correct popup menu, ensure panel doesn't disappear when empty (patches for JAL-554...

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 62ed93c..bc019fe 100755 (executable)
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -57,6 +57,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
 
   Tooltip tooltip;
 
+  private boolean hasHiddenRows;
+
   public AnnotationLabels(AlignmentPanel ap)
   {
     this.ap = ap;
@@ -77,9 +79,14 @@ public class AnnotationLabels extends Panel implements ActionListener,
     repaint();
   }
 
+  /**
+   * 
+   * @param y
+   * @return -2 if no rows are visible at all, -1 if no visible rows were selected
+   */
   int getSelectedRow(int y)
   {
-    int row = -1;
+    int row = -2;
     AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
 
     if (aa == null)
@@ -90,11 +97,11 @@ public class AnnotationLabels extends Panel implements ActionListener,
     int height = 0;
     for (int i = 0; i < aa.length; i++)
     {
+      row = -1;
       if (!aa[i].visible)
       {
         continue;
       }
-
       height += aa[i].height;
       if (y < height)
       {
@@ -248,9 +255,16 @@ public class AnnotationLabels extends Panel implements ActionListener,
     MenuItem item = new MenuItem(ADDNEW);
     item.addActionListener(this);
     popup.add(item);
-    if (aa == null)
+    if (selectedRow<0)
     {
-
+      // this never happens at moment: - see comment on JAL-563 
+      if (hasHiddenRows)
+      {
+         item = new MenuItem(SHOWALL);
+         item.addActionListener(this);
+         popup.add(item);
+      }
+      this.add(popup);
       popup.show(this, evt.getX(), evt.getY());
       return;
     }
@@ -261,9 +275,11 @@ public class AnnotationLabels extends Panel implements ActionListener,
     item = new MenuItem(HIDE);
     item.addActionListener(this);
     popup.add(item);
+    if (hasHiddenRows) {
     item = new MenuItem(SHOWALL);
     item.addActionListener(this);
     popup.add(item);
+    }
     this.add(popup);
     item = new MenuItem(OUTPUT_TEXT);
     item.addActionListener(this);
@@ -352,35 +368,26 @@ public class AnnotationLabels extends Panel implements ActionListener,
     g.setColor(Color.black);
 
     AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-    int y = g.getFont().getSize();
-    int x = 0;
+    int y = 0, fy=g.getFont().getSize();
+    int x = 0, offset;
 
     if (aa != null)
     {
+      hasHiddenRows=false;
       for (int i = 0; i < aa.length; i++)
       {
         if (!aa[i].visible)
         {
+          hasHiddenRows=true;
           continue;
         }
 
         x = width - fm.stringWidth(aa[i].label) - 3;
 
-        if (aa[i].graph > 0)
-        {
-          y += (aa[i].height / 3);
-        }
-
-        g.drawString(aa[i].label, x, y);
+        y += aa[i].height;
+        offset = -(aa[i].height-fy)/2;
 
-        if (aa[i].graph > 0)
-        {
-          y += (2 * aa[i].height / 3);
-        }
-        else
-        {
-          y += aa[i].height;
-        }
+        g.drawString(aa[i].label, x, y+offset);
       }
     }
   }