JAL-1556 initial implementation - no tests as yet but ‘works’

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

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index f4c37fd..8930629 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -66,6 +66,7 @@ import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 import jalview.io.NewickFile;
+import jalview.schemes.AnnotationColourGradient;
 import jalview.util.Comparison;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -424,82 +425,131 @@ public class AnnotationLabels extends JPanel
         consclipbrd.addActionListener(this);
         pop.add(consclipbrd);
       }
+
+      addColourOrFilterByOptions(ap,aa[selectedRow],pop);
+      
       if (aa[selectedRow].graph == AlignmentAnnotation.CONTACT_MAP)
       {
-        
-        final ContactMatrixI cm = av.getContactMatrix(aa[selectedRow]);
-        if (cm != null)
+        addContactMatrixOptions(ap,aa[selectedRow],pop);
+          // Set/adjust threshold for grouping ?
+          // colour alignment by this [type]
+          // select/hide columns by this row
+          
+        }
+      }
+    
+    pop.show(this, evt.getX(), evt.getY());
+  }
+
+  static void addColourOrFilterByOptions(final AlignmentPanel ap,
+          final AlignmentAnnotation alignmentAnnotation, final JPopupMenu pop)
+  {
+    JMenuItem item;
+    item = new JMenuItem(MessageManager.getString("label.colour_by_annotation"));
+    item.addActionListener(new ActionListener()
+    {
+      
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        AnnotationColourChooser.displayFor(ap.av, ap,alignmentAnnotation,false);
+      };
+    });
+    pop.add(item);
+    if (alignmentAnnotation.sequenceRef!=null)
+    {
+      item = new JMenuItem(MessageManager.getString("label.colour_by_annotation")+" ("+MessageManager.getString("label.per_seq")+")");
+      item.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
         {
-          pop.addSeparator();
+          AnnotationColourChooser.displayFor(ap.av, ap,alignmentAnnotation,true);
+        };
+      });
+      pop.add(item);
+    }
+    item = new JMenuItem(MessageManager.getString("action.select_by_annotation"));
+    item.addActionListener(new ActionListener()
+    {
+      
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        AnnotationColumnChooser.displayFor(ap.av,ap,alignmentAnnotation);
+      };
+    });
+    pop.add(item);
+  }
+  static void addContactMatrixOptions(final AlignmentPanel ap,
+          final AlignmentAnnotation alignmentAnnotation, final JPopupMenu pop)
+  {
+    
+    final ContactMatrixI cm = ap.av.getContactMatrix(alignmentAnnotation);
+    JMenuItem item;
+    if (cm != null)
+    {
+      pop.addSeparator();
 
-          if (cm.hasGroups())
-          {
-            JCheckBoxMenuItem chitem = new JCheckBoxMenuItem("Show Groups on Matrix");
-            boolean showGroups = aa[selectedRow].isShowGroupsForContactMatrix();
-            final AlignmentAnnotation sel_row=aa[selectedRow];
-            chitem.setState(showGroups);
-            chitem.addActionListener(new ActionListener()
-            {
+      if (cm.hasGroups())
+      {
+        JCheckBoxMenuItem chitem = new JCheckBoxMenuItem("Show Groups on Matrix");
+        boolean showGroups = alignmentAnnotation.isShowGroupsForContactMatrix();
+        final AlignmentAnnotation sel_row=alignmentAnnotation;
+        chitem.setState(showGroups);
+        chitem.addActionListener(new ActionListener()
+        {
 
-              @Override
-              public void actionPerformed(ActionEvent e)
-              {
-                sel_row.setShowGroupsForContactMatrix(chitem.getState());
-                ap.getAnnotationPanel()
-                .paint(ap.getAnnotationPanel().getGraphics());
-              }
-            });
-            pop.add(chitem);
-          }
-          if (cm.hasTree())
+          @Override
+          public void actionPerformed(ActionEvent e)
           {
-            item = new JMenuItem("Show Tree for Matrix");
-            item.addActionListener(new ActionListener()
-            {
+            sel_row.setShowGroupsForContactMatrix(chitem.getState());
+            ap.getAnnotationPanel()
+            .paint(ap.getAnnotationPanel().getGraphics());
+          }
+        });
+        pop.add(chitem);
+      }
+      if (cm.hasTree())
+      {
+        item = new JMenuItem("Show Tree for Matrix");
+        item.addActionListener(new ActionListener()
+        {
 
-              @Override
-              public void actionPerformed(ActionEvent e)
-              {
+          @Override
+          public void actionPerformed(ActionEvent e)
+          {
 
-                ap.alignFrame.showContactMapTree(aa[selectedRow], cm);
+            ap.alignFrame.showContactMapTree(alignmentAnnotation, cm);
 
-              }
-            });
-            pop.add(item);
           }
-          else
+        });
+        pop.add(item);
+      }
+      else
+      {
+        item = new JMenuItem("Calculate Tree for Matrix");
+        item.addActionListener(new ActionListener()
+        {
+          // TODO - refactor to analysis background thread
+          @Override
+          public void actionPerformed(ActionEvent e)
           {
-            item = new JMenuItem("Calculate Tree for Matrix");
-            item.addActionListener(new ActionListener()
+            new Thread(new Runnable()
             {
-              // TODO - refactor to analysis background thread
               @Override
-              public void actionPerformed(ActionEvent e)
+              public void run()
               {
-                new Thread(new Runnable()
-                {
-                  @Override
-                  public void run()
-                  {
-                    AlignmentAnnotation alan = aa[selectedRow];
-                    cm.setGroupSet(GroupSet.makeGroups(cm, 5f, true));
-                    ap.alignFrame.showContactMapTree(alan, cm);
-                  }
-                }).start();
+                AlignmentAnnotation alan = alignmentAnnotation;
+                cm.setGroupSet(GroupSet.makeGroups(cm, 5f, true));
+                ap.alignFrame.showContactMapTree(alan, cm);
               }
-            });
-            pop.add(item);
-
+            }).start();
           }
-          // Show/Hide group shading on matrix view
-          // Set/adjust threshold for grouping ?
-          // colour alignment by this [type]
-          // select/hide columns by this row
-          
-        }
+        });
+        pop.add(item);
       }
     }
-    pop.show(this, evt.getX(), evt.getY());
   }
 
   /**