X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=64339b381694bc914017709e915ae919dd734e64;hb=e9217775986fbca85770d7fe5b3763b6920b0c3f;hp=ef87c2fdda491c525f437144d17ea141b44e5b42;hpb=7e107cbd8d3112584c63396d33a69157f7d1c68d;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index ef87c2f..64339b3 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -84,7 +84,9 @@ public class PopupMenu
   JMenu jMenu1 = new JMenu();
   JMenu structureMenu = new JMenu();
   JMenu viewStructureMenu = new JMenu();
-  JMenu colStructureMenu = new JMenu();
+ // JMenu colStructureMenu = new JMenu();
+  JMenuItem editSequence = new JMenuItem();
+ // JMenuItem annotationMenuItem = new JMenuItem();
 
   /**
    * Creates a new PopupMenu object.
@@ -191,7 +193,7 @@ public class PopupMenu
           });
           viewStructureMenu.add(menuItem);
 
-          menuItem = new JMenuItem();
+       /*   menuItem = new JMenuItem();
           menuItem.setText(pdb.getId());
           menuItem.addActionListener(new java.awt.event.ActionListener()
           {
@@ -200,9 +202,14 @@ public class PopupMenu
               colourByStructure(pdb.getId());
             }
           });
-          colStructureMenu.add(menuItem);
+          colStructureMenu.add(menuItem);*/
         }
       }
+      else
+      {
+        structureMenu.remove(viewStructureMenu);
+       // structureMenu.remove(colStructureMenu);
+      }
 
       menuItem = new JMenuItem("Hide Sequences");
       menuItem.addActionListener(new java.awt.event.ActionListener()
@@ -565,7 +572,23 @@ public class PopupMenu
     jMenu1.setText("Group");
     structureMenu.setText("Structure");
     viewStructureMenu.setText("View Structure");
-    colStructureMenu.setText("Colour By Structure");
+  //  colStructureMenu.setText("Colour By Structure");
+    editSequence.setText("Edit Sequence...");
+    editSequence.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        editSequence_actionPerformed(actionEvent);
+      }
+    });
+   /* annotationMenuItem.setText("By Annotation");
+    annotationMenuItem.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        annotationMenuItem_actionPerformed(actionEvent);
+      }
+    });*/
 
     add(groupMenu);
 
@@ -614,8 +637,10 @@ public class PopupMenu
     colourMenu.addSeparator();
     colourMenu.add(abovePIDColour);
     colourMenu.add(conservationMenuItem);
+    //colourMenu.add(annotationMenuItem);
     editMenu.add(copy);
     editMenu.add(cut);
+    editMenu.add(editSequence);
     editMenu.add(upperCase);
     editMenu.add(lowerCase);
     editMenu.add(toggle);
@@ -631,7 +656,7 @@ public class PopupMenu
     jMenu1.add(outline);
     structureMenu.add(pdbMenu);
     structureMenu.add(viewStructureMenu);
-    structureMenu.add(colStructureMenu);
+   // structureMenu.add(colStructureMenu);
     noColourmenuItem.setText("None");
     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
     {
@@ -999,6 +1024,23 @@ public class PopupMenu
     refresh();
   }
 
+  public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
+  {
+    SequenceGroup sg = getGroup();
+    if (sg == null)
+    {
+      return;
+    }
+
+    AnnotationColourGradient acg = new AnnotationColourGradient(
+        sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD);
+
+    acg.predefinedColours = true;
+    sg.cs = acg;
+
+    refresh();
+  }
+
   /**
    * DOCUMENT ME!
    *
@@ -1403,4 +1445,41 @@ public class PopupMenu
     sequence.addAlignmentAnnotation(an);
 
     }
+
+  public void editSequence_actionPerformed(ActionEvent actionEvent)
+  {
+      SequenceGroup sg = ap.av.getSelectionGroup();
+
+      if(sg!=null)
+      {
+        if (sequence == null)
+          sequence = (Sequence) sg.getSequenceAt(0);
+
+        EditNameDialog dialog = new EditNameDialog(
+            sequence.getSequenceAsString(
+                sg.getStartRes(),
+                sg.getEndRes() + 1),
+            null,
+            "Edit Sequence ",
+            null,
+            "Edit Sequence");
+
+        if (dialog.accept)
+        {
+          EditCommand editCommand = new EditCommand(
+              "Edit Sequences", EditCommand.REPLACE,
+              dialog.getName(),
+              sg.getSequencesAsArray(ap.av.hiddenRepSequences),
+              sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment
+              );
+
+          ap.alignFrame.addHistoryItem(editCommand);
+
+          ap.av.firePropertyChange("alignment", null,
+                                   ap.av.getAlignment().getSequences());
+        }
+      }
+  }
+
+
 }