JAL-629 Test and fix --annotation --ssannotation args. Added a viewerType arg/subval...

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

diff --git a/src/jalview/gui/StructureViewer.java b/src/jalview/gui/StructureViewer.java
index 5effa1a..0c12eb2 100644 (file)
--- a/src/jalview/gui/StructureViewer.java
+++ b/src/jalview/gui/StructureViewer.java
@@ -119,6 +119,12 @@ public class StructureViewer
   public JalviewStructureDisplayI viewStructures(PDBEntry[] pdbs,
           SequenceI[] seqs, AlignmentPanel ap)
   {
+    return viewStructures(pdbs, seqs, ap, null);
+  }
+
+  public JalviewStructureDisplayI viewStructures(PDBEntry[] pdbs,
+          SequenceI[] seqs, AlignmentPanel ap, ViewerType viewerType)
+  {
     JalviewStructureDisplayI viewer = onlyOnePdb(pdbs, seqs, ap);
     if (viewer != null)
     {
@@ -128,7 +134,8 @@ public class StructureViewer
       return viewer;
     }
 
-    ViewerType viewerType = getViewerType();
+    if (viewerType == null)
+      viewerType = getViewerType();
 
     Map<PDBEntry, SequenceI[]> seqsForPdbs = getSequencesForPdbs(pdbs,
             seqs);
@@ -299,6 +306,12 @@ public class StructureViewer
   public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
           SequenceI[] seqsForPdb, AlignmentPanel ap)
   {
+    return viewStructures(pdb, seqsForPdb, ap, null);
+  }
+
+  public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
+          SequenceI[] seqsForPdb, AlignmentPanel ap, ViewerType viewerType)
+  {
     if (sview != null)
     {
       sview.setAlignAddedStructures(superposeAdded);
@@ -311,7 +324,8 @@ public class StructureViewer
       sview.raiseViewer();
       return sview;
     }
-    ViewerType viewerType = getViewerType();
+    if (viewerType == null)
+      viewerType = getViewerType();
     if (viewerType.equals(ViewerType.JMOL))
     {
       sview = new AppJmol(pdb, seqsForPdb, null, ap);