X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=bc5e1d89b2d58ea1092f1b5e3dfa32f07de8c614;hb=614b72c437f14dd2ddd72ae918dada3fd5d64468;hp=7093a9ab7d61663c445d3fe762d8e2b545b4236f;hpb=f53d22d39b5c18b7db1d8c7396b5ec19df6ef17b;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 7093a9a..bc5e1d8 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.analysis.Conservation;
 import jalview.api.FeatureColourI;
 import jalview.api.ViewStyleI;
 import jalview.api.structures.JalviewStructureDisplayI;
@@ -313,6 +314,7 @@ public class Jalview2XML
       }
       return sq;
     }
+
     /**
      * @return true if the forward reference was fully resolved
      */
@@ -387,35 +389,44 @@ public class Jalview2XML
 
   public void resolveFrefedSequences()
   {
-    Iterator<SeqFref> nextFref=frefedSequence.iterator();
-    int toresolve=frefedSequence.size();
-    int unresolved=0,failedtoresolve=0;
-    while (nextFref.hasNext()) {
+    Iterator<SeqFref> nextFref = frefedSequence.iterator();
+    int toresolve = frefedSequence.size();
+    int unresolved = 0, failedtoresolve = 0;
+    while (nextFref.hasNext())
+    {
       SeqFref ref = nextFref.next();
       if (ref.isResolvable())
       {
-        try {
+        try
+        {
           if (ref.resolve())
           {
             nextFref.remove();
-          } else {
+          }
+          else
+          {
             failedtoresolve++;
           }
-        } catch (Exception x) {
-          System.err.println("IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "+ref.getSref());
+        } catch (Exception x)
+        {
+          System.err
+                  .println("IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "
+                          + ref.getSref());
           x.printStackTrace();
           failedtoresolve++;
-        } 
-      } else {
+        }
+      }
+      else
+      {
         unresolved++;
       }
     }
-    if (unresolved>0)
+    if (unresolved > 0)
     {
       System.err.println("Jalview Project Import: There were " + unresolved
               + " forward references left unresolved on the stack.");
     }
-    if (failedtoresolve>0)
+    if (failedtoresolve > 0)
     {
       System.err.println("SERIOUS! " + failedtoresolve
               + " resolvable forward references failed to resolve.");
@@ -794,7 +805,7 @@ public class Jalview2XML
     JSeq jseq;
     Set<String> calcIdSet = new HashSet<String>();
     // record the set of vamsas sequence XML POJO we create.
-    HashMap<String,Sequence> vamsasSetIds = new HashMap<String,Sequence>(); 
+    HashMap<String, Sequence> vamsasSetIds = new HashMap<String, Sequence>();
     // SAVE SEQUENCES
     for (final SequenceI jds : rjal.getSequences())
     {
@@ -847,8 +858,7 @@ public class Jalview2XML
           if (av.isHiddenRepSequence(jds))
           {
             jalview.datamodel.SequenceI[] reps = av
-                    .getRepresentedSequences(jds)
-                    .getSequencesInOrder(rjal);
+                    .getRepresentedSequences(jds).getSequencesInOrder(rjal);
 
             for (int h = 0; h < reps.length; h++)
             {
@@ -982,17 +992,16 @@ 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);
@@ -1340,8 +1349,7 @@ public class Jalview2XML
           for (String featureType : renderOrder)
           {
             FeatureColourI fcol = ap.getSeqPanel().seqCanvas
-                    .getFeatureRenderer()
-                    .getFeatureStyle(featureType);
+                    .getFeatureRenderer().getFeatureStyle(featureType);
             Setting setting = new Setting();
             setting.setType(featureType);
             if (!fcol.isSimpleColour())
@@ -1354,8 +1362,8 @@ public class Jalview2XML
               setting.setAutoScale(fcol.isAutoScaled());
               setting.setThreshold(fcol.getThreshold());
               // -1 = No threshold, 0 = Below, 1 = Above
-              setting.setThreshstate(fcol.isAboveThreshold() ? 1
-                      : (fcol.isBelowThreshold() ? 0 : -1));
+              setting.setThreshstate(fcol.isAboveThreshold() ? 1 : (fcol
+                      .isBelowThreshold() ? 0 : -1));
             }
             else
             {
@@ -1377,8 +1385,7 @@ public class Jalview2XML
 
         // is groups actually supposed to be a map here ?
         Iterator<String> en = ap.getSeqPanel().seqCanvas
-                .getFeatureRenderer()
-                .getFeatureGroups().iterator();
+                .getFeatureRenderer().getFeatureGroups().iterator();
         Vector<String> groupsAdded = new Vector<String>();
         while (en.hasNext())
         {
@@ -2536,6 +2543,8 @@ 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);
@@ -2557,6 +2566,7 @@ 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");
       }
@@ -2812,7 +2822,6 @@ public class Jalview2XML
 
     List<SequenceI> hiddenSeqs = null;
 
-
     List<SequenceI> tmpseqs = new ArrayList<SequenceI>();
 
     boolean multipleView = false;
@@ -2829,13 +2838,16 @@ public class Jalview2XML
         if (!incompleteSeqs.containsKey(seqId))
         {
           // may not need this check, but keep it for at least 2.9,1 release
-          if (tmpSeq.getStart()!=jseqs[i].getStart() || tmpSeq.getEnd()!=jseqs[i].getEnd())
-          { 
+          if (tmpSeq.getStart() != jseqs[i].getStart()
+                  || tmpSeq.getEnd() != jseqs[i].getEnd())
+          {
             System.err
                     .println("Warning JAL-2154 regression: updating start/end for sequence "
                             + tmpSeq.toString() + " to " + jseqs[i]);
           }
-        } else {
+        }
+        else
+        {
           incompleteSeqs.remove(seqId);
         }
         if (vamsasSeq.length > vi && vamsasSeq[vi].getId().equals(seqId))
@@ -3005,7 +3017,8 @@ 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()))
               {
@@ -3019,12 +3032,11 @@ 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());
                 }
               }
             }
@@ -3389,9 +3401,8 @@ public class Jalview2XML
         }
         if (jGroup.getConsThreshold() != 0)
         {
-          jalview.analysis.Conservation c = new jalview.analysis.Conservation(
-                  "All", ResidueProperties.propHash, 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);
@@ -4009,11 +4020,10 @@ public class Jalview2XML
         // filename
         // translation differently.
         StructureData filedat = oldFiles.get(new File(oldfilenam));
-          if (filedat == null)
-          {
-            String reformatedOldFilename = oldfilenam.replaceAll("/",
-                    "\\\\");
-            filedat = oldFiles.get(new File(reformatedOldFilename));
+        if (filedat == null)
+        {
+          String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
+          filedat = oldFiles.get(new File(reformatedOldFilename));
         }
         newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
         pdbfilenames.add(filedat.getFilePath());