Fix phenotypes not loading properly. Fixes #219.

Author: mikekucera

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

@@ -21,10 +21,6 @@ public class DataSetFiles {
 	//colour the heading on the columns accroding to class or phenotype they belong to.
 	private String classFile = null;
 
-	//class file designations that were loaded in from a session file.
-	//need a temporary place for these class definition as
-	private String[] temp_class1 = null;
-
 	//phenotypes associated with this set of files
 	public static final String default_pheno1 = "UP";
 	public static final String default_pheno2 = "DOWN";
@@ -82,14 +78,6 @@ public void setClassFile(String classFile) {
 		this.classFile = classFile;
 	}
 
-	public String[] getTemp_class1() {
-		return temp_class1;
-	}
-
-	public void setTemp_class1(String[] temp_class1) {
-		this.temp_class1 = temp_class1;
-	}
-
 	public String getGseaHtmlReportFile() {
 		return gseaHtmlReportFile;
 	}
@@ -120,7 +108,6 @@ public void copy(DataSetFiles copy) {
 		this.enrichmentFileName1 = copy.getEnrichmentFileName1();
 		this.enrichmentFileName2 = copy.getEnrichmentFileName2();
 		this.classFile = copy.getClassFile();
-		this.temp_class1 = copy.getTemp_class1();
 		this.gseaHtmlReportFile = copy.getGseaHtmlReportFile();
 		this.RankedFile = copy.getRankedFile();
 		this.phenotype1 = copy.getPhenotype1();

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

@@ -56,7 +56,6 @@ protected EMDataSet(EnrichmentMap map, String name, Method method, DataSetFiles
 			this.enrichments.setFilename2(files.getEnrichmentFileName2());
 			this.enrichments.setPhenotype1(files.getPhenotype1());
 			this.enrichments.setPhenotype2(files.getPhenotype2());
-			this.expressionSets.setPhenotypes(files.getTemp_class1());
 			this.expressionSets.setFilename(files.getExpressionFileName());
 		} else {
 			System.out.println("There are no files initialized for this Dataset, named:" + name + "\n");

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/creation/EditDataSetPanel.java

@@ -31,6 +31,7 @@
 import org.cytoscape.util.swing.IconManager;
 import org.cytoscape.util.swing.LookAndFeelUtil;
 
+import com.google.common.base.Strings;
 import com.google.inject.Inject;
 import com.google.inject.assistedinject.Assisted;
 
@@ -52,8 +53,6 @@ public class EditDataSetPanel extends JPanel implements DetailPanel {
 	private JTextField positiveText;
 	private JTextField negativeText;
 
-	private String[] classes;
-	
 	private final @Nullable DataSetParameters initDataSet;
 
 
@@ -108,10 +107,11 @@ public DataSetParameters createDataSetParameters() {
 
 		String positive = positiveText.getText();
 		String negative = negativeText.getText();
-		if(!isNullOrEmpty(positive) && !isNullOrEmpty(negative) && classes != null) {
+		if(!isNullOrEmpty(positive)) {
 			files.setPhenotype1(positive);
+		}
+		if(!isNullOrEmpty(negative)) {
 			files.setPhenotype2(negative);
-			files.setTemp_class1(classes);
 		}
 
 		return new DataSetParameters(name, method, files);
@@ -150,7 +150,7 @@ private void createBody() {
 		expressionsText = pathTextFactory.create("Expressions:", FileBrowser.Filter.EXPRESSION);
 		ranksText = pathTextFactory.create("Ranks:", FileBrowser.Filter.RANK);
 		classesText = pathTextFactory.create("Classes:", FileBrowser.Filter.CLASS);
-		classesText.getTextField().getDocument().addDocumentListener(SwingUtil.simpleDocumentListener(this::updateClasses));
+		classesText.getTextField().getDocument().addDocumentListener(SwingUtil.simpleDocumentListener(this::preFillPhenotypes));
 
 		enrichments2Text.getLabel().setVisible(false);
 		enrichments2Text.getTextField().setVisible(false);
@@ -325,10 +325,9 @@ public List<Message> validateInput(MasterDetailDialogPage parent) {
 	}
 
 
-	private void updateClasses() {
-		if(positiveText.getText().trim().isEmpty() && negativeText.getText().trim().isEmpty() 
-				&& Files.isReadable(Paths.get(classesText.getText()))) {
-			String classFile = classesText.getText();
+	private void preFillPhenotypes() {
+		String classFile = classesText.getText();
+		if(!Strings.isNullOrEmpty(classFile) && Files.isReadable(Paths.get(classFile))) {
 			String[] phenotypes = ClassFileReaderTask.parseClasses(classFile);
 			if(phenotypes != null) {
 				LinkedHashSet<String> distinctOrdererd = new LinkedHashSet<>();
@@ -339,7 +338,6 @@ private void updateClasses() {
 					Iterator<String> iter = distinctOrdererd.iterator();
 					positiveText.setText(iter.next());
 					negativeText.setText(iter.next());
-					classes = phenotypes;
 				}
 			}
 		}

EnrichmentMapPlugin/src/test/java/org/baderlab/csplugins/enrichmentmap/model/ModelSerializerTest.java

@@ -1,10 +1,6 @@
 package org.baderlab.csplugins.enrichmentmap.model;
 
-import static org.junit.Assert.assertArrayEquals;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.*;
 
 import java.util.Map;
 import java.util.Optional;
@@ -161,7 +157,6 @@ private static void assertDataSetFilesEquals(DataSetFiles expected, DataSetFiles
 		assertEquals(expected.getEnrichmentFileName2(), actual.getEnrichmentFileName2());
 		assertEquals(expected.getRankedFile(), actual.getRankedFile());
 		assertEquals(expected.getClassFile(), actual.getClassFile());
-		assertArrayEquals(expected.getTemp_class1(), actual.getTemp_class1());
 		assertEquals(expected.getPhenotype1(), actual.getPhenotype1());
 		assertEquals(expected.getPhenotype2(), actual.getPhenotype2());
 		assertEquals(expected.getGseaHtmlReportFile(), actual.getGseaHtmlReportFile());