JAL-3063 Save/Load user defined colours using JAXB

[jalview.git] / src / jalview / schemes / ColourSchemeLoader.java

diff --git a/src/jalview/schemes/ColourSchemeLoader.java b/src/jalview/schemes/ColourSchemeLoader.java
index 9f08688..481f809 100644 (file)
--- a/src/jalview/schemes/ColourSchemeLoader.java
+++ b/src/jalview/schemes/ColourSchemeLoader.java
@@ -20,14 +20,17 @@
  */
 package jalview.schemes;
 
-import jalview.binding.JalviewUserColours;
+import jalview.xml.binding.jalview.JalviewUserColours;
 
 import java.awt.Color;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.InputStreamReader;
 
-import org.exolab.castor.xml.Unmarshaller;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamReader;
 
 public class ColourSchemeLoader
 {
@@ -51,12 +54,14 @@ public class ColourSchemeLoader
       InputStreamReader in = new InputStreamReader(
               new FileInputStream(file), "UTF-8");
 
-      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);
+      JAXBContext jc = JAXBContext
+              .newInstance("jalview.xml.binding.jalview");
+      javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
+      XMLStreamReader streamReader = XMLInputFactory.newInstance()
+              .createXMLStreamReader(in);
+      JAXBElement<JalviewUserColours> jbe = um.unmarshal(streamReader,
+              JalviewUserColours.class);
+      JalviewUserColours jucs = jbe.getValue();
 
       /*
        * non-case-sensitive colours are for 20 amino acid codes,
@@ -69,9 +74,9 @@ public class ColourSchemeLoader
 
       String name;
       int index;
-      for (int i = 0; i < jucs.getColourCount(); i++)
+      for (int i = 0; i < jucs.getColour().size(); i++)
       {
-        name = jucs.getColour(i).getName();
+        name = jucs.getColour().get(i).getName();
         if (ResidueProperties.aa3Hash.containsKey(name))
         {
           index = ResidueProperties.aa3Hash.get(name).intValue();
@@ -86,7 +91,7 @@ public class ColourSchemeLoader
         }
 
         Color color = new Color(
-                Integer.parseInt(jucs.getColour(i).getRGB(), 16));
+                Integer.parseInt(jucs.getColour().get(i).getRGB(), 16));
         if (name.toLowerCase().equals(name))
         {
           caseSensitive = true;
@@ -117,7 +122,7 @@ public class ColourSchemeLoader
 
         jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
 
-        jucs = JalviewUserColours.unmarshal(in);
+        jucs = jalview.binding.JalviewUserColours.unmarshal(in);
 
         newColours = new Color[jucs.getColourCount()];