+/*
+ * 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.ext.ensembl;
-import jalview.datamodel.Alignment;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.ext.ensembl.SeqFetcher.EnsemblSeqType;
-import jalview.io.AppletFormatAdapter;
+import jalview.datamodel.features.SequenceFeatures;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
import jalview.io.FastaFile;
-import jalview.io.FileParse;
-import jalview.util.DBRefUtils;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyLite;
import java.lang.reflect.Method;
import java.util.Arrays;
+import java.util.List;
import org.testng.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
public class EnsemblSeqProxyTest
{
- @Test
- public void testCheckEnsembl()
- {
- SeqFetcher sf = new SeqFetcher();
- sf.setTestEnsemblStatus(true);
- sf.setTesting(true);
- Assert.assertTrue(sf.isEnsemblAvailable());
- sf.setTestEnsemblStatus(false);
- Assert.assertFalse(sf.isEnsemblAvailable());
- }
- @Test(suiteName = "live")
- public void testLiveCheckEnsembl()
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
{
- SeqFetcher sf = new SeqFetcher();
- boolean isAvailable = sf.isEnsemblAvailable();
- System.out.println("Ensembl is "
- + (isAvailable ? "UP!" : "DOWN ******************* BAD!"));
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- @DataProvider(name = "ens_seqs")
- public Object[][] createData(Method m)
- {
- System.out.println(m.getName());
- return allSeqs;
- }
-
- public static Object[][] allSeqs = new Object[][]
- {
+ private static final Object[][] allSeqs = new Object[][] {
{
- EnsemblSeqType.PROTEIN,
+ new EnsemblProtein(),
"CCDS5863.1",
">CCDS5863.1\n"
+ "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
+ "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
+ "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" },
{
- EnsemblSeqType.TRANSCRIPT,
+ new EnsemblCdna(),
"CCDS5863.1",
">CCDS5863.1\n"
+ "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n"
+ "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n"
+ "GGTGCGTTTCCTGTCCACTGA\n" },
{
- EnsemblSeqType.PROTEIN,
+ new EnsemblProtein(),
"ENSP00000288602",
">ENSP00000288602\n"
+ "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
+ "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
+ "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
+ "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
- + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
+ + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDG\n"
+ // ? insertion added in ENSP00000288602.11, not in P15056
+ + "APLNQLMRCLRKYQSRTPSPLLHSVPSEIVFDFEPGPVFR\n"
+ // end insertion
+ + "GSTTGLSATPPASLPGSLTNVKALQKSP\n"
+ "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
+ "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
+ "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
+ "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
+ "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+ SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
+ }
+
+ @AfterClass(alwaysRun = true)
+ public void tearDown()
+ {
+ SequenceOntologyFactory.setInstance(null);
+ }
+
+ @DataProvider(name = "ens_seqs")
+ public Object[][] createData(Method m)
+ {
+ System.out.println(m.getName());
+ return allSeqs;
+ }
+
@Test(dataProvider = "ens_seqs", suiteName = "live")
- public void testGetOneSeqs(EnsemblSeqType type, String sq, String fastasq)
- throws Exception
+ public void testGetSequenceRecords(EnsemblSeqProxy proxy, String sq,
+ String fastasq) throws Exception
{
- SeqFetcher sf = new SeqFetcher();
- FileParse fp = sf.getSequenceReader(type, Arrays.asList(new String[]
- { sq }));
- SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
- FastaFile trueRes = new FastaFile(fastasq, AppletFormatAdapter.PASTE);
- SequenceI[] trueSqs = trueRes.getSeqsAsArray();
- Assert.assertEquals(sqs.length, trueSqs.length,
+ FastaFile trueRes = new FastaFile(fastasq, DataSourceType.PASTE);
+ SequenceI[] expected = trueRes.getSeqsAsArray();
+ AlignmentI retrieved = proxy.getSequenceRecords(sq);
+
+ Assert.assertEquals(retrieved.getHeight(), expected.length,
"Different number of sequences retrieved for query " + sq);
- Alignment ral = new Alignment(sqs);
- for (SequenceI tr : trueSqs)
+
+ for (SequenceI tr : expected)
{
SequenceI[] rseq;
Assert.assertNotNull(
- rseq = ral.findSequenceMatch(tr.getName()),
+ rseq = retrieved.findSequenceMatch(tr.getName()),
"Couldn't find sequences matching expected sequence "
+ tr.getName());
Assert.assertEquals(rseq.length, 1,
"Sequences differ for " + tr.getName() + "\n" + "Exp:"
+ tr.getSequenceAsString() + "\n" + "Got:"
+ rseq[0].getSequenceAsString());
-
}
}
- @Test(dataProvider = "ens_seqs")
- public void testRegexForProxy(EnsemblSeqType type, String sq,
- String fastasq) throws Exception
+ @Test(groups = "Functional")
+ public void getGenomicRangesFromFeatures()
+ {
+
+ }
+
+ /**
+ * Test the method that appends a single allele's reverse complement to a
+ * string buffer
+ */
+ @Test(groups = "Functional")
+ public void testReverseComplementAllele()
+ {
+ StringBuilder sb = new StringBuilder();
+ EnsemblSeqProxy.reverseComplementAllele(sb, "G"); // comp=C
+ EnsemblSeqProxy.reverseComplementAllele(sb, "g"); // comp=c
+ EnsemblSeqProxy.reverseComplementAllele(sb, "C"); // comp=G
+ EnsemblSeqProxy.reverseComplementAllele(sb, "T"); // comp=A
+ EnsemblSeqProxy.reverseComplementAllele(sb, "A"); // comp=T
+ assertEquals("C,c,G,A,T", sb.toString());
+
+ sb = new StringBuilder();
+ EnsemblSeqProxy.reverseComplementAllele(sb, "-GATt"); // revcomp=aATC-
+ EnsemblSeqProxy.reverseComplementAllele(sb, "hgmd_mutation");
+ EnsemblSeqProxy.reverseComplementAllele(sb, "PhenCode_variation");
+ assertEquals("aATC-,hgmd_mutation,PhenCode_variation", sb.toString());
+ }
+
+ /**
+ * Test the method that computes the reverse complement of the alleles in a
+ * sequence_variant feature
+ */
+ @Test(groups = "Functional")
+ public void testReverseComplementAlleles()
{
- EnsemblSeqProxy esq = new EnsemblProtein();
- Assert.assertTrue(esq.isValidReference(sq),
- "Expected reference string " + sq + " to be valid for regex "
- + esq.getAccessionValidator().toString());
-
- Assert.assertEquals(sq, DBRefUtils.processQueryToAccessionFor(esq, sq),
- "Regex for " + esq.getClass().toString() + " not correct.");
+ String alleles = "C,G,-TAC,HGMD_MUTATION,gac";
+ SequenceFeature sf = new SequenceFeature("sequence_variant", alleles,
+ 1, 2, 0f, null);
+ sf.setValue("alleles", alleles);
+ sf.setAttributes("x=y,z;alleles=" + alleles + ";a=b,c");
+
+ EnsemblSeqProxy.reverseComplementAlleles(sf);
+ String revcomp = "G,C,GTA-,HGMD_MUTATION,gtc";
+ // verify description is updated with reverse complement
+ assertEquals(revcomp, sf.getDescription());
+ // verify alleles attribute is updated with reverse complement
+ assertEquals(revcomp, sf.getValue("alleles"));
+ // verify attributes string is updated with reverse complement
+ assertEquals("x=y,z;alleles=" + revcomp + ";a=b,c", sf.getAttributes());
+ }
+
+ @Test(groups = "Functional")
+ public void testSortFeatures()
+ {
+ SequenceFeature sf1 = new SequenceFeature("", "", 10, 15, 0f, null);
+ SequenceFeature sf2 = new SequenceFeature("", "", 8, 12, 0f, null);
+ SequenceFeature sf3 = new SequenceFeature("", "", 8, 13, 0f, null);
+ SequenceFeature sf4 = new SequenceFeature("", "", 11, 11, 0f, null);
+ List<SequenceFeature> sfs = Arrays.asList(new SequenceFeature[] { sf1,
+ sf2, sf3, sf4 });
+
+ // sort by start position ascending (forward strand)
+ // sf2 and sf3 tie and should not be reordered by sorting
+ SequenceFeatures.sortFeatures(sfs, true);
+ assertSame(sfs.get(0), sf2);
+ assertSame(sfs.get(1), sf3);
+ assertSame(sfs.get(2), sf1);
+ assertSame(sfs.get(3), sf4);
+
+ // sort by end position descending (reverse strand)
+ SequenceFeatures.sortFeatures(sfs, false);
+ assertSame(sfs.get(0), sf1);
+ assertSame(sfs.get(1), sf3);
+ assertSame(sfs.get(2), sf2);
+ assertSame(sfs.get(3), sf4);
}
- // @Test(dataProvider = "ens_seqs", suiteName = "live")
- // public void testGetOneSeqs(EnsemblSeqType type, String sq, String fastasq)
- // throws Exception
- // {
- //
- // {
- // Assert.assertTrue(rseq[0].getDBRef() != null
- // && rseq[0].getDBRef().length > 0,
- // "No database references added to sequence by fetcher.");
- // Assert.assertNotNull(DBRefUtils.searchRefs(rseq[0].getDBRef(),
- // new DBRefEntry("ENSEMBL", null, sq)),
- // "Could't find database references added to sequence by fetcher.");
- //
- // }
-}
\ No newline at end of file
+}
git://source.jalview.org / jalview.git / blobdiff