X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationLabels.java;h=b6b2b0d38834ded84b4ae715f037c744480a5a39;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=67faf1109487b9ce45576da9fac5b00a0277fe20;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 67faf11..b6b2b0d 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,6 +20,14 @@
  */
 package jalview.appletgui;
 
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+import jalview.util.ParseHtmlBodyAndLinks;
+
 import java.awt.Checkbox;
 import java.awt.CheckboxMenuItem;
 import java.awt.Color;
@@ -44,14 +52,6 @@ import java.util.Arrays;
 import java.util.Collections;
 import java.util.Vector;
 
-import jalview.analysis.AlignmentUtils;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.util.MessageManager;
-import jalview.util.ParseHtmlBodyAndLinks;
-
 public class AnnotationLabels extends Panel implements ActionListener,
         MouseListener, MouseMotionListener
 {
@@ -540,7 +540,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
             if (aaa.groupRef != null)
             {
               final CheckboxMenuItem chist = new CheckboxMenuItem(
-                      MessageManager.getString("label.show_group_histogram"),
+                      MessageManager
+                              .getString("label.show_group_histogram"),
                       aa[selectedRow].groupRef.isShowConsensusHistogram());
               chist.addItemListener(new ItemListener()
               {
@@ -579,7 +580,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
 
               popup.add(cprofl);
               final CheckboxMenuItem cprofn = new CheckboxMenuItem(
-                      MessageManager.getString("label.normalise_group_logo"),
+                      MessageManager
+                              .getString("label.normalise_group_logo"),
                       aa[selectedRow].groupRef.isNormaliseSequenceLogo());
               cprofn.addItemListener(new ItemListener()
               {
@@ -602,7 +604,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
             else
             {
               final CheckboxMenuItem chist = new CheckboxMenuItem(
-                      MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram());
+                      MessageManager.getString("label.show_histogram"),
+                      av.isShowConsensusHistogram());
               chist.addItemListener(new ItemListener()
               {
                 public void itemStateChanged(ItemEvent e)
@@ -624,7 +627,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
               });
               popup.add(chist);
               final CheckboxMenuItem cprof = new CheckboxMenuItem(
-                      MessageManager.getString("label.show_logo"), av.isShowSequenceLogo());
+                      MessageManager.getString("label.show_logo"),
+                      av.isShowSequenceLogo());
               cprof.addItemListener(new ItemListener()
               {
                 public void itemStateChanged(ItemEvent e)
@@ -647,7 +651,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
               });
               popup.add(cprof);
               final CheckboxMenuItem cprofn = new CheckboxMenuItem(
-                      MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo());
+                      MessageManager.getString("label.normalise_logo"),
+                      av.isNormaliseSequenceLogo());
               cprofn.addItemListener(new ItemListener()
               {
                 public void itemStateChanged(ItemEvent e)
@@ -710,36 +715,44 @@ public class AnnotationLabels extends Panel implements ActionListener,
         {
           if (evt.getClickCount() == 1)
           {
-            ap.seqPanel.ap.idPanel.highlightSearchResults(Arrays
-                    .asList(new SequenceI[]
-                    { aa[selectedRow].sequenceRef }));
+            ap.seqPanel.ap.idPanel
+                    .highlightSearchResults(Arrays
+                            .asList(new SequenceI[] { aa[selectedRow].sequenceRef }));
           }
           else if (evt.getClickCount() >= 2)
           {
             ap.seqPanel.ap.idPanel.highlightSearchResults(null);
             SequenceGroup sg = ap.av.getSelectionGroup();
-            if (sg!=null)
+            if (sg != null)
             {
-              // we make a copy rather than edit the current selection if no modifiers pressed
+              // we make a copy rather than edit the current selection if no
+              // modifiers pressed
               // see Enhancement JAL-1557
               if (!(evt.isControlDown() || evt.isShiftDown()))
               {
                 sg = new SequenceGroup(sg);
                 sg.clear();
                 sg.addSequence(aa[selectedRow].sequenceRef, false);
-              } else {
+              }
+              else
+              {
                 if (evt.isControlDown())
                 {
                   sg.addOrRemove(aa[selectedRow].sequenceRef, true);
-                } else {
-                  // notionally, we should also add intermediate sequences from last added sequence ?
+                }
+                else
+                {
+                  // notionally, we should also add intermediate sequences from
+                  // last added sequence ?
                   sg.addSequence(aa[selectedRow].sequenceRef, true);
                 }
               }
-            } else {
+            }
+            else
+            {
               sg = new SequenceGroup();
               sg.setStartRes(0);
-              sg.setEndRes(ap.av.getAlignment().getWidth()-1);
+              sg.setEndRes(ap.av.getAlignment().getWidth() - 1);
               sg.addSequence(aa[selectedRow].sequenceRef, false);
             }
             ap.av.setSelectionGroup(sg);
@@ -776,8 +789,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
       for (int[] region : av.getColumnSelection().getHiddenColumns())
       {
         jalview.appletgui.AlignFrame.copiedHiddenColumns
-                .addElement(new int[]
-                { region[0], region[1] });
+                .addElement(new int[] { region[0], region[1] });
       }
     }
   }