X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;fp=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=5b3d78262b3602978c6bfa36adc08153759656ce;hb=04a4d60a50394d846d0479c442facebe360b5b9c;hp=fb723e6064c88ee84131f66f360860fe757de049;hpb=653e250e0a2a5dd455ae4c52794c4ce0de340418;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index fb723e6..5b3d782 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -24,6 +24,7 @@ import jalview.datamodel.features.SequenceFeaturesI;
 import jalview.util.MapList;
 
 import java.util.BitSet;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Vector;
 
@@ -45,6 +46,10 @@ public interface SequenceI extends ASequenceI
    */
   public void setName(String name);
 
+  public HiddenMarkovModel getHMM();
+
+  public void setHMM(HiddenMarkovModel hmm);
+
   /**
    * Get the display name
    */
@@ -224,6 +229,13 @@ 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.
@@ -487,6 +499,16 @@ public interface SequenceI extends ASequenceI
    */
   public List<DBRefEntry> getPrimaryDBRefs();
 
+  boolean isHMMConsensusSequence();
+
+  void setIsHMMConsensusSequence(boolean isHMMConsensusSequence);
+
+  /**
+   * Answers true if the sequence has annotation for Hidden Markov Model
+   * information content, else false
+   */
+  boolean hasHMMAnnotation();
+
   /**
    * Returns a (possibly empty) list of sequence features that overlap the given
    * alignment column range, optionally restricted to one or more specified
@@ -524,7 +546,7 @@ public interface SequenceI extends ASequenceI
    * @param c1
    * @param c2
    */
-  public int replace(char c1, char c2);
+  int replace(char c1, char c2);
 
   /**
    * Answers the GeneLociI, or null if not known
@@ -543,4 +565,26 @@ public interface SequenceI extends ASequenceI
    */
   void setGeneLoci(String speciesId, String assemblyId,
           String chromosomeId, MapList map);
+
+
+  /**
+   * Returns the sequence string constructed from the substrings of a sequence
+   * defined by the int[] ranges provided by an iterator. E.g. the iterator
+   * could iterate over all visible regions of the alignment
+   * 
+   * @param it
+   *          the iterator to use
+   * @return a String corresponding to the sequence
+   */
+  public String getSequenceStringFromIterator(Iterator<int[]> it);
+
+  /**
+   * Locate the first position in this sequence which is not contained in an
+   * iterator region. If no such position exists, return 0
+   * 
+   * @param it
+   *          iterator over regions
+   * @return first residue not contained in regions
+   */
+  public int firstResidueOutsideIterator(Iterator<int[]> it);
 }