X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2Fxdb%2Fembl%2FEmblEntryTest.java;h=46725741b8be88841939f8ba95d7d31adf6b4e39;hb=d8720fc191cba996c440171ef8e07462ef9f7035;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..4672574 100644
--- a/test/jalview/datamodel/xdb/embl/EmblEntryTest.java
+++ b/test/jalview/datamodel/xdb/embl/EmblEntryTest.java
@@ -1,308 +1,264 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel.xdb.embl;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 
-import jalview.util.MappingUtils;
+import jalview.analysis.SequenceIdMatcher;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
+import jalview.util.MapList;
 
+import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.Vector;
+import java.util.List;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class EmblEntryTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   @Test(groups = "Functional")
   public void testGetCdsRanges()
   {
     EmblEntry testee = new EmblEntry();
 
     /*
-     * Make a (CDS) Feature with 4 locations
+     * Make a (CDS) Feature with 5 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...
+    List<SequenceI> peptides = new ArrayList<SequenceI>();
+    SequenceIdMatcher matcher = new SequenceIdMatcher(peptides);
+    EmblFile ef = EmblTestHelper.getEmblFile();
+    assertEquals(1, ef.getEntries().size());
+    EmblEntry testee = ef.getEntries().get(0);
+    String sourceDb = "EMBL";
+    SequenceI dna = testee.makeSequence(sourceDb);
 
     /*
-     * Make a (CDS) Feature with 4 locations
+     * parse three CDS features, with two/one/no Uniprot cross-refs
      */
-    EmblFeature cds = new EmblFeature();
-    Vector<EmblFeatureLocations> locs = new Vector<EmblFeatureLocations>();
-    cds.setLocations(locs);
+    for (EmblFeature feature : ef.getEntries().get(0).getFeatures())
+    {
+      if ("CDS".equals(feature.getName()))
+      {
+        testee.parseCodingFeature(feature, sourceDb, dna, peptides, matcher);
+      }
+    }
 
     /*
-     * single range [10-20]
+     * 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 / "
+     * EMBL product only for the third
      */
-    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);
+    assertEquals(6, 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());
+    assertEquals("CAA12345.6", peptides.get(5).getName());
+    assertEquals("MSS", peptides.get(5).getSequenceAsString());
 
     /*
-     * single range with missing end position - should be skipped
+     * verify dna sequence has dbrefs with CDS mappings to the peptide 'products'
      */
-    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);
+    MapList cds1Map = new MapList(new int[] { 57, 46 }, new int[] { 1, 4 },
+            3, 1);
+    MapList cds2Map = new MapList(new int[] { 4, 15 }, new int[] { 1, 4 },
+            3, 1);
+    MapList cds3Map = new MapList(new int[] { 4, 6, 10, 15 }, new int[] {
+        1, 3 }, 3, 1);
+    DBRefEntry[] dbrefs = dna.getDBRefs();
+    assertEquals(4, dbrefs.length);
+    DBRefEntry dbRefEntry = dbrefs[0];
+    assertEquals("UNIPROT", dbRefEntry.getSource());
+    assertEquals("B0BCM4", dbRefEntry.getAccessionId());
+    assertSame(peptides.get(1), dbRefEntry.getMap().getTo());
+    assertEquals(cds1Map, dbRefEntry.getMap().getMap());
 
-    /*
-     * single range with extra base 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, b1, b1 });
-    elements.add(locElement);
-    loc.setLocElements(elements);
-    locs.add(loc);
+    dbRefEntry = dbrefs[1];
+    assertEquals("UNIPROT", dbRefEntry.getSource());
+    assertEquals("P0CE20", dbRefEntry.getAccessionId());
+    assertSame(peptides.get(2), dbRefEntry.getMap().getTo());
+    assertEquals(cds1Map, dbRefEntry.getMap().getMap());
+
+    dbRefEntry = dbrefs[2];
+    assertEquals("UNIPROT", dbRefEntry.getSource());
+    assertEquals("B0BCM3", dbRefEntry.getAccessionId());
+    assertSame(peptides.get(4), dbRefEntry.getMap().getTo());
+    assertEquals(cds2Map, dbRefEntry.getMap().getMap());
+
+    dbRefEntry = dbrefs[3];
+    assertEquals("EMBLCDSPROTEIN", dbRefEntry.getSource());
+    assertEquals("CAA12345.6", dbRefEntry.getAccessionId());
+    assertSame(peptides.get(5), dbRefEntry.getMap().getTo());
+    assertEquals(cds3Map, dbRefEntry.getMap().getMap());
 
     /*
-     * single valid range [50-60] to finish
+     * verify peptides have dbrefs
+     * - to EMBL sequence (with inverse 1:3 cds mapping)
+     * - to EMBLCDS (with 1:3 mapping)
+     * - direct (no mapping) to other protein accessions
      */
-    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);
+    MapList proteinToCdsMap1 = new MapList(new int[] { 1, 4 }, new int[] {
+        1, 12 }, 1, 3);
+    MapList proteinToCdsMap2 = new MapList(new int[] { 1, 3 }, new int[] {
+        1, 9 }, 1, 3);
 
-    int[] exons = testee.getCdsRanges(cds);
-    assertEquals("[10, 20, 50, 60]", Arrays.toString(exons));
+    // dbrefs for first CDS EMBL product CAA30420.1
+    dbrefs = peptides.get(0).getDBRefs();
+    assertEquals(5, dbrefs.length);
+    assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
+    assertEquals("CAA30420.1", dbrefs[0].getAccessionId());
+    // TODO: verify getPrimaryDBRefs() for peptide products
+    assertEquals(cds1Map.getInverse(), dbrefs[0].getMap().getMap());
+    assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
+    assertEquals("CAA30420.1", dbrefs[1].getAccessionId());
+    assertEquals(proteinToCdsMap1, dbrefs[1].getMap().getMap());
+    assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
+    assertEquals("CAA30420.1", dbrefs[2].getAccessionId());
+    assertNull(dbrefs[2].getMap());
+    assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "2.1", "B0BCM4"),
+            dbrefs[3]);
+    assertNull(dbrefs[3].getMap());
+    assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "P0CE20"),
+            dbrefs[4]);
+    assertNull(dbrefs[4].getMap());
+
+    // dbrefs for first CDS first Uniprot xref
+    dbrefs = peptides.get(1).getDBRefs();
+    assertEquals(2, dbrefs.length);
+    assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "2.1", "B0BCM4"),
+            dbrefs[0]);
+    assertNull(dbrefs[0].getMap());
+    assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
+    assertEquals("X07547", dbrefs[1].getAccessionId());
+    assertEquals(cds1Map.getInverse(), dbrefs[1].getMap().getMap());
+
+    // dbrefs for first CDS second Uniprot xref
+    dbrefs = peptides.get(2).getDBRefs();
+    assertEquals(2, dbrefs.length);
+    assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "P0CE20"),
+            dbrefs[0]);
+    assertNull(dbrefs[0].getMap());
+    assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
+    assertEquals("X07547", dbrefs[1].getAccessionId());
+    assertEquals(cds1Map.getInverse(), dbrefs[1].getMap().getMap());
+
+    // dbrefs for second CDS EMBL product CAA30421.1
+    dbrefs = peptides.get(3).getDBRefs();
+    assertEquals(4, dbrefs.length);
+    assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
+    assertEquals("CAA30421.1", dbrefs[0].getAccessionId());
+    assertEquals(cds2Map.getInverse(), dbrefs[0].getMap().getMap());
+    assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
+    assertEquals("CAA30421.1", dbrefs[1].getAccessionId());
+    assertEquals(proteinToCdsMap1, dbrefs[1].getMap().getMap());
+    assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
+    assertEquals("CAA30421.1", dbrefs[2].getAccessionId());
+    assertNull(dbrefs[2].getMap());
+    assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "B0BCM3"),
+            dbrefs[3]);
+    assertNull(dbrefs[3].getMap());
+
+    // dbrefs for second CDS second Uniprot xref
+    dbrefs = peptides.get(4).getDBRefs();
+    assertEquals(2, dbrefs.length);
+    assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "B0BCM3"),
+            dbrefs[0]);
+    assertNull(dbrefs[0].getMap());
+    assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
+    assertEquals("X07547", dbrefs[1].getAccessionId());
+    assertEquals(cds2Map.getInverse(), dbrefs[1].getMap().getMap());
+
+    // dbrefs for third CDS inferred EMBL product CAA12345.6
+    dbrefs = peptides.get(5).getDBRefs();
+    assertEquals(3, dbrefs.length);
+    assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
+    assertEquals("CAA12345.6", dbrefs[0].getAccessionId());
+    assertEquals(cds3Map.getInverse(), dbrefs[0].getMap().getMap());
+    assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
+    assertEquals("CAA12345.6", dbrefs[1].getAccessionId());
+    assertEquals(proteinToCdsMap2, dbrefs[1].getMap().getMap());
+    assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
+    assertEquals("CAA12345.6", dbrefs[2].getAccessionId());
+    assertNull(dbrefs[2].getMap());
   }
 
-  /**
-   * Test retrieval of exon locations matching an accession id
-   */
   @Test(groups = "Functional")
-  public void testGetCdsRanges_forAccession()
+  public void testAdjustForProteinLength()
   {
-    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));
+    int[] exons = new int[] { 11, 15, 21, 25, 31, 38 }; // 18 bp
+
+    // exact length match:
+    assertSame(exons, EmblEntry.adjustForProteinLength(6, exons));
+
+    // match if we assume exons include stop codon not in protein:
+    assertSame(exons, EmblEntry.adjustForProteinLength(5, exons));
+
+    // truncate last exon by 6bp
+    int[] truncated = EmblEntry.adjustForProteinLength(4, exons);
+    assertEquals("[11, 15, 21, 25, 31, 32]", Arrays.toString(truncated));
+
+    // remove last exon and truncate preceding by 1bp
+    truncated = EmblEntry.adjustForProteinLength(3, exons);
+    assertEquals("[11, 15, 21, 24]", Arrays.toString(truncated));
+
+    // exact removal of exon case:
+    exons = new int[] { 11, 15, 21, 27, 33, 38 }; // 18 bp
+    truncated = EmblEntry.adjustForProteinLength(4, exons);
+    assertEquals("[11, 15, 21, 27]", Arrays.toString(truncated));
+
+    // what if exons are too short for protein?
+    truncated = EmblEntry.adjustForProteinLength(7, exons);
+    assertSame(exons, truncated);
   }
 }