X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=d06adcbd4f68b5fefbef332c059de6844ffadca5;hb=b5667f39acdf309cd92881b73edfda591e0acaf4;hp=9045735594453832a054f9ce99a65b3793ee9a46;hpb=4306800413a28da102c15fe7301bcac7816445fe;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 9045735..d06adcb 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -116,9 +116,11 @@ public interface SequenceI extends ASequenceI
    * get a range on the sequence as a string
    * 
    * @param start
-   *          position relative to start of sequence including gaps (from 0)
+   *          (inclusive) position relative to start of sequence including gaps
+   *          (from 0)
    * @param end
-   *          position relative to start of sequence including gaps (from 0)
+   *          (exclusive) position relative to start of sequence including gaps
+   *          (from 0)
    * 
    * @return String containing all gap and symbols in specified range
    */
@@ -210,14 +212,17 @@ 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
+   * Returns the sequence positions for first and last residues lying within the
+   * given column positions [fromColum,toColumn] (where columns are numbered
+   * from 1), or null if no residues are included in the range
    * 
    * @param fromColum
+   *          - first column base 1
    * @param toColumn
+   *          - last column, base 1
    * @return
    */
-  public Range findPositions(int fromColum, int toColumn);
+  public ContiguousI findPositions(int fromColum, int toColumn);
 
   /**
    * Returns an int array where indices correspond to each residue in the
@@ -500,18 +505,6 @@ public interface SequenceI extends ASequenceI
   public List<DBRefEntry> getPrimaryDBRefs();
 
   /**
-   * Updates mapping of Hidden Markov Model nodes to aligned sequence positions
-   * (e.g. after an alignment edit). The nodes of the HMM (excluding the first
-   * node, with model average values), are associated in turn with non-gapped
-   * sequence positions.
-   */
-  public void updateHMMMapping();
-
-  boolean isHMMConsensusSequence();
-
-  void setIsHMMConsensusSequence(boolean isHMMConsensusSequence);
-
-  /**
    * Answers true if the sequence has annotation for Hidden Markov Model
    * information content, else false
    */
@@ -547,8 +540,6 @@ public interface SequenceI extends ASequenceI
    */
   BitSet getInsertionsAsBits();
 
-  void mapToReference(AlignmentAnnotation rf);
-
   /**
    * Replaces every occurrence of c1 in the sequence with c2 and returns the
    * number of characters changed
@@ -586,7 +577,7 @@ public interface SequenceI extends ASequenceI
    *          the iterator to use
    * @return a String corresponding to the sequence
    */
-  public String getSequenceStringFromIterator(Iterator<int[]> it);
+  String getSequenceStringFromIterator(Iterator<int[]> it);
 
   /**
    * Locate the first position in this sequence which is not contained in an
@@ -596,5 +587,12 @@ public interface SequenceI extends ASequenceI
    *          iterator over regions
    * @return first residue not contained in regions
    */
-  public int firstResidueOutsideIterator(Iterator<int[]> it);
+  int firstResidueOutsideIterator(Iterator<int[]> it);
+
+  /**
+   * Answers true if this sequence has an associated Hidden Markov Model
+   * 
+   * @return
+   */
+  boolean hasHMMProfile();
 }