Merge branch 'develop' into feature/JAL-2422ChimeraX

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

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index ef885c1..df4a93e 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;
@@ -1499,6 +1501,9 @@ public class Jalview2XML
       view.setFollowHighlight(av.isFollowHighlight());
       view.setFollowSelection(av.followSelection);
       view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
+      view.setShowComplementFeatures(av.isShowComplementFeatures());
+      view.setShowComplementFeaturesOnTop(
+              av.isShowComplementFeaturesOnTop());
       if (av.getFeaturesDisplayed() != null)
       {
         FeatureSettings fs = new FeatureSettings();
@@ -2105,7 +2110,7 @@ public class Jalview2XML
           final String viewId = viewFrame.getViewId();
           state.setViewId(viewId);
           state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
-          state.setColourwithAlignPanel(viewFrame.isUsedforcolourby(ap));
+          state.setColourwithAlignPanel(viewFrame.isUsedForColourBy(ap));
           state.setColourByJmol(viewFrame.isColouredByViewer());
           state.setType(viewFrame.getViewerType().toString());
           // pdb.addStructureState(state);
@@ -2505,21 +2510,29 @@ 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 +3163,25 @@ 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
     {
@@ -3323,8 +3336,10 @@ public class Jalview2XML
                   || tmpSeq.getEnd() != jseq.getEnd())
           {
             System.err.println(
-                    "Warning JAL-2154 regression: updating start/end for sequence "
-                            + tmpSeq.toString() + " to " + jseq);
+                    String.format("Warning JAL-2154 regression: updating start/end for sequence %s from %d/%d to %d/%d",
+                            tmpSeq.getName(), tmpSeq.getStart(),
+                            tmpSeq.getEnd(), jseq.getStart(),
+                            jseq.getEnd()));
           }
         }
         else
@@ -4434,7 +4449,7 @@ public class Jalview2XML
      */
     String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
     chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
-            "chimera", null);
+            "chimera", ".py");
 
     Set<Entry<File, StructureData>> fileData = data.getFileData()
             .entrySet();
@@ -5009,6 +5024,9 @@ public class Jalview2XML
     viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip()));
     viewport.setShowGroupConsensus(view.isShowGroupConsensus());
     viewport.setShowGroupConservation(view.isShowGroupConservation());
+    viewport.setShowComplementFeatures(view.isShowComplementFeatures());
+    viewport.setShowComplementFeaturesOnTop(
+            view.isShowComplementFeaturesOnTop());
 
     // recover feature settings
     if (jm.getFeatureSettings() != null)
@@ -5798,13 +5816,29 @@ 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()));