merge commit

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

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 4e25454..ad6f9e5 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -47,6 +47,7 @@ import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
 import java.awt.geom.AffineTransform;
 import java.awt.image.BufferedImage;
+import java.util.Arrays;
 import java.util.Vector;
 import java.util.regex.Pattern;
 
@@ -497,7 +498,9 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         this.setToolTipText(desc.toString());
       }
       else
+      {
         this.setToolTipText(null);
+      }
     }
 
   }
@@ -539,17 +542,40 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         }
         else if (aa[selectedRow].sequenceRef != null)
         {
-          Vector sr = new Vector();
-          sr.addElement(aa[selectedRow].sequenceRef);
           if (evt.getClickCount() == 1)
           {
-            ap.seqPanel.ap.idPanel.highlightSearchResults(sr);
+            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 = new SequenceGroup();
-            sg.addSequence(aa[selectedRow].sequenceRef, false);
+            SequenceGroup sg = ap.av.getSelectionGroup();
+            if (sg!=null)
+            {
+              // 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 {
+                if (evt.isControlDown())
+                {
+                  sg.addOrRemove(aa[selectedRow].sequenceRef, true);
+                } else {
+                  // notionally, we should also add intermediate sequences from last added sequence ?
+                  sg.addSequence(aa[selectedRow].sequenceRef, true);
+                }
+              }
+            } else {
+              sg = new SequenceGroup();
+              sg.setStartRes(0);
+              sg.setEndRes(ap.av.getAlignment().getWidth()-1);
+              sg.addSequence(aa[selectedRow].sequenceRef, false);
+            }
             ap.av.setSelectionGroup(sg);
             ap.av.sendSelection();
             ap.paintAlignment(false);
@@ -649,7 +675,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         pop.addSeparator();
         // av and sequencegroup need to implement same interface for
         final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
-                "Ignore Gaps In Consensus",
+                       MessageManager.getString("label.ignore_gaps_consensus"),
                 (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
                         .getIgnoreGapsConsensus() : ap.av
                         .getIgnoreGapsConsensus());
@@ -675,7 +701,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         if (aaa.groupRef != null)
         {
           final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
-                  "Show Group Histogram",
+                         MessageManager.getString("label.show_group_histogram"),
                   aa[selectedRow].groupRef.isShowConsensusHistogram());
           chist.addActionListener(new ActionListener()
           {
@@ -694,7 +720,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           });
           pop.add(chist);
           final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
-                  "Show Group Logo",
+                         MessageManager.getString("label.show_group_logo"),
                   aa[selectedRow].groupRef.isShowSequenceLogo());
           cprofl.addActionListener(new ActionListener()
           {
@@ -713,7 +739,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           });
           pop.add(cprofl);
           final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
-                  "Normalise Group Logo",
+                         MessageManager.getString("label.normalise_group_logo"),
                   aa[selectedRow].groupRef.isNormaliseSequenceLogo());
           cproflnorm.addActionListener(new ActionListener()
           {
@@ -738,7 +764,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         else
         {
           final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
-                  "Show Histogram", av.isShowConsensusHistogram());
+                         MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram());
           chist.addActionListener(new ActionListener()
           {
             public void actionPerformed(ActionEvent e)
@@ -757,7 +783,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           });
           pop.add(chist);
           final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
-                  "Show Logo", av.isShowSequenceLogo());
+                         MessageManager.getString("label.show_logo"), av.isShowSequenceLogo());
           cprof.addActionListener(new ActionListener()
           {
             public void actionPerformed(ActionEvent e)
@@ -776,7 +802,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           });
           pop.add(cprof);
           final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
-                  "Normalise Logo", av.isNormaliseSequenceLogo());
+                         MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo());
           cprofnorm.addActionListener(new ActionListener()
           {
             public void actionPerformed(ActionEvent e)
@@ -1005,7 +1031,9 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           offset -= fm.getDescent();
         }
         else
+        {
           offset += fm.getDescent();
+        }
 
         x = width - fm.stringWidth(aa[i].label) - 3;