From 4bf04707b9bb755a7cdaa829eeec02ab87b4a228 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 29 Aug 2016 22:20:23 +0100
Subject: [PATCH] =?utf8?q?JAL-2154=20don=E2=80=99t=20synthesise=20multiple=20?=
 =?utf8?q?CDS|<Acc>=20sequences=20when=20one=20is=20already=20available=20on?=
 =?utf8?q?=20dataset=20(fixes=20crossRefs2XML=20failure=20-=20CDS|ENST000002?=
 =?utf8?q?88602=20found=20duplicated=20"Pass=20(0,0,0):=20before=20start=20o?=
 =?utf8?q?f=20pass3:=20ENSEMBL=20ENSG00000157764=20->=20UNIPROT{0}:=E2=80=9D?=
 =?utf8?q?)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=utf8
Content-Transfer-Encoding: 8bit

---
 src/jalview/analysis/AlignmentUtils.java |   50 ++++++++++++++++++++++++++++--
 1 file changed, 47 insertions(+), 3 deletions(-)

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index e0ec22b..b0a2269 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -1680,15 +1680,20 @@ public class AlignmentUtils
            * didn't find mapped CDS sequence - construct it and add
            * its dataset sequence to the dataset
            */
-          cdsSeq = makeCdsSequence(dnaSeq.getDatasetSequence(), aMapping);
+          cdsSeq = makeCdsSequence(dnaSeq.getDatasetSequence(), aMapping,
+                  dataset).deriveSequence();
           // cdsSeq has a name constructed as CDS|<dbref>
           // <dbref> will be either the accession for the coding sequence,
           // marked in the /via/ dbref to the protein product accession
           // or it will be the original nucleotide accession.
-          SequenceI cdsSeqDss = cdsSeq.createDatasetSequence();
+          SequenceI cdsSeqDss = cdsSeq.getDatasetSequence();
+
           cdsSeqs.add(cdsSeq);
+
           if (!dataset.getSequences().contains(cdsSeqDss))
           {
+            // check if this sequence is a newly created one
+            // so needs adding to the dataset
             dataset.addSequence(cdsSeqDss);
           }
 
@@ -1870,9 +1875,14 @@ public class AlignmentUtils
    * 
    * @param seq
    * @param mapping
+   * @param dataset
+   *          - existing dataset. We check for sequences that look like the CDS
+   *          we are about to construct, if one exists already, then we will
+   *          just return that one.
    * @return CDS sequence (as a dataset sequence)
    */
-  static SequenceI makeCdsSequence(SequenceI seq, Mapping mapping)
+  static SequenceI makeCdsSequence(SequenceI seq, Mapping mapping,
+          AlignmentI dataset)
   {
     char[] seqChars = seq.getSequence();
     List<int[]> fromRanges = mapping.getMap().getFromRanges();
@@ -1907,6 +1917,40 @@ public class AlignmentUtils
     String mapFromId = mapping.getMappedFromId();
     String seqId = "CDS|" + (mapFromId != null ? mapFromId : seq.getName());
     SequenceI newSeq = new Sequence(seqId, newSeqChars, 1, newPos);
+    if (dataset != null)
+    {
+      SequenceI[] matches = dataset.findSequenceMatch(newSeq.getName());
+      if (matches != null)
+      {
+        boolean matched = false;
+        for (SequenceI mtch : matches)
+        {
+          if (mtch.getStart() != newSeq.getStart())
+          {
+            continue;
+          }
+          if (mtch.getEnd() != newSeq.getEnd())
+          {
+            continue;
+          }
+          if (!Arrays.equals(mtch.getSequence(), newSeq.getSequence()))
+          {
+            continue;
+          }
+          if (!matched)
+          {
+            matched = true;
+            newSeq = mtch;
+          }
+          else
+          {
+            System.err
+                    .println("JAL-2154 regression: warning - found (and ignnored a duplicate CDS sequence):"
+                            + mtch.toString());
+          }
+        }
+      }
+    }
     // newSeq.setDescription(mapFromId);
 
     return newSeq;
-- 
1.7.10.2