X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FCrossRefTest.java;h=50f38b63111eb3ddf86ca9ef65d16431a0035480;hb=6405be60655fe096cdbff89cccf0a5b12f8b7e80;hp=0c3e4d5bda13bb133d00771f6722640165c863a7;hpb=f2e52ac07216e1fa3a5d1975e6afd6bc03d6a946;p=jalview.git diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java index 0c3e4d5..50f38b6 100644 --- a/test/jalview/analysis/CrossRefTest.java +++ b/test/jalview/analysis/CrossRefTest.java @@ -27,8 +27,9 @@ import static org.testng.AssertJUnit.assertNotSame; import static org.testng.AssertJUnit.assertNull; import static org.testng.AssertJUnit.assertSame; import static org.testng.AssertJUnit.assertTrue; -import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals; +import jalview.datamodel.AlignedCodonFrame; +import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.DBRefEntry; @@ -79,12 +80,11 @@ public class CrossRefTest * Just the protein refs: */ found = DBRefUtils.selectDbRefs(false, refs); - assertEquals(5, found.length); + assertEquals(3, found.length); assertSame(ref1, found[0]); assertSame(ref2, found[1]); - assertSame(ref3, found[2]); - assertSame(ref4, found[3]); - assertSame(ref9, found[4]); + assertSame(ref4, found[2]); + // assertSame(ref9, found[3]); ENSEMBL not protein } /** @@ -248,9 +248,14 @@ public class CrossRefTest * peptide sequence with UNIPROT dbref */ SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC"); - dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2")); + 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")); SequenceI pep1 = new Sequence("Q9ZTS2", "MLAVSRGQ"); + dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2"); pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2")); AlignmentI al = new Alignment(new SequenceI[] { dna1, pep1 }); @@ -259,76 +264,100 @@ public class CrossRefTest /* * first search for a dbref nowhere on the alignment: */ - DBRefEntry dbref = new DBRefEntry("UNIPROT", "0", "P30419"); + dbref = new DBRefEntry("UNIPROT", "0", "P30419"); CrossRef testee = new CrossRef(al.getSequencesArray(), al); - boolean found = testee.searchDataset(true, dna1, dbref, result, null, + AlignedCodonFrame acf = new AlignedCodonFrame(); + boolean found = testee.searchDataset(true, dna1, dbref, result, acf, true); assertFalse(found); assertTrue(result.isEmpty()); - - // TODO we are setting direct=true here but it is set to - // false in Jalview code... + assertTrue(acf.isEmpty()); /* * search for a protein sequence with dbref UNIPROT:Q9ZTS2 */ + acf = new AlignedCodonFrame(); dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2"); found = testee.searchDataset(!dna1.isProtein(), dna1, dbref, result, - null, false); // search dataset with a protein xref from a dna + acf, false); // 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)); + assertTrue(acf.isEmpty()); /* * search for a nucleotide sequence with dbref UNIPROT:Q9ZTS2 */ result.clear(); + acf = new AlignedCodonFrame(); dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2"); found = testee.searchDataset(!pep1.isProtein(), pep1, dbref, result, - null, false); // search dataset with a protein's direct dbref to + acf, false); // 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)); + // should now have a mapping from dna to pep1 + List mappings = acf.getMappings(); + assertEquals(1, mappings.size()); + SequenceToSequenceMapping mapping = mappings.get(0); + assertSame(dna1, mapping.getFromSeq()); + assertSame(pep1, mapping.getMapping().getTo()); + MapList mapList = mapping.getMapping().getMap(); + assertEquals(1, mapList.getToRatio()); + assertEquals(3, mapList.getFromRatio()); + assertEquals(1, mapList.getFromRanges().size()); + assertEquals(1, mapList.getFromRanges().get(0)[0]); + assertEquals(21, mapList.getFromRanges().get(0)[1]); + assertEquals(1, mapList.getToRanges().size()); + assertEquals(1, mapList.getToRanges().get(0)[0]); + assertEquals(7, mapList.getToRanges().get(0)[1]); } /** * Test for finding 'product' sequences for the case where the selected - * sequence has a dbref with a mapping to a sequence + * sequence has a dbref with a mapping to a sequence. This represents the case + * where either + * */ @Test(groups = { "Functional" }) public void testFindXrefSequences_fromDbRefMap() { /* - * two peptide sequences each with a DBRef and SequenceFeature + * scenario: nucleotide sequence AF039662 + * with dbref + mapping to Q9ZTS2 and P30419 + * which themselves each have a dbref and feature */ + SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC"); SequenceI pep1 = new Sequence("Q9ZTS2", "MALFQRSV"); - pep1.addDBRef(new DBRefEntry("Pfam", "0", "PF00111")); + SequenceI pep2 = new Sequence("P30419", "MTRRSQIF"); + dna1.createDatasetSequence(); + pep1.createDatasetSequence(); + pep2.createDatasetSequence(); + + pep1.getDatasetSequence().addDBRef( + new DBRefEntry("Pfam", "0", "PF00111")); pep1.addSequenceFeature(new SequenceFeature("type", "desc", 12, 14, 1f, "group")); - SequenceI pep2 = new Sequence("P30419", "MTRRSQIF"); - pep2.addDBRef(new DBRefEntry("PDB", "0", "3JTK")); + pep2.getDatasetSequence().addDBRef(new DBRefEntry("PDB", "0", "3JTK")); pep2.addSequenceFeature(new SequenceFeature("type2", "desc2", 13, 15, 12f, "group2")); - /* - * nucleotide sequence (to go in the alignment) - */ - SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC"); - - /* - * add DBRefEntry's to dna1 with mappings from dna to both peptides - */ MapList mapList = new MapList(new int[] { 1, 24 }, new int[] { 1, 3 }, 3, 1); Mapping map = new Mapping(pep1, mapList); DBRefEntry dbRef1 = new DBRefEntry("UNIPROT", "0", "Q9ZTS2", map); - dna1.addDBRef(dbRef1); + dna1.getDatasetSequence().addDBRef(dbRef1); mapList = new MapList(new int[] { 1, 24 }, new int[] { 1, 3 }, 3, 1); map = new Mapping(pep2, mapList); DBRefEntry dbRef2 = new DBRefEntry("UNIPROT", "0", "P30419", map); - dna1.addDBRef(dbRef2); + dna1.getDatasetSequence().addDBRef(dbRef2); /* * find UNIPROT xrefs for nucleotide sequence - it should pick up @@ -348,39 +377,21 @@ public class CrossRefTest } /** - * Helper method to assert seq1 looks like a copy of seq2 + * Helper method that verifies that 'copy' has the same name, start, end, + * sequence and dataset sequence object as 'original' (but is not the same + * object) * - * @param seq1 - * @param seq2 + * @param copy + * @param original */ - private void checkCopySequence(SequenceI seq1, SequenceI seq2) + private void checkCopySequence(SequenceI copy, SequenceI original) { - assertNotSame(seq1, seq2); - assertEquals(seq1.getName(), seq2.getName()); - assertEquals(seq1.getStart(), seq2.getStart()); - assertEquals(seq1.getEnd(), seq2.getEnd()); - assertEquals(seq1.getSequenceAsString(), seq2.getSequenceAsString()); - - /* - * compare dbrefs - */ - assertArrayEquals(seq1.getDBRefs(), seq2.getDBRefs()); - // check one to verify a copy, not the same object - if (seq1.getDBRefs().length > 0) - { - assertNotSame(seq1.getDBRefs()[0], seq2.getDBRefs()[0]); - } - - /* - * compare features - */ - assertArrayEquals(seq1.getSequenceFeatures(), - seq2.getSequenceFeatures()); - if (seq1.getSequenceFeatures().length > 0) - { - assertNotSame(seq1.getSequenceFeatures()[0], - seq2.getSequenceFeatures()[0]); - } + assertNotSame(copy, original); + assertSame(copy.getDatasetSequence(), original.getDatasetSequence()); + assertEquals(copy.getName(), original.getName()); + assertEquals(copy.getStart(), original.getStart()); + assertEquals(copy.getEnd(), original.getEnd()); + assertEquals(copy.getSequenceAsString(), original.getSequenceAsString()); } /** @@ -391,11 +402,14 @@ public class CrossRefTest public void testFindXrefSequences_withFetch() { SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC"); - dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2")); - dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "P30419")); - dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "P00314")); + 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")); + final SequenceI pep2 = new Sequence("P00314", "MRKLLAASG"); + pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "P00314")); /* * argument false suppresses adding DAS sources @@ -460,7 +474,7 @@ public class CrossRefTest * 'spliced transcript' with CDS ranges */ SequenceI braf002 = new Sequence("ENST00000497784", "gCAGGCtaTCTGTTCaa"); - braf002.addDBRef(new DBRefEntry("UNIPROT", "0", "H7C5K3")); + 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, @@ -472,8 +486,9 @@ public class CrossRefTest * which happens to be true for Uniprot,PDB,EMBL but not Pfam,Rfam,Ensembl */ final SequenceI pep1 = new Sequence("UNIPROT|P15056", "MAAL"); + pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "P15056")); final SequenceI pep2 = new Sequence("UNIPROT|H7C5K3", "QALF"); - + pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "H7C5K3")); /* * argument false suppresses adding DAS sources * todo: define an interface type SequenceFetcherI and mock that