Merge branch 'feature/JAL-3181linkOrdering' into develop

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

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 8b45c40..b1f6d1b 100755 (executable)
--- 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
@@ -136,7 +139,7 @@ public class UserDefinedColours extends GUserDefinedColours
   UserDefinedColours()
   {
     super();
-    selectedButtons = new ArrayList<JButton>();
+    selectedButtons = new ArrayList<>();
   }
 
   void showFrame()
@@ -163,7 +166,7 @@ public class UserDefinedColours extends GUserDefinedColours
 
     if (upperCaseButtons == null)
     {
-      upperCaseButtons = new ArrayList<JButton>();
+      upperCaseButtons = new ArrayList<>();
     }
 
     for (int i = 0; i < 20; i++)
@@ -194,7 +197,7 @@ public class UserDefinedColours extends GUserDefinedColours
 
       if (lowerCaseButtons == null)
       {
-        lowerCaseButtons = new ArrayList<JButton>();
+        lowerCaseButtons = new ArrayList<>();
       }
 
       for (int i = 0; i < 20; i++)
@@ -631,8 +634,8 @@ public class UserDefinedColours extends GUserDefinedColours
   @Override
   protected void loadbutton_actionPerformed()
   {
-    upperCaseButtons = new ArrayList<JButton>();
-    lowerCaseButtons = new ArrayList<JButton>();
+    upperCaseButtons = new ArrayList<>();
+    lowerCaseButtons = new ArrayList<>();
 
     JalviewFileChooser chooser = new JalviewFileChooser("jc",
             "Jalview User Colours");
@@ -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)
     {
@@ -876,7 +884,7 @@ public class UserDefinedColours extends GUserDefinedColours
   protected void cancelButton_actionPerformed()
   {
     ap.alignFrame.changeColour(oldColourScheme);
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, true);
 
     try
     {