X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=b77fab6d0e4caae0eb9ebbaa3f1a94a3af8c57e1;hb=8a1017e676ae8a3ae7f0900a7023c4ad598a0ad5;hp=1033936fc764d54e28b81a18e4fc35e28439cbef;hpb=ab9c818540ef3e2599305de507b39caf34964b6e;p=jalview.git

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 1033936..b77fab6 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.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.
@@ -104,8 +104,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     {
     }
 
-    BufferedImage bi = new BufferedImage(temp.getHeight(this), temp
-            .getWidth(this), BufferedImage.TYPE_INT_RGB);
+    BufferedImage bi = new BufferedImage(temp.getHeight(this),
+            temp.getWidth(this), BufferedImage.TYPE_INT_RGB);
     Graphics2D g = (Graphics2D) bi.getGraphics();
     g.rotate(Math.toRadians(90));
     g.drawImage(temp, 0, -bi.getWidth(this), this);
@@ -453,7 +453,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             // todo: make the ap scroll to the selection
             ap.seqPanel.ap.idPanel.highlightSearchResults(null);
             ap.av.setSelectionGroup(// new SequenceGroup(
-                    aa[selectedRow].groupRef); // );
+            aa[selectedRow].groupRef); // );
             ap.av.sendSelection();
             ap.paintAlignment(false);
             PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
@@ -550,8 +550,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
                 "Ignore Gaps In Consensus",
                 (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
-                        .getIgnoreGapsConsensus()
-                        : ap.av.getIgnoreGapsConsensus());
+                        .getIgnoreGapsConsensus() : ap.av
+                        .getIgnoreGapsConsensus());
         final AlignmentAnnotation aaa = aa[selectedRow];
         cbmi.addActionListener(new ActionListener()
         {
@@ -574,8 +574,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         if (aaa.groupRef != null)
         {
           final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
-                  "Show Group Histogram", aa[selectedRow].groupRef
-                          .isShowConsensusHistogram());
+                  "Show Group Histogram",
+                  aa[selectedRow].groupRef.isShowConsensusHistogram());
           chist.addActionListener(new ActionListener()
           {
             public void actionPerformed(ActionEvent e)
@@ -592,10 +592,10 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             }
           });
           pop.add(chist);
-          final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
-                  "Show Group Logo", aa[selectedRow].groupRef
-                          .isShowSequenceLogo());
-          cprof.addActionListener(new ActionListener()
+          final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
+                  "Show Group Logo",
+                  aa[selectedRow].groupRef.isShowSequenceLogo());
+          cprofl.addActionListener(new ActionListener()
           {
             public void actionPerformed(ActionEvent e)
             {
@@ -605,12 +605,12 @@ public class AnnotationLabels extends JPanel implements MouseListener,
               // view
               // can be
               // updated.
-              aaa.groupRef.setIncludeAllConsSymbols(cprof.getState());
+              aaa.groupRef.setshowSequenceLogo(cprofl.getState());
               ap.repaint();
               // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
             }
           });
-          pop.add(cprof);
+          pop.add(cprofl);
         }
         else
         {
@@ -690,8 +690,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     String output = new FormatAdapter().formatSequences("Fasta", seqs,
             omitHidden);
 
-    Toolkit.getDefaultToolkit().getSystemClipboard().setContents(
-            new StringSelection(output), Desktop.instance);
+    Toolkit.getDefaultToolkit().getSystemClipboard()
+            .setContents(new StringSelection(output), Desktop.instance);
 
     Vector hiddenColumns = null;
     if (av.hasHiddenColumns)
@@ -824,8 +824,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
                 g.setColor(aa[gg].annotations[0].colour);
               }
 
-              g.drawLine(x, y - graphExtras - 3, x
-                      + fm.stringWidth(aa[gg].label), y - graphExtras - 3);
+              g.drawLine(x, y - graphExtras - 3,
+                      x + fm.stringWidth(aa[gg].label), y - graphExtras - 3);
 
               g.setColor(Color.black);
               graphExtras += fontHeight + 8;
@@ -846,9 +846,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     else if (dragEvent != null && aa != null)
     {
       g.setColor(Color.lightGray);
-      g.drawString(aa[selectedRow].label, dragEvent.getX(), dragEvent
-              .getY()
-              - scrollOffset);
+      g.drawString(aa[selectedRow].label, dragEvent.getX(),
+              dragEvent.getY() - scrollOffset);
     }
 
     if ((aa == null) || (aa.length < 1))