From 9cd96dd3e43ae32814fa8c62df274ff9224bfdbc Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 18 Sep 2018 17:43:03 +0100
Subject: [PATCH] JAL-3063 Save/Load user defined colours using JAXB

---
 src/jalview/gui/UserDefinedColours.java     |   16 +++++++++++----
 src/jalview/schemes/ColourSchemeLoader.java |   29 ++++++++++++++++-----------
 2 files changed, 29 insertions(+), 16 deletions(-)

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 3290500..b1f6d1b 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -24,8 +24,6 @@ import jalview.bin.Cache;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.jbgui.GUserDefinedColours;
-import jalview.schemabinding.version2.Colour;
-import jalview.schemabinding.version2.JalviewUserColours;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeLoader;
 import jalview.schemes.ColourSchemes;
@@ -34,6 +32,9 @@ import jalview.schemes.UserColourScheme;
 import jalview.util.ColorUtils;
 import jalview.util.Format;
 import jalview.util.MessageManager;
+import jalview.xml.binding.jalview.JalviewUserColours;
+import jalview.xml.binding.jalview.JalviewUserColours.Colour;
+import jalview.xml.binding.jalview.ObjectFactory;
 
 import java.awt.Color;
 import java.awt.Font;
@@ -51,6 +52,8 @@ import javax.swing.JButton;
 import javax.swing.JInternalFrame;
 import javax.swing.event.ChangeEvent;
 import javax.swing.event.ChangeListener;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.Marshaller;
 
 /**
  * This panel allows the user to assign colours to Amino Acid residue codes, and
@@ -858,9 +861,14 @@ public class UserDefinedColours extends GUserDefinedColours
         Colour col = new Colour();
         col.setName(button.getText());
         col.setRGB(Format.getHexString(button.getBackground()));
-        ucs.addColour(col);
+        ucs.getColour().add(col);
       }
-      ucs.marshal(out);
+      JAXBContext jaxbContext = JAXBContext
+              .newInstance(JalviewUserColours.class);
+      Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
+      jaxbMarshaller.marshal(
+              new ObjectFactory().createJalviewUserColours(ucs), out);
+      // ucs.marshal(out);
       out.close();
     } catch (Exception ex)
     {
diff --git a/src/jalview/schemes/ColourSchemeLoader.java b/src/jalview/schemes/ColourSchemeLoader.java
index 9f08688..481f809 100644
--- 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()];
 
-- 
1.7.10.2