X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=08fd3065670259c5e0c6ac88c7b22f3b79ac724c;hb=6a62797914bea08062a44e1b30edcdaa8fa3c96f;hp=dfacd544137b169f01c7ce82aca82aa149325829;hpb=9c37999eb4b461a5c7a94e10ac39583c1c29200a;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index dfacd54..08fd306 100644
--- 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.seqPanel.seqCanvas.getFeatureRenderer()
                     .getOrder(renderOrder[ro]);
@@ -1419,7 +1419,16 @@ public class Jalview2XML
         calcIdSet.add(aa[i].getCalcId());
         an.setCalcId(aa[i].getCalcId());
       }
-
+      if (aa[i].hasProperties())
+      {
+        for (String pr : aa[i].getProperties())
+        {
+          Property prop = new Property();
+          prop.setName(pr);
+          prop.setValue(aa[i].getProperty(pr));
+          an.addProperty(prop);
+        }
+      }
       AnnotationElement ae;
       if (aa[i].annotations != null)
       {
@@ -1447,8 +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
                     + "");
@@ -2305,7 +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);
     }
     // ///////////////////////////////
 
@@ -2631,6 +2642,14 @@ public class Jalview2XML
           jaa.belowAlignment = an[i].isBelowAlignment();
         }
         jaa.setCalcId(an[i].getCalcId());
+        if (an[i].getPropertyCount() > 0)
+        {
+          for (jalview.schemabinding.version2.Property prop : an[i]
+                  .getProperty())
+          {
+            jaa.setProperty(prop.getName(), prop.getValue());
+          }
+        }
         if (jaa.autoCalculated)
         {
           autoAlan.add(new JvAnnotRow(i, jaa));
@@ -3587,7 +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++)
@@ -3639,7 +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()));
         }
       }
@@ -3969,7 +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;
@@ -3981,7 +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)
@@ -4010,7 +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
@@ -4021,7 +4041,10 @@ public class Jalview2XML
     {
       dsq = sq.getDatasetSequence();
     }
-
+    if (sq == null && ignoreUnrefed)
+    {
+      return;
+    }
     String sqid = vamsasSeq.getDsseqid();
     if (dsq == null)
     {