JAL-845 first working linked edit protein -> cDNA

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 876db03..3ca759d 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -137,10 +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);
 
@@ -189,7 +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
    */
@@ -218,9 +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);
 
@@ -236,13 +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!
@@ -315,6 +316,8 @@ public interface SequenceI
 
   public AlignmentAnnotation[] getAnnotation();
 
+  public boolean hasAnnotation(AlignmentAnnotation ann);
+
   public void addAlignmentAnnotation(AlignmentAnnotation annotation);
 
   public void removeAlignmentAnnotation(AlignmentAnnotation annotation);