From 5088f3a5830a92aca7db379a3b1d43a891611061 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 21 Apr 2015 13:54:13 +0100
Subject: [PATCH] JAL-1693 mappings added back to the original alignment

---
 src/jalview/analysis/AlignmentUtils.java       |    9 +++--
 test/jalview/analysis/AlignmentUtilsTests.java |   48 ++++++++++++++++++++++++
 2 files changed, 54 insertions(+), 3 deletions(-)

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 7dec4ec..a4aeac7 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -27,6 +27,7 @@ import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.LinkedHashMap;
+import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
@@ -1278,7 +1279,7 @@ public class AlignmentUtils
   public static AlignmentI makeExonAlignment(SequenceI[] dna,
           Set<AlignedCodonFrame> mappings)
   {
-    Set<AlignedCodonFrame> newMappings = new HashSet<AlignedCodonFrame>();
+    Set<AlignedCodonFrame> newMappings = new LinkedHashSet<AlignedCodonFrame>();
     List<SequenceI> exonSequences = new ArrayList<SequenceI>();
     
     for (SequenceI dnaSeq : dna)
@@ -1346,8 +1347,8 @@ public class AlignmentUtils
       /*
        * Get the codon regions as { [2, 5], [7, 12], [14, 14] etc }
        */
-      List<int[]> exonRanges = seqMapping.getMap().getFromRanges();
-      for (int[] range : exonRanges)
+      final List<int[]> dnaExonRanges = seqMapping.getMap().getFromRanges();
+      for (int[] range : dnaExonRanges)
       {
         for (int pos = range[0]; pos <= range[1]; pos++)
         {
@@ -1389,6 +1390,8 @@ public class AlignmentUtils
               .getToRanges(),
               3, 1);
       newMapping.addMap(exon.getDatasetSequence(), seqMapping.getTo(), map);
+      MapList cdsToDnaMap = new MapList(dnaExonRanges, exonRange, 1, 1);
+      newMapping.addMap(dnaSeq, exon.getDatasetSequence(), cdsToDnaMap);
 
       exonSequences.add(exon);
     }
diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index c19884e..9ef1b9a 100644
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -30,6 +30,7 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.HashSet;
+import java.util.Iterator;
 import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Map;
@@ -1064,6 +1065,10 @@ public class AlignmentUtilsTests
     acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map);
     mappings.add(acf);
 
+    /*
+     * Create the Exon alignment; also replaces the dna-to-protein mappings with
+     * exon-to-protein and exon-to-dna mappings
+     */
     AlignmentI exal = AlignmentUtils.makeExonAlignment(new SequenceI[]
     { dna1 }, mappings);
 
@@ -1099,5 +1104,48 @@ public class AlignmentUtilsTests
     assertEquals("EMBLCDS", cdsRef.getSource());
     assertEquals("4", cdsRef.getVersion());
     assertEquals("A12347", cdsRef.getAccessionId());
+
+    /*
+     * Verify there are mappings from each exon sequence to its protein product
+     * and also to its dna source
+     */
+    Iterator<AlignedCodonFrame> newMappingsIterator = mappings.iterator();
+
+    // mappings for dna1 - exon1 - pep1
+    AlignedCodonFrame exonMapping = newMappingsIterator.next();
+    List<Mapping> dnaMappings = exonMapping.getMappingsForSequence(dna1);
+    assertEquals(1, dnaMappings.size());
+    assertSame(exons.get(0).getDatasetSequence(), dnaMappings.get(0)
+            .getTo());
+    assertEquals("G(1) in CDS should map to G(4) in DNA", 4, dnaMappings
+            .get(0).getMap().getToPosition(1));
+    List<Mapping> peptideMappings = exonMapping
+            .getMappingsForSequence(pep1);
+    assertEquals(1, peptideMappings.size());
+    assertSame(pep1.getDatasetSequence(), peptideMappings.get(0).getTo());
+
+    // mappings for dna1 - exon2 - pep2
+    exonMapping = newMappingsIterator.next();
+    dnaMappings = exonMapping.getMappingsForSequence(dna1);
+    assertEquals(1, dnaMappings.size());
+    assertSame(exons.get(1).getDatasetSequence(), dnaMappings.get(0)
+            .getTo());
+    assertEquals("c(4) in CDS should map to c(7) in DNA", 7, dnaMappings
+            .get(0).getMap().getToPosition(4));
+    peptideMappings = exonMapping.getMappingsForSequence(pep2);
+    assertEquals(1, peptideMappings.size());
+    assertSame(pep2.getDatasetSequence(), peptideMappings.get(0).getTo());
+
+    // mappings for dna1 - exon3 - pep3
+    exonMapping = newMappingsIterator.next();
+    dnaMappings = exonMapping.getMappingsForSequence(dna1);
+    assertEquals(1, dnaMappings.size());
+    assertSame(exons.get(2).getDatasetSequence(), dnaMappings.get(0)
+            .getTo());
+    assertEquals("T(4) in CDS should map to T(10) in DNA", 10, dnaMappings
+            .get(0).getMap().getToPosition(4));
+    peptideMappings = exonMapping.getMappingsForSequence(pep3);
+    assertEquals(1, peptideMappings.size());
+    assertSame(pep3.getDatasetSequence(), peptideMappings.get(0).getTo());
   }
 }
-- 
1.7.10.2