JAL-1605 merge commit

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 8ddd050..aa2ae7a 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -498,7 +498,7 @@ public class Jalview2XML
     for (String dssids : dsses.keySet())
     {
       AlignFrame _af = dsses.get(dssids);
-      String jfileName = MessageManager.formatMessage("label.dataset_for", new String[]{fileName,_af.getTitle()});
+      String jfileName = fileName + " Dataset for " + _af.getTitle();
       if (!jfileName.endsWith(".xml"))
       {
         jfileName = jfileName + ".xml";
@@ -1145,7 +1145,7 @@ public class Jalview2XML
       view.setFollowHighlight(av.followHighlight);
       view.setFollowSelection(av.followSelection);
       view.setIgnoreGapsinConsensus(av.getIgnoreGapsConsensus());
-      if (av.featuresDisplayed != null)
+      if (av.getFeaturesDisplayed() != null)
       {
         jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
 
@@ -1180,7 +1180,7 @@ public class Jalview2XML
                       .getColour(renderOrder[ro]).getRGB());
             }
 
-            setting.setDisplay(av.featuresDisplayed
+            setting.setDisplay(av.getFeaturesDisplayed()
                     .containsKey(renderOrder[ro]));
             float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
                     .getOrder(renderOrder[ro]);
@@ -1456,8 +1456,7 @@ public class Jalview2XML
           }
 
           ae.setPosition(a);
-          if (aa[i].annotations[a].secondaryStructure != ' '
-                  && aa[i].annotations[a].secondaryStructure != '\0')
+          if (aa[i].annotations[a].secondaryStructure > ' ')
           {
             ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure
                     + "");
@@ -2314,7 +2313,10 @@ public class Jalview2XML
     }
     else
     {
-      recoverDatasetFor(vamsasSet, al);
+      // recover dataset - passing on flag indicating if this a 'viewless'
+      // sequence set (a.k.a. a stored dataset for the project)
+      recoverDatasetFor(vamsasSet, al, object.getJalviewModelSequence()
+              .getViewportCount() == 0);
     }
     // ///////////////////////////////
 
@@ -3604,7 +3606,7 @@ public class Jalview2XML
     // recover featre settings
     if (jms.getFeatureSettings() != null)
     {
-      af.viewport.featuresDisplayed = new Hashtable();
+      af.viewport.setFeaturesDisplayed(new Hashtable());
       String[] renderOrder = new String[jms.getFeatureSettings()
               .getSettingCount()];
       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
@@ -3656,7 +3658,7 @@ public class Jalview2XML
         }
         if (setting.getDisplay())
         {
-          af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
+          af.viewport.getFeaturesDisplayed().put(setting.getType(), new Integer(
                   setting.getColour()));
         }
       }
@@ -3986,7 +3988,8 @@ public class Jalview2XML
     }
   }
 
-  private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al)
+  private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al,
+          boolean ignoreUnrefed)
   {
     jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
     Vector dseqs = null;
@@ -3998,7 +4001,7 @@ public class Jalview2XML
     for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
     {
       Sequence vamsasSeq = vamsasSet.getSequence(i);
-      ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs);
+      ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed);
     }
     // create a new dataset
     if (ds == null)
@@ -4027,7 +4030,7 @@ public class Jalview2XML
    *          vector to add new dataset sequence to
    */
   private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
-          AlignmentI ds, Vector dseqs)
+          AlignmentI ds, Vector dseqs, boolean ignoreUnrefed)
   {
     // JBP TODO: Check this is called for AlCodonFrames to support recovery of
     // xRef Codon Maps
@@ -4038,7 +4041,10 @@ public class Jalview2XML
     {
       dsq = sq.getDatasetSequence();
     }
-
+    if (sq == null && ignoreUnrefed)
+    {
+      return;
+    }
     String sqid = vamsasSeq.getDsseqid();
     if (dsq == null)
     {