X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=efefeafbada38512aa86f69d4377d8d6675873eb;hb=cce8dd5b2737f394593b3a418c7bb1836cf55c57;hp=4f0d0e88f4203ebcc08484172cbb30605ceb3141;hpb=6b544d4a85673db44b7f75f40c22d9b7425d444e;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 4f0d0e8..efefeaf 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -179,8 +179,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     AlignmentI al = av.getAlignment();
     int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
-    int maxwidth = Math.max(20, Math.min(afwidth - 200, (int) 2 * afwidth
-            / 3));
+    int maxwidth = Math.max(20,
+            Math.min(afwidth - 200, (int) 2 * afwidth / 3));
     int i = 0;
     int idWidth = 0;
     String id;
@@ -283,7 +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
+      // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); //
+      // DEBUG
       if (start < 0)
       {
         return false;
@@ -577,9 +578,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       int x = hscroll.getValue();
       av.setStartRes(x);
-      av
-              .setEndRes((x + (seqPanel.seqCanvas.getWidth() / av
-                      .getCharWidth())) - 1);
+      av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
     }
 
     if (evt.getSource() == vscroll)
@@ -859,8 +858,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
 
       pg.setColor(currentColor);
-      pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth, av
-              .getCharHeight());
+      pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
+              av.getCharHeight());
 
       pg.setColor(currentTextColor);
 
@@ -873,7 +872,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
                 - 4;
       }
 
-      pg.drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos,
+      pg.drawString(
+              seq.getDisplayId(av.getShowJVSuffix()),
+              xPos,
               (((i - startSeq) * av.charHeight) + av.getCharHeight())
                       - (av.getCharHeight() / 5));
     }
@@ -1327,7 +1328,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   public void updateAnnotation(boolean applyGlobalSettings)
   {
-    // TODO: this should be merged with other annotation update stuff - that sits on AlignViewport
+    // 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();
@@ -1346,46 +1348,46 @@ public class AlignmentPanel extends GAlignmentPanel implements
     Hashtable oldrfs = new Hashtable();
     if (aan != null)
     {
-    for (int an = 0; an < aan.length; an++)
-    {
-      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;
     if (gr != null)
     {
-    for (int g = 0; g < gr.size(); g++)
-    {
-      updateCalcs = false;
-      sg = (SequenceGroup) gr.elementAt(g);
-      if (applyGlobalSettings || !oldrfs.containsKey(sg))
-      {
-        // set defaults for this group's conservation/consensus
-        sg.setshowSequenceLogo(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)
+      for (int g = 0; g < gr.size(); g++)
       {
-        sg.recalcConservation();
+        updateCalcs = false;
+        sg = (SequenceGroup) gr.elementAt(g);
+        if (applyGlobalSettings || !oldrfs.containsKey(sg))
+        {
+          // set defaults for this group's conservation/consensus
+          sg.setshowSequenceLogo(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();
     adjustAnnotationHeight();
   }