X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FAlignmentTest.java;h=7958e9bea5be0c232f8f28b162bf2f3ee351ef5f;hb=8546ee20c998cd48567d324027d1885a771e688f;hp=5753e9799cd8c1c1b3936d9c203c48681bc64a77;hpb=36dceb54710feb97a81f4bd69ad051f316141dc3;p=jalview.git diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java index 5753e97..7958e9b 100644 --- a/test/jalview/datamodel/AlignmentTest.java +++ b/test/jalview/datamodel/AlignmentTest.java @@ -27,6 +27,7 @@ import static org.testng.AssertJUnit.assertNull; import static org.testng.AssertJUnit.assertSame; import static org.testng.AssertJUnit.assertTrue; +import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping; import jalview.io.AppletFormatAdapter; import jalview.io.FormatAdapter; import jalview.util.MapList; @@ -37,6 +38,7 @@ import java.util.Arrays; import java.util.Iterator; import java.util.List; +import org.testng.Assert; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; @@ -101,6 +103,473 @@ public class AlignmentTest return a; } + /** + * assert wrapper: tests all references in the given alignment are consistent + * + * @param alignment + */ + public static void assertAlignmentDatasetRefs(AlignmentI alignment) + { + verifyAlignmentDatasetRefs(alignment, true, null); + } + + /** + * assert wrapper: tests all references in the given alignment are consistent + * + * @param alignment + * @param message + * - prefixed to any assert failed messages + */ + public static void assertAlignmentDatasetRefs(AlignmentI alignment, + String message) + { + verifyAlignmentDatasetRefs(alignment, true, message); + } + + /** + * verify sequence and dataset references are properly contained within + * dataset + * + * @param alignment + * - the alignmentI object to verify (either alignment or dataset) + * @param raiseAssert + * - when set, testng assertions are raised. + * @param message + * - null or a string message to prepend to the assert failed + * messages. + * @return true if alignment references were in order, otherwise false. + */ + public static boolean verifyAlignmentDatasetRefs(AlignmentI alignment, + boolean raiseAssert, String message) + { + if (message == null) + { + message = ""; + } + if (alignment == null) + { + if (raiseAssert) + { + Assert.fail(message + "Alignment for verification was null."); + } + return false; + } + if (alignment.getDataset() != null) + { + AlignmentI dataset = alignment.getDataset(); + // check all alignment sequences have their dataset within the dataset + for (SequenceI seq : alignment.getSequences()) + { + SequenceI seqds = seq.getDatasetSequence(); + if (seqds.getDatasetSequence() != null) + { + if (raiseAssert) + { + Assert.fail(message + + " Alignment contained a sequence who's dataset sequence has a second dataset reference."); + } + return false; + } + if (dataset.findIndex(seqds) == -1) + { + if (raiseAssert) + { + Assert.fail(message + + " Alignment contained a sequence who's dataset sequence was not in the dataset."); + } + return false; + } + } + return verifyAlignmentDatasetRefs(alignment.getDataset(), + raiseAssert, message); + } + else + { + int dsp = -1; + // verify all dataset sequences + for (SequenceI seqds : alignment.getSequences()) + { + dsp++; + if (seqds.getDatasetSequence() != null) + { + if (raiseAssert) + { + Assert.fail(message + + " Dataset contained a sequence with non-null dataset reference (ie not a dataset sequence!)"); + } + return false; + } + int foundp = alignment.findIndex(seqds); + if (foundp != dsp) + { + if (raiseAssert) + { + Assert.fail(message + + " Dataset sequence array contains a reference at " + + dsp + " to a sequence first seen at " + foundp + " (" + + seqds.toString() + ")"); + } + return false; + } + if (seqds.getDBRefs() != null) + { + for (DBRefEntry dbr : seqds.getDBRefs()) + { + if (dbr.getMap() != null) + { + SequenceI seqdbrmapto = dbr.getMap().getTo(); + if (seqdbrmapto != null) + { + if (seqdbrmapto.getDatasetSequence() != null) + { + if (raiseAssert) + { + Assert.fail(message + + " DBRefEntry for sequence in alignment had map to sequence which was not a dataset sequence"); + } + return false; + + } + if (alignment.findIndex(dbr.getMap().getTo()) == -1) + { + if (raiseAssert) + { + Assert.fail(message + + " DBRefEntry for sequence in alignment had map to sequence not in dataset"); + } + return false; + } + } + } + } + } + } + // finally, verify codonmappings involve only dataset sequences. + if (alignment.getCodonFrames() != null) + { + for (AlignedCodonFrame alc : alignment.getCodonFrames()) + { + for (SequenceToSequenceMapping ssm : alc.getMappings()) + { + if (ssm.getFromSeq().getDatasetSequence() != null) + { + if (raiseAssert) + { + Assert.fail(message + + " CodonFrame-SSM-FromSeq is not a dataset sequence"); + } + return false; + } + if (alignment.findIndex(ssm.getFromSeq()) == -1) + { + + if (raiseAssert) + { + Assert.fail(message + + " CodonFrame-SSM-FromSeq is not contained in dataset"); + } + return false; + } + if (ssm.getMapping().getTo().getDatasetSequence() != null) + { + if (raiseAssert) + { + Assert.fail(message + + " CodonFrame-SSM-Mapping-ToSeq is not a dataset sequence"); + } + return false; + } + if (alignment.findIndex(ssm.getMapping().getTo()) == -1) + { + + if (raiseAssert) + { + Assert.fail(message + + " CodonFrame-SSM-Mapping-ToSeq is not contained in dataset"); + } + return false; + } + } + } + } + } + return true; // all relationships verified! + } + + /** + * call verifyAlignmentDatasetRefs with and without assertion raising enabled, + * to check expected pass/fail actually occurs in both conditions + * + * @param al + * @param expected + * @param msg + */ + private void assertVerifyAlignment(AlignmentI al, boolean expected, + String msg) + { + if (expected) + { + try + { + + Assert.assertTrue(verifyAlignmentDatasetRefs(al, true, null), + "Valid test alignment failed when raiseAsserts enabled:" + + msg); + } catch (AssertionError ae) + { + ae.printStackTrace(); + Assert.fail( + "Valid test alignment raised assertion errors when raiseAsserts enabled: " + + msg, ae); + } + // also check validation passes with asserts disabled + Assert.assertTrue(verifyAlignmentDatasetRefs(al, false, null), + "Valid test alignment tested false when raiseAsserts disabled:" + + msg); + } + else + { + boolean assertRaised = false; + try + { + verifyAlignmentDatasetRefs(al, true, null); + } catch (AssertionError ae) + { + // expected behaviour + assertRaised = true; + } + if (!assertRaised) + { + Assert.fail("Invalid test alignment passed when raiseAsserts enabled:" + + msg); + } + // also check validation passes with asserts disabled + Assert.assertFalse(verifyAlignmentDatasetRefs(al, false, null), + "Invalid test alignment tested true when raiseAsserts disabled:" + + msg); + } + } + + @Test(groups = { "Functional" }) + public void testVerifyAlignmentDatasetRefs() + { + SequenceI sq1 = new Sequence("sq1", "ASFDD"), sq2 = new Sequence("sq2", + "TTTTTT"); + + // construct simple valid alignment dataset + Alignment al = new Alignment(new SequenceI[] { sq1, sq2 }); + // expect this to pass + assertVerifyAlignment(al, true, "Simple valid alignment didn't verify"); + + // check test for sequence->datasetSequence validity + sq1.setDatasetSequence(sq2); + assertVerifyAlignment(al, false, + "didn't detect dataset sequence with a dataset sequence reference."); + + sq1.setDatasetSequence(null); + assertVerifyAlignment( + al, + true, + "didn't reinstate validity after nulling dataset sequence dataset reference"); + + // now create dataset and check again + al.createDatasetAlignment(); + assertNotNull(al.getDataset()); + + assertVerifyAlignment(al, true, + "verify failed after createDatasetAlignment"); + + // create a dbref on sq1 with a sequence ref to sq2 + DBRefEntry dbrs1tos2 = new DBRefEntry("UNIPROT", "1", "Q111111"); + dbrs1tos2.setMap(new Mapping(sq2.getDatasetSequence(), + new int[] { 1, 5 }, new int[] { 2, 6 }, 1, 1)); + sq1.getDatasetSequence().addDBRef(dbrs1tos2); + assertVerifyAlignment(al, true, + "verify failed after addition of valid DBRefEntry/map"); + // now create a dbref on a new sequence which maps to another sequence + // outside of the dataset + SequenceI sqout = new Sequence("sqout", "ututututucagcagcag"), sqnew = new Sequence( + "sqnew", "EEERRR"); + DBRefEntry sqnewsqout = new DBRefEntry("ENAFOO", "1", "R000001"); + sqnewsqout.setMap(new Mapping(sqout, new int[] { 1, 6 }, new int[] { 1, + 18 }, 1, 3)); + al.getDataset().addSequence(sqnew); + + assertVerifyAlignment(al, true, + "verify failed after addition of new sequence to dataset"); + // now start checking exception conditions + sqnew.addDBRef(sqnewsqout); + assertVerifyAlignment( + al, + false, + "verify passed when a dbref with map to sequence outside of dataset was added"); + // make the verify pass by adding the outsider back in + al.getDataset().addSequence(sqout); + assertVerifyAlignment(al, true, + "verify should have passed after adding dbref->to sequence in to dataset"); + // and now the same for a codon mapping... + SequenceI sqanotherout = new Sequence("sqanotherout", + "aggtutaggcagcagcag"); + + AlignedCodonFrame alc = new AlignedCodonFrame(); + alc.addMap(sqanotherout, sqnew, new MapList(new int[] { 1, 6 }, + new int[] { 1, 18 }, 3, 1)); + + al.addCodonFrame(alc); + Assert.assertEquals(al.getDataset().getCodonFrames().size(), 1); + + assertVerifyAlignment( + al, + false, + "verify passed when alCodonFrame mapping to sequence outside of dataset was added"); + // make the verify pass by adding the outsider back in + al.getDataset().addSequence(sqanotherout); + assertVerifyAlignment( + al, + true, + "verify should have passed once all sequences involved in alCodonFrame were added to dataset"); + al.getDataset().addSequence(sqanotherout); + assertVerifyAlignment(al, false, + "verify should have failed when a sequence was added twice to the dataset"); + al.getDataset().deleteSequence(sqanotherout); + assertVerifyAlignment(al, true, + "verify should have passed after duplicate entry for sequence was removed"); + } + + /** + * checks that the sequence data for an alignment's dataset is non-redundant. + * Fails if there are sequences with same id, sequence, start, and. + */ + + public static void assertDatasetIsNormalised(AlignmentI al) + { + assertDatasetIsNormalised(al, null); + } + + /** + * checks that the sequence data for an alignment's dataset is non-redundant. + * Fails if there are sequences with same id, sequence, start, and. + * + * @param al + * - alignment to verify + * @param message + * - null or message prepended to exception message. + */ + public static void assertDatasetIsNormalised(AlignmentI al, String message) + { + if (al.getDataset() != null) + { + assertDatasetIsNormalised(al.getDataset(), message); + return; + } + /* + * look for pairs of sequences with same ID, start, end, and sequence + */ + List seqSet = al.getSequences(); + for (int p = 0; p < seqSet.size(); p++) + { + SequenceI pSeq = seqSet.get(p); + for (int q = p + 1; q < seqSet.size(); q++) + { + SequenceI qSeq = seqSet.get(q); + if (pSeq.getStart() != qSeq.getStart()) + { + continue; + } + if (pSeq.getEnd() != qSeq.getEnd()) + { + continue; + } + if (!pSeq.getName().equals(qSeq.getName())) + { + continue; + } + if (!Arrays.equals(pSeq.getSequence(), qSeq.getSequence())) + { + continue; + } + Assert.fail((message == null ? "" : message + " :") + + "Found similar sequences at position " + p + " and " + q + + "\n" + pSeq.toString()); + } + } + } + + @Test(groups = { "Functional", "Asserts" }) + public void testAssertDatasetIsNormalised() + { + Sequence sq1 = new Sequence("s1/1-4", "asdf"); + Sequence sq1shift = new Sequence("s1/2-5", "asdf"); + Sequence sq1seqd = new Sequence("s1/1-4", "asdt"); + Sequence sq2 = new Sequence("s2/1-4", "asdf"); + Sequence sq1dup = new Sequence("s1/1-4", "asdf"); + + Alignment al = new Alignment(new SequenceI[] { sq1 }); + al.setDataset(null); + + try + { + assertDatasetIsNormalised(al); + } catch (AssertionError ae) + { + Assert.fail("Single sequence should be valid normalised dataset."); + } + al.addSequence(sq2); + try + { + assertDatasetIsNormalised(al); + } catch (AssertionError ae) + { + Assert.fail("Two different sequences should be valid normalised dataset."); + } + /* + * now change sq2's name in the alignment. should still be valid + */ + al.findName(sq2.getName()).setName("sq1"); + try + { + assertDatasetIsNormalised(al); + } catch (AssertionError ae) + { + Assert.fail("Two different sequences in dataset, but same name in alignment, should be valid normalised dataset."); + } + + al.addSequence(sq1seqd); + try + { + assertDatasetIsNormalised(al); + } catch (AssertionError ae) + { + Assert.fail("sq1 and sq1 with different sequence should be distinct."); + } + + al.addSequence(sq1shift); + try + { + assertDatasetIsNormalised(al); + } catch (AssertionError ae) + { + Assert.fail("sq1 and sq1 with different start/end should be distinct."); + } + /* + * finally, the failure case + */ + al.addSequence(sq1dup); + boolean ssertRaised = false; + try + { + assertDatasetIsNormalised(al); + + } catch (AssertionError ae) + { + ssertRaised = true; + } + if (!ssertRaised) + { + Assert.fail("Expected identical sequence to raise exception."); + } + } + /* * Read in Stockholm format test data including secondary structure * annotations. @@ -217,7 +686,7 @@ public class AlignmentTest * * @throws IOException */ - @Test(groups = { "Functional" }, enabled = false) + @Test(groups = { "Functional" }, enabled = true) // TODO review / update this test after redesign of alignAs method public void testAlignAs_cdnaAsProtein() throws IOException { @@ -232,7 +701,7 @@ public class AlignmentTest * Realign DNA; currently keeping existing gaps in introns only */ ((Alignment) al1).alignAs(al2, false, true); - assertEquals("ACG---GCUCCA------ACT", al1.getSequenceAt(0) + assertEquals("ACG---GCUCCA------ACT---", al1.getSequenceAt(0) .getSequenceAsString()); assertEquals("---CGT---TAACGA---AGT---", al1.getSequenceAt(1) .getSequenceAsString()); @@ -243,7 +712,7 @@ public class AlignmentTest * * @throws IOException */ - @Test(groups = { "Functional" }, enabled = false) + @Test(groups = { "Functional" }, enabled = true) // TODO review / update this test after redesign of alignAs method public void testAlignAs_cdnaAsProtein_singleSequence() throws IOException { @@ -315,7 +784,12 @@ public class AlignmentTest acf.addMap(seqFrom, seqTo, ml); } + /* + * not sure whether mappings 'belong' or protein or nucleotide + * alignment, so adding to both ;~) + */ alFrom.addCodonFrame(acf); + alTo.addCodonFrame(acf); } /** @@ -398,6 +872,8 @@ public class AlignmentTest // TODO should the copy constructor copy the dataset? // or make a new one referring to the same dataset sequences?? assertNull(copy.getDataset()); + // TODO test metadata is copied when AlignmentI is a dataset + // assertArrayEquals(copy.getDataset().getSequencesArray(), protein // .getDataset().getSequencesArray()); } @@ -453,6 +929,60 @@ public class AlignmentTest assertTrue(ds.getCodonFrames().contains(acf)); } + /** + * tests the addition of *all* sequences referred to by a sequence being added + * to the dataset + */ + @Test(groups = "Functional") + public void testCreateDatasetAlignmentWithMappedToSeqs() + { + // Alignment with two sequences, gapped. + SequenceI sq1 = new Sequence("sq1", "A--SDF"); + SequenceI sq2 = new Sequence("sq2", "G--TRQ"); + + // cross-references to two more sequences. + DBRefEntry dbr = new DBRefEntry("SQ1", "", "sq3"); + SequenceI sq3 = new Sequence("sq3", "VWANG"); + dbr.setMap(new Mapping(sq3, new MapList(new int[] { 1, 4 }, new int[] { + 2, 5 }, 1, 1))); + sq1.addDBRef(dbr); + + SequenceI sq4 = new Sequence("sq4", "ERKWI"); + DBRefEntry dbr2 = new DBRefEntry("SQ2", "", "sq4"); + dbr2.setMap(new Mapping(sq4, new MapList(new int[] { 1, 4 }, new int[] { + 2, 5 }, 1, 1))); + sq2.addDBRef(dbr2); + // and a 1:1 codonframe mapping between them. + AlignedCodonFrame alc = new AlignedCodonFrame(); + alc.addMap(sq1, sq2, new MapList(new int[] { 1, 4 }, + new int[] { 1, 4 }, 1, 1)); + + AlignmentI protein = new Alignment(new SequenceI[] { sq1, sq2 }); + + /* + * create the alignment dataset + * note this creates sequence datasets where missing + * as a side-effect (in this case, on seq2 + */ + + // TODO promote this method to AlignmentI + ((Alignment) protein).createDatasetAlignment(); + + AlignmentI ds = protein.getDataset(); + + // should be 4 sequences in dataset - two materialised, and two propagated + // from dbref + assertEquals(4, ds.getHeight()); + assertTrue(ds.getSequences().contains(sq1.getDatasetSequence())); + assertTrue(ds.getSequences().contains(sq2.getDatasetSequence())); + assertTrue(ds.getSequences().contains(sq3)); + assertTrue(ds.getSequences().contains(sq4)); + // Should have one codon frame mapping between sq1 and sq2 via dataset + // sequences + assertEquals(ds.getCodonFrame(sq1.getDatasetSequence()), + ds.getCodonFrame(sq2.getDatasetSequence())); + } + @Test(groups = "Functional") public void testAddCodonFrame() { @@ -476,6 +1006,28 @@ public class AlignmentTest } @Test(groups = "Functional") + public void testAddSequencePreserveDatasetIntegrity() + { + Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ"); + Alignment align = new Alignment(new SequenceI[] { seq }); + align.createDatasetAlignment(); + AlignmentI ds = align.getDataset(); + SequenceI copy = new Sequence(seq); + copy.insertCharAt(3, 5, '-'); + align.addSequence(copy); + Assert.assertEquals(align.getDataset().getHeight(), 1, + "Dataset shouldn't have more than one sequence."); + + Sequence seq2 = new Sequence("newtestSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ"); + align.addSequence(seq2); + Assert.assertEquals(align.getDataset().getHeight(), 2, + "Dataset should now have two sequences."); + + assertAlignmentDatasetRefs(align, + "addSequence broke dataset reference integrity"); + } + + @Test(groups = "Functional") public void getVisibleStartAndEndIndexTest() { Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ"); @@ -503,4 +1055,68 @@ public class AlignmentTest assertEquals(1, startEnd[0]); assertEquals(23, startEnd[1]); } + + /** + * Tests that dbrefs with mappings to sequence get updated if the sequence + * acquires a dataset sequence + */ + @Test(groups = "Functional") + public void testCreateDataset_updateDbrefMappings() + { + SequenceI pep = new Sequence("pep", "ASD"); + SequenceI dna = new Sequence("dna", "aaaGCCTCGGATggg"); + SequenceI cds = new Sequence("cds", "GCCTCGGAT"); + + // add dbref from dna to peptide + DBRefEntry dbr = new DBRefEntry("UNIPROT", "", "pep"); + dbr.setMap(new Mapping(pep, new MapList(new int[] { 4, 15 }, new int[] { + 1, 4 }, 3, 1))); + dna.addDBRef(dbr); + + // add dbref from dna to peptide + DBRefEntry dbr2 = new DBRefEntry("UNIPROT", "", "pep"); + dbr2.setMap(new Mapping(pep, new MapList(new int[] { 1, 12 }, new int[] + { 1, 4 }, 3, 1))); + cds.addDBRef(dbr2); + + // add dbref from peptide to dna + DBRefEntry dbr3 = new DBRefEntry("EMBL", "", "dna"); + dbr3.setMap(new Mapping(dna, new MapList(new int[] { 1, 4 }, new int[] { + 4, 15 }, 1, 3))); + pep.addDBRef(dbr3); + + // add dbref from peptide to cds + DBRefEntry dbr4 = new DBRefEntry("EMBLCDS", "", "cds"); + dbr4.setMap(new Mapping(cds, new MapList(new int[] { 1, 4 }, new int[] { + 1, 12 }, 1, 3))); + pep.addDBRef(dbr4); + + AlignmentI protein = new Alignment(new SequenceI[] { pep }); + + /* + * create the alignment dataset + */ + ((Alignment) protein).createDatasetAlignment(); + + AlignmentI ds = protein.getDataset(); + + // should be 3 sequences in dataset + assertEquals(3, ds.getHeight()); + assertTrue(ds.getSequences().contains(pep.getDatasetSequence())); + assertTrue(ds.getSequences().contains(dna)); + assertTrue(ds.getSequences().contains(cds)); + + /* + * verify peptide.cdsdbref.peptidedbref is now mapped to peptide dataset + */ + DBRefEntry[] dbRefs = pep.getDBRefs(); + assertEquals(2, dbRefs.length); + assertSame(dna, dbRefs[0].map.to); + assertSame(cds, dbRefs[1].map.to); + assertEquals(1, dna.getDBRefs().length); + assertSame(pep.getDatasetSequence(), dna.getDBRefs()[0].map.to); + assertEquals(1, cds.getDBRefs().length); + assertSame(pep.getDatasetSequence(), cds.getDBRefs()[0].map.to); + } + }