+/*
+ * 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 static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertFalse;
-import static org.testng.AssertJUnit.assertTrue;
-import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
+import static org.testng.AssertJUnit.assertSame;
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-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.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyLite;
import java.lang.reflect.Method;
-import java.net.MalformedURLException;
-import java.net.URL;
import java.util.Arrays;
import java.util.List;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
-
public class EnsemblSeqProxyTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private static final Object[][] allSeqs = new Object[][] {
{
new EnsemblProtein(),
+ "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
+ @BeforeClass(alwaysRun = true)
public void setUp()
{
SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
}
- @AfterClass
+ @AfterClass(alwaysRun = true)
public void tearDown()
{
SequenceOntologyFactory.setInstance(null);
}
@Test(dataProvider = "ens_seqs", suiteName = "live")
- public void testGetOneSeqs(EnsemblRestClient proxy, String sq, String fastasq)
- throws Exception
+ public void testGetSequenceRecords(EnsemblSeqProxy proxy, String sq,
+ String fastasq) throws Exception
{
- FileParse fp = proxy.getSequenceReader(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(suiteName = "live")
- public void testLiveCheckEnsembl()
- {
- EnsemblRestClient sf = new EnsemblRestClient()
- {
-
- @Override
- public String getDbName()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public AlignmentI getSequenceRecords(String queries) throws Exception
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- protected URL getUrl(List<String> ids) throws MalformedURLException
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- protected boolean useGetRequest()
- {
- // TODO Auto-generated method stub
- return false;
- }
-
- @Override
- protected String getRequestMimeType(boolean b)
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- protected String getResponseMimeType()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- };
- boolean isAvailable = sf.isEnsemblAvailable();
- System.out.println("Ensembl is "
- + (isAvailable ? "UP!"
- : "DOWN or unreachable ******************* BAD!"));
- }
-
@Test(groups = "Functional")
public void getGenomicRangesFromFeatures()
{
}
- @Test(groups = "Functional")
- public void testIsTranscriptIdentifier()
- {
- EnsemblSeqProxy testee = new EnsemblGene();
- assertFalse(testee.isTranscriptIdentifier(null));
- assertFalse(testee.isTranscriptIdentifier(""));
- assertFalse(testee.isTranscriptIdentifier("ENSG00000012345"));
- assertTrue(testee.isTranscriptIdentifier("ENST00000012345"));
- assertTrue(testee.isTranscriptIdentifier("ENSMUST00000012345"));
- assertFalse(testee.isTranscriptIdentifier("enst00000012345"));
- assertFalse(testee.isTranscriptIdentifier("ENST000000123456"));
- assertFalse(testee.isTranscriptIdentifier("ENST0000001234"));
- }
-
- @Test(groups = "Functional")
- public void testIsGeneIdentifier()
- {
- EnsemblSeqProxy testee = new EnsemblGene();
- assertFalse(testee.isGeneIdentifier(null));
- assertFalse(testee.isGeneIdentifier(""));
- assertFalse(testee.isGeneIdentifier("ENST00000012345"));
- assertTrue(testee.isGeneIdentifier("ENSG00000012345"));
- assertTrue(testee.isGeneIdentifier("ENSMUSG00000012345"));
- assertFalse(testee.isGeneIdentifier("ensg00000012345"));
- assertFalse(testee.isGeneIdentifier("ENSG000000123456"));
- assertFalse(testee.isGeneIdentifier("ENSG0000001234"));
- }
-
/**
* Test the method that appends a single allele's reverse complement to a
* string buffer
SequenceFeature sf2 = new SequenceFeature("", "", 8, 12, 0f, null);
SequenceFeature sf3 = new SequenceFeature("", "", 8, 13, 0f, null);
SequenceFeature sf4 = new SequenceFeature("", "", 11, 11, 0f, null);
- SequenceFeature[] sfs = new SequenceFeature[] { sf1, sf2, sf3, sf4 };
+ 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
- EnsemblSeqProxy.sortFeatures(sfs, true);
- assertArrayEquals(new SequenceFeature[] { sf2, sf3, sf1, sf4 }, sfs);
+ 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)
- EnsemblSeqProxy.sortFeatures(sfs, false);
- assertArrayEquals(new SequenceFeature[] { sf1, sf3, sf2, sf4 }, sfs);
+ SequenceFeatures.sortFeatures(sfs, false);
+ assertSame(sfs.get(0), sf1);
+ assertSame(sfs.get(1), sf3);
+ assertSame(sfs.get(2), sf2);
+ assertSame(sfs.get(3), sf4);
}
-}
\ No newline at end of file
+}
git://source.jalview.org / jalview.git / blobdiff