Jalview.isJS() --> Platform.isJS(), DBRefEntry[] --> List<DBRefEntry>

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 87b8d87..3c070dc 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -29,6 +29,7 @@ import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.GraphLine;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.RnaViewerModel;
@@ -52,7 +53,6 @@ import jalview.schemabinding.version2.Annotation;
 import jalview.schemabinding.version2.AnnotationColours;
 import jalview.schemabinding.version2.AnnotationElement;
 import jalview.schemabinding.version2.CalcIdParam;
-import jalview.schemabinding.version2.Colour;
 import jalview.schemabinding.version2.CompoundMatcher;
 import jalview.schemabinding.version2.DBRef;
 import jalview.schemabinding.version2.Features;
@@ -2110,7 +2110,7 @@ public class Jalview2XML
     vamsasSeq.setName(jds.getName());
     vamsasSeq.setSequence(jds.getSequenceAsString());
     vamsasSeq.setDescription(jds.getDescription());
-    jalview.datamodel.DBRefEntry[] dbrefs = null;
+    List<DBRefEntry> dbrefs = null;
     if (jds.getDatasetSequence() != null)
     {
       vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
@@ -2128,15 +2128,16 @@ public class Jalview2XML
     }
     if (dbrefs != null)
     {
-      for (int d = 0; d < dbrefs.length; d++)
+      for (int d = 0, n = dbrefs.size(); d < n; 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 e = dbrefs.get(d);
+        dbref.setSource(e.getSource());
+        dbref.setVersion(e.getVersion());
+        dbref.setAccessionId(e.getAccessionId());
+        if (e.hasMap())
         {
-          Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
+          Mapping mp = createVamsasMapping(e.getMap(), parentseq,
                   jds, recurse);
           dbref.setMapping(mp);
         }
@@ -2678,6 +2679,7 @@ public class Jalview2XML
     if (errorMessage != null)
     {
       final String finalErrorMessage = errorMessage;
+      errorMessage = null;
       if (raiseGUI)
       {
         javax.swing.SwingUtilities.invokeLater(new Runnable()
@@ -2695,10 +2697,10 @@ public class Jalview2XML
       }
       else
       {
-        System.err.println("Problem loading Jalview file: " + errorMessage);
+        System.err.println(
+                "Problem loading Jalview file: " + finalErrorMessage);
       }
     }
-    errorMessage = null;
   }
 
   Map<String, String> alreadyLoadedPDB = new HashMap<>();