Merge branch 'features/pca_jaxb_datasetrefs_JAL-3171_JAL-3063_JAL-1767' into develop

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

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 132bb2b..dbe3317 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;
@@ -97,6 +98,11 @@ 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
@@ -811,30 +817,39 @@ 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);
@@ -916,9 +931,9 @@ 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);
       }
 
       /*
@@ -931,16 +946,26 @@ 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)
     {