Merge remote-tracking branch

[jalview.git] / src / jalview / ws / jws1 / MsaWSThread.java

diff --git a/src/jalview/ws/jws1/MsaWSThread.java b/src/jalview/ws/jws1/MsaWSThread.java
index 3fd7c5a..72d41c9 100644 (file)
--- a/src/jalview/ws/jws1/MsaWSThread.java
+++ b/src/jalview/ws/jws1/MsaWSThread.java
@@ -26,7 +26,7 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.AlignmentView;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
@@ -632,7 +632,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
       orders[j] = null;
     }
     SequenceI[] alignment = (SequenceI[]) newview[0];
-    ColumnSelection columnselection = (ColumnSelection) newview[1];
+    HiddenColumns hidden = (HiddenColumns) newview[1];
     Alignment al = new Alignment(alignment);
     // TODO: add 'provenance' property to alignment from the method notes
     // accompanying each subjob
@@ -646,7 +646,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
 
     if (newFrame)
     {
-      AlignFrame af = new AlignFrame(al, columnselection,
+      AlignFrame af = new AlignFrame(al, hidden,
               AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
 
       // initialise with same renderer settings as in parent alignframe.
@@ -670,8 +670,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI
 
             while (j < l)
             {
-              if (((AlignmentOrder) alorders.get(i))
-                      .equals((alorders.get(j))))
+              if (((AlignmentOrder) alorders.get(i)).equals((alorders
+                      .get(j))))
               {
                 alorders.remove(j);
                 l--;