JAL-3063 Save/Load user colour scheme using JAXB

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 78c1cac..90d7c35 100644 (file)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -30,13 +30,14 @@ import jalview.datamodel.features.FeatureMatcherSetI;
 import jalview.gui.Help.HelpId;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
-import jalview.schemabinding.version2.Filter;
-import jalview.schemabinding.version2.JalviewUserColours;
-import jalview.schemabinding.version2.MatcherSet;
 import jalview.schemes.FeatureColour;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
+import jalview.xml.binding.jalview.JalviewUserColours;
+import jalview.xml.binding.jalview.JalviewUserColours.Colour;
+import jalview.xml.binding.jalview.JalviewUserColours.Filter;
+import jalview.xml.binding.jalview.ObjectFactory;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -98,6 +99,11 @@ import javax.swing.table.AbstractTableModel;
 import javax.swing.table.TableCellEditor;
 import javax.swing.table.TableCellRenderer;
 import javax.swing.table.TableColumn;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.Marshaller;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamReader;
 
 public class FeatureSettings extends JPanel
         implements FeatureSettingsControllerI
@@ -874,30 +880,39 @@ public class FeatureSettings extends JPanel
       InputStreamReader in = new InputStreamReader(
               new FileInputStream(file), "UTF-8");
 
-      JalviewUserColours jucs = JalviewUserColours.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();
+
+      // JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
 
       /*
        * load feature colours
        */
-      for (int i = jucs.getColourCount() - 1; i >= 0; i--)
+      for (int i = jucs.getColour().size() - 1; i >= 0; i--)
       {
-        jalview.schemabinding.version2.Colour newcol = jucs.getColour(i);
-        FeatureColourI colour = Jalview2XML.unmarshalColour(newcol);
+        Colour newcol = jucs.getColour().get(i);
+        FeatureColourI colour = jalview.project.Jalview2XML
+                .parseColour(newcol);
         fr.setColour(newcol.getName(), colour);
-        fr.setOrder(newcol.getName(), i / (float) jucs.getColourCount());
+        fr.setOrder(newcol.getName(), i / (float) jucs.getColour().size());
       }
 
       /*
        * load feature filters; loaded filters will replace any that are
        * currently defined, other defined filters are left unchanged 
        */
-      for (int i = 0; i < jucs.getFilterCount(); i++)
+      for (int i = 0; i < jucs.getFilter().size(); i++)
       {
-        jalview.schemabinding.version2.Filter filterModel = jucs
-                .getFilter(i);
+        Filter filterModel = jucs.getFilter().get(i);
         String featureType = filterModel.getFeatureType();
-        FeatureMatcherSetI filter = Jalview2XML.unmarshalFilter(featureType,
-                filterModel.getMatcherSet());
+        FeatureMatcherSetI filter = jalview.project.Jalview2XML
+                .parseFilter(featureType, filterModel.getMatcherSet());
         if (!filter.isEmpty())
         {
           fr.setFeatureFilter(featureType, filter);
@@ -979,9 +994,9 @@ public class FeatureSettings extends JPanel
       for (String featureType : sortedTypes)
       {
         FeatureColourI fcol = fr.getFeatureStyle(featureType);
-        jalview.schemabinding.version2.Colour col = Jalview2XML.marshalColour(
-                featureType, fcol);
-        ucs.addColour(col);
+        Colour col = jalview.project.Jalview2XML.marshalColour(featureType,
+                fcol);
+        ucs.getColour().add(col);
       }
 
       /*
@@ -994,16 +1009,26 @@ public class FeatureSettings extends JPanel
         {
           Iterator<FeatureMatcherI> iterator = filter.getMatchers().iterator();
           FeatureMatcherI firstMatcher = iterator.next();
-          MatcherSet ms = Jalview2XML.marshalFilter(firstMatcher, iterator,
+          jalview.xml.binding.jalview.FeatureMatcherSet ms = jalview.project.Jalview2XML
+                  .marshalFilter(firstMatcher, iterator,
                   filter.isAnded());
           Filter filterModel = new Filter();
           filterModel.setFeatureType(featureType);
           filterModel.setMatcherSet(ms);
-          ucs.addFilter(filterModel);
+          ucs.getFilter().add(filterModel);
         }
       }
+      JAXBContext jaxbContext = JAXBContext
+              .newInstance(JalviewUserColours.class);
+      Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
+      jaxbMarshaller.marshal(
+              new ObjectFactory().createJalviewUserColours(ucs), out);
+
+      // jaxbMarshaller.marshal(object, pout);
+      // marshaller.marshal(object);
+      out.flush();
 
-      ucs.marshal(out);
+      // ucs.marshal(out);
       out.close();
     } catch (Exception ex)
     {

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 5106e45..c4ad897 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -4815,7 +4815,7 @@ public class Jalview2XML
         if (filters != null)
         {
           FeatureMatcherSetI filter = Jalview2XML
-                  .unmarshalFilter(featureType, filters);
+                  .parseFilter(featureType, filters);
           if (!filter.isEmpty())
           {
             fr.setFeatureFilter(featureType, filter);
@@ -5873,7 +5873,7 @@ public class Jalview2XML
    * @param fcol
    * @return
    */
-  protected static Colour marshalColour(
+  public static Colour marshalColour(
           String featureType, FeatureColourI fcol)
   {
     Colour col = new Colour();
@@ -5930,7 +5930,7 @@ public class Jalview2XML
    * @param and
    *          if true, conditions are and-ed, else or-ed
    */
-  protected static jalview.xml.binding.jalview.FeatureMatcherSet marshalFilter(
+  public static jalview.xml.binding.jalview.FeatureMatcherSet marshalFilter(
           FeatureMatcherI firstMatcher, Iterator<FeatureMatcherI> filters,
           boolean and)
   {
@@ -5996,14 +5996,14 @@ public class Jalview2XML
    * @param matcherSetModel
    * @return
    */
-  protected static FeatureMatcherSetI unmarshalFilter(
+  public static FeatureMatcherSetI parseFilter(
           String featureType,
           jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel)
   {
     FeatureMatcherSetI result = new FeatureMatcherSet();
     try
     {
-      unmarshalFilterConditions(result, matcherSetModel, true);
+      parseFilterConditions(result, matcherSetModel, true);
     } catch (IllegalStateException e)
     {
       // mixing AND and OR conditions perhaps
@@ -6027,7 +6027,7 @@ public class Jalview2XML
    * @throws IllegalStateException
    *           if AND and OR conditions are mixed
    */
-  protected static void unmarshalFilterConditions(
+  protected static void parseFilterConditions(
           FeatureMatcherSetI matcherSet,
           jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel,
           boolean and)
@@ -6080,13 +6080,12 @@ public class Jalview2XML
        * compound condition
        */
       List<jalview.xml.binding.jalview.FeatureMatcherSet> matchers = matcherSetModel
-              .getCompoundMatcher()
-              .getMatcherSet();
+              .getCompoundMatcher().getMatcherSet();
       boolean anded = matcherSetModel.getCompoundMatcher().isAnd();
       if (matchers.size() == 2)
       {
-        unmarshalFilterConditions(matcherSet, matchers.get(0), anded);
-        unmarshalFilterConditions(matcherSet, matchers.get(1), anded);
+        parseFilterConditions(matcherSet, matchers.get(0), anded);
+        parseFilterConditions(matcherSet, matchers.get(1), anded);
       }
       else
       {
@@ -6101,7 +6100,7 @@ public class Jalview2XML
    * @param colourModel
    * @return
    */
-  protected static FeatureColourI unmarshalColour(Colour colourModel)
+  public static FeatureColourI parseColour(Colour colourModel)
   {
     FeatureColourI colour = null;