JAL-2738 JAL-2154 add DBRef from transcript to synthesized CDS and vice

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

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 4439bb9..7c64193 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -1044,14 +1044,18 @@ public class AlignmentUtilsTests
     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
+     * 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);
+    dna1.addDBRef(dna1xref);
+    assertEquals(2, dna1.getDBRefs().length); // to self and to pep1
     DBRefEntry dna2xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep2",
             new Mapping(mapfordna2));
-    dna2.getDatasetSequence().addDBRef(dna2xref);
+    dna2.addDBRef(dna2xref);
+    assertEquals(2, dna2.getDBRefs().length); // to self and to pep2
 
     /*
      * execute method under test:
@@ -1106,6 +1110,38 @@ public class AlignmentUtilsTests
     assertEquals(cdsMapping.getInverse(), dbref.getMap().getMap());
 
     /*
+     * verify cDNA has added a dbref with mapping to CDS
+     */
+    assertEquals(3, dna1.getDBRefs().length);
+    DBRefEntry dbRefEntry = dna1.getDBRefs()[2];
+    assertSame(cds1Dss, dbRefEntry.getMap().getTo());
+    MapList dnaToCdsMapping = new MapList(new int[] { 4, 6, 10, 12 },
+            new int[] { 1, 6 }, 1, 1);
+    assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap());
+    assertEquals(3, dna2.getDBRefs().length);
+    dbRefEntry = dna2.getDBRefs()[2];
+    assertSame(cds2Dss, dbRefEntry.getMap().getTo());
+    dnaToCdsMapping = new MapList(new int[] { 1, 3, 7, 9, 13, 15 },
+            new int[] { 1, 9 }, 1, 1);
+    assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap());
+
+    /*
+     * verify CDS has added a dbref with mapping to cDNA
+     */
+    assertEquals(2, cds1Dss.getDBRefs().length);
+    dbRefEntry = cds1Dss.getDBRefs()[1];
+    assertSame(dna1.getDatasetSequence(), dbRefEntry.getMap().getTo());
+    MapList cdsToDnaMapping = new MapList(new int[] { 1, 6 }, new int[] {
+        4, 6, 10, 12 }, 1, 1);
+    assertEquals(cdsToDnaMapping, dbRefEntry.getMap().getMap());
+    assertEquals(2, cds2Dss.getDBRefs().length);
+    dbRefEntry = cds2Dss.getDBRefs()[1];
+    assertSame(dna2.getDatasetSequence(), dbRefEntry.getMap().getTo());
+    cdsToDnaMapping = new MapList(new int[] { 1, 9 }, new int[] { 1, 3, 7,
+        9, 13, 15 }, 1, 1);
+    assertEquals(cdsToDnaMapping, dbRefEntry.getMap().getMap());
+
+    /*
      * Verify mappings from CDS to peptide, cDNA to CDS, and cDNA to peptide
      * the mappings are on the shared alignment dataset
      * 6 mappings, 2*(DNA->CDS), 2*(DNA->Pep), 2*(CDS->Pep)