From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 4 Jul 2017 15:51:34 +0000 (+0100)
Subject: JAL-147 revised update of startSeq, endSeq on unhide sequences
X-Git-Tag: Release_2_10_3b1~132^2~49
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=eeabeb4f32b679c28eb7413b638a07035e0d7eb8;p=jalview.git

JAL-147 revised update of startSeq, endSeq on unhide sequences
---

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 5e88c87..d3e502b 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1392,6 +1392,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void showAllHiddenSeqs()
   {
     int startSeq = ranges.getStartSeq();
+    int endSeq = ranges.getEndSeq();
 
     if (alignment.getHiddenSequences().getSize() > 0)
     {
@@ -1410,7 +1411,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
       hiddenRepSequences = null;
 
-      ranges.setStartSeq(startSeq);
+      ranges.setStartEndSeq(startSeq, endSeq + tmp.size());
 
       firePropertyChange("alignment", null, alignment.getSequences());
       // used to set hasHiddenRows/hiddenRepSequences here, after the property
@@ -1422,6 +1423,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void showSequence(int index)
   {
     int startSeq = ranges.getStartSeq();
+    int endSeq = ranges.getEndSeq();
 
     List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(
             index, hiddenRepSequences);
@@ -1438,7 +1440,10 @@ public abstract class AlignmentViewport implements AlignViewportI,
         selectionGroup.addSequence(seq, false);
         setSequenceAnnotationsVisible(seq, true);
       }
-      ranges.setStartSeq(startSeq);
+
+      // ranges.setStartSeq(startSeq);
+      ranges.setStartEndSeq(startSeq, endSeq + tmp.size());
+
       firePropertyChange("alignment", null, alignment.getSequences());
       sendSelection();
     }