X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FAlignmentUtilsTests.java;h=d229a3917a423d34c1152d6366efb9b842792c6c;hb=705d1c84c9a03bb0378593e4d8d8a90c8a11f831;hp=4439bb9368dd94f3bc0a640ee0858c6872269185;hpb=df2bf54c7050c42db156e96e73bbabce63e718d7;p=jalview.git

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 4439bb9..d229a39 100644
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -34,6 +34,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.GeneLociI;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResultsI;
@@ -71,7 +72,7 @@ public class AlignmentUtilsTests
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
-  public static Sequence ts = new Sequence("short",
+  private static Sequence ts = new Sequence("short",
           "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
 
   @Test(groups = { "Functional" })
@@ -1044,14 +1045,18 @@ 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 +1111,38 @@ 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) 
@@ -2533,4 +2570,67 @@ public class AlignmentUtilsTests
     assertEquals(s_as3, uas3.getSequenceAsString());
   }
 
+  @Test(groups = { "Functional" })
+  public void testTransferGeneLoci()
+  {
+    SequenceI from = new Sequence("transcript",
+            "aaacccgggTTTAAACCCGGGtttaaacccgggttt");
+    SequenceI to = new Sequence("CDS", "TTTAAACCCGGG");
+    MapList map = new MapList(new int[] { 1, 12 }, new int[] { 10, 21 }, 1,
+            1);
+
+    /*
+     * first with nothing to transfer
+     */
+    AlignmentUtils.transferGeneLoci(from, map, to);
+    assertNull(to.getGeneLoci());
+
+    /*
+     * next with gene loci set on 'from' sequence
+     */
+    int[] exons = new int[] { 100, 105, 155, 164, 210, 229 };
+    MapList geneMap = new MapList(new int[] { 1, 36 }, exons, 1, 1);
+    from.setGeneLoci("human", "GRCh38", "7", geneMap);
+    AlignmentUtils.transferGeneLoci(from, map, to);
+
+    GeneLociI toLoci = to.getGeneLoci();
+    assertNotNull(toLoci);
+    // DBRefEntry constructor upper-cases 'source'
+    assertEquals("HUMAN", toLoci.getSpeciesId());
+    assertEquals("GRCh38", toLoci.getAssemblyId());
+    assertEquals("7", toLoci.getChromosomeId());
+
+    /*
+     * transcript 'exons' are 1-6, 7-16, 17-36
+     * CDS 1:12 is transcript 10-21
+     * transcript 'CDS' is 10-16, 17-21
+     * which is 'gene' 158-164, 210-214
+     */
+    MapList toMap = toLoci.getMap();
+    assertEquals(1, toMap.getFromRanges().size());
+    assertEquals(2, toMap.getFromRanges().get(0).length);
+    assertEquals(1, toMap.getFromRanges().get(0)[0]);
+    assertEquals(12, toMap.getFromRanges().get(0)[1]);
+    assertEquals(1, toMap.getToRanges().size());
+    assertEquals(4, toMap.getToRanges().get(0).length);
+    assertEquals(158, toMap.getToRanges().get(0)[0]);
+    assertEquals(164, toMap.getToRanges().get(0)[1]);
+    assertEquals(210, toMap.getToRanges().get(0)[2]);
+    assertEquals(214, toMap.getToRanges().get(0)[3]);
+    // or summarised as (but toString might change in future):
+    assertEquals("[ [1, 12] ] 1:1 to [ [158, 164, 210, 214] ]",
+            toMap.toString());
+
+    /*
+     * an existing value is not overridden 
+     */
+    geneMap = new MapList(new int[] { 1, 36 }, new int[] { 36, 1 }, 1, 1);
+    from.setGeneLoci("inhuman", "GRCh37", "6", geneMap);
+    AlignmentUtils.transferGeneLoci(from, map, to);
+    assertEquals("GRCh38", toLoci.getAssemblyId());
+    assertEquals("7", toLoci.getChromosomeId());
+    toMap = toLoci.getMap();
+    assertEquals("[ [1, 12] ] 1:1 to [ [158, 164, 210, 214] ]",
+            toMap.toString());
+  }
 }