JAL-1894 update year/version in copyright

[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 f1879c1..903208a 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 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -34,12 +34,14 @@ 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;
@@ -49,10 +51,7 @@ import java.util.jar.JarInputStream;
 
 import javax.swing.JOptionPane;
 
-import jalview.util.MessageManager;
-import jalview.util.jarInputStreamProvider;
 import org.exolab.castor.xml.IDResolver;
-import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
 
 /**
  * DOCUMENT ME!
@@ -162,8 +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);
           }
@@ -182,7 +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);
           }
         });
@@ -242,7 +243,17 @@ 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);
@@ -339,8 +350,7 @@ 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(
@@ -373,15 +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());
 
@@ -407,6 +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)
     {
@@ -426,19 +436,21 @@ public class Jalview2XML_V1
       {
         Setting setting = jms.getFeatureSettings().getSetting(fs);
 
-        featureColours.put(
-                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())
         {
-          featuresDisplayed.put(setting.getType(), new Integer(
-                  setting.getColour()));
+          featuresDisplayed.put(setting.getType(),
+                  new Integer(setting.getColour()));
         }
       }
-      FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder, new Hashtable(), featureColours, 1.0f, null);
-      af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(frs);
+      FeatureRendererSettings frs = new FeatureRendererSettings(
+              renderOrder, new Hashtable(), featureColours, 1.0f, null);
+      af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
+              .transferSettings(frs);
     }
 
     af.setMenusFromViewport(af.viewport);