JAL-3389 add .py to restored Chimera session filename so it opens!

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

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index cf5974c..af48dba 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -38,6 +38,8 @@ import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.GeneLocus;
 import jalview.datamodel.GraphLine;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Point;
@@ -2505,21 +2507,29 @@ public class Jalview2XML
         parentseq = jds;
       }
     }
+
+    /*
+     * save any dbrefs; special subclass GeneLocus is flagged as 'locus'
+     */
     if (dbrefs != null)
     {
       for (int d = 0; d < dbrefs.length; d++)
       {
         DBRef dbref = new DBRef();
-        dbref.setSource(dbrefs[d].getSource());
-        dbref.setVersion(dbrefs[d].getVersion());
-        dbref.setAccessionId(dbrefs[d].getAccessionId());
-        if (dbrefs[d].hasMap())
+        DBRefEntry dbRefEntry = dbrefs[d];
+        dbref.setSource(dbRefEntry.getSource());
+        dbref.setVersion(dbRefEntry.getVersion());
+        dbref.setAccessionId(dbRefEntry.getAccessionId());
+        if (dbRefEntry instanceof GeneLocus)
         {
-          Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
+          dbref.setLocus(true);
+        }
+        if (dbRefEntry.hasMap())
+        {
+          Mapping mp = createVamsasMapping(dbRefEntry.getMap(), parentseq,
                   jds, recurse);
           dbref.setMapping(mp);
         }
-        // vamsasSeq.addDBRef(dbref);
         vamsasSeq.getDBRef().add(dbref);
       }
     }
@@ -3150,25 +3160,25 @@ public class Jalview2XML
    * @param prefix
    *          a prefix for the temporary file name, must be at least three
    *          characters long
-   * @param origFile
+   * @param suffixModel
    *          null or original file - so new file can be given the same suffix
    *          as the old one
    * @return
    */
   protected String copyJarEntry(jarInputStreamProvider jprovider,
-          String jarEntryName, String prefix, String origFile)
+          String jarEntryName, String prefix, String suffixModel)
   {
     BufferedReader in = null;
     PrintWriter out = null;
     String suffix = ".tmp";
-    if (origFile == null)
+    if (suffixModel == null)
     {
-      origFile = jarEntryName;
+      suffixModel = jarEntryName;
     }
-    int sfpos = origFile.lastIndexOf(".");
-    if (sfpos > -1 && sfpos < (origFile.length() - 3))
+    int sfpos = suffixModel.lastIndexOf(".");
+    if (sfpos > -1 && sfpos < (suffixModel.length() - 1))
     {
-      suffix = "." + origFile.substring(sfpos + 1);
+      suffix = "." + suffixModel.substring(sfpos + 1);
     }
     try
     {
@@ -4187,10 +4197,8 @@ public class Jalview2XML
           // TODO: verify 'associate with all views' works still
           tp.getTreeCanvas().setViewport(av); // af.viewport;
           tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
-          // FIXME: should we use safeBoolean here ?
-          tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
-
         }
+        tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
         if (tp == null)
         {
           warn("There was a problem recovering stored Newick tree: \n"
@@ -4436,7 +4444,7 @@ public class Jalview2XML
      */
     String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
     chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
-            "chimera", null);
+            "chimera", ".py");
 
     Set<Entry<File, StructureData>> fileData = data.getFileData()
             .entrySet();
@@ -4522,7 +4530,7 @@ public class Jalview2XML
           String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
           filedat = oldFiles.get(new File(reformatedOldFilename));
         }
-        newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
+        newFileLoc.append(Platform.escapeBackslashes(filedat.getFilePath()));
         pdbfilenames.add(filedat.getFilePath());
         pdbids.add(filedat.getPdbId());
         seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
@@ -5115,7 +5123,7 @@ public class Jalview2XML
         }
         else
         {
-          featureOrder.put(featureType, new Float(
+          featureOrder.put(featureType, Float.valueOf(
                   fs / jm.getFeatureSettings().getSetting().size()));
         }
         if (safeBoolean(setting.isDisplay()))
@@ -5127,7 +5135,7 @@ public class Jalview2XML
       for (int gs = 0; gs < jm.getFeatureSettings().getGroup().size(); gs++)
       {
         Group grp = jm.getFeatureSettings().getGroup().get(gs);
-        fgtable.put(grp.getName(), new Boolean(grp.isDisplay()));
+        fgtable.put(grp.getName(), Boolean.valueOf(grp.isDisplay()));
       }
       // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
       // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
@@ -5800,13 +5808,29 @@ public class Jalview2XML
     return datasetId;
   }
 
+  /**
+   * Add any saved DBRefEntry's to the sequence. An entry flagged as 'locus' is
+   * constructed as a special subclass GeneLocus.
+   * 
+   * @param datasetSequence
+   * @param sequence
+   */
   private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
   {
     for (int d = 0; d < sequence.getDBRef().size(); d++)
     {
       DBRef dr = sequence.getDBRef().get(d);
-      jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
-              dr.getSource(), dr.getVersion(), dr.getAccessionId());
+      DBRefEntry entry;
+      if (dr.isLocus())
+      {
+        entry = new GeneLocus(dr.getSource(), dr.getVersion(),
+                dr.getAccessionId());
+      }
+      else
+      {
+        entry = new DBRefEntry(dr.getSource(), dr.getVersion(),
+                dr.getAccessionId());
+      }
       if (dr.getMapping() != null)
       {
         entry.setMap(addMapping(dr.getMapping()));