JAL-1824 corrected copy'n'paste error introduced from JAL-1821 refactor which causes...

[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 b426914..cb572cd 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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;
@@ -239,8 +241,20 @@ 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);
         }
 
       }
@@ -368,15 +382,14 @@ 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());
 
@@ -402,6 +415,7 @@ public class Jalview2XML_V1
 
     af.viewport.setGlobalColourScheme(cs);
     af.viewport.setColourAppliesToAllGroups(false);
+    af.alignPanel.updateLayout();
     af.changeColour(cs);
     if (view.getConservationSelected() && cs != null)
     {
@@ -409,29 +423,31 @@ 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(
+        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(
+          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);