From 8fc03b5f923a6b80e2a7fc22f6fdd2c5c7ad9de9 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Thu, 30 Oct 2014 15:44:50 +0000
Subject: [PATCH] JAL-674 return original and replacement sequences and the
 alignment to allow more processing if needed

---
 src/jalview/analysis/AlignSeq.java |   16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index f5afa9c..c546310 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1069,11 +1069,19 @@ public class AlignSeq
    * @param ochains
    * @param al
    * @param dnaOrProtein
-   * @param removeOldAnnots when true, old annotation is cleared before new annotation transferred
+   * @param removeOldAnnots
+   *          when true, old annotation is cleared before new annotation
+   *          transferred
+   * @return List<List<SequenceI> originals, List<SequenceI> replacement,
+   *         List<AlignSeq> alignment between each>
    */
-  public static void replaceMatchingSeqsWith(List<SequenceI> seqs, List<AlignmentAnnotation> annotations, List<SequenceI> ochains,
+  public static List<List<? extends Object>> replaceMatchingSeqsWith(
+          List<SequenceI> seqs, List<AlignmentAnnotation> annotations,
+          List<SequenceI> ochains,
           AlignmentI al, String dnaOrProtein, boolean removeOldAnnots)
   {
+    List<SequenceI> orig = new ArrayList<SequenceI>(), repl = new ArrayList<SequenceI>();
+    List<AlignSeq> aligs = new ArrayList<AlignSeq>();
     if (al != null && al.getHeight() > 0)
     {
       ArrayList<SequenceI> matches = new ArrayList<SequenceI>();
@@ -1108,10 +1116,13 @@ public class AlignSeq
         if ((q = ochains.indexOf(sp)) > -1)
         {
           seqs.set(p, sq = matches.get(q));
+          orig.add(sp);
+          repl.add(sq);
           sq.setName(sp.getName());
           sq.setDescription(sp.getDescription());
           Mapping sp2sq;
           sq.transferAnnotation(sp, sp2sq = aligns.get(q).getMappingFromS1(false));
+          aligs.add(aligns.get(q));
           int inspos = -1;
           for (int ap = 0; ap < annotations.size();)
           {
@@ -1142,6 +1153,7 @@ public class AlignSeq
         }
       }
     }
+    return Arrays.asList(orig, repl, aligs);
   }
 
   /**
-- 
1.7.10.2