JAL-2629 HMMs dropped on the alignment now map to the rf annotation

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

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 2abb1f8..f4ee3a2 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -358,6 +358,8 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   HiddenSequences getHiddenSequences();
 
+  HiddenColumns getHiddenColumns();
+
   /**
    * Compact representation of alignment
    * 
@@ -578,13 +580,18 @@ public interface AlignmentI extends AnnotatedCollectionI
    */
   AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
 
+  public void setHiddenColumns(HiddenColumns cols);
+
   /**
-   * Calculate the visible start and end index of an alignment. The result is
-   * returned an int array where: int[0] = startIndex, and int[1] = endIndex.
+   * Insert a sequence at a position in an alignment
    * 
-   * @param hiddenCols
-   * @return
+   * @param i
+   *          The idnex of the position.
+   * @param snew
+   *          The new sequence.
    */
-  public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols);
+  void insertSequenceAt(int i, SequenceI snew);
+
+  
 
 }