X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FUserDefinedColours.java;h=556ae41e13ed043f96f34bd7f1f80608764357f5;hb=be545261cf6e7225da6f3ac1306b1b2609fd0e70;hp=c61db4b42f083bc6e53195f23d83b91f89840f26;hpb=7f7023facc92f28f77bc7b5b2bbd1d04c27ade28;p=jalview.git

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index c61db4b..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.
@@ -68,7 +69,7 @@ public class UserDefinedColours extends GUserDefinedColours
 
         if (System.getProperty("os.name").startsWith("Mac"))
         {
-            frame.setSize(450, 560);
+            frame.setSize(760, 370);
         }
 
         if (sg != null)
@@ -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;
     }
@@ -336,23 +382,28 @@ public class UserDefinedColours extends GUserDefinedColours
      */
     public static UserColourScheme loadDefaultColours()
     {
+        UserColourScheme ret = null;
+
         String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");
-        if ( colours != null)
+        if ( colours != null )
         {
           if(colours.indexOf("|")>-1)
             colours = colours.substring(0, colours.indexOf("|"));
 
-            return loadColours(colours);
+          ret = loadColours(colours);
         }
-        else
+
+        if(ret == null)
         {
           Color[] newColours = new Color[24];
           for (int i = 0; i < 24; i++)
           {
             newColours[i] = Color.white;
           }
-          return new UserColourScheme(newColours);
+          ret =  new UserColourScheme(newColours);
         }
+
+        return ret;
     }
 
     /**
@@ -362,7 +413,7 @@ public class UserDefinedColours extends GUserDefinedColours
      *
      * @return DOCUMENT ME!
      */
-    public static UserColourScheme loadColours(String file)
+    static UserColourScheme loadColours(String file)
     {
          UserColourScheme ucs = null;
          Color[]  newColours = null;
@@ -440,7 +491,7 @@ public class UserDefinedColours extends GUserDefinedColours
             String defaultColours = jalview.bin.Cache.getDefault("USER_DEFINED_COLOURS", choice);
             if(defaultColours.indexOf(choice)==-1)
             {
-              if(defaultColours.length()<1)
+              if(defaultColours.length()>0)
                 defaultColours = defaultColours.concat("|");
               defaultColours = defaultColours.concat(choice);
             }
@@ -485,16 +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
         {
@@ -517,9 +575,10 @@ public class UserDefinedColours extends GUserDefinedColours
     {
       userColourSchemes = new Hashtable();
 
-      if(files==null)
+      if(files==null || files.length()==0)
         return;
 
+
       // In case colours can't be loaded, we'll remove them
       // from the default list here.
       StringBuffer coloursFound = new StringBuffer();
@@ -545,7 +604,50 @@ public class UserDefinedColours extends GUserDefinedColours
       }
       if (!files.equals(coloursFound.toString()))
       {
-        jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", coloursFound.toString());
+        if (coloursFound.toString().length() > 1)
+          jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
+                                        coloursFound.toString());
+        else
+          jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");
+      }
+    }
+
+    public static void removeColourFromDefaults(String target)
+    {
+      // The only way to find colours by name is to load them in
+      // In case colours can't be loaded, we'll remove them
+      // from the default list here.
+
+      userColourSchemes = new Hashtable();
+
+      StringBuffer coloursFound = new StringBuffer();
+      StringTokenizer st = new StringTokenizer(
+           jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");
+
+      while (st.hasMoreElements())
+      {
+        String file = st.nextToken();
+        try
+        {
+          UserColourScheme ucs = loadColours(file);
+          if (ucs != null && !ucs.getName().equals(target))
+          {
+            if (coloursFound.length() > 0)
+              coloursFound.append("|");
+            coloursFound.append(file);
+            userColourSchemes.put(ucs.getName(), ucs);
+          }
+        }
+        catch (Exception ex)
+        {
+          System.out.println("Error loading User ColourFile\n" + ex);
+        }
       }
+
+      if (coloursFound.toString().length() > 1)
+        jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", coloursFound.toString());
+      else
+        jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");
+
     }
 }