javadoc and note about broken semantics for findIndex

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 293528d..21b877d 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -577,13 +577,9 @@ public class Sequence implements SequenceI
     return this.description;
   }
 
-  /**
-   * Return the alignment position for a sequence position
-   * 
-   * @param pos
-   *          lying from start to end
-   * 
-   * @return aligned position of residue pos
+  
+  /* (non-Javadoc)
+   * @see jalview.datamodel.SequenceI#findIndex(int)
    */
   public int findIndex(int pos)
   {

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 33045d0..186156d 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -164,12 +164,15 @@ 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);