X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=24f478632136404c0c4a3247b42015b6fcfb9dda;hb=a7168a947828a74899fff98c5f4f59515f60432a;hp=28fe5a8567d6dfb8c1d6d63a5d2df276e6a7c64d;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 28fe5a8..24f4786 100755
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.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 2.6)
+ * 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.appletgui;
 
@@ -465,14 +464,14 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         av.setSelectionGroup(null);
       }
 
-      SequenceFeature[] features = findFeaturesAtRes(sequence, sequence
-              .findPosition(findRes(evt)));
+      SequenceFeature[] features = findFeaturesAtRes(sequence,
+              sequence.findPosition(findRes(evt)));
 
       if (features != null && features.length > 0)
       {
         SearchResults highlight = new SearchResults();
-        highlight.addResult(sequence, features[0].getBegin(), features[0]
-                .getEnd());
+        highlight.addResult(sequence, features[0].getBegin(),
+                features[0].getEnd());
         seqCanvas.highlightSearchResults(highlight);
       }
       if (features != null && features.length > 0)
@@ -581,8 +580,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
       y -= hgap;
 
-      seq = Math.min((y % cHeight) / av.getCharHeight(), av.alignment
-              .getHeight() - 1);
+      seq = Math.min((y % cHeight) / av.getCharHeight(),
+              av.alignment.getHeight() - 1);
       if (seq < 0)
       {
         seq = -1;
@@ -641,7 +640,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   {
     seqCanvas.highlightSearchResults(results);
     if (av.followHighlight)
-    { 
+    {
       ap.scrollToPosition(results);
     }
   }
@@ -735,8 +734,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
 
     // use aa to see if the mouse pointer is on a
-    SequenceFeature[] allFeatures = findFeaturesAtRes(sequence, sequence
-            .findPosition(res));
+    SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
+            sequence.findPosition(res));
 
     int index = 0;
     while (index < allFeatures.length)
@@ -837,9 +836,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
           fontSize = 1;
         }
 
-        av
-                .setFont(new Font(av.font.getName(), av.font.getStyle(),
-                        fontSize));
+        av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
         av.charWidth = oldWidth;
       }
       else
@@ -1349,8 +1346,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     // DETECT RIGHT MOUSE BUTTON IN AWT
     if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
     {
-      SequenceFeature[] allFeatures = findFeaturesAtRes(sequence, sequence
-              .findPosition(res));
+      SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
+              sequence.findPosition(res));
 
       Vector links = null;
       if (allFeatures != null)
@@ -1359,13 +1356,13 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         {
           if (allFeatures[i].links != null)
           {
-            if (links==null)
-            { 
+            if (links == null)
+            {
               links = new Vector();
             }
             for (int j = 0; j < allFeatures[i].links.size(); j++)
             {
-            links.addElement(allFeatures[i].links.elementAt(j));
+              links.addElement(allFeatures[i].links.elementAt(j));
             }
           }
         }
@@ -1421,9 +1418,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     {
       if (stretchGroup.cs instanceof ClustalxColourScheme)
       {
-        ((ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup
-                .getSequences(av.hiddenRepSequences), stretchGroup
-                .getWidth());
+        ((ClustalxColourScheme) stretchGroup.cs).resetClustalX(
+                stretchGroup.getSequences(av.hiddenRepSequences),
+                stretchGroup.getWidth());
       }
 
       if (stretchGroup.cs instanceof Blosum62ColourScheme
@@ -1436,14 +1433,14 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
       if (stretchGroup.cs.conservationApplied())
       {
-        SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup
-                .getName());
+        SliderPanel.setConservationSlider(ap, stretchGroup.cs,
+                stretchGroup.getName());
         stretchGroup.recalcConservation();
       }
       else
       {
-        SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup
-                .getName());
+        SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
+                stretchGroup.getName());
       }
     }
     changeEndRes = false;