+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.ws.seqfetcher;
-
-import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertFalse;
-import static org.testng.AssertJUnit.assertNotNull;
-import static org.testng.AssertJUnit.assertTrue;
-
-import jalview.analysis.CrossRef;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.FeatureProperties;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.gui.JvOptionPane;
-import jalview.util.DBRefUtils;
-import jalview.ws.SequenceFetcher;
-import jalview.ws.dbsources.Pdb;
-import jalview.ws.dbsources.Uniprot;
-
-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;
-
-/**
- * @author jimp
- *
- */
-public class DbRefFetcherTest
-{
-
- @BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
- {
- JvOptionPane.setInteractiveMode(false);
- JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
- }
-
- /**
- * @throws java.lang.Exception
- */
- @BeforeClass(alwaysRun = true)
- public static void setUpBeforeClass() throws Exception
- {
- jalview.bin.Cache.initLogger();
- }
-
- /**
- * @throws java.lang.Exception
- */
- @AfterClass(alwaysRun = true)
- public static void tearDownAfterClass() throws Exception
- {
- }
-
- /**
- * Tests that standard protein database sources include Uniprot (as the first)
- * and also PDB. (Additional sources are dependent on availability of DAS
- * services.)
- */
- @Test(groups = { "Functional" })
- public void testStandardProtDbs()
- {
- List<String> defdb = new ArrayList<>();
- defdb.addAll(Arrays.asList(DBRefSource.PROTEINDBS));
- defdb.add(DBRefSource.PDB);
- List<DbSourceProxy> srces = new ArrayList<>();
- SequenceFetcher sfetcher = SequenceFetcher.getInstance();
- boolean pdbFound = false;
-
- for (String ddb : defdb)
- {
- List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
-
- if (srcesfordb != null)
- {
- // TODO is this right? get duplicate entries
- srces.addAll(srcesfordb);
- }
- }
-
- int i = 0;
- int uniprotPos = -1;
- for (DbSourceProxy s : srces)
- {
- if (s instanceof Uniprot && uniprotPos == -1)
- {
- uniprotPos = i;
- }
- if (s instanceof Pdb)
- {
- pdbFound = true;
- }
- i++;
- }
-
- assertTrue("Failed to find Uniprot source as first source amongst "
- + srces.size() + " sources (source was at position "
- + uniprotPos + ")", uniprotPos == 0);
- assertTrue("Failed to find PDB source amongst " + srces.size()
- + " sources", pdbFound);
- }
-
- /**
- * Tests retrieval of one entry from EMBL. Test is dependent on availability
- * of network and the EMBL service.
- *
- * @throws Exception
- */
- @Test(groups = { "External" })
- public void testEmblUniprotProductRecovery() throws Exception
- {
- String retrievalId = "V00488";
- DbSourceProxy embl = SequenceFetcher.getInstance().getSourceProxy(
- DBRefSource.EMBL).get(0);
- assertNotNull("Couldn't find the EMBL retrieval client", embl);
- verifyProteinNucleotideXref(retrievalId, embl);
- }
-
- /**
- * Tests retrieval of one entry from EMBLCDS. Test is dependent on
- * availability of network and the EMBLCDS service.
- *
- * @throws Exception
- */
- @Test(groups = { "External" })
- public void testEmblCDSUniprotProductRecovery() throws Exception
- {
- String retrievalId = "AAH29712";
- DbSourceProxy embl = SequenceFetcher.getInstance()
- .getSourceProxy(
- DBRefSource.EMBLCDS).get(0);
- assertNotNull("Couldn't find the EMBL retrieval client", embl);
- verifyProteinNucleotideXref(retrievalId, embl);
- }
-
- /**
- * Helper method to perform database retrieval and verification of results.
- *
- * @param retrievalId
- * @param embl
- * @throws Exception
- */
- private void verifyProteinNucleotideXref(String retrievalId,
- DbSourceProxy embl) throws Exception
- {
- AlignmentI alsq = embl.getSequenceRecords(retrievalId);
- assertNotNull("Couldn't find the EMBL record " + retrievalId, alsq);
- assertEquals("Didn't retrieve right number of records", 1,
- alsq.getHeight());
- SequenceI seq = alsq.getSequenceAt(0);
- assertEquals("Wrong sequence name", embl.getDbSource() + "|"
- + retrievalId, seq.getName());
- List<SequenceFeature> sfs = seq.getSequenceFeatures();
- assertFalse("Sequence features missing", sfs.isEmpty());
- assertTrue(
- "Feature not CDS",
- FeatureProperties.isCodingFeature(embl.getDbSource(),
- sfs.get(0).getType()));
- assertEquals(embl.getDbSource(), sfs.get(0).getFeatureGroup());
- List<DBRefEntry> dr = DBRefUtils.selectRefs(seq.getDBRefs(),
- new String[] { DBRefSource.UNIPROT });
- assertNotNull(dr);
- assertEquals("Expected a single Uniprot cross reference", 1, dr.size());
- assertEquals("Expected cross reference map to be one amino acid", dr.get(0)
- .getMap().getMappedWidth(), 1);
- assertEquals("Expected local reference map to be 3 nucleotides", dr.get(0)
- .getMap().getWidth(), 3);
- AlignmentI sprods = new CrossRef(alsq.getSequencesArray(), alsq)
- .findXrefSequences(dr.get(0).getSource(), true);
- assertNotNull(
- "Couldn't recover cross reference sequence from dataset. Was it ever added ?",
- sprods);
- assertEquals("Didn't xref right number of records", 1,
- sprods.getHeight());
- SequenceI proteinSeq = sprods.getSequenceAt(0);
- assertEquals(proteinSeq.getSequenceAsString(), dr.get(0).getMap().getTo()
- .getSequenceAsString());
- assertEquals(dr.get(0).getSource() + "|" + dr.get(0).getAccessionId(),
- proteinSeq.getName());
- }
-}
git://source.jalview.org / jalview.git / blobdiff