debugging cross references and duplicate sequence db refs

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 6694aff..5c15108 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -182,10 +182,11 @@ public interface SequenceI
   public int[] gapMap();
 
   /**
-   * DOCUMENT ME!
+   * Delete a range of aligned sequence columns, creating a new dataset sequence if necessary
+   * and adjusting start and end positions accordingly.
    *
-   * @param i DOCUMENT ME!
-   * @param j DOCUMENT ME!
+   * @param i first column in range to delete
+   * @param j last column in range to delete
    */
   public void deleteChars(int i, int j);
 
@@ -243,6 +244,12 @@ public interface SequenceI
 
   public DBRefEntry[] getDBRef();
 
+  /**
+   * add the given entry to the list of DBRefs for this sequence, 
+   * or replace a similar one if entry contains a map object 
+   * and the existing one doesnt. 
+   * @param entry
+   */
   public void addDBRef(DBRefEntry entry);
 
   public void addSequenceFeature(SequenceFeature sf);
@@ -257,10 +264,23 @@ public interface SequenceI
 
   public void addAlignmentAnnotation(AlignmentAnnotation annotation);
 
+  public void removeAlignmentAnnotation(AlignmentAnnotation annotation);
+
   /**
    * Derive a sequence (using this one's dataset or as the dataset)
    * @return duplicate sequence with valid dataset sequence
    */
   public SequenceI deriveSequence();
+  /**
+   * set the array of associated AlignmentAnnotation for this sequenceI
+   * @param revealed
+   */
+  public void setAlignmentAnnotation(AlignmentAnnotation[] annotation);
+  /**
+   * Get one or more alignment annotations with a particular label.  
+   * @param label string which each returned annotation must have as a label.
+   * @return null or array of annotations.
+   */
+  public AlignmentAnnotation[] getAnnotation(String label);
 
 }