X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=a1b268315d069a76331f360adeac4f92abb2669c;hb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;hp=57e452579fd2a1dfc6d5953bc6c1a4390e3432b3;hpb=dfc18d64376ae95cfdbf3c112825587a8891179c;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 57e4525..a1b2683 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -20,8 +20,10 @@
  */
 package jalview.datamodel;
 
+import jalview.datamodel.Sequence.DBModList;
 import jalview.datamodel.features.SequenceFeaturesI;
 import jalview.util.MapList;
+import jalview.ws.params.InvalidArgumentException;
 
 import java.util.BitSet;
 import java.util.Iterator;
@@ -46,6 +48,10 @@ public interface SequenceI extends ASequenceI
    */
   public void setName(String name);
 
+  public HiddenMarkovModel getHMM();
+
+  public void setHMM(HiddenMarkovModel hmm);
+
   /**
    * Get the display name
    */
@@ -208,14 +214,17 @@ 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. (0 and negative positions are rounded up)
    * @param toColumn
-   * @return
+   *          - last column, base 1
+   * @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
@@ -352,14 +361,17 @@ public interface SequenceI extends ASequenceI
   /**
    * set the array of Database references for the sequence.
    * 
+   * BH 2019.02.04 changes param to DBModlist 
+   * 
    * @param dbs
    * @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(DBRefEntry[] dbs);
+  public void setDBRefs(DBModList<DBRefEntry> dbs);
 
-  public DBRefEntry[] getDBRefs();
+  public DBModList<DBRefEntry> getDBRefs();
 
   /**
    * add the given entry to the list of DBRefs for this sequence, or replace a
@@ -438,6 +450,17 @@ 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
@@ -498,6 +521,12 @@ 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
@@ -534,7 +563,7 @@ 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
@@ -564,7 +593,7 @@ 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
@@ -574,5 +603,15 @@ public interface SequenceI extends ASequenceI
    *          iterator over regions
    * @return first residue not contained in regions
    */
+
   public int firstResidueOutsideIterator(Iterator<int[]> it);
+
+
+  /**
+   * Answers true if this sequence has an associated Hidden Markov Model
+   * 
+   * @return
+   */
+  boolean hasHMMProfile();
 }
+