X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FCrossRefTest.java;h=d47c2c12dfeeae265466377d530205fece1245f6;hb=c0a37536d35fb247404187b367228e71f85ce373;hp=e1d075d344ba5e528659113b492ecead8fe62363;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java index e1d075d..d47c2c1 100644 --- a/test/jalview/analysis/CrossRefTest.java +++ b/test/jalview/analysis/CrossRefTest.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -37,19 +37,29 @@ import jalview.datamodel.Mapping; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.gui.JvOptionPane; import jalview.util.DBRefUtils; import jalview.util.MapList; import jalview.ws.SequenceFetcher; -import jalview.ws.SequenceFetcherFactory; 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; public class CrossRefTest { + + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + @Test(groups = { "Functional" }) public void testFindXDbRefs() { @@ -63,28 +73,28 @@ public class CrossRefTest DBRefEntry ref8 = new DBRefEntry("PFAM", "1", "A123"); // ENSEMBL is a source of either dna or protein sequence data DBRefEntry ref9 = new DBRefEntry("ENSEMBL", "1", "A123"); - DBRefEntry[] refs = new DBRefEntry[] { ref1, ref2, ref3, ref4, ref5, - ref6, ref7, ref8, ref9 }; + List refs = Arrays.asList(new DBRefEntry[] { ref1, ref2, ref3, ref4, ref5, + ref6, ref7, ref8, ref9 }); /* * Just the DNA refs: */ - DBRefEntry[] found = DBRefUtils.selectDbRefs(true, refs); - assertEquals(4, found.length); - assertSame(ref5, found[0]); - assertSame(ref6, found[1]); - assertSame(ref7, found[2]); - assertSame(ref9, found[3]); + List found = DBRefUtils.selectDbRefs(true, refs); + assertEquals(4, found.size()); + assertSame(ref5, found.get(0)); + assertSame(ref6, found.get(1)); + assertSame(ref7, found.get(2)); + assertSame(ref9, found.get(3)); /* * Just the protein refs: */ found = DBRefUtils.selectDbRefs(false, refs); - assertEquals(4, found.length); - assertSame(ref1, found[0]); - assertSame(ref2, found[1]); - assertSame(ref4, found[2]); - assertSame(ref9, found[3]); + assertEquals(4, found.size()); + assertSame(ref1, found.get(0)); + assertSame(ref2, found.get(1)); + assertSame(ref4, found.get(2)); + assertSame(ref9, found.get(3)); } /** @@ -96,7 +106,7 @@ public class CrossRefTest public void testFindXrefSourcesForSequence_proteinToDna() { SequenceI seq = new Sequence("Seq1", "MGKYQARLSS"); - List sources = new ArrayList(); + List sources = new ArrayList<>(); AlignmentI al = new Alignment(new SequenceI[] {}); /* @@ -122,15 +132,16 @@ public class CrossRefTest sources = new CrossRef(new SequenceI[] { seq }, al) .findXrefSourcesForSequences(false); // method is patched to remove EMBL from the sources to match - assertEquals(3, sources.size()); - assertEquals("[EMBLCDS, GENEDB, ENSEMBL]", sources.toString()); + assertEquals(4, sources.size()); + assertEquals("[EMBLCDS, GENEDB, ENSEMBL, ENSEMBLGENOMES]", + sources.toString()); /* * add a sequence to the alignment which has a dbref to UNIPROT|A1234 * and others to dna coding databases */ sources.clear(); - seq.setDBRefs(null); + seq.setDBRefs(null); seq.addDBRef(new DBRefEntry("UNIPROT", "0", "A1234")); seq.addDBRef(new DBRefEntry("EMBLCDS", "0", "E2347")); SequenceI seq2 = new Sequence("Seq2", "MGKYQARLSS"); @@ -260,7 +271,7 @@ public class CrossRefTest pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2")); AlignmentI al = new Alignment(new SequenceI[] { dna1, pep1 }); - List result = new ArrayList(); + List result = new ArrayList<>(); /* * first search for a dbref nowhere on the alignment: @@ -269,7 +280,7 @@ public class CrossRefTest CrossRef testee = new CrossRef(al.getSequencesArray(), al); AlignedCodonFrame acf = new AlignedCodonFrame(); boolean found = testee.searchDataset(true, dna1, dbref, result, acf, - true); + true, DBRefUtils.SEARCH_MODE_FULL); assertFalse(found); assertTrue(result.isEmpty()); assertTrue(acf.isEmpty()); @@ -280,7 +291,7 @@ public class CrossRefTest acf = new AlignedCodonFrame(); dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2"); found = testee.searchDataset(!dna1.isProtein(), dna1, dbref, result, - acf, false); // search dataset with a protein xref from a dna + acf, false, DBRefUtils.SEARCH_MODE_FULL); // search dataset with a protein xref from a dna // sequence to locate the protein product assertTrue(found); assertEquals(1, result.size()); @@ -294,7 +305,7 @@ public class CrossRefTest acf = new AlignedCodonFrame(); dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2"); found = testee.searchDataset(!pep1.isProtein(), pep1, dbref, result, - acf, false); // search dataset with a protein's direct dbref to + acf, false, DBRefUtils.SEARCH_MODE_FULL); // search dataset with a protein's direct dbref to // locate dna sequences with matching xref assertTrue(found); assertEquals(1, result.size()); @@ -416,7 +427,7 @@ public class CrossRefTest * argument false suppresses adding DAS sources * todo: define an interface type SequenceFetcherI and mock that */ - SequenceFetcher mockFetcher = new SequenceFetcher(false) + SequenceFetcher mockFetcher = new SequenceFetcher() { @Override public boolean isFetchable(String source) @@ -430,7 +441,7 @@ public class CrossRefTest return new SequenceI[] { pep1, pep2 }; } }; - SequenceFetcherFactory.setSequenceFetcher(mockFetcher); + SequenceFetcher.setSequenceFetcher(mockFetcher); /* * find UNIPROT xrefs for nucleotide sequence @@ -443,10 +454,10 @@ public class CrossRefTest assertSame(pep2, xrefs.getSequenceAt(1)); } - @AfterClass + @AfterClass(alwaysRun = true) public void tearDown() { - SequenceFetcherFactory.setSequenceFetcher(null); + SequenceFetcher.setSequenceFetcher(null); } /** @@ -494,7 +505,7 @@ public class CrossRefTest * argument false suppresses adding DAS sources * todo: define an interface type SequenceFetcherI and mock that */ - SequenceFetcher mockFetcher = new SequenceFetcher(false) + SequenceFetcher mockFetcher = new SequenceFetcher() { @Override public boolean isFetchable(String source) @@ -508,7 +519,7 @@ public class CrossRefTest return new SequenceI[] { pep1, pep2 }; } }; - SequenceFetcherFactory.setSequenceFetcher(mockFetcher); + SequenceFetcher.setSequenceFetcher(mockFetcher); /* * find UNIPROT xrefs for gene and transcripts @@ -640,7 +651,7 @@ public class CrossRefTest * passed in calls to getSequences() - important to verify that * duplicate sequence fetches are not requested */ - SequenceFetcher mockFetcher = new SequenceFetcher(false) + SequenceFetcher mockFetcher = new SequenceFetcher() { int call = 0; @@ -668,7 +679,8 @@ public class CrossRefTest } } }; - SequenceFetcherFactory.setSequenceFetcher(mockFetcher); + + SequenceFetcher.setSequenceFetcher(mockFetcher); /* * find EMBL xrefs for Uniprot seqs and verify that @@ -696,30 +708,31 @@ public class CrossRefTest /* * verify mappings added to Uniprot-to-EMBL dbrefs */ - Mapping mapping = p0ce19.getDBRefs()[0].getMap(); + Mapping mapping = p0ce19.getDBRefs().get(0).getMap(); assertSame(j03321, mapping.getTo()); - mapping = p0ce19.getDBRefs()[1].getMap(); + mapping = p0ce19.getDBRefs().get(1).getMap(); assertSame(x06707, mapping.getTo()); - mapping = p0ce20.getDBRefs()[0].getMap(); + mapping = p0ce20.getDBRefs().get(0).getMap(); assertSame(j03321, mapping.getTo()); - mapping = p0ce20.getDBRefs()[1].getMap(); + mapping = p0ce20.getDBRefs().get(1).getMap(); assertSame(x06707, mapping.getTo()); /* * verify dbrefs on EMBL are mapped to alignment seqs */ - assertSame(p0ce19, j03321.getDBRefs()[0].getMap().getTo()); - assertSame(p0ce20, j03321.getDBRefs()[1].getMap().getTo()); - assertSame(p0ce19, x06707.getDBRefs()[0].getMap().getTo()); - assertSame(p0ce20, x06707.getDBRefs()[1].getMap().getTo()); + + assertSame(p0ce19, j03321.getDBRefs().get(0).getMap().getTo()); + assertSame(p0ce20, j03321.getDBRefs().get(1).getMap().getTo()); + assertSame(p0ce19, x06707.getDBRefs().get(0).getMap().getTo()); + assertSame(p0ce20, x06707.getDBRefs().get(1).getMap().getTo()); /* * verify new dbref on EMBL dbref mapping is copied to the * original Uniprot sequence */ - assertEquals(4, p0ce19.getDBRefs().length); - assertEquals("PIR", p0ce19.getDBRefs()[3].getSource()); - assertEquals("S01875", p0ce19.getDBRefs()[3].getAccessionId()); + assertEquals(4, p0ce19.getDBRefs().size()); + assertEquals("PIR", p0ce19.getDBRefs().get(3).getSource()); + assertEquals("S01875", p0ce19.getDBRefs().get(3).getAccessionId()); } @Test(groups = "Functional")