X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2Fxdb%2Fembl%2FEmblEntryTest.java;h=e8760bd1f12692deccf3a0363f5f81ac559c55f6;hb=1f959f4a5bc07769cde4c2577022ad64e55b4a1a;hp=9fffc45830dd634b78c09119b77639c6339ed261;hpb=4ad19b786f19aeadaf7a841e43ff8e490a39589d;p=jalview.git

diff --git a/test/jalview/datamodel/xdb/embl/EmblEntryTest.java b/test/jalview/datamodel/xdb/embl/EmblEntryTest.java
index 9fffc45..e8760bd 100644
--- a/test/jalview/datamodel/xdb/embl/EmblEntryTest.java
+++ b/test/jalview/datamodel/xdb/embl/EmblEntryTest.java
@@ -3,10 +3,13 @@ package jalview.datamodel.xdb.embl;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertSame;
 
-import jalview.util.MappingUtils;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
 
+import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.Vector;
+import java.util.List;
 
 import org.testng.annotations.Test;
 
@@ -21,288 +24,93 @@ public class EmblEntryTest
      * Make a (CDS) Feature with 4 locations
      */
     EmblFeature cds = new EmblFeature();
-    Vector<EmblFeatureLocations> locs = new Vector<EmblFeatureLocations>();
-    cds.setLocations(locs);
-
-    /*
-     * single range [10-20]
-     */
-    EmblFeatureLocations loc = new EmblFeatureLocations();
-    loc.setLocationType("single");
-    loc.setLocationComplement(false);
-    Vector<EmblFeatureLocElement> elements = new Vector<EmblFeatureLocElement>();
-    EmblFeatureLocElement locElement = new EmblFeatureLocElement();
-    BasePosition b1 = new BasePosition();
-    b1.setPos("10");
-    BasePosition b2 = new BasePosition();
-    b2.setPos("20");
-    locElement.setBasePositions(new BasePosition[] { b1, b2 });
-    elements.add(locElement);
-    loc.setLocElements(elements);
-    locs.add(loc);
-
-    /*
-     * complement range [30-40]
-     */
-    loc = new EmblFeatureLocations();
-    loc.setLocationType("single");
-    loc.setLocationComplement(true);
-    elements = new Vector<EmblFeatureLocElement>();
-    locElement = new EmblFeatureLocElement();
-    b1 = new BasePosition();
-    b1.setPos("30");
-    b2 = new BasePosition();
-    b2.setPos("40");
-    locElement.setBasePositions(new BasePosition[] { b1, b2 });
-    elements.add(locElement);
-    loc.setLocElements(elements);
-    locs.add(loc);
-
-    /*
-     * join range [50-60], [70-80]
-     */
-    loc = new EmblFeatureLocations();
-    loc.setLocationType("join");
-    loc.setLocationComplement(false);
-    elements = new Vector<EmblFeatureLocElement>();
-    locElement = new EmblFeatureLocElement();
-    b1 = new BasePosition();
-    b1.setPos("50");
-    b2 = new BasePosition();
-    b2.setPos("60");
-    locElement.setBasePositions(new BasePosition[] { b1, b2 });
-    elements.add(locElement);
-    locElement = new EmblFeatureLocElement();
-    b1 = new BasePosition();
-    b1.setPos("70");
-    b2 = new BasePosition();
-    b2.setPos("80");
-    locElement.setBasePositions(new BasePosition[] { b1, b2 });
-    elements.add(locElement);
-    loc.setLocElements(elements);
-    locs.add(loc);
-
-    /*
-     * complement range [90-100], [110-120]
-     * this should be the same as complement(join(90..100,110.120))
-     * which is "join 90-100 and 110-120, then complement"
-     */
-    loc = new EmblFeatureLocations();
-    loc.setLocationType("join");
-    loc.setLocationComplement(true);
-    elements = new Vector<EmblFeatureLocElement>();
-    locElement = new EmblFeatureLocElement();
-    b1 = new BasePosition();
-    b1.setPos("90");
-    b2 = new BasePosition();
-    b2.setPos("100");
-    locElement.setBasePositions(new BasePosition[] { b1, b2 });
-    elements.add(locElement);
-    locElement = new EmblFeatureLocElement();
-    b1 = new BasePosition();
-    b1.setPos("110");
-    b2 = new BasePosition();
-    b2.setPos("120");
-    locElement.setBasePositions(new BasePosition[] { b1, b2 });
-    elements.add(locElement);
-    loc.setLocElements(elements);
-    locs.add(loc);
+    cds.setLocation("join(10..20,complement(30..40),50..60,70..80,complement(110..120))");
 
     int[] exons = testee.getCdsRanges(cds);
-    assertEquals("[10, 20, 40, 30, 50, 60, 70, 80, 120, 110, 100, 90]",
+    assertEquals("[10, 20, 40, 30, 50, 60, 70, 80, 120, 110]",
             Arrays.toString(exons));
   }
 
   @Test(groups = "Functional")
-  public void testGetCdsRanges_badData()
+  public void testParseCodingFeature()
   {
-    EmblEntry testee = new EmblEntry();
+    // not the whole sequence but enough for this test...
+    SequenceI dna = new Sequence("J03321", "GGATCCGTAAGTTAGACGAAATT");
+    List<SequenceI> peptides = new ArrayList<SequenceI>();
+    EmblFile ef = EmblTestHelper.getEmblFile();
 
     /*
-     * Make a (CDS) Feature with 4 locations
-     */
-    EmblFeature cds = new EmblFeature();
-    Vector<EmblFeatureLocations> locs = new Vector<EmblFeatureLocations>();
-    cds.setLocations(locs);
-
-    /*
-     * single range [10-20]
-     */
-    EmblFeatureLocations loc = new EmblFeatureLocations();
-    loc.setLocationType("single");
-    loc.setLocationComplement(false);
-    Vector<EmblFeatureLocElement> elements = new Vector<EmblFeatureLocElement>();
-    EmblFeatureLocElement locElement = new EmblFeatureLocElement();
-    BasePosition b1 = new BasePosition();
-    b1.setPos("10");
-    BasePosition b2 = new BasePosition();
-    b2.setPos("20");
-    locElement.setBasePositions(new BasePosition[] { b1, b2 });
-    elements.add(locElement);
-    loc.setLocElements(elements);
-    locs.add(loc);
-
-    /*
-     * single range with missing end position - should be skipped
-     */
-    loc = new EmblFeatureLocations();
-    loc.setLocationType("single");
-    loc.setLocationComplement(false);
-    elements = new Vector<EmblFeatureLocElement>();
-    locElement = new EmblFeatureLocElement();
-    b1 = new BasePosition();
-    b1.setPos("30");
-    locElement.setBasePositions(new BasePosition[] { b1 });
-    elements.add(locElement);
-    loc.setLocElements(elements);
-    locs.add(loc);
-
-    /*
-     * single range with extra base position - should be skipped
+     * parse two CDS features, one with two Uniprot cross-refs,
+     * the other with one
      */
-    loc = new EmblFeatureLocations();
-    loc.setLocationType("single");
-    loc.setLocationComplement(false);
-    elements = new Vector<EmblFeatureLocElement>();
-    locElement = new EmblFeatureLocElement();
-    b1 = new BasePosition();
-    b1.setPos("30");
-    locElement.setBasePositions(new BasePosition[] { b1, b1, b1 });
-    elements.add(locElement);
-    loc.setLocElements(elements);
-    locs.add(loc);
-
-    /*
-     * single valid range [50-60] to finish
-     */
-    loc = new EmblFeatureLocations();
-    loc.setLocationType("single");
-    loc.setLocationComplement(false);
-    elements = new Vector<EmblFeatureLocElement>();
-    locElement = new EmblFeatureLocElement();
-    b1 = new BasePosition();
-    b1.setPos("50");
-    b2 = new BasePosition();
-    b2.setPos("60");
-    locElement.setBasePositions(new BasePosition[] { b1, b2 });
-    elements.add(locElement);
-    loc.setLocElements(elements);
-    locs.add(loc);
-
-    int[] exons = testee.getCdsRanges(cds);
-    assertEquals("[10, 20, 50, 60]", Arrays.toString(exons));
-  }
-
-  /**
-   * Test retrieval of exon locations matching an accession id
-   */
-  @Test(groups = "Functional")
-  public void testGetCdsRanges_forAccession()
-  {
     EmblEntry testee = new EmblEntry();
-    String accession = "A1234";
-    testee.setAccession(accession);
-    /*
-     * Make a (CDS) Feature with 4 locations
-     */
-    EmblFeature cds = new EmblFeature();
-    Vector<EmblFeatureLocations> locs = new Vector<EmblFeatureLocations>();
-    cds.setLocations(locs);
-  
-    /*
-     * single range [10-20] for 'this' accession
-     */
-    EmblFeatureLocations loc = new EmblFeatureLocations();
-    loc.setLocationType("single");
-    loc.setLocationComplement(false);
-    Vector<EmblFeatureLocElement> elements = new Vector<EmblFeatureLocElement>();
-    EmblFeatureLocElement locElement = new EmblFeatureLocElement();
-    locElement.setAccession(accession);
-    BasePosition b1 = new BasePosition();
-    b1.setPos("10");
-    BasePosition b2 = new BasePosition();
-    b2.setPos("20");
-    locElement.setBasePositions(new BasePosition[] { b1, b2 });
-    elements.add(locElement);
-    loc.setLocElements(elements);
-    locs.add(loc);
-  
-    /*
-     * complement range [30-40] - no accession
-     */
-    loc = new EmblFeatureLocations();
-    loc.setLocationType("single");
-    loc.setLocationComplement(true);
-    elements = new Vector<EmblFeatureLocElement>();
-    locElement = new EmblFeatureLocElement();
-    b1 = new BasePosition();
-    b1.setPos("30");
-    b2 = new BasePosition();
-    b2.setPos("40");
-    locElement.setBasePositions(new BasePosition[] { b1, b2 });
-    elements.add(locElement);
-    loc.setLocElements(elements);
-    locs.add(loc);
-  
-    /*
-     * join range [50-60] this accession, [70-80] another
-     */
-    loc = new EmblFeatureLocations();
-    loc.setLocationType("join");
-    loc.setLocationComplement(false);
-    elements = new Vector<EmblFeatureLocElement>();
-    locElement = new EmblFeatureLocElement();
-    locElement.setAccession(accession);
-    b1 = new BasePosition();
-    b1.setPos("50");
-    b2 = new BasePosition();
-    b2.setPos("60");
-    locElement.setBasePositions(new BasePosition[] { b1, b2 });
-    elements.add(locElement);
-    locElement = new EmblFeatureLocElement();
-    locElement.setAccession("notme");
-    b1 = new BasePosition();
-    b1.setPos("70");
-    b2 = new BasePosition();
-    b2.setPos("80");
-    locElement.setBasePositions(new BasePosition[] { b1, b2 });
-    elements.add(locElement);
-    loc.setLocElements(elements);
-    locs.add(loc);
-  
-    /*
-     * complement range [90-100] wrong accession, [110-120] good 
-     * this should be the same as complement(join(90..100,110.120))
-     * which is "join 90-100 and 110-120, then complement"
-     */
-    loc = new EmblFeatureLocations();
-    loc.setLocationType("join");
-    loc.setLocationComplement(true);
-    elements = new Vector<EmblFeatureLocElement>();
-    locElement = new EmblFeatureLocElement();
-    locElement.setAccession("wrong");
-    b1 = new BasePosition();
-    b1.setPos("90");
-    b2 = new BasePosition();
-    b2.setPos("100");
-    locElement.setBasePositions(new BasePosition[] { b1, b2 });
-    elements.add(locElement);
-    locElement = new EmblFeatureLocElement();
-    locElement.setAccession(accession);
-    b1 = new BasePosition();
-    b1.setPos("110");
-    b2 = new BasePosition();
-    b2.setPos("120");
-    locElement.setBasePositions(new BasePosition[] { b1, b2 });
-    elements.add(locElement);
-    loc.setLocElements(elements);
-    locs.add(loc);
-  
-    /*
-     * verify we pick out only ranges for A1234
-     */
-    int[] exons = testee.getCdsRanges(cds);
-    assertEquals("[10, 20, 50, 60, 120, 110]",
-            Arrays.toString(exons));
+    for (EmblFeature feature : ef.getEntries().get(0).getFeatures())
+    {
+      if ("CDS".equals(feature.getName()))
+      {
+        testee.parseCodingFeature(feature, "EMBL", dna, peptides);
+      }
+    }
+
+    /*
+     * peptides should now have five entries:
+     * EMBL product and two Uniprot accessions for the first CDS / translation
+     * EMBL product and one Uniprot accession for the second CDS / translation
+     */
+    assertEquals(5, peptides.size());
+    assertEquals("CAA30420.1", peptides.get(0).getName());
+    assertEquals("MLCF", peptides.get(0).getSequenceAsString());
+    assertEquals("UNIPROT|B0BCM4", peptides.get(1).getName());
+    assertEquals("MLCF", peptides.get(1).getSequenceAsString());
+    assertEquals("UNIPROT|P0CE20", peptides.get(2).getName());
+    assertEquals("MLCF", peptides.get(2).getSequenceAsString());
+    assertEquals("CAA30421.1", peptides.get(3).getName());
+    assertEquals("MSSS", peptides.get(3).getSequenceAsString());
+    assertEquals("UNIPROT|B0BCM3", peptides.get(4).getName());
+    assertEquals("MSSS", peptides.get(4).getSequenceAsString());
+
+    /*
+     * verify dna sequence has dbrefs with mappings to the peptide 'products'
+     */
+    DBRefEntry[] dbrefs = dna.getDBRefs();
+    assertEquals(3, dbrefs.length);
+    DBRefEntry dbRefEntry = dbrefs[0];
+    assertEquals("UNIPROT", dbRefEntry.getSource());
+    assertEquals("B0BCM4", dbRefEntry.getAccessionId());
+    assertSame(peptides.get(1), dbRefEntry.getMap().getTo());
+    List<int[]> fromRanges = dbRefEntry.getMap().getMap().getFromRanges();
+    assertEquals(1, fromRanges.size());
+    assertEquals(57, fromRanges.get(0)[0]);
+    assertEquals(46, fromRanges.get(0)[1]);
+    List<int[]> toRanges = dbRefEntry.getMap().getMap().getToRanges();
+    assertEquals(1, toRanges.size());
+    assertEquals(1, toRanges.get(0)[0]);
+    assertEquals(4, toRanges.get(0)[1]);
+
+    dbRefEntry = dbrefs[1];
+    assertEquals("UNIPROT", dbRefEntry.getSource());
+    assertEquals("P0CE20", dbRefEntry.getAccessionId());
+    assertSame(peptides.get(2), dbRefEntry.getMap().getTo());
+    fromRanges = dbRefEntry.getMap().getMap().getFromRanges();
+    assertEquals(1, fromRanges.size());
+    assertEquals(57, fromRanges.get(0)[0]);
+    assertEquals(46, fromRanges.get(0)[1]);
+    toRanges = dbRefEntry.getMap().getMap().getToRanges();
+    assertEquals(1, toRanges.size());
+    assertEquals(1, toRanges.get(0)[0]);
+    assertEquals(4, toRanges.get(0)[1]);
+
+    dbRefEntry = dbrefs[2];
+    assertEquals("UNIPROT", dbRefEntry.getSource());
+    assertEquals("B0BCM3", dbRefEntry.getAccessionId());
+    assertSame(peptides.get(4), dbRefEntry.getMap().getTo());
+    fromRanges = dbRefEntry.getMap().getMap().getFromRanges();
+    assertEquals(1, fromRanges.size());
+    assertEquals(4, fromRanges.get(0)[0]);
+    assertEquals(15, fromRanges.get(0)[1]);
+    toRanges = dbRefEntry.getMap().getMap().getToRanges();
+    assertEquals(1, toRanges.size());
+    assertEquals(1, toRanges.get(0)[0]);
+    assertEquals(4, toRanges.get(0)[1]);
   }
 }