JAL-1693 mappings added back to the original alignment

[jalview.git] / test / jalview / analysis / AlignmentUtilsTests.java

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index c19884e..9ef1b9a 100644 (file)
--- 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());
   }
 }