X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=c1687fe3dbe812899e70ab9d2081c91a6c6c267c;hb=e2c3b3602486cee3f85dd8dfc7856a5ce6701669;hp=6992a8db9aee7b69bea20bed1fa2fd1189569bc4;hpb=35e6fbcf5ba60709ffccaf02df6c8b414dfa2647;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 6992a8d..c1687fe 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -119,9 +119,9 @@ 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();
 
@@ -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.
@@ -515,4 +532,13 @@ public interface SequenceI extends ASequenceI
    *         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);
 }