X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fdbsources%2FUniprotTest.java;fp=test%2Fjalview%2Fws%2Fdbsources%2FUniprotTest.java;h=24f62bc42e33f12c202cb3e04b51205f36985366;hb=3459a8a691cb22508d7067f240b7254e588e77d3;hp=8bfaef0982e86d93456d5d28f567b2066f930547;hpb=5b27f1062b2203c4c31702e205f4c78e1992063e;p=jalview.git diff --git a/test/jalview/ws/dbsources/UniprotTest.java b/test/jalview/ws/dbsources/UniprotTest.java index 8bfaef0..24f62bc 100644 --- a/test/jalview/ws/dbsources/UniprotTest.java +++ b/test/jalview/ws/dbsources/UniprotTest.java @@ -62,8 +62,7 @@ public class UniprotTest + "" + "" + "A9CKP4" - + "A9CKP5" - + "A9CKP4_AGRT5" + + "A9CKP5" + "A9CKP4_AGRT5" + "A9CKP4_AGRT6" + "Mitogen-activated protein kinase 13" + "" @@ -157,31 +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 @@ -215,19 +210,20 @@ 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().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()); + 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()); + res = DBRefUtils.searchRefsForSource(seq.getDBRefs(), + DBRefSource.UNIPROT); + assertEquals(2, res.size()); /* * NB this test fragile - relies on ordering being preserved */ @@ -250,8 +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)); } /**