X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FCrossRefTest.java;h=c5f956b88836b826b59eb244afd5cc9d5a4cd282;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=9a0d610affea7e861bec1c8696af825402ab296d;hpb=49db0dff1da16c3355b43a41498c1fc93ef47e91;p=jalview.git diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java index 9a0d610..c5f956b 100644 --- a/test/jalview/analysis/CrossRefTest.java +++ b/test/jalview/analysis/CrossRefTest.java @@ -73,8 +73,9 @@ 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"); - List refs = Arrays.asList(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: @@ -141,7 +142,7 @@ public class CrossRefTest * 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"); @@ -261,8 +262,9 @@ public class CrossRefTest * peptide sequence with UNIPROT dbref */ SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC"); - Mapping map = new Mapping(new Sequence("pep2", "MLAVSRG"), new MapList( - new int[] { 1, 21 }, new int[] { 1, 7 }, 3, 1)); + Mapping map = new Mapping(new Sequence("pep2", "MLAVSRG"), + new MapList(new int[] + { 1, 21 }, new int[] { 1, 7 }, 3, 1)); DBRefEntry dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2", map); dna1.addDBRef(dbref); dna1.addDBRef(new DBRefEntry("EMBL", "0", "AF039662")); @@ -291,8 +293,9 @@ public class CrossRefTest acf = new AlignedCodonFrame(); dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2"); found = testee.searchDataset(!dna1.isProtein(), dna1, dbref, result, - acf, false, DBRefUtils.SEARCH_MODE_FULL); // search dataset with a protein xref from a dna - // sequence to locate the protein product + 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()); assertSame(pep1, result.get(0)); @@ -305,8 +308,10 @@ public class CrossRefTest acf = new AlignedCodonFrame(); dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2"); found = testee.searchDataset(!pep1.isProtein(), pep1, dbref, result, - acf, false, DBRefUtils.SEARCH_MODE_FULL); // search dataset with a protein's direct dbref to - // locate dna sequences with matching xref + 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()); assertSame(dna1, result.get(0)); @@ -353,13 +358,13 @@ public class CrossRefTest pep1.createDatasetSequence(); pep2.createDatasetSequence(); - pep1.getDatasetSequence().addDBRef( - new DBRefEntry("Pfam", "0", "PF00111")); - pep1.addSequenceFeature(new SequenceFeature("type", "desc", 12, 14, 1f, - "group")); + pep1.getDatasetSequence() + .addDBRef(new DBRefEntry("Pfam", "0", "PF00111")); + pep1.addSequenceFeature( + new SequenceFeature("type", "desc", 12, 14, 1f, "group")); pep2.getDatasetSequence().addDBRef(new DBRefEntry("PDB", "0", "3JTK")); - pep2.addSequenceFeature(new SequenceFeature("type2", "desc2", 13, 15, - 12f, "group2")); + pep2.addSequenceFeature( + new SequenceFeature("type2", "desc2", 13, 15, 12f, "group2")); MapList mapList = new MapList(new int[] { 1, 24 }, new int[] { 1, 3 }, 3, 1); @@ -403,7 +408,8 @@ public class CrossRefTest assertEquals(copy.getName(), original.getName()); assertEquals(copy.getStart(), original.getStart()); assertEquals(copy.getEnd(), original.getEnd()); - assertEquals(copy.getSequenceAsString(), original.getSequenceAsString()); + assertEquals(copy.getSequenceAsString(), + original.getSequenceAsString()); } /** @@ -413,15 +419,21 @@ public class CrossRefTest @Test(groups = { "Functional_Failing" }) public void testFindXrefSequences_withFetch() { + // JBPNote: this fails because pep1 and pep2 do not have DbRefEntrys with + // mappings + // Fix#1 would be to revise the test data so it fits with 2.11.2+ Jalview + // assumptions + // that ENA retrievals yield dbrefs with Mappings + SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC"); dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "Q9ZTS2")); dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "P30419")); dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "P00314")); final SequenceI pep1 = new Sequence("Q9ZTS2", "MYQLIRSSW"); - pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2")); + pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2", null, true)); final SequenceI pep2 = new Sequence("P00314", "MRKLLAASG"); - pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "P00314")); + pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "P00314", null, true)); /* * argument false suppresses adding DAS sources @@ -477,20 +489,22 @@ public class CrossRefTest /* * 'transcript' with CDS feature (supports mapping to protein) */ - SequenceI braf001 = new Sequence("ENST00000288602", "taagATGGCGGCGCTGa"); + SequenceI braf001 = new Sequence("ENST00000288602", + "taagATGGCGGCGCTGa"); braf001.addDBRef(new DBRefEntry("UNIPROT", "0", "P15056")); - braf001.addSequenceFeature(new SequenceFeature("CDS", "", 5, 16, 0f, - null)); + braf001.addSequenceFeature( + new SequenceFeature("CDS", "", 5, 16, 0f, null)); /* * 'spliced transcript' with CDS ranges */ - SequenceI braf002 = new Sequence("ENST00000497784", "gCAGGCtaTCTGTTCaa"); + SequenceI braf002 = new Sequence("ENST00000497784", + "gCAGGCtaTCTGTTCaa"); braf002.addDBRef(new DBRefEntry("UNIPROT", "ENSEMBL|0", "H7C5K3")); - braf002.addSequenceFeature(new SequenceFeature("CDS", "", 2, 6, 0f, - null)); - braf002.addSequenceFeature(new SequenceFeature("CDS", "", 9, 15, 0f, - null)); + braf002.addSequenceFeature( + new SequenceFeature("CDS", "", 2, 6, 0f, null)); + braf002.addSequenceFeature( + new SequenceFeature("CDS", "", 9, 15, 0f, null)); /* * TODO code is fragile - use of SequenceIdMatcher depends on fetched @@ -587,7 +601,8 @@ public class CrossRefTest /* * J03321 with mappings to P0CE19 and P0CE20 */ - final SequenceI j03321 = new Sequence("EMBL|J03321", "AAACCCTTTGGGAAAA"); + final SequenceI j03321 = new Sequence("EMBL|J03321", + "AAACCCTTTGGGAAAA"); DBRefEntry dbref1 = new DBRefEntry("UNIPROT", "0", "P0CE19"); MapList mapList = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1); @@ -610,12 +625,14 @@ public class CrossRefTest DBRefEntry dbref3 = new DBRefEntry("UNIPROT", "0", "P0CE19"); MapList map2 = new MapList(new int[] { 4, 15 }, new int[] { 1, 4 }, 3, 1); - dbref3.setMap(new Mapping(new Sequence("UNIPROT|P0CE19", "KPFG"), map2)); + dbref3.setMap( + new Mapping(new Sequence("UNIPROT|P0CE19", "KPFG"), map2)); x06707.addDBRef(dbref3); DBRefEntry dbref4 = new DBRefEntry("UNIPROT", "0", "P0CE20"); MapList map3 = new MapList(new int[] { 4, 15 }, new int[] { 1, 4 }, 3, 1); - dbref4.setMap(new Mapping(new Sequence("UNIPROT|P0CE20", "PFGK"), map3)); + dbref4.setMap( + new Mapping(new Sequence("UNIPROT|P0CE20", "PFGK"), map3)); x06707.addDBRef(dbref4); /* @@ -719,7 +736,7 @@ public class CrossRefTest /* * verify dbrefs on EMBL are mapped to alignment seqs */ - + assertSame(p0ce19, j03321.getDBRefs().get(0).getMap().getTo()); assertSame(p0ce20, j03321.getDBRefs().get(1).getMap().getTo()); assertSame(p0ce19, x06707.getDBRefs().get(0).getMap().getTo()); @@ -743,8 +760,8 @@ public class CrossRefTest assertFalse(CrossRef.sameSequence(null, seq1)); assertTrue(CrossRef.sameSequence(seq1, new Sequence("seq2", "ABCDEF"))); assertTrue(CrossRef.sameSequence(seq1, new Sequence("seq2", "abcdef"))); - assertFalse(CrossRef - .sameSequence(seq1, new Sequence("seq2", "ABCDE-F"))); + assertFalse( + CrossRef.sameSequence(seq1, new Sequence("seq2", "ABCDE-F"))); assertFalse(CrossRef.sameSequence(seq1, new Sequence("seq2", "BCDEF"))); } }