X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=61b9c31a3d3643f1094395f49a09cf2f3f2f4d4c;hb=2763845dada91cdfe266200cf852146c70392ad7;hp=0e766c4df8faf4676b9cb32f69edd84befdf89ef;hpb=330cd6b44c7c4c84c81dca69e8c8050118fb1bdd;p=jalview.git

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 0e766c4..61b9c31 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -38,6 +38,8 @@ import jalview.io.*;
 public class AnnotationLabels extends JPanel implements MouseListener,
         MouseMotionListener, ActionListener
 {
+  static String TOGGLE_LABELSCALE = "Scale Label to Column";
+
   static String ADDNEW = "Add New Row";
 
   static String EDITNAME = "Edit Label/Description";
@@ -227,6 +229,10 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       }
 
     }
+    else if (evt.getActionCommand().equals(TOGGLE_LABELSCALE))
+    {
+      aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel; 
+    }
 
     ap.annotationPanel.adjustPanelHeight();
     ap.annotationScroller.validate();
@@ -419,12 +425,50 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    */
   public void mouseClicked(MouseEvent evt)
   {
+    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+    if (SwingUtilities.isLeftMouseButton(evt))
+    {
+      if (selectedRow < aa.length)
+        {
+        if (aa[selectedRow].groupRef!=null)
+        {
+          if (evt.getClickCount()>=2)
+          {
+            // todo: make the ap scroll to the selection
+            ap.seqPanel.ap.idPanel.highlightSearchResults(null);
+            ap.av.setSelectionGroup(//new SequenceGroup(
+                    aa[selectedRow].groupRef); // );
+            ap.paintAlignment(false);
+          } else {
+            ap.seqPanel.ap.idPanel.highlightSearchResults(aa[selectedRow].groupRef.getSequences(null));
+          }
+          return;
+        } 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);
+          } else
+            if (evt.getClickCount()>=2)
+          {
+              ap.seqPanel.ap.idPanel.highlightSearchResults(null);
+              SequenceGroup sg = new SequenceGroup();
+            sg.addSequence(aa[selectedRow].sequenceRef,false);
+            ap.av.setSelectionGroup(sg);
+            ap.paintAlignment(false);
+            PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+          }
+          
+        }
+      }
+    }
     if (!SwingUtilities.isRightMouseButton(evt))
     {
       return;
     }
 
-    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
 
     JPopupMenu pop = new JPopupMenu("Annotations");
     JMenuItem item = new JMenuItem(ADDNEW);
@@ -456,30 +500,131 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     item.addActionListener(this);
     pop.add(item);
     // TODO: annotation object should be typed for autocalculated/derived property methods
-    if (selectedRow < aa.length && aa[selectedRow].autoCalculated && aa[selectedRow].label.indexOf("Consensus")>-1)
-    {
-      pop.addSeparator();
-      // av and sequencegroup need to implement same interface for 
-      final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
-              "Ignore Gaps In Consensus", ap.av.getIgnoreGapsConsensus());
-      final AlignmentAnnotation aaa = aa[selectedRow];
-      cbmi.addActionListener(new ActionListener()
+    if (selectedRow < aa.length)
+    {
+      if (!aa[selectedRow].autoCalculated) {
+        if (aa[selectedRow].graph==AlignmentAnnotation.NO_GRAPH)
+        {
+          // display formatting settings for this row.
+          pop.addSeparator();
+          // av and sequencegroup need to implement same interface for
+          item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE,
+                aa[selectedRow].scaleColLabel);
+          item.addActionListener(this);
+          pop.add(item);
+        }
+      }
+      else if (aa[selectedRow].label.indexOf("Consensus") > -1)
       {
-        public void actionPerformed(ActionEvent e)
+        pop.addSeparator();
+        // av and sequencegroup need to implement same interface for
+        final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+                "Ignore Gaps In Consensus",
+                (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
+                        .getIgnoreGapsConsensus()
+                        : ap.av.getIgnoreGapsConsensus());
+        final AlignmentAnnotation aaa = aa[selectedRow];
+        cbmi.addActionListener(new ActionListener()
         {
-          if (aaa.groupRef!=null)
+          public void actionPerformed(ActionEvent e)
           {
-            aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
+            if (aaa.groupRef != null)
+            {
+           // TODO: pass on reference to ap so the view can be updated.
+              aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState()); 
+              ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+            }
+            else
+            {
+              ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
+            }
           }
-          ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
+        });
+        pop.add(cbmi);
+        // av and sequencegroup need to implement same interface for
+        if (aaa.groupRef != null)
+        {
+          final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+                  "Show Group Histogram", aa[selectedRow].groupRef
+                          .isShowConsensusHistogram());
+          chist.addActionListener(new ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              // TODO: pass on reference
+              // to ap
+              // so the
+              // view
+              // can be
+              // updated.
+              aaa.groupRef.setShowConsensusHistogram(chist.getState());
+              ap.repaint();
+              // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+            }
+          });
+          pop.add(chist);
+          final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
+                  "Show Group Logo", aa[selectedRow].groupRef
+                          .isIncludeAllConsSymbols());
+          cprof.addActionListener(new ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              // TODO: pass on reference
+              // to ap
+              // so the
+              // view
+              // can be
+              // updated.
+              aaa.groupRef.setIncludeAllConsSymbols(cprof.getState());
+              ap.repaint();
+              // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+            }
+          });
+          pop.add(cprof);
+        } else {
+          final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+                  "Show Histogram", av.isShowConsensusHistogram());
+          chist.addActionListener(new ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              // TODO: pass on reference
+              // to ap
+              // so the
+              // view
+              // can be
+              // updated.
+              av.setShowConsensusHistogram(chist.getState());
+              ap.repaint();
+              // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+            }
+          });
+          pop.add(chist);
+          final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
+                  "Show Logo", av.isShowConsensusProfile());
+          cprof.addActionListener(new ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              // TODO: pass on reference
+              // to ap
+              // so the
+              // view
+              // can be
+              // updated.
+              av.setShowConsensusProfile(cprof.getState());
+              ap.repaint();
+              // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+            }
+          });
+          pop.add(cprof);   
         }
-      });
-      pop.add(cbmi);
-      final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
-      consclipbrd.addActionListener(this);
-      pop.add(consclipbrd);
+        final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
+        consclipbrd.addActionListener(this);
+        pop.add(consclipbrd);
+      }
     }
-
     pop.show(this, evt.getX(), evt.getY());
   }