Make sure annots are alignment width

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 45c76ee..198db44 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -209,6 +209,19 @@ public class Jalview2XML
 
     vamsasSet.setGapChar(jal.getGapCharacter() + "");
 
+    if(jal.getProperties()!=null)
+    {
+      Enumeration en = jal.getProperties().keys();
+      while(en.hasMoreElements())
+      {
+        String key = en.nextElement().toString();
+        SequenceSetProperties ssp = new SequenceSetProperties();
+        ssp.setKey(key);
+        ssp.setValue(jal.getProperties().get(key).toString());
+        vamsasSet.addSequenceSetProperties(ssp);
+      }
+    }
+
     JSeq jseq;
 
     //SAVE SEQUENCES
@@ -1207,6 +1220,13 @@ public class Jalview2XML
     jalview.datamodel.Alignment al =
         new jalview.datamodel.Alignment(orderedSeqs);
 
+    for(int i=0; i<vamsasSet.getSequenceSetPropertiesCount(); i++ )
+    {
+      SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
+      al.setProperty(ssp.getKey(), ssp.getValue());
+    }
+
+
     al.setDataset(null);
     /////////////////////////////////
 
@@ -1895,7 +1915,7 @@ public class Jalview2XML
               else if(comp!=null)
               {
                 StructureSelectionManager.getStructureSelectionManager()
-                    .setMapping(seq, pdbFile,
+                    .setMapping(seq, null, pdbFile,
                                 jalview.io.AppletFormatAdapter.FILE);
 
                 ( (AppJMol) comp).addSequence(seq);