X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fdbsources%2FUniprotTest.java;h=24f62bc42e33f12c202cb3e04b51205f36985366;hb=e3e0829f9fb59144a1ce6e3ae99f25dc2641ecb2;hp=e835724c69f316239f40b194fa09aa34b09a1f63;hpb=88515cdb74e4603a40c8c1dca14107b5ca503e04;p=jalview.git diff --git a/test/jalview/ws/dbsources/UniprotTest.java b/test/jalview/ws/dbsources/UniprotTest.java index e835724..24f62bc 100644 --- a/test/jalview/ws/dbsources/UniprotTest.java +++ b/test/jalview/ws/dbsources/UniprotTest.java @@ -20,13 +20,17 @@ */ package jalview.ws.dbsources; +import static org.testng.Assert.assertFalse; import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertNotNull; import static org.testng.AssertJUnit.assertNull; import static org.testng.AssertJUnit.assertTrue; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.DBRefSource; import jalview.datamodel.SequenceI; import jalview.gui.JvOptionPane; +import jalview.util.DBRefUtils; import jalview.xml.binding.uniprot.DbReferenceType; import jalview.xml.binding.uniprot.Entry; import jalview.xml.binding.uniprot.FeatureType; @@ -58,8 +62,7 @@ public class UniprotTest + "" + "" + "A9CKP4" - + "A9CKP5" - + "A9CKP4_AGRT5" + + "A9CKP5" + "A9CKP4_AGRT5" + "A9CKP4_AGRT6" + "Mitogen-activated protein kinase 13" + "" @@ -153,31 +156,27 @@ public class UniprotTest sf = features.get(6); assertEquals("sequence variant", sf.getType()); - assertEquals("Foo", - sf.getDescription()); + assertEquals("Foo", sf.getDescription()); assertEquals(42, sf.getLocation().getPosition().getPosition().intValue()); assertNull(sf.getLocation().getBegin()); assertNull(sf.getLocation().getEnd()); - Assert.assertEquals(Uniprot.getDescription(sf), - "p.Met42Leu" + "
  " - + "p.Met42LeuMetVal Foo"); + Assert.assertEquals(Uniprot.getDescription(sf), "p.Met42Leu" + + "
  " + "p.Met42LeuMetVal Foo"); sf = features.get(7); assertNull(sf.getLocation().getPosition()); assertEquals(42, sf.getLocation().getBegin().getPosition().intValue()); assertEquals(43, sf.getLocation().getEnd().getPosition().intValue()); - Assert.assertEquals(Uniprot.getDescription(sf), - "p.MetLeu42LeuLeu" + "
  " - + "p.MetLeu42LeuMetVal Foo"); + Assert.assertEquals(Uniprot.getDescription(sf), "p.MetLeu42LeuLeu" + + "
  " + "p.MetLeu42LeuMetVal Foo"); sf = features.get(8); assertNull(sf.getLocation().getPosition()); assertEquals(42, sf.getLocation().getBegin().getPosition().intValue()); assertEquals(45, sf.getLocation().getEnd().getPosition().intValue()); - Assert.assertEquals(Uniprot.getDescription(sf), - "p.MLML42LeuLeu" + "
  " - + "p.MLML42LMVK Foo Too"); + Assert.assertEquals(Uniprot.getDescription(sf), "p.MLML42LeuLeu" + + "
  " + "p.MLML42LMVK Foo Too"); /* * Check cross-references @@ -211,12 +210,25 @@ public class UniprotTest public void testGetUniprotSequence() throws UnsupportedEncodingException { InputStream is = new ByteArrayInputStream(UNIPROT_XML.getBytes()); - Entry entry = new Uniprot().getUniprotEntries( - is).get(0); + Entry entry = new Uniprot().getUniprotEntries(is).get(0); SequenceI seq = new Uniprot().uniprotEntryToSequence(entry); assertNotNull(seq); - assertEquals(6, seq.getDBRefs().length); // 2*Uniprot, PDB, PDBsum, 2*EMBL - + assertEquals(6, seq.getDBRefs().size()); // 2*Uniprot, PDB, PDBsum, 2*EMBL + assertEquals(seq.getSequenceAsString(), + seq.createDatasetSequence().getSequenceAsString()); + assertEquals(2, seq.getPrimaryDBRefs().size()); + List res = DBRefUtils.searchRefs(seq.getPrimaryDBRefs(), + "A9CKP4"); + assertEquals(1, res.size()); + assertTrue(res.get(0).isCanonical()); + res = DBRefUtils.searchRefsForSource(seq.getDBRefs(), + DBRefSource.UNIPROT); + assertEquals(2, res.size()); + /* + * NB this test fragile - relies on ordering being preserved + */ + assertTrue(res.get(0).isCanonical()); + assertFalse(res.get(1).isCanonical()); } /** @@ -234,8 +246,7 @@ public class UniprotTest * name formatted with Uniprot Entry name */ String expectedName = "A9CKP4_AGRT5|A9CKP4_AGRT6"; - assertEquals(expectedName, - Uniprot.getUniprotEntryId(entry)); + assertEquals(expectedName, Uniprot.getUniprotEntryId(entry)); } /**