patch re JAL-554

[jalview.git] / src / jalview / gui / AlignmentPanel.java

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 9626e80..09b7215 100755 (executable)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.gui;
 
@@ -284,6 +283,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
       int start = r[0];
       int end = r[1];
+      // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); //
+      // DEBUG
       if (start < 0)
       {
         return false;
@@ -1324,6 +1325,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     updateAnnotation(false);
   }
+
   public void updateAnnotation(boolean applyGlobalSettings)
   {
     boolean updateCalcs = false;
@@ -1331,7 +1333,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     boolean cons = av.isShowGroupConsensus();
     boolean showprf = av.isShowSequenceLogo();
     boolean showConsHist = av.isShowConsensusHistogram();
-    
+
     boolean sortg = true;
 
     // remove old automatic annotation
@@ -1342,40 +1344,46 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     AlignmentAnnotation[] aan = av.alignment.getAlignmentAnnotation();
     Hashtable oldrfs = new Hashtable();
-    for (int an = 0; an < aan.length; an++)
+    if (aan != null)
     {
-      if (aan[an].autoCalculated && aan[an].groupRef != null)
+      for (int an = 0; an < aan.length; an++)
       {
-        oldrfs.put(aan[an].groupRef, aan[an].groupRef);
-        av.alignment.deleteAnnotation(aan[an]);
-        aan[an] = null;
+        if (aan[an].autoCalculated && aan[an].groupRef != null)
+        {
+          oldrfs.put(aan[an].groupRef, aan[an].groupRef);
+          av.alignment.deleteAnnotation(aan[an]);
+          aan[an] = null;
+        }
       }
     }
     SequenceGroup sg;
-    for (int g = 0; g < gr.size(); g++)
+    if (gr != null)
     {
-      updateCalcs = false;
-      sg = (SequenceGroup) gr.elementAt(g);
-      if (applyGlobalSettings || !oldrfs.containsKey(sg))
+      for (int g = 0; g < gr.size(); g++)
       {
-        // set defaults for this group's conservation/consensus
-        sg.setIncludeAllConsSymbols(showprf);
-        sg.setShowConsensusHistogram(showConsHist);
-      }
-      if (conv)
-      {
-        updateCalcs = true;
-        av.alignment.addAnnotation(sg.getConservationRow(),0);
-      }
-      if (cons)
-      {
-        updateCalcs = true;
-        av.alignment.addAnnotation(sg.getConsensus(),0);
-      }
-      // refresh the annotation rows
-      if (updateCalcs)
-      {
-        sg.recalcConservation();
+        updateCalcs = false;
+        sg = (SequenceGroup) gr.elementAt(g);
+        if (applyGlobalSettings || !oldrfs.containsKey(sg))
+        {
+          // set defaults for this group's conservation/consensus
+          sg.setIncludeAllConsSymbols(showprf);
+          sg.setShowConsensusHistogram(showConsHist);
+        }
+        if (conv)
+        {
+          updateCalcs = true;
+          av.alignment.addAnnotation(sg.getConservationRow(), 0);
+        }
+        if (cons)
+        {
+          updateCalcs = true;
+          av.alignment.addAnnotation(sg.getConsensus(), 0);
+        }
+        // refresh the annotation rows
+        if (updateCalcs)
+        {
+          sg.recalcConservation();
+        }
       }
     }
     oldrfs.clear();