X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=test%2Fjalview%2Fdatamodel%2Fxdb%2Fembl%2FEmblEntryTest.java;h=8ed5cc402a4393d213640b8d2ce9a78079444d4a;hb=134576f5b34894218bdc4c5ce5e27fa18ad973bd;hp=d987e53eb69a5177e9e04b1ba370282e7e7c3f18;hpb=f28d892d6d2584e7eb44ff7333d49d60d787f706;p=jalview.git

diff --git a/test/jalview/datamodel/xdb/embl/EmblEntryTest.java b/test/jalview/datamodel/xdb/embl/EmblEntryTest.java
index d987e53..8ed5cc4 100644
--- a/test/jalview/datamodel/xdb/embl/EmblEntryTest.java
+++ b/test/jalview/datamodel/xdb/embl/EmblEntryTest.java
@@ -1,12 +1,34 @@
+/*
+ * 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.analysis.SequenceIdMatcher;
 import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.Sequence;
+import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceI;
+import jalview.util.MapList;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -22,7 +44,7 @@ public class EmblEntryTest
     EmblEntry testee = new EmblEntry();
 
     /*
-     * Make a (CDS) Feature with 4 locations
+     * Make a (CDS) Feature with 5 locations
      */
     EmblFeature cds = new EmblFeature();
     cds.setLocation("join(10..20,complement(30..40),50..60,70..80,complement(110..120))");
@@ -36,20 +58,22 @@ public class EmblEntryTest
   public void testParseCodingFeature()
   {
     // not the whole sequence but enough for this test...
-    SequenceI dna = new Sequence("J03321", "GGATCCGTAAGTTAGACGAAATT");
     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);
 
     /*
      * parse three CDS features, with two/one/no Uniprot cross-refs
      */
-    EmblEntry testee = new EmblEntry();
     for (EmblFeature feature : ef.getEntries().get(0).getFeatures())
     {
       if ("CDS".equals(feature.getName()))
       {
-        testee.parseCodingFeature(feature, "EMBL", dna, peptides, matcher);
+        testee.parseCodingFeature(feature, sourceDb, dna, peptides, matcher);
       }
     }
 
@@ -57,7 +81,7 @@ public class EmblEntryTest
      * 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 and synthesized EMBLCDSPROTEINaccession for the third
+     * EMBL product only for the third
      */
     assertEquals(6, peptides.size());
     assertEquals("CAA30420.1", peptides.get(0).getName());
@@ -74,63 +98,129 @@ public class EmblEntryTest
     assertEquals("MSS", peptides.get(5).getSequenceAsString());
 
     /*
-     * verify dna sequence has dbrefs with mappings to the peptide 'products'
+     * verify dna sequence has dbrefs with CDS mappings to the peptide 'products'
      */
+    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());
-    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]);
+    assertEquals(cds1Map, dbRefEntry.getMap().getMap());
 
     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]);
+    assertEquals(cds1Map, dbRefEntry.getMap().getMap());
 
     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]);
+    assertEquals(cds2Map, dbRefEntry.getMap().getMap());
 
     dbRefEntry = dbrefs[3];
     assertEquals("EMBLCDSPROTEIN", dbRefEntry.getSource());
     assertEquals("CAA12345.6", dbRefEntry.getAccessionId());
     assertSame(peptides.get(5), dbRefEntry.getMap().getTo());
-    fromRanges = dbRefEntry.getMap().getMap().getFromRanges();
-    assertEquals(2, fromRanges.size());
-    assertEquals(4, fromRanges.get(0)[0]);
-    assertEquals(6, fromRanges.get(0)[1]);
-    assertEquals(10, fromRanges.get(1)[0]);
-    assertEquals(15, fromRanges.get(1)[1]);
-    toRanges = dbRefEntry.getMap().getMap().getToRanges();
-    assertEquals(1, toRanges.size());
-    assertEquals(1, toRanges.get(0)[0]);
-    assertEquals(3, toRanges.get(0)[1]);
+    assertEquals(cds3Map, dbRefEntry.getMap().getMap());
+
+    /*
+     * 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
+     */
+    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);
+
+    // 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(groups = "Functional")
@@ -146,8 +236,7 @@ public class EmblEntryTest
 
     // truncate last exon by 6bp
     int[] truncated = EmblEntry.adjustForProteinLength(4, exons);
-    assertEquals("[11, 15, 21, 25, 31, 32]",
-            Arrays.toString(truncated));
+    assertEquals("[11, 15, 21, 25, 31, 32]", Arrays.toString(truncated));
 
     // remove last exon and truncate preceding by 1bp
     truncated = EmblEntry.adjustForProteinLength(3, exons);
@@ -161,6 +250,5 @@ public class EmblEntryTest
     // what if exons are too short for protein?
     truncated = EmblEntry.adjustForProteinLength(7, exons);
     assertSame(exons, truncated);
-    // assertEquals("[11, 15, 21, 27]", Arrays.toString(truncated));
   }
 }