+++ /dev/null
-/*
- * 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.ws.dbsources;
-
-import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertNotNull;
-import static org.testng.AssertJUnit.assertNull;
-import static org.testng.AssertJUnit.assertSame;
-import static org.testng.AssertJUnit.assertTrue;
-
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.SequenceI;
-import jalview.util.MapList;
-import jalview.xml.binding.embl.EntryType;
-import jalview.xml.binding.embl.EntryType.Feature;
-import jalview.xml.binding.embl.EntryType.Feature.Qualifier;
-import jalview.xml.binding.embl.XrefType;
-
-import java.io.ByteArrayInputStream;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import org.testng.annotations.Test;
-
-public class EmblSourceTest
-{
-
- // adapted from http://www.ebi.ac.uk/ena/data/view/X07547&display=xml
- // dna and translations truncated for convenience
- static final String TESTDATA = "<?xml version=\"1.0\" encoding=\"UTF-8\" ?>"
- + "<ROOT>"
- + "<entry accession=\"X07547\" version=\"1\" entryVersion=\"8\""
- + " dataClass=\"STD\" taxonomicDivision=\"PRO\""
- + " moleculeType=\"genomic DNA\" sequenceLength=\"7499\" topology=\"linear\""
- + " firstPublic=\"1988-11-10\" firstPublicRelease=\"18\""
- + " lastUpdated=\"1999-02-10\" lastUpdatedRelease=\"58\">"
- + "<secondaryAccession>X07574</secondaryAccession>"
- + "<description>C. trachomatis plasmid</description>"
- + "<keyword>plasmid</keyword><keyword>unidentified reading frame</keyword>"
- + "<xref db=\"EuropePMC\" id=\"PMC107176\" secondaryId=\"9573186\" />"
- + "<xref db=\"MD5\" id=\"ac73317\" />"
- /*
- * first CDS (range and translation changed to keep test data manageable)
- */
- + "<feature name=\"CDS\" location=\"complement(46..57)\">"
- // test the case of >1 cross-ref to the same database (JAL-2029)
- + "<xref db=\"UniProtKB/Swiss-Prot\" id=\"B0BCM4\" secondaryId=\"2.1\" />"
- + "<xref db=\"UniProtKB/Swiss-Prot\" id=\"P0CE20\" />"
- + "<qualifier name=\"note\"><value>ORF 8 (AA 1-330)</value></qualifier>"
- + "<qualifier name=\"protein_id\"><value>CAA30420.1</value></qualifier>"
- + "<qualifier name=\"translation\"><value>MLCF</value></qualifier>"
- + "</feature>"
- /*
- * second CDS (range and translation changed to keep test data manageable)
- */
- + "<feature name=\"CDS\" location=\"4..15\">"
- + "<xref db=\"UniProtKB/Swiss-Prot\" id=\"B0BCM3\" />"
- + "<qualifier name=\"protein_id\"><value>CAA30421.1</value></qualifier>"
- + "<qualifier name=\"translation\"><value>MSSS</value></qualifier>"
- + "</feature>"
- /*
- * third CDS is made up - has no xref - code should synthesize
- * one to an assumed EMBLCDSPROTEIN accession
- */
- + "<feature name=\"CDS\" location=\"join(4..6,10..15)\">"
- + "<qualifier name=\"protein_id\"><value>CAA12345.6</value></qualifier>"
- + "<qualifier name=\"translation\"><value>MSS</value></qualifier>"
- + "</feature>"
- /*
- * sequence (modified for test purposes)
- * emulates EMBL XML 1.2 which splits sequence data every 60 characters
- * see EmblSequence.setSequence
- */
- + "<sequence>GGTATGTCCTCTAGTACAAAC\n"
- + "ACCCCCAATATTGTGATATAATTAAAAACATAGCAT"
- + "</sequence></entry></ROOT>";
-
- @Test(groups = "Functional")
- public void testGetCdsRanges()
- {
- EmblSource testee = new EmblSource();
-
- /*
- * Make a (CDS) Feature with 5 locations
- */
- Feature cds = new Feature();
- cds.setLocation("join(10..20,complement(30..40),50..60,70..80,complement(110..120))");
-
- int[] exons = testee.getCdsRanges("EMBL", cds);
- assertEquals("[10, 20, 40, 30, 50, 60, 70, 80, 120, 110]",
- Arrays.toString(exons));
- }
-
- @Test(groups = "Functional")
- public void testGetSequence()
- {
- // not the whole sequence but enough for this test...
- List<SequenceI> peptides = new ArrayList<>();
- List<EntryType> entries = EmblSourceTest.getEmblEntries();
- assertEquals(1, entries.size());
- EntryType entry = entries.get(0);
- EmblSource testee = new EmblSource();
- String sourceDb = "EMBL";
- SequenceI dna = testee.getSequence(sourceDb, entry, peptides);
-
- /*
- * newline has been removed from sequence
- */
- String seq = dna.getSequenceAsString();
- assertEquals(
- "GGTATGTCCTCTAGTACAAACACCCCCAATATTGTGATATAATTAAAAACATAGCAT",
- seq);
-
- /*
- * 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
- */
- 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());
-
- /*
- * verify dna sequence has dbrefs
- * - to 'self' (synthesized dbref)
- * - to EuropePMC
- * - to MD5 (with null version as "0")
- * - with CDS mappings to the peptide 'products'
- */
- MapList mapToSelf = new MapList(new int[] { 1, 57 },
- new int[]
- { 1, 57 }, 1, 1);
- 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);
-
- List<DBRefEntry> dbrefs = dna.getDBRefs();
- assertEquals(7, dbrefs.size());
-
- DBRefEntry dbRefEntry = dbrefs.get(0);
- assertEquals("EMBL", dbRefEntry.getSource());
- assertEquals("X07547", dbRefEntry.getAccessionId());
- assertEquals("1", dbRefEntry.getVersion());
- assertNotNull(dbRefEntry.getMap());
- assertNull(dbRefEntry.getMap().getTo());
- assertEquals(mapToSelf, dbRefEntry.getMap().getMap());
-
- dbRefEntry = dbrefs.get(1);
- // DBRefEntry constructor puts dbSource in upper case
- assertEquals("EUROPEPMC", dbRefEntry.getSource());
- assertEquals("PMC107176", dbRefEntry.getAccessionId());
- assertEquals("9573186", dbRefEntry.getVersion());
- assertNull(dbRefEntry.getMap());
-
- dbRefEntry = dbrefs.get(2);
- assertEquals("MD5", dbRefEntry.getSource());
- assertEquals("ac73317", dbRefEntry.getAccessionId());
- assertEquals("0", dbRefEntry.getVersion());
- assertNull(dbRefEntry.getMap());
-
- dbRefEntry = dbrefs.get(3);
- assertEquals("UNIPROT", dbRefEntry.getSource());
- assertEquals("B0BCM4", dbRefEntry.getAccessionId());
- assertSame(peptides.get(1), dbRefEntry.getMap().getTo());
- assertEquals(cds1Map, dbRefEntry.getMap().getMap());
-
- dbRefEntry = dbrefs.get(4);
- assertEquals("UNIPROT", dbRefEntry.getSource());
- assertEquals("P0CE20", dbRefEntry.getAccessionId());
- assertSame(peptides.get(2), dbRefEntry.getMap().getTo());
- assertEquals(cds1Map, dbRefEntry.getMap().getMap());
-
- dbRefEntry = dbrefs.get(5);
- assertEquals("UNIPROT", dbRefEntry.getSource());
- assertEquals("B0BCM3", dbRefEntry.getAccessionId());
- assertSame(peptides.get(4), dbRefEntry.getMap().getTo());
- assertEquals(cds2Map, dbRefEntry.getMap().getMap());
-
- dbRefEntry = dbrefs.get(6);
- 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.size());
- assertEquals(DBRefSource.EMBL, dbrefs.get(0).getSource());
- assertEquals("CAA30420.1", dbrefs.get(0).getAccessionId());
- // TODO: verify getPrimaryDBRefs() for peptide products
- assertEquals(cds1Map.getInverse(), dbrefs.get(0).getMap().getMap());
- assertEquals(DBRefSource.EMBLCDS, dbrefs.get(1).getSource());
- assertEquals("CAA30420.1", dbrefs.get(1).getAccessionId());
- assertEquals(proteinToCdsMap1, dbrefs.get(1).getMap().getMap());
- assertEquals(DBRefSource.EMBLCDSProduct, dbrefs.get(2).getSource());
- assertEquals("CAA30420.1", dbrefs.get(2).getAccessionId());
- assertNull(dbrefs.get(2).getMap());
- assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "2.1", "B0BCM4"),
- dbrefs.get(3));
- assertNull(dbrefs.get(3).getMap());
- assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "P0CE20"),
- dbrefs.get(4));
- assertNull(dbrefs.get(4).getMap());
-
- // dbrefs for first CDS first Uniprot xref
- dbrefs = peptides.get(1).getDBRefs();
- assertEquals(2, dbrefs.size());
- assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "2.1", "B0BCM4"),
- dbrefs.get(0));
- assertNull(dbrefs.get(0).getMap());
- assertEquals(DBRefSource.EMBL, dbrefs.get(1).getSource());
- assertEquals("X07547", dbrefs.get(1).getAccessionId());
- assertEquals(cds1Map.getInverse(), dbrefs.get(1).getMap().getMap());
-
- // dbrefs for first CDS second Uniprot xref
- dbrefs = peptides.get(2).getDBRefs();
- assertEquals(2, dbrefs.size());
- assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "P0CE20"),
- dbrefs.get(0));
- assertNull(dbrefs.get(0).getMap());
- assertEquals(DBRefSource.EMBL, dbrefs.get(1).getSource());
- assertEquals("X07547", dbrefs.get(1).getAccessionId());
- assertEquals(cds1Map.getInverse(), dbrefs.get(1).getMap().getMap());
-
- // dbrefs for second CDS EMBL product CAA30421.1
- dbrefs = peptides.get(3).getDBRefs();
- assertEquals(4, dbrefs.size());
- assertEquals(DBRefSource.EMBL, dbrefs.get(0).getSource());
- assertEquals("CAA30421.1", dbrefs.get(0).getAccessionId());
- assertEquals(cds2Map.getInverse(), dbrefs.get(0).getMap().getMap());
- assertEquals(DBRefSource.EMBLCDS, dbrefs.get(1).getSource());
- assertEquals("CAA30421.1", dbrefs.get(1).getAccessionId());
- assertEquals(proteinToCdsMap1, dbrefs.get(1).getMap().getMap());
- assertEquals(DBRefSource.EMBLCDSProduct, dbrefs.get(2).getSource());
- assertEquals("CAA30421.1", dbrefs.get(2).getAccessionId());
- assertNull(dbrefs.get(2).getMap());
- assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "B0BCM3"),
- dbrefs.get(3));
- assertNull(dbrefs.get(3).getMap());
-
- // dbrefs for second CDS second Uniprot xref
- dbrefs = peptides.get(4).getDBRefs();
- assertEquals(2, dbrefs.size());
- assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "B0BCM3"),
- dbrefs.get(0));
- assertNull(dbrefs.get(0).getMap());
- assertEquals(DBRefSource.EMBL, dbrefs.get(1).getSource());
- assertEquals("X07547", dbrefs.get(1).getAccessionId());
- assertEquals(cds2Map.getInverse(), dbrefs.get(1).getMap().getMap());
-
- // dbrefs for third CDS inferred EMBL product CAA12345.6
- dbrefs = peptides.get(5).getDBRefs();
- assertEquals(3, dbrefs.size());
- assertEquals(DBRefSource.EMBL, dbrefs.get(0).getSource());
- assertEquals("CAA12345.6", dbrefs.get(0).getAccessionId());
- assertEquals(cds3Map.getInverse(), dbrefs.get(0).getMap().getMap());
- assertEquals(DBRefSource.EMBLCDS, dbrefs.get(1).getSource());
- assertEquals("CAA12345.6", dbrefs.get(1).getAccessionId());
- assertEquals(proteinToCdsMap2, dbrefs.get(1).getMap().getMap());
- assertEquals(DBRefSource.EMBLCDSProduct, dbrefs.get(2).getSource());
- assertEquals("CAA12345.6", dbrefs.get(2).getAccessionId());
- assertNull(dbrefs.get(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, EmblXmlSource.adjustForProteinLength(6, exons));
-
- // match if we assume exons include stop codon not in protein:
- assertSame(exons, EmblXmlSource.adjustForProteinLength(5, exons));
-
- // truncate last exon by 6bp
- int[] truncated = EmblXmlSource.adjustForProteinLength(4, exons);
- assertEquals("[11, 15, 21, 25, 31, 32]", Arrays.toString(truncated));
-
- // remove last exon and truncate preceding by 1bp
- truncated = EmblXmlSource.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 = EmblXmlSource.adjustForProteinLength(4, exons);
- assertEquals("[11, 15, 21, 27]", Arrays.toString(truncated));
-
- // what if exons are too short for protein?
- truncated = EmblXmlSource.adjustForProteinLength(7, exons);
- assertSame(exons, truncated);
- }
-
- @Test(groups = { "Functional" })
- public void testGetEmblEntries()
- {
- List<EntryType> entries = EmblSourceTest.getEmblEntries();
- assertEquals(1, entries.size());
- EntryType entry = entries.get(0);
-
- assertEquals("X07547", entry.getAccession());
- assertEquals("C. trachomatis plasmid", entry.getDescription());
- assertEquals("STD", entry.getDataClass());
- assertEquals("PRO", entry.getTaxonomicDivision());
- assertEquals("1999-02-10", entry.getLastUpdated().toString());
- assertEquals(58, entry.getLastUpdatedRelease().intValue());
- assertEquals("1988-11-10", entry.getFirstPublic().toString());
- assertEquals(18, entry.getFirstPublicRelease().intValue());
- assertEquals("genomic DNA", entry.getMoleculeType());
- assertEquals(1, entry.getVersion().intValue());
- assertEquals(8, entry.getEntryVersion().intValue());
- assertEquals("linear", entry.getTopology());
- assertEquals(7499, entry.getSequenceLength().intValue());
- assertEquals(2, entry.getKeyword().size());
- assertEquals("plasmid", entry.getKeyword().get(0));
- assertEquals("unidentified reading frame", entry.getKeyword().get(1));
-
- /*
- * dbrefs
- */
- assertEquals(2, entry.getXref().size());
- XrefType dbref = entry.getXref().get(0);
- assertEquals("EuropePMC", dbref.getDb());
- assertEquals("PMC107176", dbref.getId());
- assertEquals("9573186", dbref.getSecondaryId());
- dbref = entry.getXref().get(1);
- assertEquals("MD5", dbref.getDb());
- assertEquals("ac73317", dbref.getId());
- assertNull(dbref.getSecondaryId());
-
- /*
- * three sequence features for CDS
- */
- assertEquals(3, entry.getFeature().size());
- /*
- * first CDS
- */
- Feature ef = entry.getFeature().get(0);
- assertEquals("CDS", ef.getName());
- assertEquals("complement(46..57)", ef.getLocation());
- assertEquals(2, ef.getXref().size());
- dbref = ef.getXref().get(0);
- assertEquals("UniProtKB/Swiss-Prot", dbref.getDb());
- assertEquals("B0BCM4", dbref.getId());
- assertEquals("2.1", dbref.getSecondaryId());
- dbref = ef.getXref().get(1);
- assertEquals("UniProtKB/Swiss-Prot", dbref.getDb());
- assertEquals("P0CE20", dbref.getId());
- assertNull(dbref.getSecondaryId());
- // CDS feature qualifiers
- assertEquals(3, ef.getQualifier().size());
- Qualifier q = ef.getQualifier().get(0);
- assertEquals("note", q.getName());
- assertEquals("ORF 8 (AA 1-330)", q.getValue());
- q = ef.getQualifier().get(1);
- assertEquals("protein_id", q.getName());
- assertEquals("CAA30420.1", q.getValue());
- q = ef.getQualifier().get(2);
- assertEquals("translation", q.getName());
- assertEquals("MLCF", q.getValue());
-
- /*
- * second CDS
- */
- ef = entry.getFeature().get(1);
- assertEquals("CDS", ef.getName());
- assertEquals("4..15", ef.getLocation());
- assertEquals(1, ef.getXref().size());
- dbref = ef.getXref().get(0);
- assertEquals("UniProtKB/Swiss-Prot", dbref.getDb());
- assertEquals("B0BCM3", dbref.getId());
- assertNull(dbref.getSecondaryId());
- assertEquals(2, ef.getQualifier().size());
- q = ef.getQualifier().get(0);
- assertEquals("protein_id", q.getName());
- assertEquals("CAA30421.1", q.getValue());
- q = ef.getQualifier().get(1);
- assertEquals("translation", q.getName());
- assertEquals("MSSS", q.getValue());
-
- /*
- * third CDS
- */
- ef = entry.getFeature().get(2);
- assertEquals("CDS", ef.getName());
- assertEquals("join(4..6,10..15)", ef.getLocation());
- assertNotNull(ef.getXref());
- assertTrue(ef.getXref().isEmpty());
- assertEquals(2, ef.getQualifier().size());
- q = ef.getQualifier().get(0);
- assertEquals("protein_id", q.getName());
- assertEquals("CAA12345.6", q.getValue());
- q = ef.getQualifier().get(1);
- assertEquals("translation", q.getName());
- assertEquals("MSS", q.getValue());
-
- /*
- * Sequence - raw data before removal of newlines
- */
- String seq = entry.getSequence();
- assertEquals(
- "GGTATGTCCTCTAGTACAAAC\n"
- + "ACCCCCAATATTGTGATATAATTAAAAACATAGCAT",
- seq);
-
- /*
- * getSequence() converts empty DBRefEntry.version to "0"
- */
- assertNull(entry.getXref().get(1).getSecondaryId());
- assertNull(entry.getFeature().get(0).getXref().get(1).getSecondaryId());
- }
-
- static List<EntryType> getEmblEntries()
- {
- return new EmblSource()
- .getEmblEntries(new ByteArrayInputStream(TESTDATA.getBytes()));
- }
-}
git://source.jalview.org / jalview.git / blobdiff