From 5dd0323d078fc1f0bab425fcbd4d8bcf1528eb14 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 12 Jul 2016 17:12:10 +0100 Subject: [PATCH 1/1] JAL-2110 javadoc --- src/jalview/analysis/AlignmentUtils.java | 4 ++++ src/jalview/datamodel/SequenceI.java | 12 +++++++----- 2 files changed, 11 insertions(+), 5 deletions(-) diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java index e2f6749..7264cd2 100644 --- a/src/jalview/analysis/AlignmentUtils.java +++ b/src/jalview/analysis/AlignmentUtils.java @@ -2606,7 +2606,10 @@ public class AlignmentUtils * true; else returns false * * @param unaligned + * - sequences to be aligned based on aligned * @param aligned + * - 'guide' alignment containing sequences derived from same dataset + * as unaligned * @return */ static boolean alignAsSameSequences(AlignmentI unaligned, @@ -2617,6 +2620,7 @@ public class AlignmentUtils return false; // should only pass alignments with datasets here } + // map from dataset sequence to alignment sequence Map alignedDatasets = new HashMap(); for (SequenceI seq : aligned.getSequences()) { diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java index 355e271..45a767c 100755 --- a/src/jalview/datamodel/SequenceI.java +++ b/src/jalview/datamodel/SequenceI.java @@ -239,19 +239,21 @@ public interface SequenceI extends ASequenceI * DOCUMENT ME! * * @param i - * DOCUMENT ME! + * alignment column number * @param c - * DOCUMENT ME! + * character to insert */ public void insertCharAt(int i, char c); /** - * DOCUMENT ME! + * insert given character at alignment column position * * @param position - * DOCUMENT ME! + * alignment column number + * @param count + * length of insert * @param ch - * DOCUMENT ME! + * character to insert */ public void insertCharAt(int position, int count, char ch); -- 1.7.10.2