patched Jmol and code for embedding JmolAppConsole in a JPanel (JAL-638)

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 99c7c72..4f0d0e8 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 +283,7 @@ 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;
@@ -1324,14 +1324,16 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     updateAnnotation(false);
   }
+
   public void updateAnnotation(boolean applyGlobalSettings)
   {
+    // TODO: this should be merged with other annotation update stuff - that sits on AlignViewport
     boolean updateCalcs = false;
     boolean conv = av.isShowGroupConservation();
     boolean cons = av.isShowGroupConsensus();
-    boolean showprf = av.isShowConsensusProfile();
+    boolean showprf = av.isShowSequenceLogo();
     boolean showConsHist = av.isShowConsensusHistogram();
-    
+
     boolean sortg = true;
 
     // remove old automatic annotation
@@ -1342,6 +1344,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     AlignmentAnnotation[] aan = av.alignment.getAlignmentAnnotation();
     Hashtable oldrfs = new Hashtable();
+    if (aan != null)
+    {
     for (int an = 0; an < aan.length; an++)
     {
       if (aan[an].autoCalculated && aan[an].groupRef != null)
@@ -1351,7 +1355,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
         aan[an] = null;
       }
     }
+    }
     SequenceGroup sg;
+    if (gr != null)
+    {
     for (int g = 0; g < gr.size(); g++)
     {
       updateCalcs = false;
@@ -1359,18 +1366,18 @@ public class AlignmentPanel extends GAlignmentPanel implements
       if (applyGlobalSettings || !oldrfs.containsKey(sg))
       {
         // set defaults for this group's conservation/consensus
-        sg.setIncludeAllConsSymbols(showprf);
+        sg.setshowSequenceLogo(showprf);
         sg.setShowConsensusHistogram(showConsHist);
       }
       if (conv)
       {
         updateCalcs = true;
-        av.alignment.addAnnotation(sg.getConservationRow(),0);
+        av.alignment.addAnnotation(sg.getConservationRow(), 0);
       }
       if (cons)
       {
         updateCalcs = true;
-        av.alignment.addAnnotation(sg.getConsensus(),0);
+        av.alignment.addAnnotation(sg.getConsensus(), 0);
       }
       // refresh the annotation rows
       if (updateCalcs)
@@ -1378,6 +1385,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
         sg.recalcConservation();
       }
     }
+    }
     oldrfs.clear();
     adjustAnnotationHeight();
   }