X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FAlignmentTest.java;h=fe76df512f8244b9fc8b6c65a29ad35c3a29d164;hb=e562556addb433f911f65beba98b8d12d3f5a6b9;hp=ad1d3bf12015941b09bbb5499a9d18154b1c5a0f;hpb=2acdd7fdaa575dd5238585ad86597f808b30d281;p=jalview.git diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java index ad1d3bf..fe76df5 100644 --- a/test/jalview/datamodel/AlignmentTest.java +++ b/test/jalview/datamodel/AlignmentTest.java @@ -27,14 +27,18 @@ 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; import java.io.IOException; -import java.util.Collections; +import java.util.ArrayList; +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; @@ -99,6 +103,327 @@ 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"); + + } /* * Read in Stockholm format test data including secondary structure * annotations. @@ -180,12 +505,12 @@ public class AlignmentTest * Make mappings between sequences. The 'aligned cDNA' is playing the role * of what would normally be protein here. */ - makeMappings(al2, al1); + makeMappings(al1, al2); ((Alignment) al2).alignAs(al1, false, true); - assertEquals("GC-TC--GUC-GTA-CT", al2.getSequenceAt(0) + assertEquals("GC-TC--GUC-GTACT", al2.getSequenceAt(0) .getSequenceAsString()); - assertEquals("-GG-GTC--AGG---CAGT", al2.getSequenceAt(1) + assertEquals("-GG-GTC--AGG--CAGT", al2.getSequenceAt(1) .getSequenceAsString()); } @@ -202,38 +527,21 @@ public class AlignmentTest AlignmentI al2 = loadAlignment(AA_SEQS_1, "FASTA"); makeMappings(al1, al2); + // Fudge - alignProteinAsCdna expects mappings to be on protein + al2.getCodonFrames().addAll(al1.getCodonFrames()); + ((Alignment) al2).alignAs(al1, false, true); assertEquals("K-Q-Y-L-", al2.getSequenceAt(0).getSequenceAsString()); assertEquals("-R-F-P-W", al2.getSequenceAt(1).getSequenceAsString()); } /** - * Aligning protein from cDNA for a single sequence. This is the 'simple' case - * (as there is no need to compute codon 'alignments') but worth testing - * before tackling the multiple sequence case. - * - * @throws IOException - */ - @Test(groups = { "Functional" }) - public void testAlignAs_proteinAsCdna_singleSequence() throws IOException - { - /* - * simplest case remove all gaps - */ - verifyAlignAs(">protein\n-Q-K-\n", ">dna\nCAAaaa\n", "QK"); - - /* - * with sequence offsets - */ - verifyAlignAs(">protein/12-13\n-Q-K-\n", ">dna/20-25\nCAAaaa\n", "QK"); - } - - /** * Test aligning cdna as per protein alignment. * * @throws IOException */ - @Test(groups = { "Functional" }) + @Test(groups = { "Functional" }, enabled = true) + // TODO review / update this test after redesign of alignAs method public void testAlignAs_cdnaAsProtein() throws IOException { /* @@ -247,9 +555,9 @@ 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) + assertEquals("---CGT---TAACGA---AGT---", al1.getSequenceAt(1) .getSequenceAsString()); } @@ -258,7 +566,8 @@ public class AlignmentTest * * @throws IOException */ - @Test(groups = { "Functional" }) + @Test(groups = { "Functional" }, enabled = true) + // TODO review / update this test after redesign of alignAs method public void testAlignAs_cdnaAsProtein_singleSequence() throws IOException { /* @@ -307,32 +616,34 @@ public class AlignmentTest } /** - * Helper method to make mappings from protein to dna sequences, and add the - * mappings to the protein alignment + * Helper method to make mappings between sequences, and add the mappings to + * the 'mapped from' alignment * * @param alFrom * @param alTo */ public void makeMappings(AlignmentI alFrom, AlignmentI alTo) { - AlignmentI prot = !alFrom.isNucleotide() ? alFrom : alTo; - AlignmentI nuc = alFrom == prot ? alTo : alFrom; - int ratio = (alFrom.isNucleotide() == alTo.isNucleotide() ? 1 : 3); AlignedCodonFrame acf = new AlignedCodonFrame(); - for (int i = 0; i < nuc.getHeight(); i++) + for (int i = 0; i < alFrom.getHeight(); i++) { - SequenceI seqFrom = nuc.getSequenceAt(i); - SequenceI seqTo = prot.getSequenceAt(i); + SequenceI seqFrom = alFrom.getSequenceAt(i); + SequenceI seqTo = alTo.getSequenceAt(i); MapList ml = new MapList(new int[] { seqFrom.getStart(), seqFrom.getEnd() }, new int[] { seqTo.getStart(), seqTo.getEnd() }, ratio, 1); acf.addMap(seqFrom, seqTo, ml); } - prot.addCodonFrame(acf); + /* + * not sure whether mappings 'belong' or protein or nucleotide + * alignment, so adding to both ;~) + */ + alFrom.addCodonFrame(acf); + alTo.addCodonFrame(acf); } /** @@ -341,7 +652,8 @@ public class AlignmentTest * * @throws IOException */ - @Test(groups = { "Functional" }) + @Test(groups = { "Functional" }, enabled = false) + // TODO review / update this test after redesign of alignAs method public void testAlignAs_dnaAsProtein_withIntrons() throws IOException { /* @@ -349,14 +661,13 @@ public class AlignmentTest */ String dna1 = "A-Aa-gG-GCC-cT-TT"; String dna2 = "c--CCGgg-TT--T-AA-A"; - AlignmentI al1 = loadAlignment(">Seq1/6-17\n" + dna1 - + "\n>Seq2/20-31\n" + dna2 + "\n", "FASTA"); + AlignmentI al1 = loadAlignment(">Dna1/6-17\n" + dna1 + + "\n>Dna2/20-31\n" + dna2 + "\n", "FASTA"); AlignmentI al2 = loadAlignment( - ">Seq1/7-9\n-P--YK\n>Seq2/11-13\nG-T--F\n", "FASTA"); + ">Pep1/7-9\n-P--YK\n>Pep2/11-13\nG-T--F\n", "FASTA"); AlignedCodonFrame acf = new AlignedCodonFrame(); // Seq1 has intron at dna positions 3,4,9 so splice is AAG GCC TTT // Seq2 has intron at dna positions 1,5,6 so splice is CCG TTT AAA - // TODO sequence offsets MapList ml1 = new MapList(new int[] { 6, 7, 10, 13, 15, 17 }, new int[] { 7, 9 }, 3, 1); acf.addMap(al1.getSequenceAt(0), al2.getSequenceAt(0), ml1); @@ -397,7 +708,9 @@ public class AlignmentTest // create sequence and alignment datasets protein.setDataset(null); AlignedCodonFrame acf = new AlignedCodonFrame(); - protein.getDataset().setCodonFrames(Collections.singleton(acf)); + List acfList = Arrays.asList(new AlignedCodonFrame[] + { acf }); + protein.getDataset().setCodonFrames(acfList); AlignmentI copy = new Alignment(protein); /* @@ -413,6 +726,8 @@ 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()); } @@ -451,8 +766,7 @@ public class AlignmentTest // TODO promote this method to AlignmentI ((Alignment) protein).createDatasetAlignment(); - // TODO this method should return AlignmentI not Alignment !! - Alignment ds = protein.getDataset(); + AlignmentI ds = protein.getDataset(); // side-effect: dataset created on second sequence assertNotNull(protein.getSequenceAt(1).getDatasetSequence()); @@ -468,4 +782,130 @@ public class AlignmentTest // prove the codon frames are indeed on the dataset: 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() + { + AlignmentI align = new Alignment(new SequenceI[] {}); + AlignedCodonFrame acf = new AlignedCodonFrame(); + align.addCodonFrame(acf); + assertEquals(1, align.getCodonFrames().size()); + assertTrue(align.getCodonFrames().contains(acf)); + // can't add the same object twice: + align.addCodonFrame(acf); + assertEquals(1, align.getCodonFrames().size()); + + // create dataset alignment - mappings move to dataset + ((Alignment) align).createDatasetAlignment(); + assertSame(align.getCodonFrames(), align.getDataset().getCodonFrames()); + assertEquals(1, align.getCodonFrames().size()); + + AlignedCodonFrame acf2 = new AlignedCodonFrame(); + align.addCodonFrame(acf2); + assertTrue(align.getDataset().getCodonFrames().contains(acf)); + } + + @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"); + AlignmentI align = new Alignment(new SequenceI[] { seq }); + ArrayList hiddenCols = new ArrayList(); + + int[] startEnd = align.getVisibleStartAndEndIndex(hiddenCols); + assertEquals(0, startEnd[0]); + assertEquals(25, startEnd[1]); + + hiddenCols.add(new int[] { 0, 0 }); + startEnd = align.getVisibleStartAndEndIndex(hiddenCols); + assertEquals(1, startEnd[0]); + assertEquals(25, startEnd[1]); + + hiddenCols.add(new int[] { 6, 9 }); + hiddenCols.add(new int[] { 11, 12 }); + startEnd = align.getVisibleStartAndEndIndex(hiddenCols); + assertEquals(1, startEnd[0]); + assertEquals(25, startEnd[1]); + + hiddenCols.add(new int[] { 24, 25 }); + startEnd = align.getVisibleStartAndEndIndex(hiddenCols); + System.out.println(startEnd[0] + " : " + startEnd[1]); + assertEquals(1, startEnd[0]); + assertEquals(23, startEnd[1]); + } }