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package jalview.analysis; |
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import static org.testng.AssertJUnit.assertEquals; |
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import static org.testng.AssertJUnit.assertFalse; |
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import static org.testng.AssertJUnit.assertNotNull; |
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import static org.testng.AssertJUnit.assertNotSame; |
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import static org.testng.AssertJUnit.assertNull; |
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import static org.testng.AssertJUnit.assertSame; |
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import static org.testng.AssertJUnit.assertTrue; |
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import jalview.datamodel.AlignedCodonFrame; |
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import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping; |
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import jalview.datamodel.Alignment; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.DBRefEntry; |
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import jalview.datamodel.Mapping; |
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import jalview.datamodel.Sequence; |
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import jalview.datamodel.SequenceFeature; |
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import jalview.datamodel.SequenceI; |
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import jalview.gui.JvOptionPane; |
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import jalview.util.DBRefUtils; |
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import jalview.util.MapList; |
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import jalview.ws.SequenceFetcher; |
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import jalview.ws.SequenceFetcherFactory; |
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import jalview.ws.params.InvalidArgumentException; |
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import java.util.ArrayList; |
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import java.util.Arrays; |
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import java.util.List; |
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import org.testng.annotations.AfterClass; |
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import org.testng.annotations.BeforeClass; |
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import org.testng.annotations.Test; |
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| 57.1% |
Uncovered Elements: 127 (296) |
Complexity: 21 |
Complexity Density: 0.08 |
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public class CrossRefTest |
56 |
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{ |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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1 |
@BeforeClass(alwaysRun = true)... |
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public void setUpJvOptionPane() |
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{ |
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JvOptionPane.setInteractiveMode(false); |
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JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
63 |
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} |
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| 100% |
Uncovered Elements: 0 (22) |
Complexity: 1 |
Complexity Density: 0.05 |
1PASS
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1 |
@Test(groups = { "Functional" })... |
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public void testFindXDbRefs() |
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{ |
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DBRefEntry ref1 = new DBRefEntry("UNIPROT", "1", "A123"); |
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DBRefEntry ref2 = new DBRefEntry("UNIPROTKB/TREMBL", "1", "A123"); |
70 |
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DBRefEntry ref3 = new DBRefEntry("pdb", "1", "A123"); |
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DBRefEntry ref4 = new DBRefEntry("EMBLCDSPROTEIN", "1", "A123"); |
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DBRefEntry ref5 = new DBRefEntry("embl", "1", "A123"); |
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DBRefEntry ref6 = new DBRefEntry("emblCDS", "1", "A123"); |
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DBRefEntry ref7 = new DBRefEntry("GeneDB", "1", "A123"); |
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DBRefEntry ref8 = new DBRefEntry("PFAM", "1", "A123"); |
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DBRefEntry ref9 = new DBRefEntry("ENSEMBL", "1", "A123"); |
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List<DBRefEntry> refs = Arrays.asList(new DBRefEntry[] { ref1, ref2, ref3, ref4, ref5, |
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ref6, ref7, ref8, ref9 }); |
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List<DBRefEntry> found = DBRefUtils.selectDbRefs(true, refs); |
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assertEquals(4, found.size()); |
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assertSame(ref5, found.get(0)); |
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assertSame(ref6, found.get(1)); |
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assertSame(ref7, found.get(2)); |
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assertSame(ref9, found.get(3)); |
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found = DBRefUtils.selectDbRefs(false, refs); |
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assertEquals(4, found.size()); |
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assertSame(ref1, found.get(0)); |
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assertSame(ref2, found.get(1)); |
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assertSame(ref4, found.get(2)); |
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assertSame(ref9, found.get(3)); |
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} |
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| 100% |
Uncovered Elements: 0 (27) |
Complexity: 1 |
Complexity Density: 0.04 |
1PASS
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1 |
@Test(groups = { "Functional" }, enabled = true)... |
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public void testFindXrefSourcesForSequence_proteinToDna() |
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{ |
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SequenceI seq = new Sequence("Seq1", "MGKYQARLSS"); |
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List<String> sources = new ArrayList<>(); |
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AlignmentI al = new Alignment(new SequenceI[] {}); |
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sources = new CrossRef(new SequenceI[] { seq }, al) |
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.findXrefSourcesForSequences(false); |
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assertTrue(sources.isEmpty()); |
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seq.addDBRef(new DBRefEntry("UNIPROT", "0", "A1234")); |
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seq.addDBRef(new DBRefEntry("EMBL", "0", "E2345")); |
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seq.addDBRef(new DBRefEntry("EMBL", "0", "E2346")); |
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seq.addDBRef(new DBRefEntry("EMBLCDS", "0", "E2347")); |
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seq.addDBRef(new DBRefEntry("GENEDB", "0", "E2348")); |
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seq.addDBRef(new DBRefEntry("ENSEMBL", "0", "E2349")); |
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seq.addDBRef(new DBRefEntry("ENSEMBLGENOMES", "0", "E2350")); |
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sources = new CrossRef(new SequenceI[] { seq }, al) |
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.findXrefSourcesForSequences(false); |
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assertEquals(4, sources.size()); |
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assertEquals("[EMBLCDS, GENEDB, ENSEMBL, ENSEMBLGENOMES]", |
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sources.toString()); |
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sources.clear(); |
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seq.setDBRefs(null); |
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seq.addDBRef(new DBRefEntry("UNIPROT", "0", "A1234")); |
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seq.addDBRef(new DBRefEntry("EMBLCDS", "0", "E2347")); |
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SequenceI seq2 = new Sequence("Seq2", "MGKYQARLSS"); |
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seq2.addDBRef(new DBRefEntry("UNIPROT", "0", "A1234")); |
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seq2.addDBRef(new DBRefEntry("EMBL", "0", "E2345")); |
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seq2.addDBRef(new DBRefEntry("GENEDB", "0", "E2348")); |
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al.addSequence(seq2); |
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sources = new CrossRef(new SequenceI[] { seq, seq2 }, al) |
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.findXrefSourcesForSequences(false); |
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assertEquals(2, sources.size()); |
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assertEquals("[EMBLCDS, GENEDB]", sources.toString()); |
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} |
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165 |
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| 100% |
Uncovered Elements: 0 (9) |
Complexity: 1 |
Complexity Density: 0.11 |
1PASS
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1 |
@Test(groups = { "Functional" }, enabled = true)... |
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public void testFindXrefSequences_indirectDbrefToProtein() |
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{ |
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SequenceI emblSeq = new Sequence("AF039662", "GGGGCAGCACAAGAAC"); |
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emblSeq.addDBRef(new DBRefEntry("EMBL", "0", "AF039662")); |
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SequenceI uniprotSeq = new Sequence("Q9ZTS2", "MASVSATMISTS"); |
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uniprotSeq.addDBRef(new DBRefEntry("EMBL", "0", "AF039662")); |
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uniprotSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2")); |
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AlignmentI al = new Alignment(new SequenceI[] { emblSeq, uniprotSeq }); |
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Alignment xrefs = new CrossRef(new SequenceI[] { emblSeq }, al) |
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.findXrefSequences("UNIPROT", true); |
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assertEquals(1, xrefs.getHeight()); |
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assertSame(uniprotSeq, xrefs.getSequenceAt(0)); |
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} |
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193 |
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195 |
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196 |
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197 |
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| 100% |
Uncovered Elements: 0 (9) |
Complexity: 1 |
Complexity Density: 0.11 |
1PASS
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1 |
@Test(groups = { "Functional" }, enabled = true)... |
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public void testFindXrefSequences_indirectDbrefToNucleotide() |
200 |
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{ |
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202 |
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203 |
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204 |
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206 |
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SequenceI uniprotSeq = new Sequence("Q9ZTS2", "MASVSATMISTS"); |
207 |
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uniprotSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2")); |
208 |
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SequenceI emblSeq = new Sequence("AF039662", "GGGGCAGCACAAGAAC"); |
209 |
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emblSeq.addDBRef(new DBRefEntry("EMBL", "0", "AF039662")); |
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emblSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2")); |
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212 |
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216 |
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AlignmentI al = new Alignment(new SequenceI[] { emblSeq, uniprotSeq }); |
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Alignment xrefs = new CrossRef(new SequenceI[] { uniprotSeq }, al) |
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.findXrefSequences("EMBL", false); |
224 |
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assertEquals(1, xrefs.getHeight()); |
225 |
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assertSame(emblSeq, xrefs.getSequenceAt(0)); |
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} |
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229 |
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231 |
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232 |
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| 100% |
Uncovered Elements: 0 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
1PASS
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233 |
1 |
@Test(groups = { "Functional" })... |
234 |
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public void testFindXrefSequences_noDbrefs() |
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{ |
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237 |
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238 |
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239 |
1 |
SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC"); |
240 |
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dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2")); |
241 |
1 |
SequenceI dna2 = new Sequence("AJ307031", "AAACCCTTT"); |
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243 |
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244 |
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247 |
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248 |
1 |
AlignmentI al = new Alignment(new SequenceI[] { dna1, dna2 }); |
249 |
1 |
Alignment xrefs = new CrossRef(new SequenceI[] { dna2 }, al) |
250 |
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.findXrefSequences("UNIPROT", true); |
251 |
1 |
assertNull(xrefs); |
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} |
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254 |
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255 |
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256 |
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257 |
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| 100% |
Uncovered Elements: 0 (45) |
Complexity: 1 |
Complexity Density: 0.02 |
1PASS
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258 |
1 |
@Test(groups = { "Functional" }, enabled = true)... |
259 |
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public void testSearchDataset() |
260 |
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{ |
261 |
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262 |
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263 |
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264 |
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265 |
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SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC"); |
266 |
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Mapping map = new Mapping(new Sequence("pep2", "MLAVSRG"), new MapList( |
267 |
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new int[] { 1, 21 }, new int[] { 1, 7 }, 3, 1)); |
268 |
1 |
DBRefEntry dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2", map); |
269 |
1 |
dna1.addDBRef(dbref); |
270 |
1 |
dna1.addDBRef(new DBRefEntry("EMBL", "0", "AF039662")); |
271 |
1 |
SequenceI pep1 = new Sequence("Q9ZTS2", "MLAVSRGQ"); |
272 |
1 |
dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2"); |
273 |
1 |
pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2")); |
274 |
1 |
AlignmentI al = new Alignment(new SequenceI[] { dna1, pep1 }); |
275 |
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276 |
1 |
List<SequenceI> result = new ArrayList<>(); |
277 |
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278 |
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279 |
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280 |
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281 |
1 |
dbref = new DBRefEntry("UNIPROT", "0", "P30419"); |
282 |
1 |
CrossRef testee = new CrossRef(al.getSequencesArray(), al); |
283 |
1 |
AlignedCodonFrame acf = new AlignedCodonFrame(); |
284 |
1 |
boolean found = testee.searchDataset(true, dna1, dbref, result, acf, |
285 |
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true, DBRefUtils.SEARCH_MODE_FULL); |
286 |
1 |
assertFalse(found); |
287 |
1 |
assertTrue(result.isEmpty()); |
288 |
1 |
assertTrue(acf.isEmpty()); |
289 |
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290 |
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291 |
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292 |
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293 |
1 |
acf = new AlignedCodonFrame(); |
294 |
1 |
dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2"); |
295 |
1 |
found = testee.searchDataset(!dna1.isProtein(), dna1, dbref, result, |
296 |
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acf, false, DBRefUtils.SEARCH_MODE_FULL); |
297 |
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298 |
1 |
assertTrue(found); |
299 |
1 |
assertEquals(1, result.size()); |
300 |
1 |
assertSame(pep1, result.get(0)); |
301 |
1 |
assertTrue(acf.isEmpty()); |
302 |
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303 |
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304 |
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305 |
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306 |
1 |
result.clear(); |
307 |
1 |
acf = new AlignedCodonFrame(); |
308 |
1 |
dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2"); |
309 |
1 |
found = testee.searchDataset(!pep1.isProtein(), pep1, dbref, result, |
310 |
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acf, false, DBRefUtils.SEARCH_MODE_FULL); |
311 |
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312 |
1 |
assertTrue(found); |
313 |
1 |
assertEquals(1, result.size()); |
314 |
1 |
assertSame(dna1, result.get(0)); |
315 |
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|
316 |
1 |
List<SequenceToSequenceMapping> mappings = acf.getMappings(); |
317 |
1 |
assertEquals(1, mappings.size()); |
318 |
1 |
SequenceToSequenceMapping mapping = mappings.get(0); |
319 |
1 |
assertSame(dna1, mapping.getFromSeq()); |
320 |
1 |
assertSame(pep1, mapping.getMapping().getTo()); |
321 |
1 |
MapList mapList = mapping.getMapping().getMap(); |
322 |
1 |
assertEquals(1, mapList.getToRatio()); |
323 |
1 |
assertEquals(3, mapList.getFromRatio()); |
324 |
1 |
assertEquals(1, mapList.getFromRanges().size()); |
325 |
1 |
assertEquals(1, mapList.getFromRanges().get(0)[0]); |
326 |
1 |
assertEquals(21, mapList.getFromRanges().get(0)[1]); |
327 |
1 |
assertEquals(1, mapList.getToRanges().size()); |
328 |
1 |
assertEquals(1, mapList.getToRanges().get(0)[0]); |
329 |
1 |
assertEquals(7, mapList.getToRanges().get(0)[1]); |
330 |
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} |
331 |
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332 |
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333 |
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334 |
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335 |
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336 |
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337 |
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338 |
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339 |
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340 |
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341 |
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342 |
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| 100% |
Uncovered Elements: 0 (23) |
Complexity: 1 |
Complexity Density: 0.04 |
1PASS
|
|
343 |
1 |
@Test(groups = { "Functional" })... |
344 |
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public void testFindXrefSequences_fromDbRefMap() |
345 |
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{ |
346 |
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347 |
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348 |
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349 |
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350 |
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351 |
1 |
SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC"); |
352 |
1 |
SequenceI pep1 = new Sequence("Q9ZTS2", "MALFQRSV"); |
353 |
1 |
SequenceI pep2 = new Sequence("P30419", "MTRRSQIF"); |
354 |
1 |
dna1.createDatasetSequence(); |
355 |
1 |
pep1.createDatasetSequence(); |
356 |
1 |
pep2.createDatasetSequence(); |
357 |
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|
358 |
1 |
pep1.getDatasetSequence().addDBRef( |
359 |
|
new DBRefEntry("Pfam", "0", "PF00111")); |
360 |
1 |
pep1.addSequenceFeature(new SequenceFeature("type", "desc", 12, 14, 1f, |
361 |
|
"group")); |
362 |
1 |
pep2.getDatasetSequence().addDBRef(new DBRefEntry("PDB", "0", "3JTK")); |
363 |
1 |
pep2.addSequenceFeature(new SequenceFeature("type2", "desc2", 13, 15, |
364 |
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12f, "group2")); |
365 |
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366 |
1 |
MapList mapList = new MapList(new int[] { 1, 24 }, new int[] { 1, 3 }, |
367 |
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3, 1); |
368 |
1 |
Mapping map = new Mapping(pep1, mapList); |
369 |
1 |
DBRefEntry dbRef1 = new DBRefEntry("UNIPROT", "0", "Q9ZTS2", map); |
370 |
1 |
dna1.getDatasetSequence().addDBRef(dbRef1); |
371 |
1 |
mapList = new MapList(new int[] { 1, 24 }, new int[] { 1, 3 }, 3, 1); |
372 |
1 |
map = new Mapping(pep2, mapList); |
373 |
1 |
DBRefEntry dbRef2 = new DBRefEntry("UNIPROT", "0", "P30419", map); |
374 |
1 |
dna1.getDatasetSequence().addDBRef(dbRef2); |
375 |
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376 |
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377 |
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378 |
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379 |
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|
380 |
1 |
AlignmentI al = new Alignment(new SequenceI[] { dna1 }); |
381 |
1 |
Alignment xrefs = new CrossRef(new SequenceI[] { dna1 }, al) |
382 |
|
.findXrefSequences("UNIPROT", true); |
383 |
1 |
assertEquals(2, xrefs.getHeight()); |
384 |
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|
385 |
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|
386 |
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387 |
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388 |
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389 |
1 |
checkCopySequence(pep1, xrefs.getSequenceAt(0)); |
390 |
1 |
checkCopySequence(pep2, xrefs.getSequenceAt(1)); |
391 |
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} |
392 |
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393 |
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394 |
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395 |
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396 |
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397 |
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398 |
|
@param |
399 |
|
@param |
400 |
|
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|
| 100% |
Uncovered Elements: 0 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
|
401 |
2 |
private void checkCopySequence(SequenceI copy, SequenceI original)... |
402 |
|
{ |
403 |
2 |
assertNotSame(copy, original); |
404 |
2 |
assertSame(copy.getDatasetSequence(), original.getDatasetSequence()); |
405 |
2 |
assertEquals(copy.getName(), original.getName()); |
406 |
2 |
assertEquals(copy.getStart(), original.getStart()); |
407 |
2 |
assertEquals(copy.getEnd(), original.getEnd()); |
408 |
2 |
assertEquals(copy.getSequenceAsString(), original.getSequenceAsString()); |
409 |
|
} |
410 |
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411 |
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412 |
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|
413 |
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|
414 |
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|
| 0% |
Uncovered Elements: 15 (15) |
Complexity: 1 |
Complexity Density: 0.07 |
1PASS
|
|
415 |
0 |
@Test(groups = { "Functional_Failing" })... |
416 |
|
public void testFindXrefSequences_withFetch() |
417 |
|
{ |
418 |
0 |
SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC"); |
419 |
0 |
dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "Q9ZTS2")); |
420 |
0 |
dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "P30419")); |
421 |
0 |
dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "P00314")); |
422 |
0 |
final SequenceI pep1 = new Sequence("Q9ZTS2", "MYQLIRSSW"); |
423 |
0 |
pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2")); |
424 |
|
|
425 |
0 |
final SequenceI pep2 = new Sequence("P00314", "MRKLLAASG"); |
426 |
0 |
pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "P00314")); |
427 |
|
|
428 |
|
|
429 |
|
|
430 |
|
|
431 |
|
|
432 |
0 |
SequenceFetcher mockFetcher = new SequenceFetcher() |
433 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
434 |
0 |
@Override... |
435 |
|
public boolean isFetchable(String source) |
436 |
|
{ |
437 |
0 |
return true; |
438 |
|
} |
439 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
440 |
0 |
@Override... |
441 |
|
public SequenceI[] getSequences(List<DBRefEntry> refs, boolean dna) |
442 |
|
{ |
443 |
0 |
return new SequenceI[] { pep1, pep2 }; |
444 |
|
} |
445 |
|
}; |
446 |
0 |
SequenceFetcherFactory.setSequenceFetcher(mockFetcher); |
447 |
|
|
448 |
|
|
449 |
|
|
450 |
|
|
451 |
0 |
AlignmentI al = new Alignment(new SequenceI[] { dna1 }); |
452 |
0 |
Alignment xrefs = new CrossRef(new SequenceI[] { dna1 }, al) |
453 |
|
.findXrefSequences("UNIPROT", true); |
454 |
0 |
assertEquals(2, xrefs.getHeight()); |
455 |
0 |
assertSame(pep1, xrefs.getSequenceAt(0)); |
456 |
0 |
assertSame(pep2, xrefs.getSequenceAt(1)); |
457 |
|
} |
458 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
459 |
1 |
@AfterClass(alwaysRun = true)... |
460 |
|
public void tearDown() |
461 |
|
{ |
462 |
1 |
SequenceFetcherFactory.setSequenceFetcher(null); |
463 |
|
} |
464 |
|
|
465 |
|
|
466 |
|
|
467 |
|
|
468 |
|
|
|
|
| 0% |
Uncovered Elements: 22 (22) |
Complexity: 1 |
Complexity Density: 0.05 |
1PASS
|
|
469 |
0 |
@Test(groups = { "Functional_Failing" })... |
470 |
|
public void testFindXrefSequences_forGeneAndTranscripts() |
471 |
|
{ |
472 |
|
|
473 |
|
|
474 |
|
|
475 |
0 |
SequenceI gene = new Sequence("ENSG00000157764", "CGCCTCCCTTCCCC"); |
476 |
0 |
gene.addDBRef(new DBRefEntry("UNIPROT", "0", "P15056")); |
477 |
0 |
gene.addDBRef(new DBRefEntry("UNIPROT", "0", "H7C5K3")); |
478 |
|
|
479 |
|
|
480 |
|
|
481 |
|
|
482 |
0 |
SequenceI braf001 = new Sequence("ENST00000288602", "taagATGGCGGCGCTGa"); |
483 |
0 |
braf001.addDBRef(new DBRefEntry("UNIPROT", "0", "P15056")); |
484 |
0 |
braf001.addSequenceFeature(new SequenceFeature("CDS", "", 5, 16, 0f, |
485 |
|
null)); |
486 |
|
|
487 |
|
|
488 |
|
|
489 |
|
|
490 |
0 |
SequenceI braf002 = new Sequence("ENST00000497784", "gCAGGCtaTCTGTTCaa"); |
491 |
0 |
braf002.addDBRef(new DBRefEntry("UNIPROT", "ENSEMBL|0", "H7C5K3")); |
492 |
0 |
braf002.addSequenceFeature(new SequenceFeature("CDS", "", 2, 6, 0f, |
493 |
|
null)); |
494 |
0 |
braf002.addSequenceFeature(new SequenceFeature("CDS", "", 9, 15, 0f, |
495 |
|
null)); |
496 |
|
|
497 |
|
|
498 |
|
|
499 |
|
|
500 |
|
|
501 |
|
|
502 |
0 |
final SequenceI pep1 = new Sequence("UNIPROT|P15056", "MAAL"); |
503 |
0 |
pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "P15056")); |
504 |
0 |
final SequenceI pep2 = new Sequence("UNIPROT|H7C5K3", "QALF"); |
505 |
0 |
pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "H7C5K3")); |
506 |
|
|
507 |
|
|
508 |
|
|
509 |
|
|
510 |
0 |
SequenceFetcher mockFetcher = new SequenceFetcher() |
511 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
512 |
0 |
@Override... |
513 |
|
public boolean isFetchable(String source) |
514 |
|
{ |
515 |
0 |
return true; |
516 |
|
} |
517 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
518 |
0 |
@Override... |
519 |
|
public SequenceI[] getSequences(List<DBRefEntry> refs, boolean dna) |
520 |
|
{ |
521 |
0 |
return new SequenceI[] { pep1, pep2 }; |
522 |
|
} |
523 |
|
}; |
524 |
0 |
SequenceFetcherFactory.setSequenceFetcher(mockFetcher); |
525 |
|
|
526 |
|
|
527 |
|
|
528 |
|
|
529 |
|
|
530 |
|
|
531 |
|
|
532 |
|
|
533 |
0 |
SequenceI[] seqs = new SequenceI[] { gene, braf001, braf002 }; |
534 |
0 |
AlignmentI al = new Alignment(seqs); |
535 |
0 |
Alignment xrefs = new CrossRef(seqs, al).findXrefSequences("UNIPROT", |
536 |
|
true); |
537 |
0 |
assertEquals(2, xrefs.getHeight()); |
538 |
0 |
assertSame(pep1, xrefs.getSequenceAt(0)); |
539 |
0 |
assertSame(pep2, xrefs.getSequenceAt(1)); |
540 |
|
} |
541 |
|
|
542 |
|
|
543 |
|
|
544 |
|
|
545 |
|
|
546 |
|
|
547 |
|
|
548 |
|
|
549 |
|
|
550 |
|
|
551 |
|
|
552 |
|
|
553 |
|
|
554 |
|
|
555 |
|
|
556 |
|
|
557 |
|
|
558 |
|
|
559 |
|
|
560 |
|
|
561 |
|
|
562 |
|
|
563 |
|
|
564 |
|
|
565 |
|
|
|
|
| 0% |
Uncovered Elements: 68 (68) |
Complexity: 1 |
Complexity Density: 0.01 |
1PASS
|
|
566 |
0 |
@Test(groups = { "Functional_Failing" })... |
567 |
|
public void testFindXrefSequences_uniprotEmblManyToMany() |
568 |
|
{ |
569 |
|
|
570 |
|
|
571 |
|
|
572 |
|
|
573 |
0 |
SequenceI p0ce19 = new Sequence("UNIPROT|P0CE19", "KPFG"); |
574 |
0 |
p0ce19.addDBRef(new DBRefEntry("EMBL", "0", "J03321")); |
575 |
0 |
p0ce19.addDBRef(new DBRefEntry("EMBL", "0", "X06707")); |
576 |
0 |
p0ce19.addDBRef(new DBRefEntry("EMBL", "0", "M19487")); |
577 |
0 |
SequenceI p0ce20 = new Sequence("UNIPROT|P0CE20", "PFGK"); |
578 |
0 |
p0ce20.addDBRef(new DBRefEntry("EMBL", "0", "J03321")); |
579 |
0 |
p0ce20.addDBRef(new DBRefEntry("EMBL", "0", "X06707")); |
580 |
0 |
p0ce20.addDBRef(new DBRefEntry("EMBL", "0", "X07547")); |
581 |
|
|
582 |
|
|
583 |
|
|
584 |
|
|
585 |
|
|
586 |
|
|
587 |
|
|
588 |
|
|
589 |
|
|
590 |
|
|
591 |
|
|
592 |
0 |
final SequenceI j03321 = new Sequence("EMBL|J03321", "AAACCCTTTGGGAAAA"); |
593 |
0 |
DBRefEntry dbref1 = new DBRefEntry("UNIPROT", "0", "P0CE19"); |
594 |
0 |
MapList mapList = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, |
595 |
|
3, 1); |
596 |
0 |
Mapping map = new Mapping(new Sequence("UNIPROT|P0CE19", "KPFG"), |
597 |
|
mapList); |
598 |
|
|
599 |
0 |
map.getTo().addDBRef(new DBRefEntry("PIR", "0", "S01875")); |
600 |
0 |
dbref1.setMap(map); |
601 |
0 |
j03321.addDBRef(dbref1); |
602 |
0 |
DBRefEntry dbref2 = new DBRefEntry("UNIPROT", "0", "P0CE20"); |
603 |
0 |
mapList = new MapList(new int[] { 4, 15 }, new int[] { 2, 5 }, 3, 1); |
604 |
0 |
dbref2.setMap(new Mapping(new Sequence("UNIPROT|P0CE20", "PFGK"), |
605 |
|
new MapList(mapList))); |
606 |
0 |
j03321.addDBRef(dbref2); |
607 |
|
|
608 |
|
|
609 |
|
|
610 |
|
|
611 |
0 |
final SequenceI x06707 = new Sequence("EMBL|X06707", "atgAAACCCTTTGGG"); |
612 |
0 |
DBRefEntry dbref3 = new DBRefEntry("UNIPROT", "0", "P0CE19"); |
613 |
0 |
MapList map2 = new MapList(new int[] { 4, 15 }, new int[] { 1, 4 }, 3, |
614 |
|
1); |
615 |
0 |
dbref3.setMap(new Mapping(new Sequence("UNIPROT|P0CE19", "KPFG"), map2)); |
616 |
0 |
x06707.addDBRef(dbref3); |
617 |
0 |
DBRefEntry dbref4 = new DBRefEntry("UNIPROT", "0", "P0CE20"); |
618 |
0 |
MapList map3 = new MapList(new int[] { 4, 15 }, new int[] { 1, 4 }, 3, |
619 |
|
1); |
620 |
0 |
dbref4.setMap(new Mapping(new Sequence("UNIPROT|P0CE20", "PFGK"), map3)); |
621 |
0 |
x06707.addDBRef(dbref4); |
622 |
|
|
623 |
|
|
624 |
|
|
625 |
|
|
626 |
0 |
final SequenceI m19487 = new Sequence("EMBL|M19487", "AAACCCTTTGGG"); |
627 |
0 |
DBRefEntry dbref5 = new DBRefEntry("UNIPROT", "0", "P0CE19"); |
628 |
0 |
dbref5.setMap(new Mapping(new Sequence("UNIPROT|P0CE19", "KPFG"), |
629 |
|
new MapList(mapList))); |
630 |
0 |
m19487.addDBRef(dbref5); |
631 |
0 |
DBRefEntry dbref6 = new DBRefEntry("UNIPROT", "0", "Q46432"); |
632 |
0 |
dbref6.setMap(new Mapping(new Sequence("UNIPROT|Q46432", "KPFG"), |
633 |
|
new MapList(mapList))); |
634 |
0 |
m19487.addDBRef(dbref6); |
635 |
|
|
636 |
|
|
637 |
|
|
638 |
|
|
639 |
0 |
final SequenceI x07547 = new Sequence("EMBL|X07547", "cccAAACCCTTTGGG"); |
640 |
0 |
DBRefEntry dbref7 = new DBRefEntry("UNIPROT", "0", "P0CE20"); |
641 |
0 |
dbref7.setMap(new Mapping(new Sequence("UNIPROT|P0CE20", "PFGK"), |
642 |
|
new MapList(map2))); |
643 |
0 |
x07547.addDBRef(dbref7); |
644 |
0 |
DBRefEntry dbref8 = new DBRefEntry("UNIPROT", "0", "B0BCM4"); |
645 |
0 |
dbref8.setMap(new Mapping(new Sequence("UNIPROT|B0BCM4", "KPFG"), |
646 |
|
new MapList(map2))); |
647 |
0 |
x07547.addDBRef(dbref8); |
648 |
|
|
649 |
|
|
650 |
|
|
651 |
|
|
652 |
|
|
653 |
|
|
654 |
|
|
655 |
|
|
656 |
0 |
SequenceFetcher mockFetcher = new SequenceFetcher() |
657 |
|
{ |
658 |
|
int call = 0; |
659 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
660 |
0 |
@Override... |
661 |
|
public boolean isFetchable(String source) |
662 |
|
{ |
663 |
0 |
return true; |
664 |
|
} |
665 |
|
|
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
|
666 |
0 |
@Override... |
667 |
|
public SequenceI[] getSequences(List<DBRefEntry> refs, boolean dna) |
668 |
|
{ |
669 |
0 |
call++; |
670 |
0 |
if (call == 1) |
671 |
|
{ |
672 |
0 |
assertEquals("Expected 3 embl seqs in first fetch", 3, |
673 |
|
refs.size()); |
674 |
0 |
return new SequenceI[] { j03321, x06707, m19487 }; |
675 |
|
} |
676 |
|
else |
677 |
|
{ |
678 |
0 |
assertEquals("Expected 1 embl seq in second fetch", 1, |
679 |
|
refs.size()); |
680 |
0 |
return new SequenceI[] { x07547 }; |
681 |
|
} |
682 |
|
} |
683 |
|
}; |
684 |
0 |
SequenceFetcherFactory.setSequenceFetcher(mockFetcher); |
685 |
|
|
686 |
|
|
687 |
|
|
688 |
|
|
689 |
|
|
690 |
|
|
691 |
|
|
692 |
|
|
693 |
|
|
694 |
0 |
SequenceI[] seqs = new SequenceI[] { p0ce19, p0ce20 }; |
695 |
0 |
AlignmentI al = new Alignment(seqs); |
696 |
0 |
Alignment xrefs = new CrossRef(seqs, al).findXrefSequences("EMBL", |
697 |
|
false); |
698 |
|
|
699 |
|
|
700 |
|
|
701 |
|
|
702 |
0 |
assertNotNull(xrefs); |
703 |
0 |
assertEquals(4, xrefs.getHeight()); |
704 |
0 |
assertSame(j03321, xrefs.getSequenceAt(0)); |
705 |
0 |
assertSame(x06707, xrefs.getSequenceAt(1)); |
706 |
0 |
assertSame(m19487, xrefs.getSequenceAt(2)); |
707 |
0 |
assertSame(x07547, xrefs.getSequenceAt(3)); |
708 |
|
|
709 |
|
|
710 |
|
|
711 |
|
|
712 |
0 |
Mapping mapping = p0ce19.getDBRefs().get(0).getMap(); |
713 |
0 |
assertSame(j03321, mapping.getTo()); |
714 |
0 |
mapping = p0ce19.getDBRefs().get(1).getMap(); |
715 |
0 |
assertSame(x06707, mapping.getTo()); |
716 |
0 |
mapping = p0ce20.getDBRefs().get(0).getMap(); |
717 |
0 |
assertSame(j03321, mapping.getTo()); |
718 |
0 |
mapping = p0ce20.getDBRefs().get(1).getMap(); |
719 |
0 |
assertSame(x06707, mapping.getTo()); |
720 |
|
|
721 |
|
|
722 |
|
|
723 |
|
|
724 |
|
|
725 |
0 |
assertSame(p0ce19, j03321.getDBRefs().get(0).getMap().getTo()); |
726 |
0 |
assertSame(p0ce20, j03321.getDBRefs().get(1).getMap().getTo()); |
727 |
0 |
assertSame(p0ce19, x06707.getDBRefs().get(0).getMap().getTo()); |
728 |
0 |
assertSame(p0ce20, x06707.getDBRefs().get(1).getMap().getTo()); |
729 |
|
|
730 |
|
|
731 |
|
|
732 |
|
|
733 |
|
|
734 |
0 |
assertEquals(4, p0ce19.getDBRefs().size()); |
735 |
0 |
assertEquals("PIR", p0ce19.getDBRefs().get(3).getSource()); |
736 |
0 |
assertEquals("S01875", p0ce19.getDBRefs().get(3).getAccessionId()); |
737 |
|
} |
738 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (8) |
Complexity: 1 |
Complexity Density: 0.12 |
1PASS
|
|
739 |
1 |
@Test(groups = "Functional")... |
740 |
|
public void testSameSequence() |
741 |
|
{ |
742 |
1 |
assertTrue(CrossRef.sameSequence(null, null)); |
743 |
1 |
SequenceI seq1 = new Sequence("seq1", "ABCDEF"); |
744 |
1 |
assertFalse(CrossRef.sameSequence(seq1, null)); |
745 |
1 |
assertFalse(CrossRef.sameSequence(null, seq1)); |
746 |
1 |
assertTrue(CrossRef.sameSequence(seq1, new Sequence("seq2", "ABCDEF"))); |
747 |
1 |
assertTrue(CrossRef.sameSequence(seq1, new Sequence("seq2", "abcdef"))); |
748 |
1 |
assertFalse(CrossRef |
749 |
|
.sameSequence(seq1, new Sequence("seq2", "ABCDE-F"))); |
750 |
1 |
assertFalse(CrossRef.sameSequence(seq1, new Sequence("seq2", "BCDEF"))); |
751 |
|
} |
752 |
|
} |