Merge branch 'develop' into features/JAL-845splitPaneMergeDevelop

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

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index f732a36..91332b1 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -408,8 +408,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       Dimension d = ap.annotationScroller.getPreferredSize();
       int dif = evt.getY() - oldY;
 
-      dif /= ap.av.charHeight;
-      dif *= ap.av.charHeight;
+      dif /= ap.av.getCharHeight();
+      dif *= ap.av.getCharHeight();
 
       if ((d.height - dif) > 20)
       {
@@ -683,10 +683,10 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         pop.addSeparator();
         // av and sequencegroup need to implement same interface for
         final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
-                       MessageManager.getString("label.ignore_gaps_consensus"),
+                        MessageManager.getString("label.ignore_gaps_consensus"),
                 (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
                         .getIgnoreGapsConsensus() : ap.av
-                        .getIgnoreGapsConsensus());
+                        .isIgnoreGapsConsensus());
         final AlignmentAnnotation aaa = aa[selectedRow];
         cbmi.addActionListener(new ActionListener()
         {
@@ -709,7 +709,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         if (aaa.groupRef != null)
         {
           final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
-                         MessageManager.getString("label.show_group_histogram"),
+                          MessageManager.getString("label.show_group_histogram"),
                   aa[selectedRow].groupRef.isShowConsensusHistogram());
           chist.addActionListener(new ActionListener()
           {
@@ -728,7 +728,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           });
           pop.add(chist);
           final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
-                         MessageManager.getString("label.show_group_logo"),
+                          MessageManager.getString("label.show_group_logo"),
                   aa[selectedRow].groupRef.isShowSequenceLogo());
           cprofl.addActionListener(new ActionListener()
           {
@@ -747,7 +747,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           });
           pop.add(cprofl);
           final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
-                         MessageManager.getString("label.normalise_group_logo"),
+                          MessageManager.getString("label.normalise_group_logo"),
                   aa[selectedRow].groupRef.isNormaliseSequenceLogo());
           cproflnorm.addActionListener(new ActionListener()
           {
@@ -772,7 +772,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         else
         {
           final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
-                         MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram());
+                          MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram());
           chist.addActionListener(new ActionListener()
           {
             public void actionPerformed(ActionEvent e)
@@ -791,7 +791,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           });
           pop.add(chist);
           final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
-                         MessageManager.getString("label.show_logo"), av.isShowSequenceLogo());
+                          MessageManager.getString("label.show_logo"), av.isShowSequenceLogo());
           cprof.addActionListener(new ActionListener()
           {
             public void actionPerformed(ActionEvent e)
@@ -810,7 +810,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           });
           pop.add(cprof);
           final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
-                         MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo());
+                          MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo());
           cprofnorm.addActionListener(new ActionListener()
           {
             public void actionPerformed(ActionEvent e)
@@ -1122,7 +1122,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
               dragEvent.getY() - getScrollOffset());
     }
 
-    if (!av.wrapAlignment && ((aa == null) || (aa.length < 1)))
+    if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
     {
       g.drawString(MessageManager.getString("label.right_click"), 2, 8);
       g.drawString(MessageManager.getString("label.to_add_annotation"), 2,