JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / src / jalview / gui / Jalview2XML_V1.java

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index 9e4a8ec..f8a296f 100755 (executable)
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.analysis.Conservation;
 import jalview.binding.Annotation;
 import jalview.binding.AnnotationElement;
 import jalview.binding.Features;
@@ -34,14 +35,17 @@ import jalview.binding.Setting;
 import jalview.binding.Tree;
 import jalview.binding.UserColours;
 import jalview.binding.Viewport;
+import jalview.datamodel.PDBEntry;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 import jalview.util.jarInputStreamProvider;
+import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
 
 import java.io.InputStreamReader;
+import java.io.Reader;
+import java.net.UnknownHostException;
 import java.util.Hashtable;
 import java.util.Vector;
 import java.util.jar.JarEntry;
@@ -49,8 +53,6 @@ import java.util.jar.JarInputStream;
 
 import javax.swing.JOptionPane;
 
-import org.exolab.castor.xml.IDResolver;
-
 /**
  * DOCUMENT ME!
  * 
@@ -125,33 +127,29 @@ public class Jalview2XML_V1
           jarentry = jin.getNextJarEntry();
         }
 
-        class NoDescIDResolver implements IDResolver
-        {
-          public Object resolve(String idref)
-          {
-            System.out.println(idref + " used");
-            return null;
-          }
-        }
-
         if (jarentry != null)
         {
-          InputStreamReader in = new InputStreamReader(jin, "UTF-8");
-          JalviewModel object = new JalviewModel();
+          entryCount++;
+          if (jarentry.getName().endsWith(".xml"))
+          {
+            Reader in = new InputStreamReader(jin, "UTF-8");
+            JalviewModel object = new JalviewModel();
 
-          object = object.unmarshal(in);
+            object = object.unmarshal(in);
 
-          af = LoadFromObject(object, file);
-          entryCount++;
+            af = LoadFromObject(object, file);
+          }
         }
+        jin.close();
       } while (jarentry != null);
-    } catch (final java.net.UnknownHostException ex)
+    } catch (final UnknownHostException ex)
     {
       ex.printStackTrace();
       if (raiseGUI)
       {
         javax.swing.SwingUtilities.invokeLater(new Runnable()
         {
+          @Override
           public void run()
           {
 
@@ -159,8 +157,7 @@ public class Jalview2XML_V1
                     + "\n");
             JOptionPane.showInternalMessageDialog(Desktop.desktop,
                     MessageManager.formatMessage("label.couldnt_locate",
-                            new String[]
-                            { file }), MessageManager
+                            new String[] { file }), MessageManager
                             .getString("label.url_not_found"),
                     JOptionPane.WARNING_MESSAGE);
           }
@@ -175,11 +172,15 @@ public class Jalview2XML_V1
       {
         javax.swing.SwingUtilities.invokeLater(new Runnable()
         {
+          @Override
           public void run()
           {
 
             JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                    MessageManager.formatMessage("label.error_loading_file_params", new String[]{file}), MessageManager.getString("label.error_loading_jalview_file"),
+                    MessageManager.formatMessage(
+                            "label.error_loading_file_params", new String[]
+                            { file }), MessageManager
+                            .getString("label.error_loading_jalview_file"),
                     JOptionPane.WARNING_MESSAGE);
           }
         });
@@ -239,7 +240,17 @@ public class Jalview2XML_V1
         {
           jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
           entry.setId(ids[p].getId());
-          entry.setType(ids[p].getType());
+          if (ids[p].getType() != null)
+          {
+            if (ids[p].getType().equalsIgnoreCase("PDB"))
+            {
+              entry.setType(PDBEntry.Type.PDB);
+            }
+            else
+            {
+              entry.setType(PDBEntry.Type.FILE);
+            }
+          }
           al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
           StructureSelectionManager.getStructureSelectionManager(
                   Desktop.instance).registerPDBEntry(entry);
@@ -336,8 +347,7 @@ public class Jalview2XML_V1
 
         for (int s = 0; s < ids.length; s++)
         {
-          seqs.addElement(seqids
-                  .elementAt(ids[s]));
+          seqs.addElement(seqids.elementAt(ids[s]));
         }
 
         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
@@ -349,8 +359,7 @@ public class Jalview2XML_V1
 
         if (groups[i].getConsThreshold() != 0)
         {
-          jalview.analysis.Conservation c = new jalview.analysis.Conservation(
-                  "All", ResidueProperties.propHash, 3,
+          Conservation c = new Conservation("All", 3,
                   sg.getSequences(null), 0, sg.getWidth() - 1);
           c.calculate();
           c.verdict(false, 25);
@@ -370,15 +379,14 @@ public class Jalview2XML_V1
     af.viewport.setColourText(view.getShowColourText());
     af.viewport.setConservationSelected(view.getConservationSelected());
     af.viewport.setShowJVSuffix(view.getShowFullId());
-    af.viewport.setFont(new java.awt.Font(view.getFontName(), view
-            .getFontStyle(), view.getFontSize()));
-    af.alignPanel.fontChanged();
+    af.viewport.setFont(
+            new java.awt.Font(view.getFontName(), view.getFontStyle(), view
+                    .getFontSize()), true);
 
     af.viewport.setRenderGaps(view.getRenderGaps());
     af.viewport.setWrapAlignment(view.getWrapAlignment());
-    af.alignPanel.setWrapAlignment(view.getWrapAlignment());
-    af.viewport.setShowAnnotation(view.getShowAnnotation());
-    af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
+
+    af.viewport.setShowAnnotation(view.isShowAnnotation());
     af.viewport.setShowBoxes(view.getShowBoxes());
     af.viewport.setShowText(view.getShowText());
 
@@ -404,6 +412,7 @@ public class Jalview2XML_V1
 
     af.viewport.setGlobalColourScheme(cs);
     af.viewport.setColourAppliesToAllGroups(false);
+    af.alignPanel.updateLayout();
     af.changeColour(cs);
     if (view.getConservationSelected() && cs != null)
     {
@@ -411,29 +420,33 @@ public class Jalview2XML_V1
     }
 
     af.viewport.setColourAppliesToAllGroups(true);
-    af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();
+    af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
 
     if (jms.getFeatureSettings() != null)
     {
-      af.viewport.featuresDisplayed = new Hashtable();
+      Hashtable featuresDisplayed = new Hashtable();
+      Hashtable featureColours = new Hashtable();
       String[] renderOrder = new String[jms.getFeatureSettings()
               .getSettingCount()];
       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
       {
         Setting setting = jms.getFeatureSettings().getSetting(fs);
 
-        af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
-                setting.getType(), new java.awt.Color(setting.getColour()));
+        featureColours.put(setting.getType(),
+                new java.awt.Color(setting.getColour()));
 
         renderOrder[fs] = setting.getType();
 
         if (setting.getDisplay())
         {
-          af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
-                  setting.getColour()));
+          featuresDisplayed.put(setting.getType(),
+                  new Integer(setting.getColour()));
         }
       }
-      af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
+      FeatureRendererSettings frs = new FeatureRendererSettings(
+              renderOrder, new Hashtable(), featureColours, 1.0f, null);
+      af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
+              .transferSettings(frs);
     }
 
     af.setMenusFromViewport(af.viewport);