X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureViewerBase.java;h=e73ce07bcee5dddc98d8a078295d55de919061de;hb=983d1a8699629252cde6bf5eb47f74064049884e;hp=d7f7c3156d02e3c5295efbd40f52161b72faefdd;hpb=bdf1428136ce701e58a90f346973dbdf9d42b316;p=jalview.git

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index d7f7c31..e73ce07 100644
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -23,7 +23,7 @@ package jalview.gui;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.gui.StructureViewer.ViewerType;
@@ -812,7 +812,7 @@ public abstract class StructureViewerBase extends GStructureViewer
     try
     {
       AlignmentI[] als = new Alignment[_alignwith.size()];
-      ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];
+      HiddenColumns[] alc = new HiddenColumns[_alignwith.size()];
       int[] alm = new int[_alignwith.size()];
       int a = 0;
   
@@ -820,7 +820,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       {
         als[a] = ap.av.getAlignment();
         alm[a] = -1;
-        alc[a++] = ap.av.getColumnSelection();
+        alc[a++] = ap.av.getAlignment().getHiddenColumns();
       }
       reply = getBinding().superposeStructures(als, alm, alc);
       if (reply != null)
@@ -919,7 +919,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       {
         // TODO: cope with multiple PDB files in view
         in = new BufferedReader(
-                new FileReader(getBinding().getPdbFile()[0]));
+                new FileReader(getBinding().getStructureFiles()[0]));
         File outFile = chooser.getSelectedFile();
   
         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
@@ -991,7 +991,7 @@ public abstract class StructureViewerBase extends GStructureViewer
      * enable 'Superpose with' if more than one mapped structure
      */
     viewSelectionMenu.setEnabled(false);
-    if (getBinding().getPdbFile().length > 1
+    if (getBinding().getStructureFiles().length > 1
             && getBinding().getSequence().length > 1)
     {
       viewSelectionMenu.setEnabled(true);