X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FCrossRefTest.java;h=31f9728a242f64b48e674c3682300b9488da28d7;hb=4ad1fc4f0e441e2562cbc2ecaf1f89fa4a475c25;hp=35606f0f6efe689585639dbf5e83aca9232b0bc0;hpb=3ef44bef1f825d26977dedd1608469712a87fe15;p=jalview.git
diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java
index 35606f0..31f9728 100644
--- a/test/jalview/analysis/CrossRefTest.java
+++ b/test/jalview/analysis/CrossRefTest.java
@@ -1,15 +1,54 @@
+/*
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.analysis;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertSame;
-
-import org.junit.Test;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+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 static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
+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.util.DBRefUtils;
+import jalview.util.MapList;
+import jalview.ws.SequenceFetcher;
+import jalview.ws.SequenceFetcherFactory;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.Test;
public class CrossRefTest
{
- @Test
+ @Test(groups = { "Functional" })
public void testFindXDbRefs()
{
DBRefEntry ref1 = new DBRefEntry("UNIPROT", "1", "A123");
@@ -20,27 +59,370 @@ public class CrossRefTest
DBRefEntry ref6 = new DBRefEntry("emblCDS", "1", "A123");
DBRefEntry ref7 = new DBRefEntry("GeneDB", "1", "A123");
DBRefEntry ref8 = new DBRefEntry("PFAM", "1", "A123");
- DBRefEntry[] refs = new DBRefEntry[]
- { ref1, ref2, ref3, ref4, ref5, ref6, ref7, ref8 };
+ // ENSEMBL is a source of either dna or protein sequence data
+ DBRefEntry ref9 = new DBRefEntry("ENSEMBL", "1", "A123");
+ DBRefEntry[] refs = new DBRefEntry[] { ref1, ref2, ref3, ref4, ref5,
+ ref6, ref7, ref8, ref9 };
/*
* Just the DNA refs:
*/
- DBRefEntry[] found = CrossRef.findXDbRefs(false, refs);
- assertEquals(3, found.length);
+ DBRefEntry[] found = DBRefUtils.selectDbRefs(true, refs);
+ assertEquals(4, found.length);
assertSame(ref5, found[0]);
assertSame(ref6, found[1]);
assertSame(ref7, found[2]);
+ assertSame(ref9, found[3]);
/*
* Just the protein refs:
*/
- found = CrossRef.findXDbRefs(true, refs);
- assertEquals(4, found.length);
+ found = DBRefUtils.selectDbRefs(false, refs);
+ assertEquals(5, found.length);
assertSame(ref1, found[0]);
assertSame(ref2, found[1]);
assertSame(ref3, found[2]);
assertSame(ref4, found[3]);
+ assertSame(ref9, found[4]);
+ }
+
+ /**
+ * 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" })
+ public void testFindXrefSourcesForSequence_proteinToDna()
+ {
+ SequenceI seq = new Sequence("Seq1", "MGKYQARLSS");
+ List sources = new ArrayList();
+ AlignmentI al = new Alignment(new SequenceI[] {});
+
+ /*
+ * first with no dbrefs to search
+ */
+ CrossRef.findXrefSourcesForSequence(seq, false, al, sources);
+ 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"));
+ CrossRef.findXrefSourcesForSequence(seq, false, al, sources);
+ assertEquals(4, sources.size());
+ assertEquals("[EMBL, EMBLCDS, GENEDB, ENSEMBL]",
+ 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);
+ CrossRef.findXrefSourcesForSequence(seq, false, al, sources);
+ assertEquals(3, sources.size());
+ assertEquals("[EMBLCDS, EMBL, 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" })
+ 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 = CrossRef.findXrefSequences(
+ new SequenceI[] { emblSeq }, true, "UNIPROT", al);
+ 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" })
+ 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 = CrossRef.findXrefSequences(
+ new SequenceI[] { uniprotSeq }, false, "EMBL", al);
+ 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 = CrossRef.findXrefSequences(new SequenceI[] { dna2 },
+ true, "UNIPROT", al);
+ 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" })
+ public void testSearchDataset()
+ {
+ /*
+ * nucleotide sequence with UNIPROT AND EMBL dbref
+ * peptide sequence with UNIPROT dbref
+ */
+ SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
+ dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
+ dna1.addDBRef(new DBRefEntry("EMBL", "0", "AF039662"));
+ SequenceI pep1 = new Sequence("Q9ZTS2", "MLAVSRGQ");
+ pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
+ AlignmentI al = new Alignment(new SequenceI[] { dna1, pep1 });
+
+ List result = new ArrayList();
+
+ /*
+ * first search for a dbref nowhere on the alignment:
+ */
+ DBRefEntry dbref = new DBRefEntry("UNIPROT", "0", "P30419");
+ boolean found = CrossRef.searchDataset(dna1, dbref, al, result, null,
+ true, true);
+ assertFalse(found);
+ assertTrue(result.isEmpty());
+
+ // TODO we are setting direct=true here but it is set to
+ // false in Jalview code...
+
+ /*
+ * search for a protein sequence with dbref UNIPROT:Q9ZTS2
+ */
+ dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2");
+ found = CrossRef.searchDataset(dna1, dbref, al, result, null, true,
+ true);
+ assertTrue(found);
+ assertEquals(1, result.size());
+ assertSame(pep1, result.get(0));
+
+ /*
+ * search for a nucleotide sequence with dbref UNIPROT:Q9ZTS2
+ */
+ result.clear();
+ dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2");
+ found = CrossRef.searchDataset(pep1, dbref, al, result, null, true,
+ false);
+ assertTrue(found);
+ assertEquals(1, result.size());
+ assertSame(dna1, result.get(0));
+ }
+
+ /**
+ * Test for finding 'product' sequences for the case where the selected
+ * sequence has a dbref with a mapping to a sequence
+ */
+ @Test(groups = { "Functional" })
+ public void testFindXrefSequences_fromDbRefMap()
+ {
+ /*
+ * two peptide sequences each with a DBRef and SequenceFeature
+ */
+ SequenceI pep1 = new Sequence("Q9ZTS2", "MALFQRSV");
+ pep1.addDBRef(new DBRefEntry("Pfam", "0", "PF00111"));
+ pep1.addSequenceFeature(new SequenceFeature("type", "desc", 12, 14, 1f,
+ "group"));
+ SequenceI pep2 = new Sequence("P30419", "MTRRSQIF");
+ pep2.addDBRef(new DBRefEntry("PDB", "0", "3JTK"));
+ pep2.addSequenceFeature(new SequenceFeature("type2", "desc2", 13, 15,
+ 12f, "group2"));
+
+ /*
+ * nucleotide sequence (to go in the alignment)
+ */
+ SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
+
+ /*
+ * add DBRefEntry's to dna1 with mappings from dna to both peptides
+ */
+ 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.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.addDBRef(dbRef2);
+
+ /*
+ * find UNIPROT xrefs for nucleotide sequence - it should pick up
+ * mapped sequences
+ */
+ AlignmentI al = new Alignment(new SequenceI[] { dna1 });
+ Alignment xrefs = CrossRef.findXrefSequences(new SequenceI[] { dna1 },
+ true, "UNIPROT", al);
+ 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 to assert seq1 looks like a copy of seq2
+ *
+ * @param seq1
+ * @param seq2
+ */
+ private void checkCopySequence(SequenceI seq1, SequenceI seq2)
+ {
+ assertNotSame(seq1, seq2);
+ assertEquals(seq1.getName(), seq2.getName());
+ assertEquals(seq1.getStart(), seq2.getStart());
+ assertEquals(seq1.getEnd(), seq2.getEnd());
+ assertEquals(seq1.getSequenceAsString(), seq2.getSequenceAsString());
+
+ /*
+ * compare dbrefs
+ */
+ assertArrayEquals(seq1.getDBRefs(), seq2.getDBRefs());
+ // check one to verify a copy, not the same object
+ if (seq1.getDBRefs().length > 0)
+ {
+ assertNotSame(seq1.getDBRefs()[0], seq2.getDBRefs()[0]);
+ }
+
+ /*
+ * compare features
+ */
+ assertArrayEquals(seq1.getSequenceFeatures(),
+ seq2.getSequenceFeatures());
+ if (seq1.getSequenceFeatures().length > 0)
+ {
+ assertNotSame(seq1.getSequenceFeatures()[0],
+ seq2.getSequenceFeatures()[0]);
+ }
+ }
+
+ /**
+ * 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", "0", "Q9ZTS2"));
+ dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "P30419"));
+ dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "P00314"));
+ final SequenceI pep1 = new Sequence("Q9ZTS2", "MYQLIRSSW");
+ final SequenceI pep2 = new Sequence("P00314", "MRKLLAASG");
+
+ SequenceFetcher mockFetcher = new SequenceFetcher()
+ {
+
+ @Override
+ public boolean isFetchable(String source)
+ {
+ return true;
+ }
+
+ @Override
+ public SequenceI[] getSequences(List refs, boolean dna)
+ {
+ return new SequenceI[] { pep1, pep2 };
+ }
+ };
+ SequenceFetcherFactory.setSequenceFetcher(mockFetcher);
+
+ /*
+ * find UNIPROT xrefs for nucleotide sequence
+ */
+ AlignmentI al = new Alignment(new SequenceI[] { dna1 });
+ Alignment xrefs = CrossRef.findXrefSequences(new SequenceI[] { dna1 },
+ true, "UNIPROT", al);
+ assertEquals(2, xrefs.getHeight());
+ assertSame(pep1, xrefs.getSequenceAt(0));
+ assertSame(pep2, xrefs.getSequenceAt(1));
+ }
+
+ @AfterClass
+ public void tearDown()
+ {
+ SequenceFetcherFactory.setSequenceFetcher(null);
}
}