From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Tue, 25 Sep 2012 14:22:09 +0000 (+0100)
Subject: JAL-1179 note and patch for exceptions raised when jalview.viewmodel.AlignmentViewpor... 
X-Git-Tag: Jalview_2_9~289
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=cd05157564b53f68ca9eb3ade15d0e687b57572d;hp=af4a464ed5537d777ec821929704e9169d8fba9e;p=jalview.git

JAL-1179 note and patch for exceptions raised when jalview.viewmodel.AlignmentViewport.getAlignmentView() called with non-null selection that contains no sequences. Needed for JAL-1031 and JAL-1032
---

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index a23aad5..662145e 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -72,7 +72,7 @@ public class AlignmentView
   /**
    * Construct an alignmentView from a live jalview alignment view. Note -
    * hidden rows will be excluded from alignmentView
-   * 
+   * Note: JAL-1179
    * @param alignment
    *          - alignment as referenced by an AlignViewport
    * @param columnSelection
@@ -104,7 +104,7 @@ public class AlignmentView
     // and record non-empty groups in group list.
     // record / sub-select selected region on the alignment view
     SequenceI[] selseqs;
-    if (selection != null)
+    if (selection != null && selection.getSize()>0)
     {
       List<SequenceI> sel = selection.getSequences(null);
       this.selected = new Vector();
@@ -174,7 +174,7 @@ public class AlignmentView
     {
       if (selseqs[i] != null)
       {
-        if (selection != null && !selectedRegionOnly)
+        if (selection != null && selection.getSize()>0 && !selectedRegionOnly)
         {
           sequences[csi].setGroupMembership(selected);
           selected.addElement(sequences[csi]);