X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=6992a8db9aee7b69bea20bed1fa2fd1189569bc4;hb=35e6fbcf5ba60709ffccaf02df6c8b414dfa2647;hp=dbf3ed363b3f19b2d2cecf0d0d260b553f842887;hpb=ffa5c07d90b4a933762a5d9faa0578c11693d63a;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index dbf3ed3..6992a8d 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -22,6 +22,7 @@ package jalview.datamodel;
 
 import jalview.datamodel.features.SequenceFeaturesI;
 
+import java.util.BitSet;
 import java.util.List;
 import java.util.Vector;
 
@@ -202,30 +203,6 @@ public interface SequenceI extends ASequenceI
   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
    * 
@@ -289,7 +266,7 @@ public interface SequenceI extends ASequenceI
    * Answers a list of all sequence features associated with this sequence. The
    * list may be held by the sequence's dataset sequence if that is defined.
    * 
-   * @return hard reference to array
+   * @return
    */
   public List<SequenceFeature> getSequenceFeatures();
 
@@ -510,14 +487,32 @@ public interface SequenceI extends ASequenceI
   public List<DBRefEntry> getPrimaryDBRefs();
 
   /**
-   * Returns a (possibly empty) list of sequence features that overlap the range
-   * from-to (inclusive), optionally restricted to one or more specified feature
-   * types
+   * Returns a (possibly empty) list of sequence features that overlap the given
+   * alignment column range, optionally restricted to one or more specified
+   * feature types. If the range is all gaps, then features which enclose it are
+   * included (but not contact features).
    * 
-   * @param from
-   * @param to
+   * @param fromCol
+   *          start column of range inclusive (1..)
+   * @param toCol
+   *          end column of range inclusive (1..)
    * @param types
+   *          optional feature types to restrict results to
    * @return
    */
-  List<SequenceFeature> findFeatures(int from, int to, String... types);
+  List<SequenceFeature> findFeatures(int fromCol, int toCol, String... types);
+
+  /**
+   * Method to call to indicate that the sequence (characters or alignment/gaps)
+   * has been modified. Provided to allow any cursors on residue/column
+   * positions to be invalidated.
+   */
+  void sequenceChanged();
+  
+  /**
+   * 
+   * @return BitSet corresponding to index [0,length) where Comparison.isGap()
+   *         returns true.
+   */
+  BitSet getInsertionsAsBits();
 }