Merge branch 'develop' into features/mchmmer

[jalview.git] / src / jalview / datamodel / SequenceI.java

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 52072bb..6d34d07 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -21,6 +21,7 @@
 package jalview.datamodel;
 
 import jalview.datamodel.features.SequenceFeaturesI;
+import jalview.util.MapList;
 
 import java.util.BitSet;
 import java.util.Iterator;
@@ -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
    */
@@ -495,6 +500,12 @@ public interface SequenceI extends ASequenceI
   public List<DBRefEntry> getPrimaryDBRefs();
 
   /**
+   * 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
    * feature types. If the range is all gaps, then features which enclose it are
@@ -531,7 +542,26 @@ 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
+   * 
+   * @return
+   */
+  GeneLociI getGeneLoci();
+
+  /**
+   * Sets the mapping to gene loci for the sequence
+   * 
+   * @param speciesId
+   * @param assemblyId
+   * @param chromosomeId
+   * @param map
+   */
+  void setGeneLoci(String speciesId, String assemblyId,
+          String chromosomeId, MapList map);
+
 
   /**
    * Returns the sequence string constructed from the substrings of a sequence
@@ -542,5 +572,22 @@ 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
+   * iterator region. If no such position exists, return 0
+   * 
+   * @param it
+   *          iterator over regions
+   * @return first residue not contained in regions
+   */
+  int firstResidueOutsideIterator(Iterator<int[]> it);
+
+  /**
+   * Answers true if this sequence has an associated Hidden Markov Model
+   * 
+   * @return
+   */
+  boolean hasHMMProfile();
 }