Merge branch 'develop' into trialMerge

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index d24daa1..d09e7c2 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -37,6 +37,8 @@ import jalview.datamodel.StructureViewerModel;
 import jalview.datamodel.StructureViewerModel.StructureData;
 import jalview.ext.varna.RnaModel;
 import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
 import jalview.schemabinding.version2.AlcodMap;
 import jalview.schemabinding.version2.AlcodonFrame;
 import jalview.schemabinding.version2.Annotation;
@@ -992,17 +994,16 @@ public class Jalview2XML
             }
           }
 
-          if (entry.getProperty() != null && !entry.getProperty().isEmpty())
+          Enumeration<String> props = entry.getProperties();
+          if (props.hasMoreElements())
           {
             PdbentryItem item = new PdbentryItem();
-            Hashtable properties = entry.getProperty();
-            Enumeration en2 = properties.keys();
-            while (en2.hasMoreElements())
+            while (props.hasMoreElements())
             {
               Property prop = new Property();
-              String key = en2.nextElement().toString();
+              String key = props.nextElement();
               prop.setName(key);
-              prop.setValue(properties.get(key).toString());
+              prop.setValue(entry.getProperty(key).toString());
               item.addProperty(prop);
             }
             pdb.addPdbentryItem(item);
@@ -2544,6 +2545,8 @@ public class Jalview2XML
           SplitFrame sf = createSplitFrame(dnaFrame, af);
           addedToSplitFrames.add(dnaFrame);
           addedToSplitFrames.add(af);
+          dnaFrame.setMenusForViewport();
+          af.setMenusForViewport();
           if (af.viewport.isGatherViewsHere())
           {
             gatherTo.add(sf);
@@ -2565,6 +2568,7 @@ public class Jalview2XML
         Viewport view = candidate.getKey();
         Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
                 view.getHeight());
+        af.setMenusForViewport();
         System.err.println("Failed to restore view " + view.getTitle()
                 + " to split frame");
       }
@@ -3015,7 +3019,8 @@ public class Jalview2XML
                 entry.setType(PDBEntry.Type.FILE);
               }
             }
-            if (ids[p].getFile() != null)
+            // jprovider is null when executing 'New View'
+            if (ids[p].getFile() != null && jprovider != null)
             {
               if (!pdbloaded.containsKey(ids[p].getFile()))
               {
@@ -3029,12 +3034,11 @@ public class Jalview2XML
             }
             if (ids[p].getPdbentryItem() != null)
             {
-              entry.setProperty(new Hashtable());
               for (PdbentryItem item : ids[p].getPdbentryItem())
               {
                 for (Property pr : item.getProperty())
                 {
-                  entry.getProperty().put(pr.getName(), pr.getValue());
+                  entry.setProperty(pr.getName(), pr.getValue());
                 }
               }
             }
@@ -3399,8 +3403,8 @@ public class Jalview2XML
         }
         if (jGroup.getConsThreshold() != 0)
         {
-          Conservation c = new Conservation("All", 3,
-                  sg.getSequences(null), 0, sg.getWidth() - 1);
+          Conservation c = new Conservation("All", sg.getSequences(null),
+                  0, sg.getWidth() - 1);
           c.calculate();
           c.verdict(false, 25);
           sg.cs.setConservation(c);
@@ -4228,8 +4232,7 @@ public class Jalview2XML
       StructureData filedat = oldFiles.get(id);
       String pdbFile = filedat.getFilePath();
       SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
-      binding.getSsm().setMapping(seq, null, pdbFile,
-              jalview.io.AppletFormatAdapter.FILE);
+      binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE);
       binding.addSequenceForStructFile(pdbFile, seq);
     }
     // and add the AlignmentPanel's reference to the view panel
@@ -4344,7 +4347,7 @@ public class Jalview2XML
     af = new AlignFrame(al, view.getWidth(), view.getHeight(),
             uniqueSeqSetId, viewId);
 
-    af.setFileName(file, "Jalview");
+    af.setFileName(file, FileFormat.Jalview);
 
     for (int i = 0; i < JSEQ.length; i++)
     {