Merge branch 'develop' into feature/JAL-3187linkedFeatures

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

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 11404dc..9a303e2 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;
@@ -58,7 +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;
@@ -92,6 +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;
@@ -1503,7 +1505,7 @@ public class Jalview2XML
       {
         FeatureSettings fs = new FeatureSettings();
 
-        FeatureRenderer fr = ap.getSeqPanel().seqCanvas
+        FeatureRendererModel fr = ap.getSeqPanel().seqCanvas
                 .getFeatureRenderer();
         String[] renderOrder = fr.getRenderOrder().toArray(new String[0]);
 
@@ -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);
       }
     }
@@ -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"
@@ -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]));
@@ -4978,21 +4986,22 @@ public class Jalview2XML
       }
     }
 
+    /*
+     * turn off 'alignment colour applies to all groups'
+     * while restoring global colour scheme
+     */
+    viewport.setColourAppliesToAllGroups(false);
     viewport.setGlobalColourScheme(cs);
     viewport.getResidueShading().setThreshold(pidThreshold,
             view.isIgnoreGapsinConsensus());
     viewport.getResidueShading()
             .setConsensus(viewport.getSequenceConsensusHash());
-    viewport.setColourAppliesToAllGroups(false);
-
     if (safeBoolean(view.isConservationSelected()) && cs != null)
     {
       viewport.getResidueShading()
               .setConservationInc(safeInt(view.getConsThreshold()));
     }
-
     af.changeColour(cs);
-
     viewport.setColourAppliesToAllGroups(true);
 
     viewport
@@ -5014,7 +5023,7 @@ public class Jalview2XML
     // 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());
@@ -5114,7 +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()))
@@ -5126,7 +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() ?
@@ -5799,13 +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()));