+++ /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.analysis;
-
-import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertFalse;
-import static org.testng.AssertJUnit.assertNotNull;
-import static org.testng.AssertJUnit.assertNotSame;
-import static org.testng.AssertJUnit.assertNull;
-import static org.testng.AssertJUnit.assertSame;
-import static org.testng.AssertJUnit.assertTrue;
-
-import jalview.datamodel.AlignedCodonFrame;
-import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.Mapping;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.gui.JvOptionPane;
-import jalview.util.DBRefUtils;
-import jalview.util.MapList;
-import jalview.ws.SequenceFetcher;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
-public class CrossRefTest
-{
-
- @BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
- {
- JvOptionPane.setInteractiveMode(false);
- JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
- }
-
- @Test(groups = { "Functional" })
- public void testFindXDbRefs()
- {
- DBRefEntry ref1 = new DBRefEntry("UNIPROT", "1", "A123");
- DBRefEntry ref2 = new DBRefEntry("UNIPROTKB/TREMBL", "1", "A123");
- DBRefEntry ref3 = new DBRefEntry("pdb", "1", "A123");
- DBRefEntry ref4 = new DBRefEntry("EMBLCDSPROTEIN", "1", "A123");
- DBRefEntry ref5 = new DBRefEntry("embl", "1", "A123");
- DBRefEntry ref6 = new DBRefEntry("emblCDS", "1", "A123");
- DBRefEntry ref7 = new DBRefEntry("GeneDB", "1", "A123");
- DBRefEntry ref8 = new DBRefEntry("PFAM", "1", "A123");
- // ENSEMBL is a source of either dna or protein sequence data
- DBRefEntry ref9 = new DBRefEntry("ENSEMBL", "1", "A123");
- List<DBRefEntry> refs = Arrays.asList(new DBRefEntry[] { ref1, ref2, ref3, ref4, ref5,
- ref6, ref7, ref8, ref9 });
-
- /*
- * Just the DNA refs:
- */
- List<DBRefEntry> found = DBRefUtils.selectDbRefs(true, refs);
- assertEquals(4, found.size());
- assertSame(ref5, found.get(0));
- assertSame(ref6, found.get(1));
- assertSame(ref7, found.get(2));
- assertSame(ref9, found.get(3));
-
- /*
- * Just the protein refs:
- */
- found = DBRefUtils.selectDbRefs(false, refs);
- assertEquals(4, found.size());
- assertSame(ref1, found.get(0));
- assertSame(ref2, found.get(1));
- assertSame(ref4, found.get(2));
- assertSame(ref9, found.get(3));
- }
-
- /**
- * Test the method that finds a sequence's "product" xref source databases,
- * which may be direct (dbrefs on the sequence), or indirect (dbrefs on
- * sequences which share a dbref with the sequence
- */
- @Test(groups = { "Functional" }, enabled = true)
- public void testFindXrefSourcesForSequence_proteinToDna()
- {
- SequenceI seq = new Sequence("Seq1", "MGKYQARLSS");
- List<String> sources = new ArrayList<>();
- AlignmentI al = new Alignment(new SequenceI[] {});
-
- /*
- * first with no dbrefs to search
- */
- sources = new CrossRef(new SequenceI[] { seq }, al)
- .findXrefSourcesForSequences(false);
- assertTrue(sources.isEmpty());
-
- /*
- * add some dbrefs to sequence
- */
- // protein db is not a candidate for findXrefSources
- seq.addDBRef(new DBRefEntry("UNIPROT", "0", "A1234"));
- // dna coding databatases are
- seq.addDBRef(new DBRefEntry("EMBL", "0", "E2345"));
- // a second EMBL xref should not result in a duplicate
- seq.addDBRef(new DBRefEntry("EMBL", "0", "E2346"));
- seq.addDBRef(new DBRefEntry("EMBLCDS", "0", "E2347"));
- seq.addDBRef(new DBRefEntry("GENEDB", "0", "E2348"));
- seq.addDBRef(new DBRefEntry("ENSEMBL", "0", "E2349"));
- seq.addDBRef(new DBRefEntry("ENSEMBLGENOMES", "0", "E2350"));
- sources = new CrossRef(new SequenceI[] { seq }, al)
- .findXrefSourcesForSequences(false);
- // method is patched to remove EMBL from the sources to match
- assertEquals(4, sources.size());
- assertEquals("[EMBLCDS, GENEDB, ENSEMBL, ENSEMBLGENOMES]",
- sources.toString());
-
- /*
- * add a sequence to the alignment which has a dbref to UNIPROT|A1234
- * and others to dna coding databases
- */
- sources.clear();
- seq.setDBRefs(null);
- seq.addDBRef(new DBRefEntry("UNIPROT", "0", "A1234"));
- seq.addDBRef(new DBRefEntry("EMBLCDS", "0", "E2347"));
- SequenceI seq2 = new Sequence("Seq2", "MGKYQARLSS");
- seq2.addDBRef(new DBRefEntry("UNIPROT", "0", "A1234"));
- seq2.addDBRef(new DBRefEntry("EMBL", "0", "E2345"));
- seq2.addDBRef(new DBRefEntry("GENEDB", "0", "E2348"));
- // TODO include ENSEMBLGENOMES in DBRefSource.DNACODINGDBS ?
- al.addSequence(seq2);
- sources = new CrossRef(new SequenceI[] { seq, seq2 }, al)
- .findXrefSourcesForSequences(false);
- // method removed EMBL from sources to match
- assertEquals(2, sources.size());
- assertEquals("[EMBLCDS, GENEDB]", sources.toString());
- }
-
- /**
- * Test for finding 'product' sequences for the case where only an indirect
- * xref is found - not on the nucleotide sequence but on a peptide sequence in
- * the alignment which which it shares a nucleotide dbref
- */
- @Test(groups = { "Functional" }, enabled = true)
- public void testFindXrefSequences_indirectDbrefToProtein()
- {
- /*
- * Alignment setup:
- * - nucleotide dbref EMBL|AF039662
- * - peptide dbrefs EMBL|AF039662, UNIPROT|Q9ZTS2
- */
- SequenceI emblSeq = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
- emblSeq.addDBRef(new DBRefEntry("EMBL", "0", "AF039662"));
- SequenceI uniprotSeq = new Sequence("Q9ZTS2", "MASVSATMISTS");
- uniprotSeq.addDBRef(new DBRefEntry("EMBL", "0", "AF039662"));
- uniprotSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
-
- /*
- * Find UNIPROT xrefs for nucleotide
- * - it has no UNIPROT dbref of its own
- * - but peptide with matching nucleotide dbref does, so is returned
- */
- AlignmentI al = new Alignment(new SequenceI[] { emblSeq, uniprotSeq });
- Alignment xrefs = new CrossRef(new SequenceI[] { emblSeq }, al)
- .findXrefSequences("UNIPROT", true);
- assertEquals(1, xrefs.getHeight());
- assertSame(uniprotSeq, xrefs.getSequenceAt(0));
- }
-
- /**
- * Test for finding 'product' sequences for the case where only an indirect
- * xref is found - not on the peptide sequence but on a nucleotide sequence in
- * the alignment which which it shares a protein dbref
- */
- @Test(groups = { "Functional" }, enabled = true)
- public void testFindXrefSequences_indirectDbrefToNucleotide()
- {
- /*
- * Alignment setup:
- * - peptide dbref UNIPROT|Q9ZTS2
- * - nucleotide dbref EMBL|AF039662, UNIPROT|Q9ZTS2
- */
- SequenceI uniprotSeq = new Sequence("Q9ZTS2", "MASVSATMISTS");
- uniprotSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
- SequenceI emblSeq = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
- emblSeq.addDBRef(new DBRefEntry("EMBL", "0", "AF039662"));
- emblSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
-
- /*
- * find EMBL xrefs for peptide sequence - it has no direct
- * dbrefs, but the 'corresponding' nucleotide sequence does, so is returned
- */
- /*
- * Find EMBL xrefs for peptide
- * - it has no EMBL dbref of its own
- * - but nucleotide with matching peptide dbref does, so is returned
- */
- AlignmentI al = new Alignment(new SequenceI[] { emblSeq, uniprotSeq });
- Alignment xrefs = new CrossRef(new SequenceI[] { uniprotSeq }, al)
- .findXrefSequences("EMBL", false);
- assertEquals(1, xrefs.getHeight());
- assertSame(emblSeq, xrefs.getSequenceAt(0));
- }
-
- /**
- * Test for finding 'product' sequences for the case where the selected
- * sequence has no dbref to the desired source, and there are no indirect
- * references via another sequence in the alignment
- */
- @Test(groups = { "Functional" })
- public void testFindXrefSequences_noDbrefs()
- {
- /*
- * two nucleotide sequences, one with UNIPROT dbref
- */
- SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
- dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
- SequenceI dna2 = new Sequence("AJ307031", "AAACCCTTT");
-
- /*
- * find UNIPROT xrefs for peptide sequence - it has no direct
- * dbrefs, and the other sequence (which has a UNIPROT dbref) is not
- * equatable to it, so no results found
- */
- AlignmentI al = new Alignment(new SequenceI[] { dna1, dna2 });
- Alignment xrefs = new CrossRef(new SequenceI[] { dna2 }, al)
- .findXrefSequences("UNIPROT", true);
- assertNull(xrefs);
- }
-
- /**
- * Tests for the method that searches an alignment (with one sequence
- * excluded) for protein/nucleotide sequences with a given cross-reference
- */
- @Test(groups = { "Functional" }, enabled = true)
- public void testSearchDataset()
- {
- /*
- * nucleotide sequence with UNIPROT AND EMBL dbref
- * peptide sequence with UNIPROT dbref
- */
- SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
- Mapping map = new Mapping(new Sequence("pep2", "MLAVSRG"), new MapList(
- new int[] { 1, 21 }, new int[] { 1, 7 }, 3, 1));
- DBRefEntry dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2", map);
- dna1.addDBRef(dbref);
- dna1.addDBRef(new DBRefEntry("EMBL", "0", "AF039662"));
- SequenceI pep1 = new Sequence("Q9ZTS2", "MLAVSRGQ");
- dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2");
- pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
- AlignmentI al = new Alignment(new SequenceI[] { dna1, pep1 });
-
- List<SequenceI> result = new ArrayList<>();
-
- /*
- * first search for a dbref nowhere on the alignment:
- */
- dbref = new DBRefEntry("UNIPROT", "0", "P30419");
- CrossRef testee = new CrossRef(al.getSequencesArray(), al);
- AlignedCodonFrame acf = new AlignedCodonFrame();
- boolean found = testee.searchDataset(true, dna1, dbref, result, acf,
- true, DBRefUtils.SEARCH_MODE_FULL);
- assertFalse(found);
- assertTrue(result.isEmpty());
- assertTrue(acf.isEmpty());
-
- /*
- * search for a protein sequence with dbref UNIPROT:Q9ZTS2
- */
- acf = new AlignedCodonFrame();
- dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2");
- found = testee.searchDataset(!dna1.isProtein(), dna1, dbref, result,
- acf, false, DBRefUtils.SEARCH_MODE_FULL); // search dataset with a protein xref from a dna
- // sequence to locate the protein product
- assertTrue(found);
- assertEquals(1, result.size());
- assertSame(pep1, result.get(0));
- assertTrue(acf.isEmpty());
-
- /*
- * search for a nucleotide sequence with dbref UNIPROT:Q9ZTS2
- */
- result.clear();
- acf = new AlignedCodonFrame();
- dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2");
- found = testee.searchDataset(!pep1.isProtein(), pep1, dbref, result,
- acf, false, DBRefUtils.SEARCH_MODE_FULL); // search dataset with a protein's direct dbref to
- // locate dna sequences with matching xref
- assertTrue(found);
- assertEquals(1, result.size());
- assertSame(dna1, result.get(0));
- // should now have a mapping from dna to pep1
- List<SequenceToSequenceMapping> mappings = acf.getMappings();
- assertEquals(1, mappings.size());
- SequenceToSequenceMapping mapping = mappings.get(0);
- assertSame(dna1, mapping.getFromSeq());
- assertSame(pep1, mapping.getMapping().getTo());
- MapList mapList = mapping.getMapping().getMap();
- assertEquals(1, mapList.getToRatio());
- assertEquals(3, mapList.getFromRatio());
- assertEquals(1, mapList.getFromRanges().size());
- assertEquals(1, mapList.getFromRanges().get(0)[0]);
- assertEquals(21, mapList.getFromRanges().get(0)[1]);
- assertEquals(1, mapList.getToRanges().size());
- assertEquals(1, mapList.getToRanges().get(0)[0]);
- assertEquals(7, mapList.getToRanges().get(0)[1]);
- }
-
- /**
- * Test for finding 'product' sequences for the case where the selected
- * sequence has a dbref with a mapping to a sequence. This represents the case
- * where either
- * <ul>
- * <li>a fetched sequence is already decorated with its cross-reference (e.g.
- * EMBL + translation), or</li>
- * <li>Get Cross-References has been done once resulting in instantiated
- * cross-reference mappings</li>
- * </ul>
- */
- @Test(groups = { "Functional" })
- public void testFindXrefSequences_fromDbRefMap()
- {
- /*
- * scenario: nucleotide sequence AF039662
- * with dbref + mapping to Q9ZTS2 and P30419
- * which themselves each have a dbref and feature
- */
- SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
- SequenceI pep1 = new Sequence("Q9ZTS2", "MALFQRSV");
- SequenceI pep2 = new Sequence("P30419", "MTRRSQIF");
- dna1.createDatasetSequence();
- pep1.createDatasetSequence();
- pep2.createDatasetSequence();
-
- pep1.getDatasetSequence().addDBRef(
- new DBRefEntry("Pfam", "0", "PF00111"));
- pep1.addSequenceFeature(new SequenceFeature("type", "desc", 12, 14, 1f,
- "group"));
- pep2.getDatasetSequence().addDBRef(new DBRefEntry("PDB", "0", "3JTK"));
- pep2.addSequenceFeature(new SequenceFeature("type2", "desc2", 13, 15,
- 12f, "group2"));
-
- MapList mapList = new MapList(new int[] { 1, 24 }, new int[] { 1, 3 },
- 3, 1);
- Mapping map = new Mapping(pep1, mapList);
- DBRefEntry dbRef1 = new DBRefEntry("UNIPROT", "0", "Q9ZTS2", map);
- dna1.getDatasetSequence().addDBRef(dbRef1);
- mapList = new MapList(new int[] { 1, 24 }, new int[] { 1, 3 }, 3, 1);
- map = new Mapping(pep2, mapList);
- DBRefEntry dbRef2 = new DBRefEntry("UNIPROT", "0", "P30419", map);
- dna1.getDatasetSequence().addDBRef(dbRef2);
-
- /*
- * find UNIPROT xrefs for nucleotide sequence - it should pick up
- * mapped sequences
- */
- AlignmentI al = new Alignment(new SequenceI[] { dna1 });
- Alignment xrefs = new CrossRef(new SequenceI[] { dna1 }, al)
- .findXrefSequences("UNIPROT", true);
- assertEquals(2, xrefs.getHeight());
-
- /*
- * cross-refs alignment holds copies of the mapped sequences
- * including copies of their dbrefs and features
- */
- checkCopySequence(pep1, xrefs.getSequenceAt(0));
- checkCopySequence(pep2, xrefs.getSequenceAt(1));
- }
-
- /**
- * Helper method that verifies that 'copy' has the same name, start, end,
- * sequence and dataset sequence object as 'original' (but is not the same
- * object)
- *
- * @param copy
- * @param original
- */
- private void checkCopySequence(SequenceI copy, SequenceI original)
- {
- assertNotSame(copy, original);
- assertSame(copy.getDatasetSequence(), original.getDatasetSequence());
- assertEquals(copy.getName(), original.getName());
- assertEquals(copy.getStart(), original.getStart());
- assertEquals(copy.getEnd(), original.getEnd());
- assertEquals(copy.getSequenceAsString(), original.getSequenceAsString());
- }
-
- /**
- * Test for finding 'product' sequences for the case where the selected
- * sequence has a dbref with no mapping, triggering a fetch from database
- */
- @Test(groups = { "Functional" })
- public void testFindXrefSequences_withFetch()
- {
- SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
- dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "Q9ZTS2"));
- dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "P30419"));
- dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "P00314"));
- final SequenceI pep1 = new Sequence("Q9ZTS2", "MYQLIRSSW");
- pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
-
- final SequenceI pep2 = new Sequence("P00314", "MRKLLAASG");
- pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "P00314"));
-
- /*
- * argument false suppresses adding DAS sources
- * todo: define an interface type SequenceFetcherI and mock that
- */
- SequenceFetcher mockFetcher = new SequenceFetcher()
- {
- @Override
- public boolean isFetchable(String source)
- {
- return true;
- }
-
- @Override
- public SequenceI[] getSequences(List<DBRefEntry> refs, boolean dna)
- {
- return new SequenceI[] { pep1, pep2 };
- }
- };
- SequenceFetcher.setSequenceFetcher(mockFetcher);
-
- /*
- * find UNIPROT xrefs for nucleotide sequence
- */
- AlignmentI al = new Alignment(new SequenceI[] { dna1 });
- Alignment xrefs = new CrossRef(new SequenceI[] { dna1 }, al)
- .findXrefSequences("UNIPROT", true);
- assertEquals(2, xrefs.getHeight());
- assertSame(pep1, xrefs.getSequenceAt(0));
- assertSame(pep2, xrefs.getSequenceAt(1));
- }
-
- @AfterClass(alwaysRun = true)
- public void tearDown()
- {
- SequenceFetcher.setSequenceFetcher(null);
- }
-
- /**
- * Test for finding 'product' sequences for the case where both gene and
- * transcript sequences have dbrefs to Uniprot.
- */
- @Test(groups = { "Functional" })
- public void testFindXrefSequences_forGeneAndTranscripts()
- {
- /*
- * 'gene' sequence
- */
- SequenceI gene = new Sequence("ENSG00000157764", "CGCCTCCCTTCCCC");
- gene.addDBRef(new DBRefEntry("UNIPROT", "0", "P15056"));
- gene.addDBRef(new DBRefEntry("UNIPROT", "0", "H7C5K3"));
-
- /*
- * 'transcript' with CDS feature (supports mapping to protein)
- */
- SequenceI braf001 = new Sequence("ENST00000288602", "taagATGGCGGCGCTGa");
- braf001.addDBRef(new DBRefEntry("UNIPROT", "0", "P15056"));
- braf001.addSequenceFeature(new SequenceFeature("CDS", "", 5, 16, 0f,
- null));
-
- /*
- * 'spliced transcript' with CDS ranges
- */
- SequenceI braf002 = new Sequence("ENST00000497784", "gCAGGCtaTCTGTTCaa");
- braf002.addDBRef(new DBRefEntry("UNIPROT", "ENSEMBL|0", "H7C5K3"));
- braf002.addSequenceFeature(new SequenceFeature("CDS", "", 2, 6, 0f,
- null));
- braf002.addSequenceFeature(new SequenceFeature("CDS", "", 9, 15, 0f,
- null));
-
- /*
- * TODO code is fragile - use of SequenceIdMatcher depends on fetched
- * sequences having a name starting Source|Accession
- * which happens to be true for Uniprot,PDB,EMBL but not Pfam,Rfam,Ensembl
- */
- final SequenceI pep1 = new Sequence("UNIPROT|P15056", "MAAL");
- pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "P15056"));
- final SequenceI pep2 = new Sequence("UNIPROT|H7C5K3", "QALF");
- pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "H7C5K3"));
- /*
- * argument false suppresses adding DAS sources
- * todo: define an interface type SequenceFetcherI and mock that
- */
- SequenceFetcher mockFetcher = new SequenceFetcher()
- {
- @Override
- public boolean isFetchable(String source)
- {
- return true;
- }
-
- @Override
- public SequenceI[] getSequences(List<DBRefEntry> refs, boolean dna)
- {
- return new SequenceI[] { pep1, pep2 };
- }
- };
- SequenceFetcher.setSequenceFetcher(mockFetcher);
-
- /*
- * find UNIPROT xrefs for gene and transcripts
- * verify that
- * - the two proteins are retrieved but not duplicated
- * - mappings are built from transcript (CDS) to proteins
- * - no mappings from gene to proteins
- */
- SequenceI[] seqs = new SequenceI[] { gene, braf001, braf002 };
- AlignmentI al = new Alignment(seqs);
- Alignment xrefs = new CrossRef(seqs, al).findXrefSequences("UNIPROT",
- true);
- assertEquals(2, xrefs.getHeight());
- assertSame(pep1, xrefs.getSequenceAt(0));
- assertSame(pep2, xrefs.getSequenceAt(1));
- }
-
- /**
- * <pre>
- * Test that emulates this (real but simplified) case:
- * Alignment: DBrefs
- * UNIPROT|P0CE19 EMBL|J03321, EMBL|X06707, EMBL|M19487
- * UNIPROT|P0CE20 EMBL|J03321, EMBL|X06707, EMBL|X07547
- * Find cross-references for EMBL. These are mocked here as
- * EMBL|J03321 with mappings to P0CE18, P0CE19, P0CE20
- * EMBL|X06707 with mappings to P0CE17, P0CE19, P0CE20
- * EMBL|M19487 with mappings to P0CE19, Q46432
- * EMBL|X07547 with mappings to P0CE20, B0BCM4
- * EMBL sequences are first 'fetched' (mocked here) for P0CE19.
- * The 3 EMBL sequences are added to the alignment dataset.
- * Their dbrefs to Uniprot products P0CE19 and P0CE20 should be matched in the
- * alignment dataset and updated to reference the original Uniprot sequences.
- * For the second Uniprot sequence, the J03321 and X06707 xrefs should be
- * resolved from the dataset, and only the X07547 dbref fetched.
- * So the end state to verify is:
- * - 4 cross-ref sequences returned: J03321, X06707, M19487, X07547
- * - P0CE19/20 dbrefs to EMBL sequences now have mappings
- * - J03321 dbrefs to P0CE19/20 mapped to original Uniprot sequences
- * - X06707 dbrefs to P0CE19/20 mapped to original Uniprot sequences
- * </pre>
- */
- @Test(groups = { "Functional" })
- public void testFindXrefSequences_uniprotEmblManyToMany()
- {
- /*
- * Uniprot sequences, both with xrefs to EMBL|J03321
- * and EMBL|X07547
- */
- SequenceI p0ce19 = new Sequence("UNIPROT|P0CE19", "KPFG");
- p0ce19.addDBRef(new DBRefEntry("EMBL", "0", "J03321"));
- p0ce19.addDBRef(new DBRefEntry("EMBL", "0", "X06707"));
- p0ce19.addDBRef(new DBRefEntry("EMBL", "0", "M19487"));
- SequenceI p0ce20 = new Sequence("UNIPROT|P0CE20", "PFGK");
- p0ce20.addDBRef(new DBRefEntry("EMBL", "0", "J03321"));
- p0ce20.addDBRef(new DBRefEntry("EMBL", "0", "X06707"));
- p0ce20.addDBRef(new DBRefEntry("EMBL", "0", "X07547"));
-
- /*
- * EMBL sequences to be 'fetched', complete with dbrefs and mappings
- * to their protein products (CDS location and translations are provided
- * in EMBL XML); these should be matched to, and replaced with,
- * the corresponding uniprot sequences after fetching
- */
-
- /*
- * J03321 with mappings to P0CE19 and P0CE20
- */
- final SequenceI j03321 = new Sequence("EMBL|J03321", "AAACCCTTTGGGAAAA");
- DBRefEntry dbref1 = new DBRefEntry("UNIPROT", "0", "P0CE19");
- MapList mapList = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 },
- 3, 1);
- Mapping map = new Mapping(new Sequence("UNIPROT|P0CE19", "KPFG"),
- mapList);
- // add a dbref to the mapped to sequence - should get copied to p0ce19
- map.getTo().addDBRef(new DBRefEntry("PIR", "0", "S01875"));
- dbref1.setMap(map);
- j03321.addDBRef(dbref1);
- DBRefEntry dbref2 = new DBRefEntry("UNIPROT", "0", "P0CE20");
- mapList = new MapList(new int[] { 4, 15 }, new int[] { 2, 5 }, 3, 1);
- dbref2.setMap(new Mapping(new Sequence("UNIPROT|P0CE20", "PFGK"),
- new MapList(mapList)));
- j03321.addDBRef(dbref2);
-
- /*
- * X06707 with mappings to P0CE19 and P0CE20
- */
- final SequenceI x06707 = new Sequence("EMBL|X06707", "atgAAACCCTTTGGG");
- DBRefEntry dbref3 = new DBRefEntry("UNIPROT", "0", "P0CE19");
- MapList map2 = new MapList(new int[] { 4, 15 }, new int[] { 1, 4 }, 3,
- 1);
- dbref3.setMap(new Mapping(new Sequence("UNIPROT|P0CE19", "KPFG"), map2));
- x06707.addDBRef(dbref3);
- DBRefEntry dbref4 = new DBRefEntry("UNIPROT", "0", "P0CE20");
- MapList map3 = new MapList(new int[] { 4, 15 }, new int[] { 1, 4 }, 3,
- 1);
- dbref4.setMap(new Mapping(new Sequence("UNIPROT|P0CE20", "PFGK"), map3));
- x06707.addDBRef(dbref4);
-
- /*
- * M19487 with mapping to P0CE19 and Q46432
- */
- final SequenceI m19487 = new Sequence("EMBL|M19487", "AAACCCTTTGGG");
- DBRefEntry dbref5 = new DBRefEntry("UNIPROT", "0", "P0CE19");
- dbref5.setMap(new Mapping(new Sequence("UNIPROT|P0CE19", "KPFG"),
- new MapList(mapList)));
- m19487.addDBRef(dbref5);
- DBRefEntry dbref6 = new DBRefEntry("UNIPROT", "0", "Q46432");
- dbref6.setMap(new Mapping(new Sequence("UNIPROT|Q46432", "KPFG"),
- new MapList(mapList)));
- m19487.addDBRef(dbref6);
-
- /*
- * X07547 with mapping to P0CE20 and B0BCM4
- */
- final SequenceI x07547 = new Sequence("EMBL|X07547", "cccAAACCCTTTGGG");
- DBRefEntry dbref7 = new DBRefEntry("UNIPROT", "0", "P0CE20");
- dbref7.setMap(new Mapping(new Sequence("UNIPROT|P0CE20", "PFGK"),
- new MapList(map2)));
- x07547.addDBRef(dbref7);
- DBRefEntry dbref8 = new DBRefEntry("UNIPROT", "0", "B0BCM4");
- dbref8.setMap(new Mapping(new Sequence("UNIPROT|B0BCM4", "KPFG"),
- new MapList(map2)));
- x07547.addDBRef(dbref8);
-
- /*
- * mock sequence fetcher to 'return' the EMBL sequences
- * TODO: Mockito would allow .thenReturn().thenReturn() here,
- * and also capture and verification of the parameters
- * passed in calls to getSequences() - important to verify that
- * duplicate sequence fetches are not requested
- */
- SequenceFetcher mockFetcher = new SequenceFetcher()
- {
- int call = 0;
-
- @Override
- public boolean isFetchable(String source)
- {
- return true;
- }
-
- @Override
- public SequenceI[] getSequences(List<DBRefEntry> refs, boolean dna)
- {
- call++;
- if (call == 1)
- {
- assertEquals("Expected 3 embl seqs in first fetch", 3,
- refs.size());
- return new SequenceI[] { j03321, x06707, m19487 };
- }
- else
- {
- assertEquals("Expected 1 embl seq in second fetch", 1,
- refs.size());
- return new SequenceI[] { x07547 };
- }
- }
- };
-
- SequenceFetcher.setSequenceFetcher(mockFetcher);
-
- /*
- * find EMBL xrefs for Uniprot seqs and verify that
- * - the EMBL xref'd sequences are retrieved without duplicates
- * - mappings are added to the Uniprot dbrefs
- * - mappings in the EMBL-to-Uniprot dbrefs are updated to the
- * alignment sequences
- * - dbrefs on the EMBL sequences are added to the original dbrefs
- */
- SequenceI[] seqs = new SequenceI[] { p0ce19, p0ce20 };
- AlignmentI al = new Alignment(seqs);
- Alignment xrefs = new CrossRef(seqs, al).findXrefSequences("EMBL",
- false);
-
- /*
- * verify retrieved sequences
- */
- assertNotNull(xrefs);
- assertEquals(4, xrefs.getHeight());
- assertSame(j03321, xrefs.getSequenceAt(0));
- assertSame(x06707, xrefs.getSequenceAt(1));
- assertSame(m19487, xrefs.getSequenceAt(2));
- assertSame(x07547, xrefs.getSequenceAt(3));
-
- /*
- * verify mappings added to Uniprot-to-EMBL dbrefs
- */
- Mapping mapping = p0ce19.getDBRefs().get(0).getMap();
- assertSame(j03321, mapping.getTo());
- mapping = p0ce19.getDBRefs().get(1).getMap();
- assertSame(x06707, mapping.getTo());
- mapping = p0ce20.getDBRefs().get(0).getMap();
- assertSame(j03321, mapping.getTo());
- mapping = p0ce20.getDBRefs().get(1).getMap();
- assertSame(x06707, mapping.getTo());
-
- /*
- * verify dbrefs on EMBL are mapped to alignment seqs
- */
-
- assertSame(p0ce19, j03321.getDBRefs().get(0).getMap().getTo());
- assertSame(p0ce20, j03321.getDBRefs().get(1).getMap().getTo());
- assertSame(p0ce19, x06707.getDBRefs().get(0).getMap().getTo());
- assertSame(p0ce20, x06707.getDBRefs().get(1).getMap().getTo());
-
- /*
- * verify new dbref on EMBL dbref mapping is copied to the
- * original Uniprot sequence
- */
- assertEquals(4, p0ce19.getDBRefs().size());
- assertEquals("PIR", p0ce19.getDBRefs().get(3).getSource());
- assertEquals("S01875", p0ce19.getDBRefs().get(3).getAccessionId());
- }
-
- @Test(groups = "Functional")
- public void testSameSequence()
- {
- assertTrue(CrossRef.sameSequence(null, null));
- SequenceI seq1 = new Sequence("seq1", "ABCDEF");
- assertFalse(CrossRef.sameSequence(seq1, null));
- assertFalse(CrossRef.sameSequence(null, seq1));
- assertTrue(CrossRef.sameSequence(seq1, new Sequence("seq2", "ABCDEF")));
- assertTrue(CrossRef.sameSequence(seq1, new Sequence("seq2", "abcdef")));
- assertFalse(CrossRef
- .sameSequence(seq1, new Sequence("seq2", "ABCDE-F")));
- assertFalse(CrossRef.sameSequence(seq1, new Sequence("seq2", "BCDEF")));
- }
-}
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