JAL-3518 basic refactoring / pull up of superposeStructures; to tidy!

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

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index aa39ee7..6dd7d50 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -22,9 +22,7 @@ package jalview.gui;
 
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
-import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.gui.StructureViewer.ViewerType;
@@ -772,19 +770,8 @@ public abstract class StructureViewerBase extends GStructureViewer
     String reply = null;
     try
     {
-      AlignmentI[] als = new Alignment[_alignwith.size()];
-      HiddenColumns[] alc = new HiddenColumns[_alignwith.size()];
-      int[] alm = new int[_alignwith.size()];
-      int a = 0;
-
-      for (AlignmentViewPanel alignPanel : _alignwith)
-      {
-        als[a] = alignPanel.getAlignment();
-        alm[a] = -1;
-        alc[a++] = alignPanel.getAlignment().getHiddenColumns();
-      }
-      reply = getBinding().superposeStructures(als, alm, alc);
-      if (reply != null)
+      reply = getBinding().superposeStructures(_alignwith);
+      if (reply != null && !reply.isEmpty())
       {
         String text = MessageManager
                 .formatMessage("error.superposition_failed", reply);