Add canvas parameter to AnnotatationTree methods. Some cleanup. Refs

#4314
cytoscape · Sep 13, 2018 · 689b4e4 · 689b4e4
1 parent a62aaa6
commit 689b4e4
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Showing 10 changed files with 176 additions and 139 deletions.
diff --git a/...g-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/AnnotationNode.java b/...g-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/AnnotationNode.java
@@ -74,16 +74,16 @@ public String toString() {
 	}
 
 	void removeEmptyGroups() {
+		for(AnnotationNode n : children) {
+			n.removeEmptyGroups();
+		}
 		Iterator<AnnotationNode> iter = children.iterator();
 		while(iter.hasNext()) {
 			AnnotationNode n = iter.next();
 			if(n.getAnnotation() instanceof GroupAnnotation && n.getChildCount() == 0) {
 				iter.remove();
 			}
 		}
-		for(AnnotationNode n : children) {
-			n.removeEmptyGroups();
-		}
 	}
 
 

diff --git a/...g-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/AnnotationTree.java b/...g-presentation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/AnnotationTree.java
@@ -8,6 +8,7 @@
 import java.util.Comparator;
 import java.util.HashMap;
 import java.util.HashSet;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -57,33 +58,36 @@ public AnnotationNode getRoot(String canvas) {
 		}
 	}
 
-	public AnnotationNode get(Annotation a) {
-		AnnotationNode node = foregroundLookup.get(a);
-		if(node != null)
-			return node;
-		return backgroundLookup.get(a);
-	} 
+	public AnnotationNode get(String canvas, Annotation a) {
+		switch(canvas) {
+			case Annotation.FOREGROUND: return foregroundLookup.get(a);
+			case Annotation.BACKGROUND: return backgroundLookup.get(a);
+			default: return null;
+		}
+	}
 
 
-	public void shift(int direction, Collection<? extends Annotation> annotations) {
-		groupByParent(annotations).forEach((parent, childrenToShift) -> parent.shift(direction, childrenToShift));
+	public void shift(int direction, String canvas, Collection<? extends Annotation> annotations) {
+		groupByParent(canvas, annotations).forEach((parent, childrenToShift) -> parent.shift(direction, childrenToShift));
 	}
 
-	public boolean shiftAllowed(int direction, Collection<? extends Annotation> annotations) {
+	public boolean shiftAllowed(int direction, String canvas, Collection<? extends Annotation> annotations) {
 		if(annotations.isEmpty())
 			return false;
 
-		for(Map.Entry<AnnotationNode,List<AnnotationNode>> entry : groupByParent(annotations).entrySet()) {
-			if(!entry.getKey().shiftAllowed(direction, entry.getValue())) {
+		for(Map.Entry<AnnotationNode,List<AnnotationNode>> entry : groupByParent(canvas, annotations).entrySet()) {
+			AnnotationNode parent = entry.getKey();
+			List<AnnotationNode> childrenToShift = entry.getValue();
+			if(!parent.shiftAllowed(direction, childrenToShift)) {
 				return false;
 			}
 		}
 		return true;
 	}
 
-	private Map<AnnotationNode,List<AnnotationNode>> groupByParent(Collection<? extends Annotation> annotations) {
+	private Map<AnnotationNode,List<AnnotationNode>> groupByParent(String canvas, Collection<? extends Annotation> annotations) {
 		return annotations.stream()
-			.map(this::get)
+			.map(a -> this.get(canvas, a))
 			.filter(a -> a != null)
 			.collect(groupingBy(AnnotationNode::getParent)); // doesn't matter which tree they are already separate
 	}
@@ -242,6 +246,27 @@ private static boolean containsCycle(DingAnnotation a, Collection<DingAnnotation
 		}
 		return false;
 	}
+
+
+	public static boolean hasSameParent(Collection<? extends Annotation> annotations) {
+		if(annotations.isEmpty())
+			return false;
+
+		Iterator<? extends Annotation> iter = annotations.iterator();
+		GroupAnnotation parent = null;
+		if(iter.hasNext()) {
+			DingAnnotation a = (DingAnnotation)iter.next();
+			parent = a.getGroupParent();
+		}
+		while(iter.hasNext()) {
+			DingAnnotation a = (DingAnnotation)iter.next();
+			if(parent != a.getGroupParent()) {
+				return false;
+			}
+		}
+
+		return true;
+	}
 
 
 	private static void sortAnnotations(List<Annotation> annotations) {

diff --git a/...on-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/GroupAnnotationsTask.java b/...on-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/GroupAnnotationsTask.java
@@ -4,6 +4,7 @@
 import java.util.Collections;
 
 import org.cytoscape.ding.impl.DGraphView;
+import org.cytoscape.ding.impl.cyannotator.AnnotationTree;
 import org.cytoscape.ding.impl.cyannotator.CyAnnotator;
 import org.cytoscape.ding.impl.cyannotator.annotations.DingAnnotation;
 import org.cytoscape.ding.impl.cyannotator.annotations.GroupAnnotationImpl;
@@ -59,6 +60,9 @@ public GroupAnnotationsTask(CyNetworkView view, Collection<DingAnnotation> annot
 
 	@Override
 	public void run(TaskMonitor tm) throws Exception {
+		if(annotations.isEmpty() || !AnnotationTree.hasSameParent(annotations))
+			return;
+
 		if (view instanceof DGraphView) {
 			DGraphView dView = (DGraphView) view;
 
@@ -72,6 +76,8 @@ public void run(TaskMonitor tm) throws Exception {
 
 			cyAnnotator.markUndoEdit("Group Annotations");
 
+			GroupAnnotation parent = annotations.iterator().next().getGroupParent(); // may be null
+
 			// remove the annotations from any existing groups
 			for(DingAnnotation a : selectedAnnotations) {
 				GroupAnnotation group = a.getGroupParent();
@@ -80,21 +86,24 @@ public void run(TaskMonitor tm) throws Exception {
 				}
 			}
 
-			GroupAnnotationImpl group = new GroupAnnotationImpl(dView, Collections.emptyMap());
-			group.addComponent(null); // Need to add this first so we can update things appropriately
+			GroupAnnotationImpl newGroup = new GroupAnnotationImpl(dView, Collections.emptyMap());
+			newGroup.addComponent(null); // Need to add this first so we can update things appropriately
 
 			// Now, add all of the children--do not iterate AnnotationSelection directly or that can throw
 			// ConcurrentModifcationExceptions
 			for(DingAnnotation a : selectedAnnotations) {
-				group.addMember(a);
+				newGroup.addMember(a);
 				a.setSelected(false);
 			};
 
-			cyAnnotator.addAnnotation(group);
+			if(parent != null)
+				parent.addMember(newGroup);
+
+			cyAnnotator.addAnnotation(newGroup);
 
-			// Finally, set ourselves to be the selected component
-			group.setSelected(true);
-			group.update();
+			// Finally, set ourselves to be the selected components 
+			newGroup.setSelected(true);
+			newGroup.update();
 
 			cyAnnotator.postUndoEdit();
 		}

diff --git a/.../src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/GroupAnnotationsTaskFactory.java b/.../src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/GroupAnnotationsTaskFactory.java
@@ -1,41 +1,12 @@
 package org.cytoscape.ding.impl.cyannotator.tasks;
 
-/*
- * #%L
- * Cytoscape Ding View/Presentation Impl (ding-presentation-impl)
- * $Id:$
- * $HeadURL:$
- * %%
- * Copyright (C) 2006 - 2013 The Cytoscape Consortium
- * %%
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as 
- * published by the Free Software Foundation, either version 2.1 of the 
- * License, or (at your option) any later version.
- * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Lesser Public License for more details.
- * 
- * You should have received a copy of the GNU General Lesser Public 
- * License along with this program.  If not, see
- * <http://www.gnu.org/licenses/lgpl-2.1.html>.
- * #L%
- */
-
-
-
-import java.awt.geom.Point2D;
-
+import org.cytoscape.ding.impl.DGraphView;
+import org.cytoscape.ding.impl.cyannotator.AnnotationTree;
+import org.cytoscape.ding.impl.cyannotator.CyAnnotator;
 import org.cytoscape.task.NetworkViewTaskFactory;
 import org.cytoscape.view.model.CyNetworkView;
 import org.cytoscape.work.TaskIterator;
 
-import org.cytoscape.ding.impl.DGraphView;
-import org.cytoscape.ding.impl.cyannotator.CyAnnotator;
-import org.cytoscape.ding.impl.cyannotator.annotations.DingAnnotation;
-
 public class GroupAnnotationsTaskFactory implements NetworkViewTaskFactory {
 
 	@Override
@@ -47,9 +18,6 @@ public TaskIterator createTaskIterator(CyNetworkView networkView) {
 	@Override
 	public boolean isReady(CyNetworkView networkView) {
 		CyAnnotator cyAnnotator = ((DGraphView)networkView).getCyAnnotator();
-		// Get all of the selected annotations
-		if (cyAnnotator.getAnnotationSelection().count() > 1)
-			return true;
-		return false;
+		return AnnotationTree.hasSameParent(cyAnnotator.getAnnotationSelection().getSelectedAnnotations());
 	}
 }
diff --git a/...-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/ReorderAnnotationsTask.java b/...-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/ReorderAnnotationsTask.java
@@ -4,13 +4,17 @@
 import java.util.Collection;
 import java.util.Collections;
 import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
 
 import org.cytoscape.ding.impl.DGraphView;
 import org.cytoscape.ding.impl.cyannotator.AnnotationTree;
 import org.cytoscape.ding.impl.cyannotator.CyAnnotator;
 import org.cytoscape.ding.impl.cyannotator.annotations.DingAnnotation;
 import org.cytoscape.task.AbstractNetworkViewTask;
 import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.presentation.annotations.Annotation;
+import org.cytoscape.view.presentation.annotations.GroupAnnotation;
 import org.cytoscape.work.TaskMonitor;
 
 /*
@@ -79,7 +83,11 @@ public void run(TaskMonitor tm) throws Exception {
 
 	private void changeCanvas() {
 		for (int i = annotations.size() - 1; i >= 0; i--) {
-			annotations.get(i).changeCanvas(canvasName);
+			DingAnnotation da = annotations.get(i);
+			// group annotations must stay on the foreground canvas
+			if(!(da instanceof GroupAnnotation && Annotation.BACKGROUND.equals(canvasName))) {
+				da.changeCanvas(canvasName);
+			}
 		}
 
 		// need to rebuild the tree AFTER changing the canvas
@@ -93,7 +101,17 @@ private void reorder(Integer offset) {
 		CyAnnotator cyAnnotator = ((DGraphView)view).getCyAnnotator();
 		AnnotationTree tree = cyAnnotator.getAnnotationTree();
 
-		tree.shift(offset, annotations);
+		Map<String,List<DingAnnotation>> byCanvas = 
+				annotations.stream().collect(Collectors.groupingBy(DingAnnotation::getCanvasName));
+
+		List<DingAnnotation> fga = byCanvas.get(Annotation.FOREGROUND);
+		if(fga != null && !fga.isEmpty())
+			tree.shift(offset, Annotation.FOREGROUND, fga);
+
+		List<DingAnnotation> bga = byCanvas.get(Annotation.BACKGROUND);
+		if(bga != null && !bga.isEmpty())
+			tree.shift(offset, Annotation.BACKGROUND, bga);
+
 		tree.resetZOrder();
 	}
 

diff --git a/...java/org/cytoscape/ding/impl/cyannotator/tasks/ReorderSelectedAnnotationsTaskFactory.java b/...java/org/cytoscape/ding/impl/cyannotator/tasks/ReorderSelectedAnnotationsTaskFactory.java
@@ -8,6 +8,7 @@
 import org.cytoscape.ding.impl.cyannotator.annotations.DingAnnotation;
 import org.cytoscape.task.NetworkViewTaskFactory;
 import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.presentation.annotations.Annotation;
 import org.cytoscape.work.TaskIterator;
 
 /*
@@ -75,7 +76,9 @@ public boolean isReady(CyNetworkView view) {
 
 
 		if (offset != null) {
-			return cyAnnotator.getAnnotationTree().shiftAllowed(offset, annotations);
+			boolean fg = cyAnnotator.getAnnotationTree().shiftAllowed(offset, Annotation.FOREGROUND, annotations);
+			boolean bg = cyAnnotator.getAnnotationTree().shiftAllowed(offset, Annotation.BACKGROUND, annotations);
+			return fg || bg;
 		}
 
 		if (canvasName != null) {

diff --git a/...-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/UngroupAnnotationsTask.java b/...-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/tasks/UngroupAnnotationsTask.java
@@ -3,6 +3,7 @@
 import java.util.Collection;
 import java.util.Collections;
 import java.util.LinkedHashSet;
+import java.util.List;
 import java.util.Set;
 
 import org.cytoscape.ding.impl.DGraphView;
@@ -55,19 +56,29 @@ public UngroupAnnotationsTask(CyNetworkView view, Collection<GroupAnnotation> an
 	}
 
 	@Override
-	public void run(TaskMonitor tm) throws Exception {
+	public void run(TaskMonitor tm) {
 		if (view instanceof DGraphView) {
 
 			CyAnnotator annotator = ((DGraphView)view).getCyAnnotator();
 			annotator.markUndoEdit("Ungroup Annotations");
 
 			for(GroupAnnotation ga : groups) {
-				for(Annotation a : ga.getMembers()) {
+				GroupAnnotation parent = ((DingAnnotation)ga).getGroupParent();
+				List<Annotation> members = ga.getMembers();
+
+				for(Annotation a : members) {
 					ga.removeMember(a);
 					a.setSelected(true);
 				}
 
-				ga.removeAnnotation();
+				// move the annotations into the parent
+				if(parent != null) {
+					for(Annotation a : members) {
+						parent.addMember(a);
+					}
+				}
+
+				ga.removeAnnotation(); // this fires an event so it must go at the end
 			}
 
 			annotator.postUndoEdit();