Fixed recursion bug for going down the tree looking for invalid taxa …

…to a term May have fixed problem with dialog boxes not listening for the mouse on drag and drop
geneontology · Nov 28, 2016 · ac79096 · ac79096
1 parent bace96b
commit ac79096
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Showing 7 changed files with 131 additions and 60 deletions.
diff --git a/.classpath b/.classpath
@@ -11,15 +11,11 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
 	<classpathentry excluding="**" kind="src" output="target/classes" path="resources">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
 	<classpathentry kind="output" path="target/classes"/>
 </classpath>
diff --git a/.settings/org.eclipse.jdt.core.prefs b/.settings/org.eclipse.jdt.core.prefs
@@ -1,12 +1,2 @@
 eclipse.preferences.version=1
-org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7
-org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
-org.eclipse.jdt.core.compiler.compliance=1.7
-org.eclipse.jdt.core.compiler.debug.lineNumber=generate
-org.eclipse.jdt.core.compiler.debug.localVariable=generate
-org.eclipse.jdt.core.compiler.debug.sourceFile=generate
-org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
-org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
 org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
-org.eclipse.jdt.core.compiler.source=1.7
diff --git a/resources/org/paint/resources/VERSION b/resources/org/paint/resources/VERSION
@@ -1 +1 @@
-v2.28
+v2.28.1
diff --git a/src/org/paint/dialog/AnnotUtil.java b/src/org/paint/dialog/AnnotUtil.java
@@ -0,0 +1,47 @@
+package org.paint.dialog;
+
+import java.util.List;
+
+import org.bbop.framework.GUIManager;
+import org.bbop.phylo.annotate.PaintAction;
+import org.bbop.phylo.annotate.WithEvidence;
+import org.bbop.phylo.model.Bioentity;
+import org.bbop.phylo.model.Tree;
+import org.bbop.phylo.util.TaxonChecker;
+import org.paint.gui.event.AnnotationChangeEvent;
+import org.paint.gui.event.EventManager;
+import org.paint.main.PaintManager;
+
+public class AnnotUtil {
+
+	private static AnnotUtil INSTANCE;
+
+	private AnnotUtil() {
+	}
+
+	public static AnnotUtil inst() {
+		if (INSTANCE == null) {
+			INSTANCE = new AnnotUtil();
+		}
+		return INSTANCE;
+	}
+
+	public void propagateAssociation(Bioentity node, Tree tree, String term, String date) {
+		boolean valid_for_all_descendents = TaxonChecker.checkTaxons(tree, node, term, false);
+		if (!valid_for_all_descendents) {
+			List<String> invalid_taxa = TaxonChecker.getInvalidTaxa(node, term);
+			TaxonDialog taxon_dialog = new TaxonDialog(GUIManager.getManager().getFrame(), term, invalid_taxa);
+			valid_for_all_descendents = taxon_dialog.isLost();
+		}
+		if (valid_for_all_descendents) {
+			WithEvidence withs = new WithEvidence(tree, node, term);
+			int qualifiers = withs.getWithQualifiers();
+			if (qualifiers > 0) {
+				QualifierDialog qual_dialog = new QualifierDialog(GUIManager.getManager().getFrame(), qualifiers);
+				qualifiers = qual_dialog.getQualifiers();
+			}
+			PaintAction.inst().propagateAssociation(PaintManager.inst().getFamily(), node, term, withs, date, qualifiers);
+			EventManager.inst().fireAnnotationChangeEvent(new AnnotationChangeEvent(node));
+		}
+	}
+}
diff --git a/src/org/paint/gui/matrix/AnnotMatrix.java b/src/org/paint/gui/matrix/AnnotMatrix.java
@@ -55,6 +55,7 @@
 import org.bbop.phylo.tracking.LogEntry;
 import org.bbop.phylo.util.OWLutil;
 import org.bbop.phylo.util.TaxonChecker;
+import org.paint.dialog.AnnotUtil;
 import org.paint.dialog.QualifierDialog;
 import org.paint.dialog.TaxonDialog;
 import org.paint.displaymodel.DisplayBioentity;
@@ -551,22 +552,23 @@ private class AnnotateActionListener implements ActionListener{
 
 		public void actionPerformed(ActionEvent e){
 			Tree tree = PaintManager.inst().getTree().getTreeModel();
-			boolean valid_for_all_descendents = TaxonChecker.checkTaxons(tree, ancestor, term, false);
-			if (!valid_for_all_descendents) {
-				List<String> invalid_taxa = TaxonChecker.getInvalidTaxa(ancestor, term);
-				TaxonDialog taxon_dialog = new TaxonDialog(GUIManager.getManager().getFrame(), term, invalid_taxa);
-				valid_for_all_descendents = taxon_dialog.isLost();
-			}
-			if (valid_for_all_descendents) {
-				WithEvidence withs = new WithEvidence(tree, ancestor, term);
-				int qualifiers = withs.getWithQualifiers();
-				if (qualifiers > 0) {
-					QualifierDialog qual_dialog = new QualifierDialog(GUIManager.getManager().getFrame(), qualifiers);
-					qualifiers = qual_dialog.getQualifiers();
-				}
-				PaintAction.inst().propagateAssociation(PaintManager.inst().getFamily(), ancestor, term, withs, null, qualifiers);
-				EventManager.inst().fireAnnotationChangeEvent(new AnnotationChangeEvent(ancestor));
-			}
+			AnnotUtil.inst().propagateAssociation(ancestor, tree, term, null);
+//			boolean valid_for_all_descendents = TaxonChecker.checkTaxons(tree, ancestor, term, false);
+//			if (!valid_for_all_descendents) {
+//				List<String> invalid_taxa = TaxonChecker.getInvalidTaxa(ancestor, term);
+//				TaxonDialog taxon_dialog = new TaxonDialog(GUIManager.getManager().getFrame(), term, invalid_taxa);
+//				valid_for_all_descendents = taxon_dialog.isLost();
+//			}
+//			if (valid_for_all_descendents) {
+//				WithEvidence withs = new WithEvidence(tree, ancestor, term);
+//				int qualifiers = withs.getWithQualifiers();
+//				if (qualifiers > 0) {
+//					QualifierDialog qual_dialog = new QualifierDialog(GUIManager.getManager().getFrame(), qualifiers);
+//					qualifiers = qual_dialog.getQualifiers();
+//				}
+//				PaintAction.inst().propagateAssociation(PaintManager.inst().getFamily(), ancestor, term, withs, null, qualifiers);
+//				EventManager.inst().fireAnnotationChangeEvent(new AnnotationChangeEvent(ancestor));
+//			}
 		}
 
 	}

diff --git a/src/org/paint/gui/matrix/AnnotMatrixModel.java b/src/org/paint/gui/matrix/AnnotMatrixModel.java
@@ -141,17 +141,17 @@ private void sortTerms(List<Bioentity> nodes, List<String> cellular_list) {
 
 		/* Hack alert - hard coded the GO id for cellular process here */
 		/* Only applies to biological process */
-		if (aspect_name.equals(AspectSelector.Aspect.BIOLOGICAL_PROCESS.toString())) {
-			String cellular = "GO:0009987";
-			for (String term : cellular_list) {
-				if (!OWLutil.inst().moreSpecific(term, cellular)) {
-					noncellular_list.add(term);
-				}
-			}
-			for (String term : noncellular_list) {
-				cellular_list.remove(term);
-			}
-		}
+//		if (aspect_name.equals(AspectSelector.Aspect.BIOLOGICAL_PROCESS.toString())) {
+//			String cellular = "GO:0009987";
+//			for (String term : cellular_list) {
+//				if (!OWLutil.inst().moreSpecific(term, cellular)) {
+//					noncellular_list.add(term);
+//				}
+//			}
+//			for (String term : noncellular_list) {
+//				cellular_list.remove(term);
+//			}
+//		}
 
 		/*
 		 * First an alphabetic sort

diff --git a/src/org/paint/gui/matrix/AnnotationTransferHandler.java b/src/org/paint/gui/matrix/AnnotationTransferHandler.java
@@ -49,17 +49,21 @@
 
 import javax.swing.Icon;
 import javax.swing.JComponent;
+import javax.swing.SwingUtilities;
 import javax.swing.TransferHandler;
 
 import org.apache.log4j.Logger;
 import org.bbop.framework.GUIManager;
 import org.bbop.phylo.annotate.PaintAction;
 import org.bbop.phylo.annotate.WithEvidence;
+import org.bbop.phylo.model.Bioentity;
+import org.bbop.phylo.model.Family;
 import org.bbop.phylo.model.Tree;
 import org.bbop.phylo.tracking.LogEntry;
 import org.bbop.phylo.tracking.LogEntry.LOG_ENTRY_TYPE;
 import org.bbop.phylo.util.OWLutil;
 import org.bbop.phylo.util.TaxonChecker;
+import org.paint.dialog.AnnotUtil;
 import org.paint.dialog.QualifierDialog;
 import org.paint.dialog.TaxonDialog;
 import org.paint.displaymodel.DisplayBioentity;
@@ -256,22 +260,30 @@ public boolean importData(TransferHandler.TransferSupport support) {
 		Point p = support.getDropLocation().getDropPoint();
 		DisplayBioentity node = tree.getClickedInNodeArea(p);
 
-		boolean valid_for_all_descendents = TaxonChecker.checkTaxons(tree.getTreeModel(), node, term, false);
-		if (!valid_for_all_descendents) {
-			List<String> invalid_taxa = TaxonChecker.getInvalidTaxa(node, term);
-			TaxonDialog taxon_dialog = new TaxonDialog(GUIManager.getManager().getFrame(), term, invalid_taxa);
-			valid_for_all_descendents = taxon_dialog.isLost();
-		}
-		if (valid_for_all_descendents) {
-			WithEvidence withs = new WithEvidence(tree.getTreeModel(), node, term);
-			int qualifiers = withs.getWithQualifiers();
-			if (qualifiers > 0) {
-				QualifierDialog qual_dialog = new QualifierDialog(GUIManager.getManager().getFrame(), qualifiers);
-				qualifiers = qual_dialog.getQualifiers();
-			}
-			PaintAction.inst().propagateAssociation(PaintManager.inst().getFamily(), node, term, withs, null, qualifiers);
-			EventManager.inst().fireAnnotationChangeEvent(new AnnotationChangeEvent(node));
-		}
+		AnnotUtil.inst().propagateAssociation(node, tree.getTreeModel(), term, null);
+//		boolean valid_for_all_descendents = TaxonChecker.checkTaxons(tree.getTreeModel(), node, term, false);
+//		if (!valid_for_all_descendents) {
+//			List<String> invalid_taxa = TaxonChecker.getInvalidTaxa(node, term);
+//			doTaxonDialog taxon_dialog_runner = new doTaxonDialog(term, invalid_taxa);
+//			Thread t1 = new Thread(taxon_dialog_runner);
+//			t1.start();
+//			try {
+//				t1.join();
+//			} catch (InterruptedException e) {
+//				log.info("Not sure what to do here if it ever happens");
+//			}
+//			valid_for_all_descendents = taxon_dialog_runner.valid();
+//		}
+//		if (valid_for_all_descendents) {
+//			WithEvidence withs = new WithEvidence(tree.getTreeModel(), node, term);
+//			int qualifiers = withs.getWithQualifiers();
+//			if (qualifiers > 0) {
+//				QualifierDialog qual_dialog = new QualifierDialog(GUIManager.getManager().getFrame(), qualifiers);
+//				qualifiers = qual_dialog.getQualifiers();
+//			}
+//			PaintAction.inst().propagateAssociation(PaintManager.inst().getFamily(), node, term, withs, null, qualifiers);
+//			EventManager.inst().fireAnnotationChangeEvent(new AnnotationChangeEvent(node));
+//		}
 		clearVisitedNodes(tree);
 		return true;
 	}
@@ -434,4 +446,28 @@ public void dropActionChanged(DragSourceDragEvent dsde)
 		{
 		}
 	}
-}
+
+//	private class doTaxonDialog implements Runnable{
+//		private final String term;
+//		private final List<String> invalid_taxa;
+//		private boolean valid_for_all_descendents;
+//
+//		doTaxonDialog(String term, List<String> invalid_taxa) {
+//			this.term = term;
+//			this.invalid_taxa = invalid_taxa;
+//		}
+//
+//		public void run() {
+//			SwingUtilities.invokeLater(new Runnable() {
+//				public void run() {
+//					TaxonDialog taxon_dialog = new TaxonDialog(GUIManager.getManager().getFrame(), term, invalid_taxa);
+//					valid_for_all_descendents = taxon_dialog.isLost();
+//				}
+//			});
+//		}
+//		
+//		public boolean valid() {
+//			return valid_for_all_descendents;
+//		}
+//	}
+}