X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=c1687fe3dbe812899e70ab9d2081c91a6c6c267c;hb=e2c3b3602486cee3f85dd8dfc7856a5ce6701669;hp=6840df83edce2ea4cbf02b16b7c38a85df38c7fe;hpb=ff450fad8709ae81919af7a15ea382af7292794c;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 6840df8..c1687fe 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -203,6 +203,16 @@ public interface SequenceI extends ASequenceI
   public int findPosition(int i);
 
   /**
+   * Returns the from-to sequence positions (start..) for the given column
+   * positions (1..), or null if no residues are included in the range
+   * 
+   * @param fromColum
+   * @param toColumn
+   * @return
+   */
+  public Range findPositions(int fromColum, int toColumn);
+
+  /**
    * Returns an int array where indices correspond to each residue in the
    * sequence and the element value gives its position in the alignment
    * 
@@ -212,6 +222,13 @@ public interface SequenceI extends ASequenceI
   public int[] gapMap();
 
   /**
+   * Build a bitset corresponding to sequence gaps
+   * 
+   * @return a BitSet where set values correspond to gaps in the sequence
+   */
+  public BitSet gapBitset();
+
+  /**
    * Returns an int array where indices correspond to each position in sequence
    * char array and the element value gives the result of findPosition for that
    * index in the sequence.