Bug #144. Save and restore classes properly. Fix HeatMap column title

colors.

Author: mikekucera

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/actions/EnrichmentMapSessionAction.java

@@ -415,7 +415,7 @@ public void handleEvent(SessionAboutToBeSavedEvent e) {
 		String tmpDir = System.getProperty("java.io.tmpdir");
 		System.out.println("java.io.tmpdir: [" + tmpDir + "]");
 
-		String prop_file_content = "";
+		StringBuilder prop_file_content = new StringBuilder();
 
 		//get the networks
 		HashMap<Long, EnrichmentMap> networks = EnrichmentMapManager.getInstance().getCyNetworkList();
@@ -447,8 +447,9 @@ public void handleEvent(SessionAboutToBeSavedEvent e) {
 			//geneset file for PostAnalysis Signature Genesets
 			File siggmt = new File(tmpDir,name+".signature.gmt");
 
-			prop_file_content = prop_file_content + "Version\t2.0\n";
-			prop_file_content = prop_file_content + params.toString();
+			prop_file_content.append("Version\t2.0\n");
+			prop_file_content.append(params.toString());
+			
 			try{
 				if (!em.getSignatureGenesets().isEmpty() ) {
 					BufferedWriter sigGmtwriter = new BufferedWriter(new FileWriter(siggmt));
@@ -474,7 +475,7 @@ public void handleEvent(SessionAboutToBeSavedEvent e) {
 					HashMap<String, DataSet> all_datasets = em.getDatasets();
 
 					//output to the property file how many datasets we have (so we know on reload)
-					prop_file_content = prop_file_content + "Datasets\t"+  all_datasets.keySet().toString() +"\n";
+					prop_file_content.append("Datasets\t"+  all_datasets.keySet().toString() + "\n");
 
 					for(Iterator<String> k  = all_datasets.keySet().iterator(); k.hasNext();){
 						String dataset_name = k.next().toString();
@@ -499,7 +500,7 @@ public void handleEvent(SessionAboutToBeSavedEvent e) {
 						enr1writer_backcomp.close();
 						pFileList.add(enrichmentresults_backcomp);    
 
-						prop_file_content = prop_file_content + em.getDataset(current).getSetofgenesets().toString(current);
+						prop_file_content.append(em.getDataset(current).getSetofgenesets().toString(current));
 
 						//enrichments
 						File enrichmentresults = new File(tmpDir, name+"." + dataset_name +".ENR.txt");
@@ -509,7 +510,7 @@ public void handleEvent(SessionAboutToBeSavedEvent e) {
 						enr1writer.close();
 						pFileList.add(enrichmentresults);            				
 
-						prop_file_content = prop_file_content + em.getDataset(current).getEnrichments().toString(current);
+						prop_file_content.append(em.getDataset(current).getEnrichments().toString(current));
 
 						//expression
 						if(em.getDataset(current).getExpressionSets() != null){
@@ -521,7 +522,7 @@ public void handleEvent(SessionAboutToBeSavedEvent e) {
 							pFileList.add(expression);
 
 							//print out the information about the expression files
-							prop_file_content = prop_file_content + em.getDataset(current).getExpressionSets().toString(current);
+							prop_file_content.append(em.getDataset(current).getExpressionSets().toString(current));
 
 							//save all the rank files
 							if(!em.getDataset(current).getExpressionSets().getRanks().isEmpty()){
@@ -553,7 +554,7 @@ public void handleEvent(SessionAboutToBeSavedEvent e) {
 						}        			        			
 					}
 					BufferedWriter writer = new BufferedWriter(new FileWriter(session_prop_file));
-					writer.write(prop_file_content);
+					writer.write(prop_file_content.toString());
 					writer.close();
 					pFileList.add(session_prop_file);
 				}  

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/heatmap/ColumnHeaderVerticalRenderer.java

@@ -43,12 +43,14 @@
 
 package org.baderlab.csplugins.enrichmentmap.heatmap;
 
+import java.awt.Color;
 import java.awt.Component;
 import java.awt.Font;
 import java.awt.FontMetrics;
 import java.awt.Graphics2D;
 import java.awt.RenderingHints;
 import java.awt.image.BufferedImage;
+import java.util.Optional;
 
 import javax.swing.Icon;
 import javax.swing.ImageIcon;
@@ -66,41 +68,54 @@
  * <p>
  * Flips column headers to vertical position
  */
+@SuppressWarnings("serial")
 public class ColumnHeaderVerticalRenderer extends DefaultTableCellRenderer {
 
+	private Optional<Color> labelBackgroundColor;
+	
+	public ColumnHeaderVerticalRenderer(Color labelBackgroundColor) {
+		this.labelBackgroundColor = Optional.ofNullable(labelBackgroundColor);
+	}
+	
+	public ColumnHeaderVerticalRenderer() {
+		this.labelBackgroundColor = Optional.empty();
+	}
+	
 
     @Override
     public Component getTableCellRendererComponent(JTable table,
                                                    Object value, boolean isSelected, boolean hasFocus,
                                                    int row, int column) {
-
         JLabel label = new JLabel();
 
         label.setBorder(UIManager.getBorder("TableHeader.cellBorder"));
         label.setBackground(this.getBackground());
         label.setForeground(UIManager.getColor("TableHeader.foreground"));
         label.setFont(UIManager.getFont("TableHeader.font"));
 
-        Icon icon = VerticalCaption.getVerticalCaption(label, value.toString(), false);
+        Icon icon = getVerticalCaption(label, value.toString(), false);
 
         label.setIcon(icon);
         label.setVerticalAlignment(JLabel.BOTTOM);
         label.setHorizontalAlignment(JLabel.CENTER);
 
         return label;
     }
-}
-
-class VerticalCaption {
 
-    static Icon getVerticalCaption(JComponent component, String caption, boolean clockwise) {
+    
+    private Icon getVerticalCaption(JComponent component, String caption, boolean clockwise) {
 		Font f = component.getFont();
 		FontMetrics fm = component.getFontMetrics(f);
 		int captionHeight = fm.getHeight();
 		int captionWidth = fm.stringWidth(caption);
 		BufferedImage bi = new BufferedImage(captionHeight + 4, captionWidth + 4, BufferedImage.TYPE_INT_ARGB);
         Graphics2D g = (Graphics2D) bi.getGraphics();
 
+        if(labelBackgroundColor.isPresent()) {
+	        g.setColor(labelBackgroundColor.get()); 
+	        g.fillRect(0, 0, bi.getWidth(), bi.getHeight());
+        }
+        
         g.setColor(component.getForeground());
         g.setFont(f);
         g.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON);

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/model/GeneExpressionMatrix.java

@@ -43,6 +43,7 @@
 
 package org.baderlab.csplugins.enrichmentmap.model;
 
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Iterator;
@@ -409,7 +410,7 @@ public String toString(String ds) {
         paramVariables.append(ds + "%" + simpleName + "%expressionUniverse\t" + expressionUniverse   + "\n");
 
         if(phenotypes != null)
-            paramVariables.append(ds + "%" + simpleName + "%phenotypes\t" + phenotypes.toString()   + "\n");
+            paramVariables.append(ds + "%" + simpleName + "%phenotypes\t" + Arrays.toString(phenotypes)   + "\n");
 
         return paramVariables.toString();
     }
@@ -418,14 +419,41 @@ public String toString(String ds) {
      * Restores parameters saved in the session file.
      * Note, most of this object is restored by the ExpressionFileReaderTask.
      */
-    public void restoreProps(String ds, Map<String, String> props) {
+	public void restoreProps(String ds, Map<String, String> props) {
     	String simpleName = this.getClass().getSimpleName();
 		String val = props.get(ds + "%" + simpleName + "%expressionUniverse");
 		if(val != null) {
 			try {
 				expressionUniverse = Integer.parseInt(val);
 			} catch(NumberFormatException e) {}
 		}
+		
+		if(props.containsKey(ds + "%" + simpleName + "%phenotype1")) {
+			String prop = props.get(ds + "%" + simpleName + "%phenotype1");
+			if(!"null".equals(prop)) {
+				this.phenotype1 = prop;
+			}
+		}
+		if(props.containsKey(ds + "%" + simpleName + "%phenotype2")) {
+			String prop = props.get(ds + "%" + simpleName + "%phenotype2");
+			if(!"null".equals(prop)) {
+				this.phenotype2 = prop;
+			}
+		}
+		
+		String[] col_names = getColumnNames();
+		
+		if(props.containsKey(ds + "%" + simpleName + "%phenotypes") && col_names != null && col_names.length > 0) {
+			try {
+				String prop = props.get(ds + "%" + simpleName + "%phenotypes");
+				if(!prop.startsWith("[Ljava.lang.String")) { // avoid bug #144
+					String[] restored_phenotypes = prop.replace("[", "").replace("]", "").split(", ");
+					if(restored_phenotypes.length == col_names.length-2) {
+						this.phenotypes = restored_phenotypes;
+					}
+				}
+			} catch(Exception e) { }
+		}
 	}
 
 

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/HeatMapPanel.java

@@ -439,13 +439,9 @@ public void updatePanel() {
 			table.setCellSelectionEnabled(true);
 
 			//set the table header renderer to the vertical renderer
-			ColumnHeaderVerticalRenderer pheno1_renderer = new ColumnHeaderVerticalRenderer();
-			pheno1_renderer.setBackground(EnrichmentMapVisualStyle.LIGHTEST_PHENOTYPE_1);
-			ColumnHeaderVerticalRenderer pheno2_renderer = new ColumnHeaderVerticalRenderer();
-			pheno2_renderer.setBackground(EnrichmentMapVisualStyle.LIGHTEST_PHENOTYPE_2);
-
+			ColumnHeaderVerticalRenderer pheno1_renderer  = new ColumnHeaderVerticalRenderer(EnrichmentMapVisualStyle.LIGHTEST_PHENOTYPE_1);
+			ColumnHeaderVerticalRenderer pheno2_renderer  = new ColumnHeaderVerticalRenderer(EnrichmentMapVisualStyle.LIGHTEST_PHENOTYPE_2);
 			ColumnHeaderVerticalRenderer default_renderer = new ColumnHeaderVerticalRenderer();
-			default_renderer.setBackground(Color.white);
 
 			if (params.isData2() && map.getDataset(EnrichmentMap.DATASET2).getExpressionSets() != null && !map.getDataset(EnrichmentMap.DATASET1)
 					.getExpressionSets().getFilename().equalsIgnoreCase(map.getDataset(EnrichmentMap.DATASET2).getExpressionSets().getFilename())) {