JAL-2388 last separation of hidden columns/col selection

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

diff --git a/src/jalview/ws/jws1/JPredThread.java b/src/jalview/ws/jws1/JPredThread.java
index 078f189..b0210d8 100644 (file)
--- a/src/jalview/ws/jws1/JPredThread.java
+++ b/src/jalview/ws/jws1/JPredThread.java
@@ -27,7 +27,6 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
-import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
@@ -115,7 +114,7 @@ class JPredThread extends JWS1Thread implements WSClientI
         return null;
       }
       AlignmentI al = null;
-      ColumnSelection alcsel = null;
+      HiddenColumns alhidden = null;
       int FirstSeq = -1; // the position of the query sequence in Alignment al
 
       JpredResult result = (JpredResult) this.result;
@@ -145,7 +144,7 @@ class JPredThread extends JWS1Thread implements WSClientI
                     .getAlignmentAndHiddenColumns(getGapChar());
             sqs = (SequenceI[]) alandcolsel[0];
             al = new Alignment(sqs);
-            alcsel = (ColumnSelection) alandcolsel[1];
+            alhidden = (HiddenColumns) alandcolsel[1];
           }
           else
           {
@@ -238,7 +237,7 @@ class JPredThread extends JWS1Thread implements WSClientI
           {
             // Adjust input view for gaps
             // propagate insertions into profile
-            alcsel = ColumnSelection.propagateInsertions(profileseq, al,
+            alhidden = HiddenColumns.propagateInsertions(profileseq, al,
                     input);
           }
         }
@@ -253,7 +252,7 @@ class JPredThread extends JWS1Thread implements WSClientI
                   alant.sequenceRef);
         }
       }
-      return new Object[] { al, alcsel }; // , FirstSeq, noMsa};
+      return new Object[] { al, alhidden }; // , FirstSeq, noMsa};
     }
 
     /**