X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=03fc545434ecb15c82ed8f3ce405b10fb3229201;hb=2780a5c99798d048f690752f69a61c131e5e24d1;hp=ec76cb99abaf45a1264721752e550ffceba7f99f;hpb=4c6cd08af580ff73cfce39bec34ae4658a4b4b34;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index ec76cb9..03fc545 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -21,7 +21,9 @@
 package jalview.datamodel;
 
 import jalview.datamodel.features.SequenceFeaturesI;
+import jalview.util.MapList;
 
+import java.util.BitSet;
 import java.util.List;
 import java.util.Vector;
 
@@ -118,9 +120,9 @@ public interface SequenceI extends ASequenceI
   public String getSequenceAsString(int start, int end);
 
   /**
-   * Get the sequence as a character array
+   * Answers a copy of the sequence as a character array
    * 
-   * @return seqeunce and any gaps
+   * @return
    */
   public char[] getSequence();
 
@@ -202,6 +204,16 @@ 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
    * 
@@ -265,7 +277,7 @@ 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();
 
@@ -500,4 +512,32 @@ public interface SequenceI extends ASequenceI
    * @return
    */
   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();
+
+  /**
+   * Replaces every occurrence of c1 in the sequence with c2 and returns the
+   * number of characters changed
+   * 
+   * @param c1
+   * @param c2
+   */
+  public int replace(char c1, char c2);
+
+  GeneLociI getGeneLoci();
+
+  void setGeneLoci(String speciesId, String assemblyId,
+          String chromosomeId, MapList map);
 }