JAL-2106 JAL-2154 fix test for additional reference transferred from locus to CDS...

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

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index a0c9ace..7e8442d 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -994,29 +994,44 @@ public class AlignmentUtilsTests
 
     /*
      * need a sourceDbRef if we are to construct dbrefs to the CDS
-     * sequence
+     * sequence from the dna contig sequences
      */
     DBRefEntry dbref = new DBRefEntry("ENSEMBL", "0", "dna1");
-    dna1.getDatasetSequence().setSourceDBRef(dbref);
+    dna1.getDatasetSequence().addDBRef(dbref);
+    org.testng.Assert.assertEquals(dbref, dna1.getPrimaryDBRefs().get(0));
     dbref = new DBRefEntry("ENSEMBL", "0", "dna2");
-    dna2.getDatasetSequence().setSourceDBRef(dbref);
+    dna2.getDatasetSequence().addDBRef(dbref);
+    org.testng.Assert.assertEquals(dbref, dna2.getPrimaryDBRefs().get(0));
 
     /*
      * CDS sequences are 'discovered' from dna-to-protein mappings on the alignment
      * dataset (e.g. added from dbrefs by CrossRef.findXrefSequences)
      */
-    MapList map = new MapList(new int[] { 4, 6, 10, 12 },
+    MapList mapfordna1 = new MapList(new int[] { 4, 6, 10, 12 },
             new int[] { 1, 2 }, 3, 1);
     AlignedCodonFrame acf = new AlignedCodonFrame();
-    acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
+    acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
+            mapfordna1);
     dna.addCodonFrame(acf);
-    map = new MapList(new int[] { 1, 3, 7, 9, 13, 15 }, new int[] { 1, 3 },
+    MapList mapfordna2 = new MapList(new int[] { 1, 3, 7, 9, 13, 15 },
+            new int[] { 1, 3 },
             3, 1);
     acf = new AlignedCodonFrame();
-    acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
+    acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(),
+            mapfordna2);
     dna.addCodonFrame(acf);
 
     /*
+     * In this case, mappings originally came from matching Uniprot accessions - so need an xref on dna involving those regions. These are normally constructed from CDS annotation
+     */
+    DBRefEntry dna1xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep1",
+            new Mapping(mapfordna1));
+    dna1.getDatasetSequence().addDBRef(dna1xref);
+    DBRefEntry dna2xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep2",
+            new Mapping(mapfordna2));
+    dna2.getDatasetSequence().addDBRef(dna2xref);
+
+    /*
      * execute method under test:
      */
     AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
@@ -1042,11 +1057,12 @@ public class AlignmentUtilsTests
      * verify CDS has a dbref with mapping to peptide
      */
     assertNotNull(cds1Dss.getDBRefs());
-    assertEquals(1, cds1Dss.getDBRefs().length);
+    assertEquals(2, cds1Dss.getDBRefs().length);
     dbref = cds1Dss.getDBRefs()[0];
-    assertEquals("UNIPROT", dbref.getSource());
-    assertEquals("0", dbref.getVersion());
-    assertEquals("pep1", dbref.getAccessionId());
+    assertEquals(dna1xref.getSource(), dbref.getSource());
+    // version is via ensembl's primary ref
+    assertEquals(dna1xref.getVersion(), dbref.getVersion());
+    assertEquals(dna1xref.getAccessionId(), dbref.getAccessionId());
     assertNotNull(dbref.getMap());
     assertSame(pep1.getDatasetSequence(), dbref.getMap().getTo());
     MapList cdsMapping = new MapList(new int[] { 1, 6 },
@@ -1057,6 +1073,7 @@ public class AlignmentUtilsTests
      * verify peptide has added a dbref with reverse mapping to CDS
      */
     assertNotNull(pep1.getDBRefs());
+    // FIXME pep1.getDBRefs() is 1 - is that the correct behaviour ?
     assertEquals(2, pep1.getDBRefs().length);
     dbref = pep1.getDBRefs()[1];
     assertEquals("ENSEMBL", dbref.getSource());
@@ -2440,6 +2457,7 @@ public class AlignmentUtilsTests
     SequenceI dna6 = new Sequence("dna6", "CCCgggtttAAA");
     dna6.createDatasetSequence();
     al1.addSequence(dna6);
+    // JAL-2110 JBP Comment: what's the use case for this behaviour ?
     assertFalse(AlignmentUtils.alignAsSameSequences(al1, al2));
   }
 
@@ -2448,8 +2466,9 @@ public class AlignmentUtilsTests
   {
     SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
     SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
-    SequenceI as1 = dna1.deriveSequence(), as2 = dna1.deriveSequence()
-            .getSubSequence(3, 7), as3 = dna2.deriveSequence();
+    SequenceI as1 = dna1.deriveSequence();
+    SequenceI as2 = dna1.deriveSequence().getSubSequence(3, 7);
+    SequenceI as3 = dna2.deriveSequence();
     as1.insertCharAt(6, 5, '-');
     String s_as1 = as1.getSequenceAsString();
     as2.insertCharAt(6, 5, '-');
@@ -2460,8 +2479,9 @@ public class AlignmentUtilsTests
 
     // why do we need to cast this still ?
     ((Alignment) aligned).createDatasetAlignment();
-    SequenceI uas1 = dna1.deriveSequence(), uas2 = dna1.deriveSequence()
-            .getSubSequence(3, 7), uas3 = dna2.deriveSequence();
+    SequenceI uas1 = dna1.deriveSequence();
+    SequenceI uas2 = dna1.deriveSequence().getSubSequence(3, 7);
+    SequenceI uas3 = dna2.deriveSequence();
     AlignmentI tobealigned = new Alignment(new SequenceI[] { uas1, uas2,
         uas3 });
     ((Alignment) tobealigned).createDatasetAlignment();