X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=8d747c2f02f29915c5fc1bd4e06cd51bc27e326d;hb=24efbd38f2c3dceaf6d3e305eef41ba0b0c9ebdc;hp=38c32500838c229949292ba657e45a0ca79d3de3;hpb=c3c4dc54c7f7667de14e1dc797190a8e5b5699ae;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 38c3250..8d747c2 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -3,6 +3,7 @@ package jalview.gui;
 import jalview.datamodel.*;
 import jalview.analysis.*;
 import jalview.schemes.*;
+import java.awt.*;
 import javax.swing.*;
 import java.awt.event.*;
 import jalview.io.*;
@@ -40,6 +41,7 @@ public class PopupMenu extends JPopupMenu
   Sequence sequence;
   JMenuItem unGroupMenuItem = new JMenuItem();
   JMenuItem pdbMenuItem = new JMenuItem();
+  JMenuItem outline = new JMenuItem();
 
   public PopupMenu(AlignmentPanel ap, Sequence seq)
   {
@@ -73,7 +75,7 @@ public class PopupMenu extends JPopupMenu
     catch(Exception e)
     {    e.printStackTrace();    }
 
-    SequenceGroup sg = ap.av.getRubberbandGroup();
+    SequenceGroup sg = ap.av.getSelectionGroup();
     if(sg!=null)
     {
       groupName.setText(sg.getName());
@@ -133,6 +135,7 @@ public class PopupMenu extends JPopupMenu
         groupName_actionPerformed(e);
       }
     });
+    groupAnnotation.setEnabled(false);
     groupAnnotation.setText("Annotation");
     groupAnnotation.addActionListener(new java.awt.event.ActionListener()
     {
@@ -151,6 +154,8 @@ public class PopupMenu extends JPopupMenu
       }
     });
     residueMenu.setText("Residue");
+    annotateResidue.setEnabled(false);
+    annotateResidue.setActionCommand("annotate residue");
     annotateResidue.setText("annotate residue???");
     PIDColour.setFocusPainted(false);
     unGroupMenuItem.setText("Remove Group");
@@ -169,6 +174,14 @@ public class PopupMenu extends JPopupMenu
         pdbMenuItem_actionPerformed(e);
       }
     });
+    outline.setText("Border colour");
+    outline.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        outline_actionPerformed(e);
+      }
+    });
     add(groupMenu);
     this.add(sequenceMenu);
     this.add(residueMenu);
@@ -179,6 +192,8 @@ public class PopupMenu extends JPopupMenu
     defineMenu.add(groupName);
     defineMenu.add(groupAnnotation);
     defineMenu.addSeparator();
+    defineMenu.add(outline);
+    defineMenu.addSeparator();
     defineMenu.add(noColourmenuItem);
     defineMenu.add(clustalColour);
     defineMenu.add(zappoColour);
@@ -324,7 +339,6 @@ public class PopupMenu extends JPopupMenu
     if( superG !=null)
       superG.setSuperGroupProperties( sg );
 
-    ap.seqPanel.seqCanvas.paintFlag=true;
     ap.seqPanel.repaint();
   }
 
@@ -381,7 +395,23 @@ public class PopupMenu extends JPopupMenu
 
   protected void abovePIDColour_actionPerformed(ActionEvent e)
   {
-    Desktop.setPIDSliderSource(ap, getGroup().cs, getGroup().getName());
+    if(abovePIDColour.isSelected())
+{
+
+   Desktop.setPIDSliderSource(ap, getGroup().cs, getGroup().getName());
+   refresh();
+}
+else // remove PIDColouring
+{
+    ColourSchemeI cs = getGroup().cs;
+      ResidueColourScheme rcs = (ResidueColourScheme)cs;
+      rcs.setThreshold(0);
+      getGroup().cs = rcs;
+      refresh();
+}
+
+
+
   }
 
 
@@ -486,10 +516,11 @@ public class PopupMenu extends JPopupMenu
 
   SequenceGroup getGroup()
   {
-    SequenceGroup sg = ap.av.getRubberbandGroup();
+    SequenceGroup sg = ap.av.getSelectionGroup();
 
     // this method won't add a new group if it already exists
     ap.av.alignment.addGroup(sg);
+
     return sg;
   }
 
@@ -515,9 +546,9 @@ public class PopupMenu extends JPopupMenu
 
   void unGroupMenuItem_actionPerformed(ActionEvent e)
   {
-     SequenceGroup sg = ap.av.getRubberbandGroup();
+     SequenceGroup sg = ap.av.getSelectionGroup();
      ap.av.alignment.deleteGroup(sg);
-     ap.av.setRubberbandGroup(null);
+     ap.av.setSelectionGroup(null);
      ap.RefreshPanels();
   }
 
@@ -549,4 +580,12 @@ public class PopupMenu extends JPopupMenu
     }
   }
 
+  protected void outline_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = getGroup();
+    Color col = JColorChooser.showDialog(this, "Select Outline Colour", Color.BLUE);
+    if(col!=null)
+      sg.setOutlineColour(col);
+  }
+
 }