JAL-3878 update branch from 2.12 merge from 2.11.2

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 7c3eb41..8f1d160 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -48,6 +48,9 @@ public interface SequenceI extends ASequenceI
    */
   public void setName(String name);
 
+  public HiddenMarkovModel getHMM();
+
+  public void setHMM(HiddenMarkovModel hmm);
   /**
    * Get the display name
    */
@@ -215,10 +218,10 @@ 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 ContiguousI findPositions(int fromColum, int toColumn);
 
@@ -515,6 +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
@@ -596,5 +604,11 @@ 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();
 }