X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=3ca759dfdf50c5744d9cfe7fa565a736c6acb5f0;hb=61f1a8b75ea5ce352d6214c34fbdcd58bafbbb73;hp=2e68371243c224c8d409addf5e7698cd021659de;hpb=57c4f810f995895293ef4a9d956dd9c9a767d41f;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 2e68371..3ca759d 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -21,6 +21,7 @@
 package jalview.datamodel;
 
 import java.util.List;
+import java.util.Vector;
 
 import fr.orsay.lri.varna.models.rna.RNA;
 
@@ -136,10 +137,12 @@ public interface SequenceI
    * create a new sequence object from start to end of this sequence
    * 
    * @param start
-   *          int
+   *          int index for start position
    * @param end
-   *          int
+   *          int index for end position
+   * 
    * @return SequenceI
+   * @note implementations may use getSequence to get the sequence data
    */
   public SequenceI getSubSequence(int start, int end);
 
@@ -188,7 +191,7 @@ public interface SequenceI
    * Returns the sequence position for an alignment position
    * 
    * @param i
-   *          column index in alignment (from 1)
+   *          column index in alignment (from 0..<length)
    * 
    * @return residue number for residue (left of and) nearest ith column
    */
@@ -217,9 +220,9 @@ public interface SequenceI
    * if necessary and adjusting start and end positions accordingly.
    * 
    * @param i
-   *          first column in range to delete
+   *          first column in range to delete (inclusive)
    * @param j
-   *          last column in range to delete
+   *          last column in range to delete (exclusive)
    */
   public void deleteChars(int i, int j);
 
@@ -235,13 +238,12 @@ public interface SequenceI
 
   /**
    * DOCUMENT ME!
-   * 
-   * @param i
+   * @param position
    *          DOCUMENT ME!
-   * @param c
+   * @param ch
    *          DOCUMENT ME!
    */
-  public void insertCharAt(int i, int length, char c);
+  public void insertCharAt(int position, int count, char ch);
 
   /**
    * DOCUMENT ME!
@@ -314,6 +316,8 @@ public interface SequenceI
 
   public AlignmentAnnotation[] getAnnotation();
 
+  public boolean hasAnnotation(AlignmentAnnotation ann);
+
   public void addAlignmentAnnotation(AlignmentAnnotation annotation);
 
   public void removeAlignmentAnnotation(AlignmentAnnotation annotation);