X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FUserDefinedColours.java;h=556ae41e13ed043f96f34bd7f1f80608764357f5;hb=e25f63a72efddff9e071abdeff0ae5599431e4f8;hp=79df106d8c7eb51c381b643641203fb6b29f8448;hpb=a67402c4b5b2bc1c97d2624af72c941dec51ea40;p=jalview.git

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 79df106..556ae41 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -52,6 +52,7 @@ public class UserDefinedColours extends GUserDefinedColours
     Vector selectedButtons;
     ColourSchemeI oldColourScheme;
     JInternalFrame frame;
+    MCview.PDBCanvas pdbcanvas;
 
     /**
      * Creates a new UserDefinedColours object.
@@ -106,6 +107,40 @@ public class UserDefinedColours extends GUserDefinedColours
         makeButton("Gap", "-");
     }
 
+    public UserDefinedColours(MCview.PDBCanvas pdb, ColourSchemeI oldcs)
+    {
+        super();
+        frame = new JInternalFrame();
+        frame.setContentPane(this);
+        Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true);
+        pdbcanvas = pdb;
+
+        if (System.getProperty("os.name").startsWith("Mac"))
+        {
+            frame.setSize(760, 370);
+        }
+
+        colorChooser.getSelectionModel().addChangeListener(this);
+
+        oldColourScheme = oldcs;
+
+        if (oldColourScheme instanceof UserColourScheme)
+        {
+              schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());
+        }
+        for (int i = 0; i < 20; i++)
+        {
+            makeButton(ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i]) +
+                "", ResidueProperties.aa[i]);
+        }
+
+        makeButton("B", "B");
+        makeButton("Z", "Z");
+        makeButton("X", "X");
+        makeButton("Gap", "-");
+    }
+
+
     /**
      * DOCUMENT ME!
      *
@@ -139,8 +174,12 @@ public class UserDefinedColours extends GUserDefinedColours
 
       if(e.isShiftDown())
       {
-        JButton start = (JButton)selectedButtons.elementAt(selectedButtons.size()-1);
-        JButton end = (JButton) e.getSource();
+        JButton start, end = (JButton) e.getSource();
+        if(selectedButtons.size()>0)
+          start = (JButton)selectedButtons.elementAt(selectedButtons.size()-1);
+        else
+          start = (JButton) e.getSource();
+
         int startIndex=0, endIndex=0;
         for(int b=0; b<buttonPanel.getComponentCount(); b++)
         {
@@ -265,10 +304,15 @@ public class UserDefinedColours extends GUserDefinedColours
             seqGroup.cs = ucs;
             ap.repaint();
         }
-        else
+        else if(ap!=null)
         {
             ap.alignFrame.changeColour(ucs);
         }
+        else if(pdbcanvas!=null)
+        {
+          pdbcanvas.pdb.setColours(ucs);
+          pdbcanvas.updateSeqColours();
+        }
     }
 
     UserColourScheme getSchemeFromGUI()
@@ -282,7 +326,9 @@ public class UserDefinedColours extends GUserDefinedColours
       }
 
       UserColourScheme ucs = new UserColourScheme(newColours);
-      ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+      if(ap!=null)
+        ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+
 
       return ucs;
     }
@@ -490,16 +536,23 @@ public class UserDefinedColours extends GUserDefinedColours
      */
     protected void cancelButton_actionPerformed(ActionEvent e)
     {
+      if (ap != null)
+      {
         if (seqGroup != null)
         {
-            seqGroup.cs = oldColourScheme;
+          seqGroup.cs = oldColourScheme;
         }
-        else
+        else if (ap != null)
         {
-            ap.av.setGlobalColourScheme(oldColourScheme);
+          ap.av.setGlobalColourScheme(oldColourScheme);
         }
-
         ap.repaint();
+      }
+
+      if(pdbcanvas!=null)
+      {
+        pdbcanvas.pdb.setColours(oldColourScheme);
+      }
 
         try
         {