X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationLabels.java;h=3e8166415416344c27ede87174735efa1b1376d7;hb=13f678a057d4bf84c0b7bd0dbf37c42599158d7e;hp=a884c05aa734dd2e80329dfdefd6042ac068469e;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index a884c05..3e81664 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -21,7 +21,6 @@
 package jalview.appletgui;
 
 import java.util.*;
-
 import java.awt.*;
 import java.awt.event.*;
 
@@ -412,7 +411,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
     if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
     {
 
-      PopupMenu popup = new PopupMenu(MessageManager.getString("label.annotations"));
+      PopupMenu popup = new PopupMenu(
+              MessageManager.getString("label.annotations"));
 
       MenuItem item = new MenuItem(ADDNEW);
       item.addActionListener(this);
@@ -455,7 +455,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
           {
             popup.addSeparator();
             final CheckboxMenuItem cbmi = new CheckboxMenuItem(
-                    "Ignore Gaps In Consensus",
+                    MessageManager.getString("label.ignore_gaps_consensus"),
                     (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
                             .getIgnoreGapsConsensus() : ap.av
                             .getIgnoreGapsConsensus());
@@ -480,7 +480,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
             if (aaa.groupRef != null)
             {
               final CheckboxMenuItem chist = new CheckboxMenuItem(
-                      "Show Group Histogram",
+                      MessageManager.getString("label.show_group_histogram"),
                       aa[selectedRow].groupRef.isShowConsensusHistogram());
               chist.addItemListener(new ItemListener()
               {
@@ -499,7 +499,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
               });
               popup.add(chist);
               final CheckboxMenuItem cprofl = new CheckboxMenuItem(
-                      "Show Group Logo",
+                      MessageManager.getString("label.show_group_logo"),
                       aa[selectedRow].groupRef.isShowSequenceLogo());
               cprofl.addItemListener(new ItemListener()
               {
@@ -519,7 +519,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
 
               popup.add(cprofl);
               final CheckboxMenuItem cprofn = new CheckboxMenuItem(
-                      "Normalise Group Logo",
+                      MessageManager.getString("label.normalise_group_logo"),
                       aa[selectedRow].groupRef.isNormaliseSequenceLogo());
               cprofn.addItemListener(new ItemListener()
               {
@@ -542,7 +542,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
             else
             {
               final CheckboxMenuItem chist = new CheckboxMenuItem(
-                      "Show Histogram", av.isShowConsensusHistogram());
+                      MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram());
               chist.addItemListener(new ItemListener()
               {
                 public void itemStateChanged(ItemEvent e)
@@ -564,7 +564,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
               });
               popup.add(chist);
               final CheckboxMenuItem cprof = new CheckboxMenuItem(
-                      "Show Logo", av.isShowSequenceLogo());
+                      MessageManager.getString("label.show_logo"), av.isShowSequenceLogo());
               cprof.addItemListener(new ItemListener()
               {
                 public void itemStateChanged(ItemEvent e)
@@ -587,7 +587,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
               });
               popup.add(cprof);
               final CheckboxMenuItem cprofn = new CheckboxMenuItem(
-                      "Normalise Logo", av.isNormaliseSequenceLogo());
+                      MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo());
               cprofn.addItemListener(new ItemListener()
               {
                 public void itemStateChanged(ItemEvent e)
@@ -648,17 +648,40 @@ public class AnnotationLabels extends Panel implements ActionListener,
         }
         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.paintAlignment(false);
             PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
@@ -773,7 +796,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
     {
       g.setColor(Color.black);
       g.drawString(MessageManager.getString("label.right_click"), 2, 8);
-      g.drawString(MessageManager.getString("label.to_add_annotation"), 2, 18);
+      g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
+              18);
     }
   }
 }