JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

[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 946181c..b9d4391 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 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,17 +20,38 @@
  */
 package jalview.gui;
 
-import java.io.*;
-import java.util.*;
-import java.util.jar.*;
-
-import javax.swing.*;
-
-import org.exolab.castor.xml.*;
-import jalview.binding.*;
-import jalview.schemes.*;
+import jalview.binding.Annotation;
+import jalview.binding.AnnotationElement;
+import jalview.binding.Features;
+import jalview.binding.JGroup;
+import jalview.binding.JSeq;
+import jalview.binding.JalviewModel;
+import jalview.binding.JalviewModelSequence;
+import jalview.binding.Pdbids;
+import jalview.binding.Sequence;
+import jalview.binding.SequenceSet;
+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.util.Hashtable;
+import java.util.Vector;
+import java.util.jar.JarEntry;
+import java.util.jar.JarInputStream;
+
+import javax.swing.JOptionPane;
+
+import org.exolab.castor.xml.IDResolver;
 
 /**
  * DOCUMENT ME!
@@ -120,7 +141,7 @@ public class Jalview2XML_V1
           InputStreamReader in = new InputStreamReader(jin, "UTF-8");
           JalviewModel object = new JalviewModel();
 
-          object = (JalviewModel) object.unmarshal(in);
+          object = object.unmarshal(in);
 
           af = LoadFromObject(object, file);
           entryCount++;
@@ -140,8 +161,7 @@ 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);
           }
@@ -160,7 +180,10 @@ public class Jalview2XML_V1
           {
 
             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);
           }
         });
@@ -220,8 +243,20 @@ 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);
         }
 
       }
@@ -315,8 +350,7 @@ public class Jalview2XML_V1
 
         for (int s = 0; s < ids.length; s++)
         {
-          seqs.addElement((jalview.datamodel.SequenceI) seqids
-                  .elementAt(ids[s]));
+          seqs.addElement(seqids.elementAt(ids[s]));
         }
 
         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
@@ -349,15 +383,14 @@ 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());
 
@@ -383,6 +416,7 @@ public class Jalview2XML_V1
 
     af.viewport.setGlobalColourScheme(cs);
     af.viewport.setColourAppliesToAllGroups(false);
+    af.alignPanel.updateLayout();
     af.changeColour(cs);
     if (view.getConservationSelected() && cs != null)
     {
@@ -390,29 +424,33 @@ 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);