Merge branch 'develop' into bug/JAL-1803_JAL-2157

[jalview.git] / src / jalview / gui / AnnotationLabels.java

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 68df498..92c6dc6 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -244,6 +244,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     else if (evt.getActionCommand().equals(DELETE))
     {
       ap.av.getAlignment().deleteAnnotation(aa[selectedRow]);
+      ap.av.getCalcManager().removeWorkerForAnnotation(aa[selectedRow]);
     }
     else if (evt.getActionCommand().equals(SHOWALL))
     {
@@ -331,12 +332,20 @@ public class AnnotationLabels extends JPanel implements MouseListener,
   {
     getSelectedRow(evt.getY() - getScrollOffset());
     oldY = evt.getY();
-    if (!evt.isPopupTrigger())
+    if (evt.isPopupTrigger())
     {
-      return;
+      showPopupMenu(evt);
     }
+  }
+
+  /**
+   * Build and show the Pop-up menu at the right-click mouse position
+   * 
+   * @param evt
+   */
+  void showPopupMenu(MouseEvent evt)
+  {
     evt.consume();
-    // handle popup menu event
     final AlignmentAnnotation[] aa = ap.av.getAlignment()
             .getAlignmentAnnotation();
 
@@ -594,7 +603,6 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       }
     }
     pop.show(this, evt.getX(), evt.getY());
-
   }
 
   /**
@@ -606,6 +614,12 @@ public class AnnotationLabels extends JPanel implements MouseListener,
   @Override
   public void mouseReleased(MouseEvent evt)
   {
+    if (evt.isPopupTrigger())
+    {
+      showPopupMenu(evt);
+      return;
+    }
+
     int start = selectedRow;
     getSelectedRow(evt.getY() - getScrollOffset());
     int end = selectedRow;
@@ -802,8 +816,45 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             // todo: make the ap scroll to the selection - not necessary, first
             // click highlights/scrolls, second selects
             ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
-            ap.av.setSelectionGroup(// new SequenceGroup(
-            aa[selectedRow].groupRef); // );
+            // process modifiers
+            SequenceGroup sg = ap.av.getSelectionGroup();
+            if (sg == null
+                    || sg == aa[selectedRow].groupRef
+                    || !(jalview.util.Platform.isControlDown(evt) || evt
+                            .isShiftDown()))
+            {
+              if (jalview.util.Platform.isControlDown(evt)
+                      || evt.isShiftDown())
+              {
+                // clone a new selection group from the associated group
+                ap.av.setSelectionGroup(new SequenceGroup(
+                        aa[selectedRow].groupRef));
+              }
+              else
+              {
+                // set selection to the associated group so it can be edited
+                ap.av.setSelectionGroup(aa[selectedRow].groupRef);
+              }
+            }
+            else
+            {
+              // modify current selection with associated group
+              int remainToAdd = aa[selectedRow].groupRef.getSize();
+              for (SequenceI sgs : aa[selectedRow].groupRef.getSequences())
+              {
+                if (jalview.util.Platform.isControlDown(evt))
+                {
+                  sg.addOrRemove(sgs, --remainToAdd == 0);
+                }
+                else
+                {
+                  // notionally, we should also add intermediate sequences from
+                  // last added sequence ?
+                  sg.addSequence(sgs, --remainToAdd == 0);
+                }
+              }
+            }
+
             ap.paintAlignment(false);
             PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
             ap.av.sendSelection();
@@ -833,7 +884,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
               // we make a copy rather than edit the current selection if no
               // modifiers pressed
               // see Enhancement JAL-1557
-              if (!(evt.isControlDown() || evt.isShiftDown()))
+              if (!(jalview.util.Platform.isControlDown(evt) || evt
+                      .isShiftDown()))
               {
                 sg = new SequenceGroup(sg);
                 sg.clear();
@@ -841,7 +893,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
               }
               else
               {
-                if (evt.isControlDown())
+                if (jalview.util.Platform.isControlDown(evt))
                 {
                   sg.addOrRemove(aa[selectedRow].sequenceRef, true);
                 }
@@ -861,9 +913,9 @@ public class AnnotationLabels extends JPanel implements MouseListener,
               sg.addSequence(aa[selectedRow].sequenceRef, false);
             }
             ap.av.setSelectionGroup(sg);
-            ap.av.sendSelection();
             ap.paintAlignment(false);
             PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+            ap.av.sendSelection();
           }
 
         }