JAL-2822 verify start/end is correctly updated and restored after edit, undo, and...

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 538b791..f1a4140 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -192,22 +192,26 @@ public interface SequenceI extends ASequenceI
   public int findIndex(int pos);
 
   /**
-   * Returns the sequence position for an alignment position.
+   * Returns the sequence position for an alignment (column) position. If at a
+   * gap, returns the position of the next residue to the right. If beyond the
+   * end of the sequence, returns 1 more than the last residue position.
    * 
    * @param i
    *          column index in alignment (from 0..<length)
    * 
-   * @return TODO: JAL-2562 - residue number for residue (left of and) nearest
-   *         ith column
+   * @return
    */
   public int findPosition(int i);
 
   /**
-   * Returns the from-to sequence positions (start..) for the given column
-   * positions (1..), or null if no residues are included in the range
+   * Returns the sequence positions for first and last residues lying within the
+   * given column positions [fromColum,toColumn] (where columns are numbered
+   * from 1), or null if no residues are included in the range
    * 
    * @param fromColum
+   *          - first column base 1
    * @param toColumn
+   *          - last column, base 1
    * @return
    */
   public Range findPositions(int fromColum, int toColumn);
@@ -534,22 +538,4 @@ public interface SequenceI extends ASequenceI
    * @param c2
    */
   int replace(char c1, char c2);
-
-  /**
-   * Adjusts position and extent of features to allow for cut of the specified
-   * (inclusive) column range. Returns a list of {originalFeature,
-   * amendedFeature} for
-   * <ul>
-   * <li>features that have been deleted (as within the cut) - amendedFeature is
-   * null</li>
-   * <li>truncated features (as overlapping or spanning the cut)</li>
-   * </ul>
-   * Contact features that overlap the cut region are deleted. Contact features
-   * that enclose the cut region are shortened.
-   * 
-   * @param fromColumn
-   * @param toColumn
-   * @return
-   */
-  List<SequenceFeature[]> adjustFeatures(int fromColumn, int toColumn);
 }