javadoc

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 470497e..c3396b6 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -258,9 +258,10 @@ public class AlignmentAnnotation
       }
 
       /**
-       * Attach the annotation to seqRef, starting from startRes position.
+       * Attach the annotation to seqRef, starting from startRes position. If alreadyMapped is true then the indices of the annotation[] array are sequence positions rather than alignment column positions.
        * @param seqRef
        * @param startRes
+       * @param alreadyMapped
        */
       public void createSequenceMapping(SequenceI seqRef,
                                         int startRes,

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 635043b..fc52190 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -455,13 +455,12 @@ public class Sequence implements SequenceI
     }
 
     /**
-     * DOCUMENT ME!
+     * Returns an int array where indices correspond to each residue in the sequence and the element value gives its position in the alignment
      *
-     * @return DOCUMENT ME!
+     * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no residues in SequenceI object
      */
     public int[] gapMap()
     {
-        // Returns an int array giving the position of each residue in the sequence in the alignment
         String seq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars, sequence);
         int[] map = new int[seq.length()];
         int j = 0;

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index f2d9e74..8291026 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -151,18 +151,18 @@ public interface SequenceI
     public int findIndex(int pos);
 
     /**
-     * DOCUMENT ME!
+     * Returns the sequence position for an alignment position
      *
-     * @param i DOCUMENT ME!
+     * @param i column index in alignment (from 1)
      *
-     * @return DOCUMENT ME!
+     * @return residue number for residue (left of and) nearest ith column
      */
     public int findPosition(int i);
 
     /**
-     * DOCUMENT ME!
+     * Returns an int array where indices correspond to each residue in the sequence and the element value gives its position in the alignment
      *
-     * @return DOCUMENT ME!
+     * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no residues in SequenceI object
      */
     public int[] gapMap();