X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=8f1d1602114789394801aaefef5d5ab35f8a5722;hb=747167089ecf8d6afc70d417f5a20352e029bd95;hp=72ce22c9fca0880fbba67bc6707e18788daf9858;hpb=c794c5033adeee182b03a5ea92c0a7495a29661f;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 72ce22c..8f1d160 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -51,7 +51,6 @@ public interface SequenceI extends ASequenceI
   public HiddenMarkovModel getHMM();
 
   public void setHMM(HiddenMarkovModel hmm);
-
   /**
    * Get the display name
    */
@@ -450,6 +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
@@ -508,7 +518,6 @@ 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
@@ -552,7 +561,7 @@ public interface SequenceI extends ASequenceI
    * @param c1
    * @param c2
    */
-  int replace(char c1, char c2);
+  public int replace(char c1, char c2);
 
   /**
    * Answers the GeneLociI, or null if not known
@@ -582,7 +591,7 @@ public interface SequenceI extends ASequenceI
    *          the iterator to use
    * @return a String corresponding to the sequence
    */
-  String getSequenceStringFromIterator(Iterator<int[]> it);
+  public String getSequenceStringFromIterator(Iterator<int[]> it);
 
   /**
    * Locate the first position in this sequence which is not contained in an
@@ -592,7 +601,6 @@ public interface SequenceI extends ASequenceI
    *          iterator over regions
    * @return first residue not contained in regions
    */
-
   public int firstResidueOutsideIterator(Iterator<int[]> it);