X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FAlignmentUtilsTests.java;h=d229a3917a423d34c1152d6366efb9b842792c6c;hb=705d1c84c9a03bb0378593e4d8d8a90c8a11f831;hp=7c64193bd4578f71686bfd76e8cdb5a0a901ef03;hpb=6fe36904fddf9ecb85e67974f48081bba373e8ab;p=jalview.git

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 7c64193..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" })
@@ -2569,4 +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());
+  }
 }