Merge: 497958b 68dcaa7

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 2ceb245..5d11901 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -500,7 +500,7 @@ 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";
@@ -1129,7 +1129,7 @@ public class Jalview2XML
       view.setShowBoxes(av.getShowBoxes());
       view.setShowColourText(av.getColourText());
       view.setShowFullId(av.getShowJVSuffix());
-      view.setRightAlignIds(av.rightAlignIds);
+      view.setRightAlignIds(av.isRightAlignIds());
       view.setShowSequenceFeatures(av.isShowSequenceFeatures());
       view.setShowText(av.getShowText());
       view.setShowUnconserved(av.getShowUnconserved());
@@ -1151,7 +1151,7 @@ public class Jalview2XML
       {
         jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
 
-        String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer()
+        String[] renderOrder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
                 .getRenderOrder().toArray(new String[0]);
 
         Vector settingsAdded = new Vector();
@@ -1161,7 +1161,7 @@ public class Jalview2XML
         {
           for (int ro = 0; ro < renderOrder.length; ro++)
           {
-            gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer()
+            gstyle = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
                     .getFeatureStyle(renderOrder[ro]);
             Setting setting = new Setting();
             setting.setType(renderOrder[ro]);
@@ -1179,13 +1179,13 @@ public class Jalview2XML
             }
             else
             {
-              setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
+              setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer()
                       .getColour(renderOrder[ro]).getRGB());
             }
 
             setting.setDisplay(av.getFeaturesDisplayed().isVisible(
                     renderOrder[ro]));
-            float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer()
+            float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
                     .getOrder(renderOrder[ro]);
             if (rorder > -1)
             {
@@ -1197,7 +1197,7 @@ public class Jalview2XML
         }
 
         // Make sure we save none displayed feature settings
-        Iterator en = ap.seqPanel.seqCanvas.getFeatureRenderer()
+        Iterator en = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
                 .getFeatureColours().keySet().iterator();
         while (en.hasNext())
         {
@@ -1209,11 +1209,11 @@ public class Jalview2XML
 
           Setting setting = new Setting();
           setting.setType(key);
-          setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
+          setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer()
                   .getColour(key).getRGB());
 
           setting.setDisplay(false);
-          float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer()
+          float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
                   .getOrder(key);
           if (rorder > -1)
           {
@@ -1223,7 +1223,7 @@ public class Jalview2XML
           settingsAdded.addElement(key);
         }
         // is groups actually supposed to be a map here ?
-        en = ap.seqPanel.seqCanvas.getFeatureRenderer().getFeatureGroups()
+        en = ap.getSeqPanel().seqCanvas.getFeatureRenderer().getFeatureGroups()
                 .iterator();
         Vector groupsAdded = new Vector();
         while (en.hasNext())
@@ -1235,7 +1235,7 @@ public class Jalview2XML
           }
           Group g = new Group();
           g.setName(grp);
-          g.setDisplay(((Boolean) ap.seqPanel.seqCanvas
+          g.setDisplay(((Boolean) ap.getSeqPanel().seqCanvas
                   .getFeatureRenderer().checkGroupVisibility(grp, false))
                   .booleanValue());
           fs.addGroup(g);
@@ -1461,8 +1461,7 @@ 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
                     + "");
@@ -2319,7 +2318,10 @@ 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);
     }
     // ///////////////////////////////
 
@@ -3477,7 +3479,7 @@ public class Jalview2XML
 
     af.viewport.setConservationSelected(view.getConservationSelected());
     af.viewport.setShowJVSuffix(view.getShowFullId());
-    af.viewport.rightAlignIds = view.getRightAlignIds();
+    af.viewport.setRightAlignIds(view.getRightAlignIds());
     af.viewport.setFont(new java.awt.Font(view.getFontName(), view
             .getFontStyle(), view.getFontSize()));
     af.alignPanel.fontChanged();
@@ -3674,7 +3676,7 @@ public class Jalview2XML
       // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
       FeatureRendererSettings frs = new FeatureRendererSettings(
               renderOrder, fgtable, featureColours, 1.0f, featureOrder);
-      af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
+      af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
               .transferSettings(frs);
 
     }
@@ -3995,7 +3997,8 @@ 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;
@@ -4007,7 +4010,7 @@ 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)
@@ -4020,7 +4023,7 @@ public class Jalview2XML
       addDatasetRef(vamsasSet.getDatasetId(), ds);
     }
     // set the dataset for the newly imported alignment.
-    if (al.getDataset() == null)
+    if (al.getDataset() == null && !ignoreUnrefed)
     {
       al.setDataset(ds);
     }
@@ -4036,7 +4039,7 @@ 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
@@ -4047,7 +4050,10 @@ public class Jalview2XML
     {
       dsq = sq.getDatasetSequence();
     }
-
+    if (sq == null && ignoreUnrefed)
+    {
+      return;
+    }
     String sqid = vamsasSeq.getDsseqid();
     if (dsq == null)
     {