patches for JAL-554 and JAL-570

focus is explicitly handed back to caller (JAL-566)

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index bd46613..bf2f152 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -73,6 +73,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
   Font font = new Font("Arial", Font.PLAIN, 11);
 
+  private boolean hasHiddenRows;
+
   /**
    * Creates a new AnnotationLabels object.
    * 
@@ -130,15 +132,23 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     repaint();
   }
 
+  /**
+   * sets selectedRow to -2 if no annotation preset, -1 if no visible row is at
+   * y
+   * 
+   * @param y
+   *          coordinate position to search for a row
+   */
   void getSelectedRow(int y)
   {
     int height = 0;
     AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-
+    selectedRow = -2;
     if (aa != null)
     {
       for (int i = 0; i < aa.length; i++)
       {
+        selectedRow = -1;
         if (!aa[i].visible)
         {
           continue;
@@ -153,8 +163,6 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           break;
         }
       }
-    } else {
-      selectedRow = -1;
     }
   }
 
@@ -252,7 +260,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
   {
     EditNameDialog dialog = new EditNameDialog(annotation.label,
             annotation.description, "       Annotation Name ",
-            "Annotation Description ", "Edit Annotation Name/Description");
+            "Annotation Description ", "Edit Annotation Name/Description",
+            ap.alignFrame);
 
     if (!dialog.accept)
     {
@@ -300,6 +309,10 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       // Swap these annotations
       AlignmentAnnotation startAA = ap.av.alignment
               .getAlignmentAnnotation()[start];
+      if (end == -1)
+      {
+        end = ap.av.alignment.getAlignmentAnnotation().length - 1;
+      }
       AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
 
       ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
@@ -431,7 +444,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
     if (SwingUtilities.isLeftMouseButton(evt))
     {
-      if (aa!=null && selectedRow < aa.length)
+      if (selectedRow > -1 && selectedRow < aa.length)
       {
         if (aa[selectedRow].groupRef != null)
         {
@@ -480,17 +493,18 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     JPopupMenu pop = new JPopupMenu("Annotations");
     JMenuItem item = new JMenuItem(ADDNEW);
     item.addActionListener(this);
-
-    if ((aa == null) || (aa.length == 0))
+    pop.add(item);
+    if (selectedRow < 0)
     {
-      item = new JMenuItem(SHOWALL);
-      item.addActionListener(this);
-      pop.add(item);
+      if (hasHiddenRows)
+      { // let the user make everything visible again
+        item = new JMenuItem(SHOWALL);
+        item.addActionListener(this);
+        pop.add(item);
+      }
       pop.show(this, evt.getX(), evt.getY());
       return;
     }
-
-    pop.add(item);
     item = new JMenuItem(EDITNAME);
     item.addActionListener(this);
     pop.add(item);
@@ -500,9 +514,12 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     item = new JMenuItem(DELETE);
     item.addActionListener(this);
     pop.add(item);
-    item = new JMenuItem(SHOWALL);
-    item.addActionListener(this);
-    pop.add(item);
+    if (hasHiddenRows)
+    {
+      item = new JMenuItem(SHOWALL);
+      item.addActionListener(this);
+      pop.add(item);
+    }
     item = new JMenuItem(OUTPUT_TEXT);
     item.addActionListener(this);
     pop.add(item);
@@ -752,12 +769,14 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
     if (aa != null)
     {
+      hasHiddenRows = false;
       for (int i = 0; i < aa.length; i++)
       {
         g.setColor(Color.black);
 
         if (!aa[i].visible)
         {
+          hasHiddenRows = true;
           continue;
         }