X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=8f1d1602114789394801aaefef5d5ab35f8a5722;hb=747167089ecf8d6afc70d417f5a20352e029bd95;hp=9e9758cd2528df0008225cbb3591eea466b34ed9;hpb=26b115b0a77d521da92a06572d9b7819c2d0d49a;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 9e9758c..8f1d160 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -20,6 +20,7 @@
  */
 package jalview.datamodel;
 
+import jalview.datamodel.Sequence.DBModList;
 import jalview.datamodel.features.SequenceFeaturesI;
 import jalview.util.MapList;
 import jalview.ws.params.InvalidArgumentException;
@@ -47,6 +48,9 @@ public interface SequenceI extends ASequenceI
    */
   public void setName(String name);
 
+  public HiddenMarkovModel getHMM();
+
+  public void setHMM(HiddenMarkovModel hmm);
   /**
    * Get the display name
    */
@@ -113,9 +117,11 @@ 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
    */
@@ -212,12 +218,12 @@ public interface SequenceI extends ASequenceI
    * from 1), or null if no residues are included in the range
    * 
    * @param fromColum
-   *          - first column base 1
+   *          - first column base 1. (0 and negative positions are rounded up)
    * @param toColumn
    *          - last column, base 1
-   * @return
+   * @return null if fromColum>toColumn
    */
-  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
@@ -354,20 +360,17 @@ public interface SequenceI extends ASequenceI
   /**
    * set the array of Database references for the sequence.
    * 
-   * BH 2019.01.25 added throw
+   * BH 2019.02.04 changes param to DBModlist 
    * 
    * @param dbs
- * @throws InvalidArgumentException 
    * @deprecated - use is discouraged since side-effects may occur if DBRefEntry
    *             set are not normalised.
    * @throws InvalidArgumentException if the is not one created by Sequence itself
    */
   @Deprecated
-  public void setDBRefs(List<DBRefEntry> dbs) throws InvalidArgumentException;
-
-  public List<DBRefEntry> getDBRefs();
+  public void setDBRefs(DBModList<DBRefEntry> dbs);
 
-  public void getDBRefsFrom(SequenceI seq);
+  public DBModList<DBRefEntry> getDBRefs();
 
   /**
    * add the given entry to the list of DBRefs for this sequence, or replace a
@@ -446,6 +449,17 @@ public interface SequenceI extends ASequenceI
           String label);
 
   /**
+   * Returns a (possibly empty) list of any annotations that match on given
+   * calcId (source), label (type) and description (observation instance).
+   * Null values do not match.
+   * 
+   * @param calcId
+   * @param label
+   * @param description
+   */
+  public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+          String label, String description);
+  /**
    * create a new dataset sequence (if necessary) for this sequence and sets
    * this sequence to refer to it. This call will move any features or
    * references on the sequence onto the dataset. It will also make a duplicate
@@ -504,6 +518,11 @@ public interface SequenceI extends ASequenceI
    *         list
    */
   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
@@ -584,5 +603,12 @@ public interface SequenceI extends ASequenceI
    */
   public int firstResidueOutsideIterator(Iterator<int[]> it);
 
+
+  /**
+   * Answers true if this sequence has an associated Hidden Markov Model
+   * 
+   * @return
+   */
+  boolean hasHMMProfile();
 }