JAL-2629 add basic parameter adjustment to hmmsearch/align

[jalview.git] / src / jalview / datamodel / AllColsCollection.java

diff --git a/src/jalview/datamodel/AllColsCollection.java b/src/jalview/datamodel/AllColsCollection.java
index 1b1a5dd..4ac4f83 100644 (file)
--- a/src/jalview/datamodel/AllColsCollection.java
+++ b/src/jalview/datamodel/AllColsCollection.java
@@ -27,20 +27,22 @@ import java.util.Iterator;
 public class AllColsCollection implements AlignmentColsCollectionI
 {
   int start;
+
   int end;
-  ColumnSelection hidden;
-  
-  public AllColsCollection(int s, int e, ColumnSelection colsel)
+
+  HiddenColumns hidden;
+
+  public AllColsCollection(int s, int e, AlignmentI al)
   {
     start = s;
     end = e;
-    hidden = colsel;
+    hidden = al.getHiddenColumns();
   }
-  
+
   @Override
   public Iterator<Integer> iterator()
   {
-    return new AllColsIterator(start,end,hidden);
+    return new AllColsIterator(start, end, hidden);
   }
 
   @Override