Merge branch 'develop' into menard

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index bf3c031..194f144 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -167,12 +167,15 @@ public interface SequenceI
   public String getDescription();
 
   /**
-   * DOCUMENT ME!
+   * Return the alignment column for a sequence position
+   *    * Return the alignment position for a sequence position
    * 
    * @param pos
-   *          DOCUMENT ME!
+   *          lying from start to end
+   * 
+   * @return aligned column for residue (0 if residue is upstream from alignment, -1 if residue is downstream from alignment)
+   * note. Sequence object returns sequence.getEnd() for positions upstream currently. TODO: change sequence for assert(findIndex(seq.getEnd()+1)==-1) and fix incremental bugs
    * 
-   * @return DOCUMENT ME!
    */
   public int findIndex(int pos);