X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=0f78bdb4f1fd6341b6d011d4e4fb8063a5a2909d;hb=0e65ec37e2c956e0ad94feda6fd07b7c3a9003ee;hp=e4be5ee3dd299f7f7e46844082f8e2f580e3f318;hpb=df2bf54c7050c42db156e96e73bbabce63e718d7;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index e4be5ee..0f78bdb 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -176,7 +176,7 @@ public interface SequenceI extends ASequenceI
   public String getDescription();
 
   /**
-   * Return the alignment column for a sequence position
+   * Return the alignment column (from 1..) for a sequence position
    * 
    * @param pos
    *          lying from start to end
@@ -191,16 +191,41 @@ public interface SequenceI extends ASequenceI
   public int findIndex(int pos);
 
   /**
-   * Returns the sequence position for an alignment position
+   * Returns the sequence position for an alignment position.
    * 
    * @param i
    *          column index in alignment (from 0..<length)
    * 
-   * @return residue number for residue (left of and) nearest ith column
+   * @return TODO: JAL-2562 - residue number for residue (left of and) nearest
+   *         ith column
    */
   public int findPosition(int i);
 
   /**
+   * Returns the range of sequence positions included in the given alignment
+   * position range. If no positions are included (the range is entirely gaps),
+   * then returns null.
+   * 
+   * <pre>
+   * Example: 
+   * >Seq/8-13
+   * ABC--DE-F
+   * findPositions(1, 4) returns Range(9, 9) // B only
+   * findPositions(3, 4) returns null // all gaps
+   * findPositions(2, 6) returns Range(10, 12) // CDE
+   * findPositions(3, 7) returns Range(11,12) // DE
+   * </pre>
+   * 
+   * @param fromCol
+   *          first aligned column position (base 0, inclusive)
+   * @param toCol
+   *          last aligned column position (base 0, inclusive)
+   * 
+   * @return
+   */
+  public Range findPositions(int fromCol, int toCol);
+
+  /**
    * Returns an int array where indices correspond to each residue in the
    * sequence and the element value gives its position in the alignment
    * 
@@ -495,4 +520,9 @@ public interface SequenceI extends ASequenceI
    * @return
    */
   List<SequenceFeature> findFeatures(int from, int to, String... types);
+
+  /**
+   * Invalidate any cursors on the sequence (e.g. after an edit)
+   */
+  public void zapCursor();
 }