From 06118a7ac64edb37e3d741f9a768dba9ebb949fc Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 6 Oct 2006 16:16:04 +0000 Subject: [PATCH] javadoc --- src/jalview/datamodel/AlignmentAnnotation.java | 3 ++- src/jalview/datamodel/Sequence.java | 5 ++--- src/jalview/datamodel/SequenceI.java | 10 +++++----- 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index 470497e..c3396b6 100755 --- 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 --- 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 --- 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(); -- 1.7.10.2