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package jalview.ws.seqfetcher; |
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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.assertTrue; |
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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.junit.Assert; |
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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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import jalview.analysis.CrossRef; |
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import jalview.datamodel.AlignmentAnnotation; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.DBRefEntry; |
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import jalview.datamodel.DBRefSource; |
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import jalview.datamodel.FeatureProperties; |
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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.ws.DBRefFetcher; |
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import jalview.ws.SequenceFetcher; |
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import jalview.ws.dbsources.EBIAlfaFold; |
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import jalview.ws.dbsources.Pdb; |
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import jalview.ws.dbsources.Uniprot; |
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@author |
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| 36.4% |
Uncovered Elements: 56 (88) |
Complexity: 14 |
Complexity Density: 0.2 |
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public class DbRefFetcherTest |
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{ |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
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@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); |
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} |
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@throws |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@BeforeClass(alwaysRun = true)... |
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public static void setUpBeforeClass() throws Exception |
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{ |
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jalview.bin.Console.initLogger(); |
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} |
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@throws |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
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@AfterClass(alwaysRun = true)... |
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public static void tearDownAfterClass() throws Exception |
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{ |
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} |
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| 0% |
Uncovered Elements: 11 (11) |
Complexity: 1 |
Complexity Density: 0.09 |
4-
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@Test(groups = { "Network" })... |
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public void checkUniprotCanonicalFlagSet() |
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{ |
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SequenceI uniprotSeq = new Sequence("FER1_SPIOL", |
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"MAATTTTMMGMATTFVPKPQAPPMMAALPSNTGRSLFGLKTGSRGGRMTMAAYKVTLVTPTGNVEFQCPDDV" |
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+ "YILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEE" |
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+ "LTA"); |
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DBRefFetcher dbr = new DBRefFetcher(new SequenceI[] { uniprotSeq }); |
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dbr.fetchDBRefs(true); |
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List<DBRefEntry> primRefs = uniprotSeq.getPrimaryDBRefs(); |
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assertNotNull(primRefs); |
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assertTrue(primRefs.size() > 0); |
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boolean canonicalUp = false; |
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for (DBRefEntry ref : primRefs) |
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{ |
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assertEquals(DBRefSource.UNIPROT, ref.getCanonicalSourceName()); |
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canonicalUp |= ref.isCanonical(); |
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} |
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assertTrue("No Canonical Uniprot reference detected", canonicalUp); |
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} |
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| 96.2% |
Uncovered Elements: 1 (26) |
Complexity: 5 |
Complexity Density: 0.25 |
1PASS
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@Test(groups = { "Functional" })... |
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public void testStandardProtDbs() |
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{ |
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List<String> defdb = new ArrayList<String>(); |
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defdb.addAll(Arrays.asList(DBRefSource.PROTEINDBS)); |
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defdb.add(DBRefSource.PDB); |
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List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>(); |
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SequenceFetcher sfetcher = new SequenceFetcher(); |
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boolean pdbFound = false; |
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for (String ddb : defdb) |
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{ |
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List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb); |
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if (srcesfordb != null) |
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{ |
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srces.addAll(srcesfordb); |
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} |
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} |
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int i = 0; |
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int uniprotPos = -1; |
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for (DbSourceProxy s : srces) |
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{ |
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if (s instanceof Uniprot && uniprotPos == -1) |
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{ |
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uniprotPos = i; |
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} |
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if (s instanceof Pdb) |
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{ |
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pdbFound = true; |
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} |
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i++; |
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} |
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assertTrue("Failed to find Uniprot source as first source amongst " |
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+ srces.size() + " sources (source was at position " |
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+ uniprotPos + ")", uniprotPos == 0); |
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assertTrue("Failed to find PDB source amongst " + srces.size() |
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+ " sources", pdbFound); |
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} |
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@throws |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
1PASS
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@Test(groups = { "External" })... |
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public void testEmblUniprotProductRecovery() throws Exception |
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{ |
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String retrievalId = "V00488"; |
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DbSourceProxy embl = new SequenceFetcher() |
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.getSourceProxy(DBRefSource.EMBL).get(0); |
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assertNotNull("Couldn't find the EMBL retrieval client", embl); |
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verifyProteinNucleotideXref(retrievalId, embl); |
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} |
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@throws |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
1PASS
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@Test(groups = { "External" })... |
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public void testEmblCDSUniprotProductRecovery() throws Exception |
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{ |
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String retrievalId = "AAH29712"; |
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DbSourceProxy embl = new SequenceFetcher() |
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.getSourceProxy(DBRefSource.EMBLCDS).get(0); |
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assertNotNull("Couldn't find the EMBL retrieval client", embl); |
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verifyProteinNucleotideXref(retrievalId, embl); |
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} |
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@param |
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@param |
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@throws |
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| 0% |
Uncovered Elements: 20 (20) |
Complexity: 1 |
Complexity Density: 0.05 |
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private void verifyProteinNucleotideXref(String retrievalId,... |
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DbSourceProxy embl) throws Exception |
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{ |
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AlignmentI alsq = embl.getSequenceRecords(retrievalId); |
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assertNotNull("Couldn't find the EMBL record " + retrievalId, alsq); |
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assertEquals("Didn't retrieve right number of records", 1, |
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alsq.getHeight()); |
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SequenceI seq = alsq.getSequenceAt(0); |
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assertEquals("Wrong sequence name", |
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embl.getDbSource() + "|" + retrievalId, seq.getName()); |
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List<SequenceFeature> sfs = seq.getSequenceFeatures(); |
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assertFalse("Sequence features missing", sfs.isEmpty()); |
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assertTrue("Feature not CDS", FeatureProperties |
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.isCodingFeature(embl.getDbSource(), sfs.get(0).getType())); |
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assertEquals(embl.getDbSource(), sfs.get(0).getFeatureGroup()); |
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List<DBRefEntry> dr = DBRefUtils.selectRefs(seq.getDBRefs(), |
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new String[] |
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{ DBRefSource.UNIPROT }); |
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assertNotNull(dr); |
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assertEquals("Expected a single Uniprot cross reference", 1, dr.size()); |
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assertEquals("Expected cross reference map to be one amino acid", |
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dr.get(0).getMap().getMappedWidth(), 1); |
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assertEquals("Expected local reference map to be 3 nucleotides", |
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dr.get(0).getMap().getWidth(), 3); |
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AlignmentI sprods = new CrossRef(alsq.getSequencesArray(), alsq) |
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.findXrefSequences(dr.get(0).getSource(), true); |
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assertNotNull( |
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"Couldn't recover cross reference sequence from dataset. Was it ever added ?", |
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sprods); |
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assertEquals("Didn't xref right number of records", 1, |
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sprods.getHeight()); |
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SequenceI proteinSeq = sprods.getSequenceAt(0); |
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assertEquals(proteinSeq.getSequenceAsString(), |
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dr.get(0).getMap().getTo().getSequenceAsString()); |
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assertEquals(dr.get(0).getSource() + "|" + dr.get(0).getAccessionId(), |
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proteinSeq.getName()); |
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} |
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@throws |
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| 0% |
Uncovered Elements: 11 (11) |
Complexity: 2 |
Complexity Density: 0.22 |
1PASS
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@Test(groups = { "External" })... |
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public void testAlphaFoldClien() throws Exception |
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{ |
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DbSourceProxy alphafold = new EBIAlfaFold(); |
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AlignmentI resp = alphafold |
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.getSequenceRecords(alphafold.getTestQuery()); |
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assertNotNull(resp); |
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assertEquals("One sequence only", resp.getHeight(), 1); |
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for (AlignmentAnnotation aa : resp.getAlignmentAnnotation()) |
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{ |
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if (aa.graph == AlignmentAnnotation.CONTACT_MAP) |
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{ |
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assertTrue("Contact map didn't provide valid contact", |
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resp.getContactListFor(aa, 1).getContactAt(1) != -1d); |
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return; |
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} |
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} |
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Assert.fail("No pAE matrix found for alphafold structure."); |
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} |
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} |