTaskResult taskResult, String prefix, TaskMonitor taskMonitor) {
 		createNodeBypassForColor(taskResult);
 		CyNetwork network = taskResult.getNetwork();
-        
-        CyTable networkTable = network.getDefaultNetworkTable();
-        if(networkTable.getColumn(EDGE_WIDTH_PARAMETERS_COLUMN) == null) {
-        	networkTable.createColumn(EDGE_WIDTH_PARAMETERS_COLUMN, String.class, false);
-        }
-        
-		applyWidthEquation(equationCompiler, prefix, network);
+		
+		WidthFunction widthFunction = new WidthFunction(vmfFactoryContinuous);
+		widthFunction.setEdgeWidths(network, prefix, taskMonitor);
 	}
 
 
@@ -109,7 +86,7 @@ private void createPostAnalysisAppearance(VisualStyle vs, String prefix) {
         vs.addVisualMappingFunction(disMapping_nodeShape);
 
         // Replace the edge width mapping that was created by EnrichmentMapVisualStyle
-        String widthAttribute = prefix + EDGE_WIDTH_FORMULA_COLUMN;
+        String widthAttribute = prefix + WidthFunction.EDGE_WIDTH_FORMULA_COLUMN;
         PassthroughMapping<Double,Double> edgeWidthMapping = (PassthroughMapping<Double,Double>) vmfFactoryPassthrough.createVisualMappingFunction(widthAttribute, Double.class, BasicVisualLexicon.EDGE_WIDTH);
         vs.addVisualMappingFunction(edgeWidthMapping);
 	}
@@ -126,90 +103,4 @@ private void createNodeBypassForColor(BuildDiseaseSignatureTaskResult taskResult
 	}
 
 
-	public static void applyWidthEquation(EquationCompiler equationCompiler, String prefix, CyNetwork network) {
-		String widthAttribute = prefix + EDGE_WIDTH_FORMULA_COLUMN;
-        CyTable edgeTable = network.getDefaultEdgeTable();
-        if(edgeTable.getColumn(widthAttribute) == null) {
-        	edgeTable.createColumn(widthAttribute, Double.class, false);
-        }
-        
-        String formula = "=" + WidthFunction.NAME + "($SUID)";
-        
-        Equation equation = compileEquation(equationCompiler, edgeTable, formula);
-        for(CyRow row : edgeTable.getAllRows()) {
-        	row.set(widthAttribute, equation);
-        }
-	}
-	
-	
-	private static Equation compileEquation(EquationCompiler equationCompiler, CyTable edgeTable, String formula) {
-		Map<String, Class<?>> attribNameToType = attributeToTypeMap(edgeTable);
-        if(equationCompiler.compile(formula, attribNameToType)) {
-			return equationCompiler.getEquation();
-        }
-        else {
-        	throw new RuntimeException(equationCompiler.getLastErrorMsg());
-        }
-	}
-	
-	private static Map<String,Class<?>> attributeToTypeMap(CyTable table) {
-		Map<String,Class<?>> map = new HashMap<>();
-		for(CyColumn column : table.getColumns())
-			map.put(column.getName(), column.getType());
-		return map;
-	}
-	
-	
-	public static boolean appliesTo(CyNetwork network) {
-		CyTable networkTable = network.getDefaultNetworkTable();
-	    return networkTable.getColumn(EDGE_WIDTH_PARAMETERS_COLUMN) != null;
-	}
-	
-	
-	/**
-	 * Parameters typically used by the EdgeWidthDialog and stored in the network table.
-	 */
-	public static class EdgeWidthParams {
-		public final double em_lower;
-		public final double em_upper;
-		public final double pa_lessThan100;
-		public final double pa_lessThan10;
-		public final double pa_greater;
-		
-		public EdgeWidthParams(double em_lower, double em_upper, double pa_lessThan100, double pa_lessThan10, double pa_greater) {
-			this.em_lower = em_lower;
-			this.em_upper = em_upper;
-			this.pa_lessThan100 = pa_lessThan100;
-			this.pa_lessThan10 = pa_lessThan10;
-			this.pa_greater = pa_greater;
-		}
-		
-		public static EdgeWidthParams defaultValues() {
-			return new EdgeWidthParams(DEFAULT_WIDTH_EM_LOWER, DEFAULT_WIDTH_EM_UPPER,
-					                   DEFAULT_WIDTH_PA_LESS_THAN_100, DEFAULT_WIDTH_PA_LESS_THAN_10, DEFAULT_WIDTH_PA_GREATER);
-		}
-		
-		public static EdgeWidthParams restore(CyNetwork network) {
-			try {
-				String val = network.getRow(network).get(EDGE_WIDTH_PARAMETERS_COLUMN, String.class);
-				String[] params = val.split(",");
-				double em_lower = Double.parseDouble(params[0]);
-				double em_upper = Double.parseDouble(params[1]);
-				double pa_lessThan100 = Double.parseDouble(params[2]);
-				double pa_lessThan10 = Double.parseDouble(params[3]);
-				double pa_greater = Double.parseDouble(params[4]);
-				return new EdgeWidthParams(em_lower, em_upper, pa_lessThan100, pa_lessThan10, pa_greater);
-			} catch(NullPointerException | ArrayIndexOutOfBoundsException | IllegalArgumentException e) {
-				return defaultValues();
-			}
-		}
-		
-		public void save(CyNetwork network) {
-			CyRow row = network.getRow(network);
-			String val = String.format("%f,%f,%f,%f,%f", em_lower, em_upper, pa_lessThan100, pa_lessThan10, pa_greater);
-			row.set(EDGE_WIDTH_PARAMETERS_COLUMN, val);
-		}
-	}
-	
-	
 }