X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2Fxdb%2Fembl%2FEmblEntryTest.java;h=abe5099ff49096944b9e179990a5a9422da4cd4d;hb=a3b6803932b6b0ce73a44982bc58c56b7b4def4b;hp=3de5e3f25343518d9eb4d23e57987d11540ba9b7;hpb=77a7aa4d0c1be9ac6d0e6195a3b0ac3cd73f2875;p=jalview.git diff --git a/test/jalview/datamodel/xdb/embl/EmblEntryTest.java b/test/jalview/datamodel/xdb/embl/EmblEntryTest.java index 3de5e3f..abe5099 100644 --- a/test/jalview/datamodel/xdb/embl/EmblEntryTest.java +++ b/test/jalview/datamodel/xdb/embl/EmblEntryTest.java @@ -1,12 +1,14 @@ 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 +24,7 @@ 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))"); @@ -36,30 +38,32 @@ public class EmblEntryTest public void testParseCodingFeature() { // not the whole sequence but enough for this test... - SequenceI dna = new Sequence("J03321", "GGATCCGTAAGTTAGACGAAATT"); List peptides = new ArrayList(); 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 two CDS features, one with two Uniprot cross-refs, - * the other with one + * 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); } } /* * 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 + * EMBL product and one Uniprot accession for the second CDS / " + * EMBL product only for the third */ - assertEquals(5, peptides.size()); + assertEquals(6, peptides.size()); assertEquals("CAA30420.1", peptides.get(0).getName()); assertEquals("MLCF", peptides.get(0).getSequenceAsString()); assertEquals("UNIPROT|B0BCM4", peptides.get(1).getName()); @@ -70,49 +74,162 @@ public class EmblEntryTest 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()); /* - * 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(3, dbrefs.length); + assertEquals(4, dbrefs.length); DBRefEntry dbRefEntry = dbrefs[0]; assertEquals("UNIPROT", dbRefEntry.getSource()); assertEquals("B0BCM4", dbRefEntry.getAccessionId()); assertSame(peptides.get(1), dbRefEntry.getMap().getTo()); - List fromRanges = dbRefEntry.getMap().getMap().getFromRanges(); - assertEquals(1, fromRanges.size()); - assertEquals(57, fromRanges.get(0)[0]); - assertEquals(46, fromRanges.get(0)[1]); - List 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()); + 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") + public void testAdjustForProteinLength() + { + 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); } }