Multi-select in heat map table.

mikekucera · mikekucera · commit 3a9e1e88c405 · 2021-01-28T13:45:14.000-05:00
Refs #426
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/genemania/GeneManiaTaskFactory.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/genemania/GeneManiaTaskFactory.java
@@ -47,7 +47,7 @@ public class GeneManiaTaskFactory {
 	@Inject private OpenBrowser openBrowser;
 	
 	
-	public TaskIterator createTaskIterator(EnrichmentMap map, List<String> genes, List<GSEALeadingEdgeRankingOption> leadingEdgeRanks) {
+	public TaskIterator createTaskIterator(EnrichmentMap map, List<String> genes, List<String> selectedGenes, List<GSEALeadingEdgeRankingOption> leadingEdgeRanks) {
 		// Show message to user if genemania not installed
 		List<String> commands = availableCommands.getCommands(GENEMANIA_NAMESPACE);
 		
@@ -67,7 +67,7 @@ public TaskIterator createTaskIterator(EnrichmentMap map, List<String> genes, Li
 		
 		
 		
-		QueryGeneManiaTask queryTask = queryGeneManiaTaskFactory.create(map, genes, leadingEdgeRanks);
+		QueryGeneManiaTask queryTask = queryGeneManiaTaskFactory.create(map, genes, selectedGenes, leadingEdgeRanks);
 		
 		// Get list of organisms from GeneMANIA
 		TaskIterator ti = commandExecutorTaskFactory.createTaskIterator(
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/genemania/QueryGeneManiaNodeViewTaskFactory.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/genemania/QueryGeneManiaNodeViewTaskFactory.java
@@ -34,7 +34,7 @@ public TaskIterator createTaskIterator(View<CyNode> nodeView, CyNetworkView netw
 		
 		List<GSEALeadingEdgeRankingOption> rankOptions = rankingOptionFactory.getGSEADataSetSetRankOptions(map);
 		
-		TaskIterator tasks = geneManiaTaskFactory.createTaskIterator(map, genes, rankOptions);
+		TaskIterator tasks = geneManiaTaskFactory.createTaskIterator(map, genes, null, rankOptions);
 		return tasks;
 	}
 
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/genemania/QueryGeneManiaTask.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/genemania/QueryGeneManiaTask.java
@@ -24,6 +24,7 @@
 import com.google.gson.Gson;
 import com.google.inject.Inject;
 import com.google.inject.assistedinject.Assisted;
+import com.google.inject.assistedinject.AssistedInject;
 
 public class QueryGeneManiaTask extends AbstractTask {
 	
@@ -43,6 +44,9 @@ public class QueryGeneManiaTask extends AbstractTask {
 	@Tunable(description = "Network Weighting:")
 	public ListSingleSelection<GMWeightingMethod> weightingMethods;
 	
+	// not a tunable, used just for the UI
+	public List<String> selectedGenes;
+	
 	private GMSearchResult result;
 	
 	private static long lastTaxonomyId = 9606; // H.sapiens
@@ -51,12 +55,21 @@ public class QueryGeneManiaTask extends AbstractTask {
 	@Inject private SynchronousTaskManager<?> syncTaskManager;
 	
 	public static interface Factory {
-		QueryGeneManiaTask create(EnrichmentMap map, List<String> geneList, List<GSEALeadingEdgeRankingOption> leadingEdgeRanks);
+		QueryGeneManiaTask create(
+				EnrichmentMap map, 
+				@Assisted("geneList") List<String> geneList, 
+				@Assisted("selectedGenes") List<String> selectedGenes, 
+				List<GSEALeadingEdgeRankingOption> leadingEdgeRanks);
 	}
 	
-	@Inject
-	public QueryGeneManiaTask(@Assisted EnrichmentMap map, @Assisted List<String> geneList, @Assisted List<GSEALeadingEdgeRankingOption> leadingEdgeRanks) {
-		this.geneList = new GeneListTunable(map, geneList, leadingEdgeRanks);
+	@AssistedInject
+	public QueryGeneManiaTask(
+			@Assisted EnrichmentMap map, 
+			@Assisted("geneList") List<String> geneList, 
+			@Assisted("selectedGenes") List<String> selectedGenes, 
+			@Assisted List<GSEALeadingEdgeRankingOption> leadingEdgeRanks)
+	{
+		this.geneList = new GeneListTunable(map, geneList, selectedGenes, leadingEdgeRanks);
 		this.organisms = new ListSingleSelection<>();
 		this.weightingMethods = new ListSingleSelection<>(GMWeightingMethod.values());
 		this.weightingMethods.setSelectedValue(weightingMethods.getPossibleValues().get(0));
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/string/QueryStringNodeViewTaskFactory.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/string/QueryStringNodeViewTaskFactory.java
@@ -34,7 +34,7 @@ public TaskIterator createTaskIterator(View<CyNode> nodeView, CyNetworkView netw
 		
 		List<GSEALeadingEdgeRankingOption> rankOptions = rankingOptionFactory.getGSEADataSetSetRankOptions(map);
 		
-		return stringAppFactory.createTaskIterator(map, genes, rankOptions);
+		return stringAppFactory.createTaskIterator(map, genes, null, rankOptions);
 	}
 
 	@Override
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/string/QueryStringTask.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/string/QueryStringTask.java
@@ -24,6 +24,7 @@
 import com.google.gson.Gson;
 import com.google.inject.Inject;
 import com.google.inject.assistedinject.Assisted;
+import com.google.inject.assistedinject.AssistedInject;
 
 public class QueryStringTask extends AbstractTask {
 	
@@ -50,12 +51,21 @@ public class QueryStringTask extends AbstractTask {
 	@Inject private CommandExecutorTaskFactory commandExecutorTaskFactory;
 	
 	public static interface Factory {
-		QueryStringTask create(EnrichmentMap map, List<String> geneList, List<GSEALeadingEdgeRankingOption> leadingEdgeRanks);
+		QueryStringTask create(
+				EnrichmentMap map, 
+				@Assisted("geneList") List<String> geneList,
+				@Assisted("selectedGenes") List<String> selectedGenes,
+				List<GSEALeadingEdgeRankingOption> leadingEdgeRanks);
 	}
 	
-	@Inject
-	public QueryStringTask(@Assisted EnrichmentMap map, @Assisted List<String> geneList, @Assisted List<GSEALeadingEdgeRankingOption> leadingEdgeRanks) {		
-		this.geneList = new GeneListTunable(map, geneList, leadingEdgeRanks);
+	@AssistedInject
+	public QueryStringTask(
+			@Assisted EnrichmentMap map, 
+			@Assisted("geneList") List<String> geneList,
+			@Assisted("selectedGenes") List<String> selectedGenes,
+			@Assisted List<GSEALeadingEdgeRankingOption> leadingEdgeRanks)
+	{		
+		this.geneList = new GeneListTunable(map, geneList, selectedGenes, leadingEdgeRanks);
 		this.organisms = new ListSingleSelection<>();
 	}
 	
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/string/StringAppTaskFactory.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/string/StringAppTaskFactory.java
@@ -44,7 +44,7 @@ public class StringAppTaskFactory {
 	@Inject private OpenBrowser openBrowser;
 
 	
-	public TaskIterator createTaskIterator(EnrichmentMap map, List<String> genes, List<GSEALeadingEdgeRankingOption> leadingEdgeRanks) {
+	public TaskIterator createTaskIterator(EnrichmentMap map, List<String> genes, List<String> selectedGenes, List<GSEALeadingEdgeRankingOption> leadingEdgeRanks) {
 		// Show message to user if STRING App not installed
 		List<String> commands = availableCommands.getCommands(STRING_NAMESPACE);
 		
@@ -62,7 +62,7 @@ public TaskIterator createTaskIterator(EnrichmentMap map, List<String> genes, Li
 			return null;
 		}
 		
-		QueryStringTask queryTask = queryStringTaskFactory.create(map, genes, leadingEdgeRanks);
+		QueryStringTask queryTask = queryStringTaskFactory.create(map, genes, selectedGenes, leadingEdgeRanks);
 		
 		// Get list of organisms from STRING App
 		TaskIterator ti = commandExecutorTaskFactory.createTaskIterator(
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/tunables/GeneListGUITunableHandler.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/tunables/GeneListGUITunableHandler.java
@@ -47,9 +47,10 @@ private JPanel createGeneListPanel() {
 		GeneListTunable geneListTunable = getGeneListTunable();
 		EnrichmentMap map = geneListTunable.getEnrichmentMap();
 		List<String> genes = geneListTunable.getGenes();
+		List<String> selectedGenes = geneListTunable.getSelectedGenes();
 		List<GSEALeadingEdgeRankingOption> leadingEdgeRanks = geneListTunable.getLeadingEdgeRanks();
 		
-		checkboxPanel = new GeneListPanel(map, genes, leadingEdgeRanks);
+		checkboxPanel = new GeneListPanel(map, genes, selectedGenes, leadingEdgeRanks);
 		
 		JPanel panel = new JPanel();
 		
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/tunables/GeneListPanel.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/tunables/GeneListPanel.java
@@ -7,8 +7,11 @@
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 import java.util.function.Consumer;
 import java.util.stream.Collectors;
 
@@ -42,12 +45,21 @@ public class GeneListPanel extends JPanel {
 	private JButton selectNoneButton;
 	private JButton selectEdgeButton;
 	
-	public GeneListPanel(EnrichmentMap map, List<String> genes, List<GSEALeadingEdgeRankingOption> leadingEdgeRanks) {
+	public GeneListPanel(
+			EnrichmentMap map, 
+			List<String> genes, 
+			List<String> selectedGenes, 
+			List<GSEALeadingEdgeRankingOption> leadingEdgeRanks) 
+	{
 		this.map = map;
 		
+		
+		Set<String> selected = selectedGenes == null ? Collections.emptySet() : new HashSet<>(selectedGenes);
+		
 		checkboxListModel = new CheckboxListModel<>();
 		genes.stream().sorted().forEach(gene -> {
-			checkboxListModel.addElement(new CheckboxData<>(gene, gene, true));
+			boolean sel = selected.isEmpty() || selected.contains(gene);
+			checkboxListModel.addElement(new CheckboxData<>(gene, gene, sel));
 		});
 		
 		checkboxList = new CheckboxList<>(checkboxListModel);
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/tunables/GeneListTunable.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/tunables/GeneListTunable.java
@@ -15,11 +15,16 @@ public class GeneListTunable {
 	private List<GSEALeadingEdgeRankingOption> leadingEdgeRanks;
 	
 	
-	public GeneListTunable(EnrichmentMap map, List<String> genes, List<GSEALeadingEdgeRankingOption> leadingEdgeRanks) {
+	public GeneListTunable(
+			EnrichmentMap map, 
+			List<String> genes, 
+			List<String> selectedGenes, 
+			List<GSEALeadingEdgeRankingOption> leadingEdgeRanks)
+	{
 		this.map = map;
 		this.genes = Objects.requireNonNull(genes);
 		this.leadingEdgeRanks = leadingEdgeRanks == null ? Collections.emptyList() : leadingEdgeRanks;
-		this.selectedGenes = genes;
+		this.selectedGenes = selectedGenes == null ? Collections.emptyList() : selectedGenes;
 	}
 	
 	public List<GSEALeadingEdgeRankingOption> getLeadingEdgeRanks() {
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/heatmap/HeatMapContentPanel.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/heatmap/HeatMapContentPanel.java
@@ -288,7 +288,7 @@ JTable getTable() {
 			table.setFillsViewportHeight(true);
 			table.setAutoResizeMode(JTable.AUTO_RESIZE_OFF);
 			table.setCellSelectionEnabled(true);
-			table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+			table.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
 			table.setDefaultRenderer(Double.class, new HeatMapCellRenderer());
 			table.setDefaultRenderer(RankValue.class, new RankValueRenderer());
 			table.setRowSorter(new HeatMapRowSorter(model));
@@ -345,6 +345,28 @@ public List<String> getGenes() {
 		return ((HeatMapTableModel) getTable().getModel()).getGenes();
 	}
 	
+	public List<String> getSelectedGenes() {
+		JTable table = getTable();
+		
+		int[] selectedCols = table.getSelectedColumns();
+		if(selectedCols == null || selectedCols.length == 0)
+			return Collections.emptyList();
+		Arrays.sort(selectedCols);
+		if(Arrays.binarySearch(selectedCols, HeatMapTableModel.GENE_COL) < 0)
+			return Collections.emptyList(); // Genes column not selected
+		
+		List<String> selectedGenes = new ArrayList<>();
+		for(int row : table.getSelectedRows()) {
+			Object value = table.getValueAt(row, HeatMapTableModel.GENE_COL);
+			if(value != null) {
+				String gene = value.toString();
+				selectedGenes.add(gene);
+			}
+			
+		}
+		return selectedGenes;
+	}
+	
 	public Set<String> getLeadingEdgeGenes() {
 		return ((HeatMapTableModel) getTable().getModel()).getLeadingEdgeGenes();
 	}
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/heatmap/HeatMapMediator.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/heatmap/HeatMapMediator.java
@@ -547,16 +547,18 @@ public static Collection<Integer> getGenes(EnrichmentMap map, Map<String,Set<Int
 	private void runGeneMANIA() {
 		EnrichmentMap map = getContentPanel().getEnrichmentMap();
 		List<String> genes = getContentPanel().getGenes();
+		List<String> selectedGenes = getContentPanel().getSelectedGenes();
 		List<GSEALeadingEdgeRankingOption> gseaOptions = rankingOptionFactory.getGSEADataSetSetRankOptions(map);
-		TaskIterator tasks = geneManiaTaskFactory.createTaskIterator(map, genes, gseaOptions);
+		TaskIterator tasks = geneManiaTaskFactory.createTaskIterator(map, genes, selectedGenes, gseaOptions);
 		taskManager.execute(tasks);
 	}
 	
 	private void runString() {
 		EnrichmentMap map = getContentPanel().getEnrichmentMap();
 		List<String> genes = getContentPanel().getGenes();
+		List<String> selectedGenes = getContentPanel().getSelectedGenes();
 		List<GSEALeadingEdgeRankingOption> gseaOptions = rankingOptionFactory.getGSEADataSetSetRankOptions(map);
-		TaskIterator tasks = stringAppTaskFactoy.createTaskIterator(map, genes, gseaOptions);
+		TaskIterator tasks = stringAppTaskFactoy.createTaskIterator(map, genes, selectedGenes, gseaOptions);
 		taskManager.execute(tasks);
 	}
 	

Original file line number	Diff line number	Diff line change
`@@ -34,7 +34,7 @@ public TaskIterator createTaskIterator(View<CyNode> nodeView, CyNetworkView netw`
`34`	`34`
`35`	`35`	`List<GSEALeadingEdgeRankingOption> rankOptions = rankingOptionFactory.getGSEADataSetSetRankOptions(map);`
`36`	`36`
`37`		`- TaskIterator tasks = geneManiaTaskFactory.createTaskIterator(map, genes, rankOptions);`
	`37`	`+ TaskIterator tasks = geneManiaTaskFactory.createTaskIterator(map, genes, null, rankOptions);`
`38`	`38`	`return tasks;`
`39`	`39`	`}`
`40`	`40`