X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FUserDefinedColours.java;h=ede020c6101fd71d3c79968e9024763c3adb4123;hb=e02486484d33e20dedb020a34f31f6024d5720a2;hp=ec4ad5526196ea40068f3f33e2ae59039709102b;hpb=5ad6d650b6726eb880d8342d19711e626f6ae2f0;p=jalview.git

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index ec4ad55..ede020c 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!
      *
@@ -140,7 +175,7 @@ public class UserDefinedColours extends GUserDefinedColours
       if(e.isShiftDown())
       {
         JButton start, end = (JButton) e.getSource();
-        if(selectedButtons.size()>1)
+        if(selectedButtons.size()>0)
           start = (JButton)selectedButtons.elementAt(selectedButtons.size()-1);
         else
           start = (JButton) e.getSource();
@@ -269,10 +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()
@@ -286,7 +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;
     }
@@ -381,10 +423,14 @@ public class UserDefinedColours extends GUserDefinedColours
             InputStreamReader in = new InputStreamReader(new FileInputStream(
                         file), "UTF-8");
 
-            jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
-            jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
+              jalview.schemabinding.version2.JalviewUserColours jucs
+                  = new jalview.schemabinding.version2.JalviewUserColours();
+
+              org.exolab.castor.xml.Unmarshaller unmar
+                  = new org.exolab.castor.xml.Unmarshaller(jucs);
+              jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar.unmarshal( in );
 
-            newColours = new Color[jucs.getColourCount()];
+              newColours = new Color[jucs.getColourCount()];
 
             for (int i = 0; i < 24; i++)
             {
@@ -400,9 +446,34 @@ public class UserDefinedColours extends GUserDefinedColours
         }
         catch (Exception ex)
         {
-            System.out.println("Error loading User ColourFile\n"+ex);
-        }
+            //Could be Archive Jalview format
+            try{
+              InputStreamReader in = new InputStreamReader(new FileInputStream(
+                  file), "UTF-8");
 
+              jalview.binding.JalviewUserColours jucs
+                  = new jalview.binding.JalviewUserColours();
+
+              jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
+
+              newColours = new Color[jucs.getColourCount()];
+
+              for (int i = 0; i < 24; i++)
+              {
+                newColours[i] = new Color(Integer.parseInt(
+                    jucs.getColour(i).getRGB(), 16));
+              }
+              if (newColours != null)
+              {
+                ucs = new UserColourScheme(newColours);
+                ucs.setName(jucs.getSchemeName());
+              }
+            }catch(Exception ex2)
+            { ex2.printStackTrace(); }
+
+            if(newColours==null)
+              System.out.println("Error loading User ColourFile\n"+ex);
+        }
 
        return ucs;
     }
@@ -494,16 +565,23 @@ 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
         {