spelling err

[jalview.git] / src / jalview / gui / UserDefinedColours.java

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index ec4ad55..ede020c 100755 (executable)
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -52,6 +52,7 @@ public class UserDefinedColours extends GUserDefinedColours
     Vector selectedButtons;\r
     ColourSchemeI oldColourScheme;\r
     JInternalFrame frame;\r
+    MCview.PDBCanvas pdbcanvas;\r
 \r
     /**\r
      * Creates a new UserDefinedColours object.\r
@@ -106,6 +107,40 @@ public class UserDefinedColours extends GUserDefinedColours
         makeButton("Gap", "-");\r
     }\r
 \r
+    public UserDefinedColours(MCview.PDBCanvas pdb, ColourSchemeI oldcs)\r
+    {\r
+        super();\r
+        frame = new JInternalFrame();\r
+        frame.setContentPane(this);\r
+        Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true);\r
+        pdbcanvas = pdb;\r
+\r
+        if (System.getProperty("os.name").startsWith("Mac"))\r
+        {\r
+            frame.setSize(760, 370);\r
+        }\r
+\r
+        colorChooser.getSelectionModel().addChangeListener(this);\r
+\r
+        oldColourScheme = oldcs;\r
+\r
+        if (oldColourScheme instanceof UserColourScheme)\r
+        {\r
+              schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());\r
+        }\r
+        for (int i = 0; i < 20; i++)\r
+        {\r
+            makeButton(ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i]) +\r
+                "", ResidueProperties.aa[i]);\r
+        }\r
+\r
+        makeButton("B", "B");\r
+        makeButton("Z", "Z");\r
+        makeButton("X", "X");\r
+        makeButton("Gap", "-");\r
+    }\r
+\r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -140,7 +175,7 @@ public class UserDefinedColours extends GUserDefinedColours
       if(e.isShiftDown())\r
       {\r
         JButton start, end = (JButton) e.getSource();\r
-        if(selectedButtons.size()>1)\r
+        if(selectedButtons.size()>0)\r
           start = (JButton)selectedButtons.elementAt(selectedButtons.size()-1);\r
         else\r
           start = (JButton) e.getSource();\r
@@ -269,10 +304,15 @@ public class UserDefinedColours extends GUserDefinedColours
             seqGroup.cs = ucs;\r
             ap.repaint();\r
         }\r
-        else\r
+        else if(ap!=null)\r
         {\r
             ap.alignFrame.changeColour(ucs);\r
         }\r
+        else if(pdbcanvas!=null)\r
+        {\r
+          pdbcanvas.pdb.setColours(ucs);\r
+          pdbcanvas.updateSeqColours();\r
+        }\r
     }\r
 \r
     UserColourScheme getSchemeFromGUI()\r
@@ -286,7 +326,9 @@ public class UserDefinedColours extends GUserDefinedColours
       }\r
 \r
       UserColourScheme ucs = new UserColourScheme(newColours);\r
-      ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
+      if(ap!=null)\r
+        ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
+\r
 \r
       return ucs;\r
     }\r
@@ -381,10 +423,14 @@ public class UserDefinedColours extends GUserDefinedColours
             InputStreamReader in = new InputStreamReader(new FileInputStream(\r
                         file), "UTF-8");\r
 \r
-            jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();\r
-            jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);\r
+              jalview.schemabinding.version2.JalviewUserColours jucs\r
+                  = new jalview.schemabinding.version2.JalviewUserColours();\r
+\r
+              org.exolab.castor.xml.Unmarshaller unmar\r
+                  = new org.exolab.castor.xml.Unmarshaller(jucs);\r
+              jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar.unmarshal( in );\r
 \r
-            newColours = new Color[jucs.getColourCount()];\r
+              newColours = new Color[jucs.getColourCount()];\r
 \r
             for (int i = 0; i < 24; i++)\r
             {\r
@@ -400,9 +446,34 @@ public class UserDefinedColours extends GUserDefinedColours
         }\r
         catch (Exception ex)\r
         {\r
-            System.out.println("Error loading User ColourFile\n"+ex);\r
-        }\r
+            //Could be Archive Jalview format\r
+            try{\r
+              InputStreamReader in = new InputStreamReader(new FileInputStream(\r
+                  file), "UTF-8");\r
 \r
+              jalview.binding.JalviewUserColours jucs\r
+                  = new jalview.binding.JalviewUserColours();\r
+\r
+              jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);\r
+\r
+              newColours = new Color[jucs.getColourCount()];\r
+\r
+              for (int i = 0; i < 24; i++)\r
+              {\r
+                newColours[i] = new Color(Integer.parseInt(\r
+                    jucs.getColour(i).getRGB(), 16));\r
+              }\r
+              if (newColours != null)\r
+              {\r
+                ucs = new UserColourScheme(newColours);\r
+                ucs.setName(jucs.getSchemeName());\r
+              }\r
+            }catch(Exception ex2)\r
+            { ex2.printStackTrace(); }\r
+\r
+            if(newColours==null)\r
+              System.out.println("Error loading User ColourFile\n"+ex);\r
+        }\r
 \r
        return ucs;\r
     }\r
@@ -494,16 +565,23 @@ public class UserDefinedColours extends GUserDefinedColours
      */\r
     protected void cancelButton_actionPerformed(ActionEvent e)\r
     {\r
+      if (ap != null)\r
+      {\r
         if (seqGroup != null)\r
         {\r
-            seqGroup.cs = oldColourScheme;\r
+          seqGroup.cs = oldColourScheme;\r
         }\r
-        else\r
+        else if (ap != null)\r
         {\r
-            ap.av.setGlobalColourScheme(oldColourScheme);\r
+          ap.av.setGlobalColourScheme(oldColourScheme);\r
         }\r
-\r
         ap.repaint();\r
+      }\r
+\r
+      if(pdbcanvas!=null)\r
+      {\r
+        pdbcanvas.pdb.setColours(oldColourScheme);\r
+      }\r
 \r
         try\r
         {\r