Merge branch 'develop' into Jalview-JS/develop

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

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 4d772a1..6340e64 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -39,6 +39,7 @@ 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;
@@ -59,7 +60,6 @@ import jalview.gui.AlignmentPanel;
 import jalview.gui.AppVarna;
 import jalview.gui.ChimeraViewFrame;
 import jalview.gui.Desktop;
-import jalview.gui.FeatureRenderer;
 import jalview.gui.JvOptionPane;
 import jalview.gui.OOMWarning;
 import jalview.gui.PCAPanel;
@@ -93,6 +93,7 @@ import jalview.util.matcher.Condition;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.PCAModel;
 import jalview.viewmodel.ViewportRanges;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
 import jalview.ws.jws2.Jws2Discoverer;
@@ -1512,11 +1513,14 @@ 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();
 
-        FeatureRenderer fr = ap.getSeqPanel().seqCanvas
+        FeatureRendererModel fr = ap.getSeqPanel().seqCanvas
                 .getFeatureRenderer();
         String[] renderOrder = fr.getRenderOrder().toArray(new String[0]);
 
@@ -2520,6 +2524,10 @@ public class Jalview2XML
         parentseq = jds;
       }
     }
+
+    /*
+     * save any dbrefs; special subclass GeneLocus is flagged as 'locus'
+     */
     if (dbrefs != null)
     {
       for (int d = 0, nd = dbrefs.size(); d < nd; d++)
@@ -2529,13 +2537,16 @@ public class Jalview2XML
         dbref.setSource(ref.getSource());
         dbref.setVersion(ref.getVersion());
         dbref.setAccessionId(ref.getAccessionId());
+        if (ref instanceof GeneLocus)
+        {
+          dbref.setLocus(true);
+        }
         if (ref.hasMap())
         {
           Mapping mp = createVamsasMapping(ref.getMap(), parentseq,
                   jds, recurse);
           dbref.setMapping(mp);
         }
-        // vamsasSeq.addDBRef(dbref);
         vamsasSeq.getDBRef().add(dbref);
       }
     }
@@ -3166,25 +3177,25 @@ 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
     {
@@ -3339,8 +3350,10 @@ 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
@@ -4450,7 +4463,7 @@ public class Jalview2XML
      */
     String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
     chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
-            "chimera", null);
+            "chimera", ".py");
 
     Set<Entry<File, StructureData>> fileData = data.getFileData()
             .entrySet();
@@ -4536,7 +4549,7 @@ 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]));
@@ -5036,11 +5049,14 @@ 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)
     {
-      FeatureRenderer fr = af.alignPanel.getSeqPanel().seqCanvas
+      FeatureRendererModel fr = af.alignPanel.getSeqPanel().seqCanvas
               .getFeatureRenderer();
       FeaturesDisplayed fdi;
       viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
@@ -5140,7 +5156,7 @@ public class Jalview2XML
         }
         else
         {
-          featureOrder.put(featureType, new Float(
+          featureOrder.put(featureType, Float.valueOf(
                   fs / jm.getFeatureSettings().getSetting().size()));
         }
         if (safeBoolean(setting.isDisplay()))
@@ -5152,7 +5168,7 @@ 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() ?
@@ -5825,13 +5841,29 @@ 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()));