From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 18 Aug 2016 15:33:06 +0000 (+0100)
Subject: Merge branch 'develop' into bug/JAL-1841rnaSecStr
X-Git-Tag: Release_2_10_0~70^2~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=71d6099d5246bdaf7b667e02620f403937582780;p=jalview.git

Merge branch 'develop' into bug/JAL-1841rnaSecStr
---

71d6099d5246bdaf7b667e02620f403937582780
diff --cc src/jalview/appletgui/AnnotationPanel.java
index ee8c9ca,e5475f8..6012c1a
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@@ -25,9 -25,9 +25,10 @@@ import jalview.datamodel.Annotation
  import jalview.datamodel.SequenceI;
  import jalview.renderer.AnnotationRenderer;
  import jalview.renderer.AwtRenderPanelI;
+ import jalview.schemes.ResidueProperties;
  import jalview.util.Comparison;
  import jalview.util.MessageManager;
 +import jalview.util.Platform;
  
  import java.awt.Color;
  import java.awt.Dimension;
diff --cc src/jalview/gui/AnnotationPanel.java
index 61a3f8c,3c9a13e..6a621ff
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@@ -287,15 -290,17 +290,18 @@@ public class AnnotationPanel extends JP
        aa[activeRow].annotations = anot;
      }
  
 -    if (evt.getActionCommand().equals(REMOVE))
 +    String action = evt.getActionCommand();
 +    if (action.equals(REMOVE))
      {
-       for (int sel : av.getColumnSelection().getSelected())
+       for (int index : av.getColumnSelection().getSelected())
        {
-         anot[sel] = null;
+         if (av.getColumnSelection().isVisible(index))
+         {
+           anot[index] = null;
+         }
        }
      }
 -    else if (evt.getActionCommand().equals(LABEL))
 +    else if (action.equals(LABEL))
      {
        String exMesg = collectAnnotVals(anot, LABEL);
        String label = JOptionPane.showInputDialog(this,