X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=d8537bba4a6908777b00bab339d4a11c98ecbbc1;hb=7dc7fb2a35c435d825bc91c5ae60ec6073419a69;hp=47a8fafe6a8ad0a20c9591e765aeeb78741e723d;hpb=2bd3c28fe234c6883bec5412db83a809ab8d1500;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 47a8faf..d8537bb 100644
--- 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;
@@ -127,7 +129,6 @@ import java.util.jar.JarInputStream;
 import java.util.jar.JarOutputStream;
 
 import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
 import javax.swing.SwingUtilities;
 
 import org.exolab.castor.xml.Marshaller;
@@ -314,6 +315,7 @@ public class Jalview2XML
       }
       return sq;
     }
+
     /**
      * @return true if the forward reference was fully resolved
      */
@@ -388,35 +390,44 @@ 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.");
@@ -795,7 +806,7 @@ 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())
     {
@@ -848,8 +859,7 @@ 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++)
             {
@@ -983,17 +993,16 @@ 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);
@@ -1341,8 +1350,7 @@ 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())
@@ -1355,8 +1363,8 @@ 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
             {
@@ -1378,8 +1386,7 @@ 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())
         {
@@ -2537,6 +2544,8 @@ 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);
@@ -2558,6 +2567,7 @@ 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");
       }
@@ -2627,10 +2637,10 @@ public class Jalview2XML
           @Override
           public void run()
           {
-            JOptionPane.showInternalMessageDialog(Desktop.desktop,
+            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                     finalErrorMessage, "Error "
                             + (saving ? "saving" : "loading")
-                            + " Jalview file", JOptionPane.WARNING_MESSAGE);
+                            + " Jalview file", JvOptionPane.WARNING_MESSAGE);
           }
         });
       }
@@ -2813,7 +2823,6 @@ public class Jalview2XML
 
     List<SequenceI> hiddenSeqs = null;
 
-
     List<SequenceI> tmpseqs = new ArrayList<SequenceI>();
 
     boolean multipleView = false;
@@ -2830,13 +2839,16 @@ 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))
@@ -3006,7 +3018,8 @@ 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()))
               {
@@ -3020,12 +3033,11 @@ 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());
                 }
               }
             }
@@ -3390,8 +3402,8 @@ 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);
@@ -4009,11 +4021,10 @@ 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());
@@ -4220,8 +4231,7 @@ 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
@@ -4336,7 +4346,7 @@ 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++)
     {
@@ -4411,10 +4421,12 @@ public class Jalview2XML
 
     af.viewport.setShowAnnotation(view.getShowAnnotation());
     af.viewport.setAbovePIDThreshold(view.getPidSelected());
+    af.viewport.setThreshold(view.getPidThreshold());
 
     af.viewport.setColourText(view.getShowColourText());
 
     af.viewport.setConservationSelected(view.getConservationSelected());
+    af.viewport.setIncrement(view.getConsThreshold());
     af.viewport.setShowJVSuffix(view.getShowFullId());
     af.viewport.setRightAlignIds(view.getRightAlignIds());
     af.viewport.setFont(
@@ -4464,7 +4476,6 @@ public class Jalview2XML
 
       if (cs != null)
       {
-        cs.setThreshold(view.getPidThreshold(), true);
         cs.setConsensus(af.viewport.getSequenceConsensusHash());
       }
     }