X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FAlignmentTest.java;h=06be9827351abb9fa78eb8db379551f2d2f1bbbd;hp=915d860017f613bee10c3af5119bc58e365dbf87;hb=391467e57959e2c71a5051de06da2028dc07f2ba;hpb=dedd44136e37982fc2c713ae229b5a97a9b0b639 diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java index 915d860..06be982 100644 --- a/test/jalview/datamodel/AlignmentTest.java +++ b/test/jalview/datamodel/AlignmentTest.java @@ -27,21 +27,26 @@ 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.ArrayList; import java.util.Arrays; import java.util.Iterator; import java.util.List; import org.testng.Assert; +import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; +import jalview.analysis.AlignmentGenerator; +import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping; +import jalview.gui.JvOptionPane; +import jalview.io.DataSourceType; +import jalview.io.FileFormat; +import jalview.io.FileFormatI; +import jalview.io.FormatAdapter; +import jalview.util.Comparison; +import jalview.util.MapList; + /** * Unit tests for Alignment datamodel. * @@ -50,6 +55,14 @@ import org.testng.annotations.Test; */ public class AlignmentTest { + + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + // @formatter:off private static final String TEST_DATA = "# STOCKHOLM 1.0\n" + @@ -94,11 +107,11 @@ public class AlignmentTest * @return * @throws IOException */ - protected AlignmentI loadAlignment(final String data, String format) + protected AlignmentI loadAlignment(final String data, FileFormatI format) throws IOException { - AlignmentI a = new FormatAdapter().readFile(data, - AppletFormatAdapter.PASTE, format); + AlignmentI a = new FormatAdapter().readFile(data, DataSourceType.PASTE, + format); a.setDataset(null); return a; } @@ -134,19 +147,23 @@ public class AlignmentTest * - 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. + * @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 (message == null) + { + message = ""; + } if (alignment == null) { if (raiseAssert) { - Assert.fail(message+"Alignment for verification was null."); + Assert.fail(message + "Alignment for verification was null."); } return false; } @@ -161,7 +178,8 @@ public class AlignmentTest { if (raiseAssert) { - Assert.fail(message+" Alignment contained a sequence who's dataset sequence has a second dataset reference."); + Assert.fail(message + + " Alignment contained a sequence who's dataset sequence has a second dataset reference."); } return false; } @@ -169,23 +187,40 @@ public class AlignmentTest { if (raiseAssert) { - Assert.fail(message+" Alignment contained a sequence who's dataset sequence was not in the dataset."); + Assert.fail(message + + " Alignment contained a sequence who's dataset sequence was not in the dataset."); } return false; } } - return verifyAlignmentDatasetRefs(alignment.getDataset(), raiseAssert, message); + 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!)"); + 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; } @@ -202,7 +237,8 @@ public class AlignmentTest { if (raiseAssert) { - Assert.fail(message+" DBRefEntry for sequence in alignment had map to sequence which was not a dataset sequence"); + Assert.fail(message + + " DBRefEntry for sequence in alignment had map to sequence which was not a dataset sequence"); } return false; @@ -211,7 +247,9 @@ public class AlignmentTest { if (raiseAssert) { - Assert.fail(message+" DBRefEntry for sequence in alignment had map to sequence not in dataset"); + Assert.fail(message + " DBRefEntry " + dbr + + " for sequence " + seqds + + " in alignment has map to sequence not in dataset"); } return false; } @@ -231,7 +269,8 @@ public class AlignmentTest { if (raiseAssert) { - Assert.fail(message+" CodonFrame-SSM-FromSeq is not a dataset sequence"); + Assert.fail(message + + " CodonFrame-SSM-FromSeq is not a dataset sequence"); } return false; } @@ -240,7 +279,8 @@ public class AlignmentTest if (raiseAssert) { - Assert.fail(message+" CodonFrame-SSM-FromSeq is not contained in dataset"); + Assert.fail(message + + " CodonFrame-SSM-FromSeq is not contained in dataset"); } return false; } @@ -248,7 +288,8 @@ public class AlignmentTest { if (raiseAssert) { - Assert.fail(message+" CodonFrame-SSM-Mapping-ToSeq is not a dataset sequence"); + Assert.fail(message + + " CodonFrame-SSM-Mapping-ToSeq is not a dataset sequence"); } return false; } @@ -257,7 +298,8 @@ public class AlignmentTest if (raiseAssert) { - Assert.fail(message+" CodonFrame-SSM-Mapping-ToSeq is not contained in dataset"); + Assert.fail(message + + " CodonFrame-SSM-Mapping-ToSeq is not contained in dataset"); } return false; } @@ -292,53 +334,56 @@ public class AlignmentTest ae.printStackTrace(); Assert.fail( "Valid test alignment raised assertion errors when raiseAsserts enabled: " - + msg, ae); + + msg, + ae); } // also check validation passes with asserts disabled Assert.assertTrue(verifyAlignmentDatasetRefs(al, false, null), - "Valid test alignment failed when raiseAsserts disabled:" + "Valid test alignment tested false when raiseAsserts disabled:" + msg); } else { + boolean assertRaised = false; try { - Assert.assertFalse(verifyAlignmentDatasetRefs(al, true, null)); - Assert.fail("Invalid test alignment passed but no assertion raised when raiseAsserts enabled:" - + msg); + 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 passed when raiseAsserts disabled:" + "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"); + SequenceI sq1 = new Sequence("sq1", "ASFDD"), + sq2 = new Sequence("sq2", "TTTTTT"); // construct simple valid alignment dataset - Alignment al = new Alignment(new SequenceI[] { - sq1, sq2 }); + 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, + assertVerifyAlignment(al, false, "didn't detect dataset sequence with a dataset sequence reference."); sq1.setDatasetSequence(null); - assertVerifyAlignment( - al, - true, + assertVerifyAlignment(al, true, "didn't reinstate validity after nulling dataset sequence dataset reference"); // now create dataset and check again @@ -350,27 +395,27 @@ public class AlignmentTest // 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)); + 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"); + 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)); + 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, + 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); @@ -381,27 +426,166 @@ public class AlignmentTest "aggtutaggcagcagcag"); AlignedCodonFrame alc = new AlignedCodonFrame(); - alc.addMap(sqanotherout, sqnew, new MapList(new int[] { 1, 6 }, - new int[] { 1, 18 }, 3, 1)); + 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, + 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, + 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. @@ -409,7 +593,7 @@ public class AlignmentTest @BeforeMethod(alwaysRun = true) public void setUp() throws IOException { - al = loadAlignment(TEST_DATA, "STH"); + al = loadAlignment(TEST_DATA, FileFormat.Stockholm); int i = 0; for (AlignmentAnnotation ann : al.getAlignmentAnnotation()) { @@ -431,6 +615,84 @@ public class AlignmentTest AlignmentAnnotation ann = iter.next(); assertEquals("D.melanogaster.2", ann.sequenceRef.getName()); assertFalse(iter.hasNext()); + + // invalid id + anns = al.findAnnotation("CalcIdForD.melanogaster.?"); + assertFalse(iter.hasNext()); + anns = al.findAnnotation(null); + assertFalse(iter.hasNext()); + } + + /** + * Test method that returns annotations that match on reference sequence, + * label, or calcId. + */ + @Test(groups = { "Functional" }) + public void testFindAnnotations_bySeqLabelandorCalcId() + { + // TODO: finish testFindAnnotations_bySeqLabelandorCalcId test + /* Note - this is an incomplete test - need to check null or + * non-null [ matches, not matches ] behaviour for each of the three + * parameters..*/ + + // search for a single, unique calcId with wildcards on other params + Iterable anns = al.findAnnotations(null, + "CalcIdForD.melanogaster.2", null); + Iterator iter = anns.iterator(); + assertTrue(iter.hasNext()); + AlignmentAnnotation ann = iter.next(); + assertEquals("D.melanogaster.2", ann.sequenceRef.getName()); + assertFalse(iter.hasNext()); + + // save reference to test sequence reference parameter + SequenceI rseq = ann.sequenceRef; + + // search for annotation associated with a single sequence + anns = al.findAnnotations(rseq, null, null); + iter = anns.iterator(); + assertTrue(iter.hasNext()); + ann = iter.next(); + assertEquals("D.melanogaster.2", ann.sequenceRef.getName()); + assertFalse(iter.hasNext()); + + // search for annotation with a non-existant calcId + anns = al.findAnnotations(null, "CalcIdForD.melanogaster.?", null); + iter = anns.iterator(); + assertFalse(iter.hasNext()); + + // search for annotation with a particular label - expect three + anns = al.findAnnotations(null, null, "Secondary Structure"); + iter = anns.iterator(); + assertTrue(iter.hasNext()); + iter.next(); + assertTrue(iter.hasNext()); + iter.next(); + assertTrue(iter.hasNext()); + iter.next(); + // third found.. so + assertFalse(iter.hasNext()); + + // search for annotation on one sequence with a particular label - expect + // one + SequenceI sqfound; + anns = al.findAnnotations(sqfound = al.getSequenceAt(1), null, + "Secondary Structure"); + iter = anns.iterator(); + assertTrue(iter.hasNext()); + // expect reference to sequence 1 in the alignment + assertTrue(sqfound == iter.next().sequenceRef); + assertFalse(iter.hasNext()); + + // null on all parameters == find all annotations + anns = al.findAnnotations(null, null, null); + iter = anns.iterator(); + int n = al.getAlignmentAnnotation().length; + while (iter.hasNext()) + { + n--; + iter.next(); + } + assertTrue("Found " + n + " fewer annotations from search.", n == 0); } @Test(groups = { "Functional" }) @@ -475,9 +737,9 @@ public class AlignmentTest public void testAlignAs_dnaAsDna() throws IOException { // aligned cDNA: - AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA"); + AlignmentI al1 = loadAlignment(CDNA_SEQS_1, FileFormat.Fasta); // unaligned cDNA: - AlignmentI al2 = loadAlignment(CDNA_SEQS_2, "FASTA"); + AlignmentI al2 = loadAlignment(CDNA_SEQS_2, FileFormat.Fasta); /* * Make mappings between sequences. The 'aligned cDNA' is playing the role @@ -486,10 +748,10 @@ public class AlignmentTest makeMappings(al1, al2); ((Alignment) al2).alignAs(al1, false, true); - assertEquals("GC-TC--GUC-GTACT", al2.getSequenceAt(0) - .getSequenceAsString()); - assertEquals("-GG-GTC--AGG--CAGT", al2.getSequenceAt(1) - .getSequenceAsString()); + assertEquals("GC-TC--GUC-GTACT", + al2.getSequenceAt(0).getSequenceAsString()); + assertEquals("-GG-GTC--AGG--CAGT", + al2.getSequenceAt(1).getSequenceAsString()); } /** @@ -501,8 +763,8 @@ public class AlignmentTest public void testAlignAs_proteinAsCdna() throws IOException { // see also AlignmentUtilsTests - AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA"); - AlignmentI al2 = loadAlignment(AA_SEQS_1, "FASTA"); + AlignmentI al1 = loadAlignment(CDNA_SEQS_1, FileFormat.Fasta); + AlignmentI al2 = loadAlignment(AA_SEQS_1, FileFormat.Fasta); makeMappings(al1, al2); // Fudge - alignProteinAsCdna expects mappings to be on protein @@ -525,18 +787,18 @@ public class AlignmentTest /* * Load alignments and add mappings for cDNA to protein */ - AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA"); - AlignmentI al2 = loadAlignment(AA_SEQS_1, "FASTA"); + AlignmentI al1 = loadAlignment(CDNA_SEQS_1, FileFormat.Fasta); + AlignmentI al2 = loadAlignment(AA_SEQS_1, FileFormat.Fasta); makeMappings(al1, al2); /* * Realign DNA; currently keeping existing gaps in introns only */ ((Alignment) al1).alignAs(al2, false, true); - assertEquals("ACG---GCUCCA------ACT---", al1.getSequenceAt(0) - .getSequenceAsString()); - assertEquals("---CGT---TAACGA---AGT---", al1.getSequenceAt(1) - .getSequenceAsString()); + assertEquals("ACG---GCUCCA------ACT---", + al1.getSequenceAt(0).getSequenceAsString()); + assertEquals("---CGT---TAACGA---AGT---", + al1.getSequenceAt(1).getSequenceAsString()); } /** @@ -582,8 +844,8 @@ public class AlignmentTest * Load alignments and add mappings from nucleotide to protein (or from * first to second if both the same type) */ - AlignmentI al1 = loadAlignment(fromSeqs, "FASTA"); - AlignmentI al2 = loadAlignment(toSeqs, "FASTA"); + AlignmentI al1 = loadAlignment(fromSeqs, FileFormat.Fasta); + AlignmentI al2 = loadAlignment(toSeqs, FileFormat.Fasta); makeMappings(al1, al2); /* @@ -610,9 +872,11 @@ public class AlignmentTest { 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); + MapList ml = new MapList( + new int[] + { seqFrom.getStart(), seqFrom.getEnd() }, + new int[] + { seqTo.getStart(), seqTo.getEnd() }, ratio, 1); acf.addMap(seqFrom, seqTo, ml); } @@ -639,18 +903,21 @@ public class AlignmentTest */ String dna1 = "A-Aa-gG-GCC-cT-TT"; String dna2 = "c--CCGgg-TT--T-AA-A"; - AlignmentI al1 = loadAlignment(">Dna1/6-17\n" + dna1 - + "\n>Dna2/20-31\n" + dna2 + "\n", "FASTA"); + AlignmentI al1 = loadAlignment( + ">Dna1/6-17\n" + dna1 + "\n>Dna2/20-31\n" + dna2 + "\n", + FileFormat.Fasta); AlignmentI al2 = loadAlignment( - ">Pep1/7-9\n-P--YK\n>Pep2/11-13\nG-T--F\n", "FASTA"); + ">Pep1/7-9\n-P--YK\n>Pep2/11-13\nG-T--F\n", FileFormat.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 - MapList ml1 = new MapList(new int[] { 6, 7, 10, 13, 15, 17 }, new int[] - { 7, 9 }, 3, 1); + 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); - MapList ml2 = new MapList(new int[] { 21, 23, 26, 31 }, new int[] { 11, - 13 }, 3, 1); + MapList ml2 = new MapList(new int[] { 21, 23, 26, 31 }, + new int[] + { 11, 13 }, 3, 1); acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml2); al2.addCodonFrame(acf); @@ -658,11 +925,11 @@ public class AlignmentTest * Align ignoring gaps in dna introns and exons */ ((Alignment) al1).alignAs(al2, false, false); - assertEquals("---AAagG------GCCcTTT", al1.getSequenceAt(0) - .getSequenceAsString()); + assertEquals("---AAagG------GCCcTTT", + al1.getSequenceAt(0).getSequenceAsString()); // note 1 gap in protein corresponds to 'gg-' in DNA (3 positions) - assertEquals("cCCGgg-TTT------AAA", al1.getSequenceAt(1) - .getSequenceAsString()); + assertEquals("cCCGgg-TTT------AAA", + al1.getSequenceAt(1).getSequenceAsString()); /* * Reset and realign, preserving gaps in dna introns and exons @@ -673,21 +940,22 @@ public class AlignmentTest // String dna1 = "A-Aa-gG-GCC-cT-TT"; // String dna2 = "c--CCGgg-TT--T-AA-A"; // assumption: we include 'the greater of' protein/dna gap lengths, not both - assertEquals("---A-Aa-gG------GCC-cT-TT", al1.getSequenceAt(0) - .getSequenceAsString()); - assertEquals("c--CCGgg-TT--T------AA-A", al1.getSequenceAt(1) - .getSequenceAsString()); + assertEquals("---A-Aa-gG------GCC-cT-TT", + al1.getSequenceAt(0).getSequenceAsString()); + assertEquals("c--CCGgg-TT--T------AA-A", + al1.getSequenceAt(1).getSequenceAsString()); } @Test(groups = "Functional") public void testCopyConstructor() throws IOException { - AlignmentI protein = loadAlignment(AA_SEQS_1, FormatAdapter.PASTE); + AlignmentI protein = loadAlignment(AA_SEQS_1, FileFormat.Fasta); // create sequence and alignment datasets protein.setDataset(null); AlignedCodonFrame acf = new AlignedCodonFrame(); - List acfList = Arrays.asList(new AlignedCodonFrame[] - { acf }); + List acfList = Arrays + .asList(new AlignedCodonFrame[] + { acf }); protein.getDataset().setCodonFrames(acfList); AlignmentI copy = new Alignment(protein); @@ -696,10 +964,10 @@ public class AlignmentTest */ assertFalse(copy.getSequenceAt(0) == protein.getSequenceAt(0)); assertFalse(copy.getSequenceAt(1) == protein.getSequenceAt(1)); - assertSame(copy.getSequenceAt(0).getDatasetSequence(), protein - .getSequenceAt(0).getDatasetSequence()); - assertSame(copy.getSequenceAt(1).getDatasetSequence(), protein - .getSequenceAt(1).getDatasetSequence()); + assertSame(copy.getSequenceAt(0).getDatasetSequence(), + protein.getSequenceAt(0).getDatasetSequence()); + assertSame(copy.getSequenceAt(1).getDatasetSequence(), + protein.getSequenceAt(1).getDatasetSequence()); // TODO should the copy constructor copy the dataset? // or make a new one referring to the same dataset sequences?? @@ -719,7 +987,7 @@ public class AlignmentTest public void testCreateDatasetAlignment() throws IOException { AlignmentI protein = new FormatAdapter().readFile(AA_SEQS_1, - AppletFormatAdapter.PASTE, "FASTA"); + DataSourceType.PASTE, FileFormat.Fasta); /* * create a dataset sequence on first sequence * leave the second without one @@ -749,10 +1017,10 @@ public class AlignmentTest // side-effect: dataset created on second sequence assertNotNull(protein.getSequenceAt(1).getDatasetSequence()); // dataset alignment has references to dataset sequences - assertEquals(ds.getSequenceAt(0), protein.getSequenceAt(0) - .getDatasetSequence()); - assertEquals(ds.getSequenceAt(1), protein.getSequenceAt(1) - .getDatasetSequence()); + assertEquals(ds.getSequenceAt(0), + protein.getSequenceAt(0).getDatasetSequence()); + assertEquals(ds.getSequenceAt(1), + protein.getSequenceAt(1).getDatasetSequence()); // codon frames should have been moved to the dataset // getCodonFrames() should delegate to the dataset: @@ -775,19 +1043,22 @@ public class AlignmentTest // 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))); + 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))); + 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)); + alc.addMap(sq1, sq2, + new MapList(new int[] + { 1, 4 }, new int[] { 1, 4 }, 1, 1)); AlignmentI protein = new Alignment(new SequenceI[] { sq1, sq2 }); @@ -838,31 +1109,486 @@ public class AlignmentTest } @Test(groups = "Functional") - public void getVisibleStartAndEndIndexTest() + public void testAddSequencePreserveDatasetIntegrity() { 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]); + 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"); + } + + /** + * 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 + */ + List dbRefs = pep.getDBRefs(); + assertEquals(2, dbRefs.size()); + assertSame(dna, dbRefs.get(0).map.to); + assertSame(cds, dbRefs.get(1).map.to); + assertEquals(1, dna.getDBRefs().size()); + assertSame(pep.getDatasetSequence(), dna.getDBRefs().get(0).map.to); + assertEquals(1, cds.getDBRefs().size()); + assertSame(pep.getDatasetSequence(), cds.getDBRefs().get(0).map.to); + } + + @Test(groups = { "Functional" }) + public void testFindGroup() + { + SequenceI seq1 = new Sequence("seq1", "ABCDEF---GHI"); + SequenceI seq2 = new Sequence("seq2", "---JKLMNO---"); + AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2 }); + + assertNull(a.findGroup(null, 0)); + assertNull(a.findGroup(seq1, 1)); + assertNull(a.findGroup(seq1, -1)); + + /* + * add a group consisting of just "DEF" + */ + SequenceGroup sg1 = new SequenceGroup(); + sg1.addSequence(seq1, false); + sg1.setStartRes(3); + sg1.setEndRes(5); + a.addGroup(sg1); + + assertNull(a.findGroup(seq1, 2)); // position not in group + assertNull(a.findGroup(seq1, 6)); // position not in group + assertNull(a.findGroup(seq2, 5)); // sequence not in group + assertSame(a.findGroup(seq1, 3), sg1); // yes + assertSame(a.findGroup(seq1, 4), sg1); + assertSame(a.findGroup(seq1, 5), sg1); + + /* + * add a group consisting of + * EF-- + * KLMN + */ + SequenceGroup sg2 = new SequenceGroup(); + sg2.addSequence(seq1, false); + sg2.addSequence(seq2, false); + sg2.setStartRes(4); + sg2.setEndRes(7); + a.addGroup(sg2); + + assertNull(a.findGroup(seq1, 2)); // unchanged + assertSame(a.findGroup(seq1, 3), sg1); // unchanged + /* + * if a residue is in more than one group, method returns + * the first found (in order groups were added) + */ + assertSame(a.findGroup(seq1, 4), sg1); + assertSame(a.findGroup(seq1, 5), sg1); + + /* + * seq2 only belongs to the second group + */ + assertSame(a.findGroup(seq2, 4), sg2); + assertSame(a.findGroup(seq2, 5), sg2); + assertSame(a.findGroup(seq2, 6), sg2); + assertSame(a.findGroup(seq2, 7), sg2); + assertNull(a.findGroup(seq2, 3)); + assertNull(a.findGroup(seq2, 8)); + } + + @Test(groups = { "Functional" }) + public void testDeleteSequenceByIndex() + { + // create random alignment + AlignmentGenerator gen = new AlignmentGenerator(false); + AlignmentI a = gen.generate(20, 15, 123, 5, 5); + + // delete sequence 10, alignment reduced by 1 + int height = a.getAbsoluteHeight(); + a.deleteSequence(10); + assertEquals(a.getAbsoluteHeight(), height - 1); + + // try to delete -ve index, nothing happens + a.deleteSequence(-1); + assertEquals(a.getAbsoluteHeight(), height - 1); + + // try to delete beyond end of alignment, nothing happens + a.deleteSequence(14); + assertEquals(a.getAbsoluteHeight(), height - 1); + } + + @Test(groups = { "Functional" }) + public void testDeleteSequenceBySeq() + { + // create random alignment + AlignmentGenerator gen = new AlignmentGenerator(false); + AlignmentI a = gen.generate(20, 15, 123, 5, 5); + + // delete sequence 10, alignment reduced by 1 + int height = a.getAbsoluteHeight(); + SequenceI seq = a.getSequenceAt(10); + a.deleteSequence(seq); + assertEquals(a.getAbsoluteHeight(), height - 1); + + // try to delete non-existent sequence, nothing happens + seq = new Sequence("cds", "GCCTCGGAT"); + assertEquals(a.getAbsoluteHeight(), height - 1); + } + + @Test(groups = { "Functional" }) + public void testDeleteHiddenSequence() + { + // create random alignment + AlignmentGenerator gen = new AlignmentGenerator(false); + AlignmentI a = gen.generate(20, 15, 123, 5, 5); + + // delete a sequence which is hidden, check it is NOT removed from hidden + // sequences + int height = a.getAbsoluteHeight(); + SequenceI seq = a.getSequenceAt(2); + a.getHiddenSequences().hideSequence(seq); + assertEquals(a.getHiddenSequences().getSize(), 1); + a.deleteSequence(2); + assertEquals(a.getAbsoluteHeight(), height - 1); + assertEquals(a.getHiddenSequences().getSize(), 1); + + // delete a sequence which is not hidden, check hiddenSequences are not + // affected + a.deleteSequence(10); + assertEquals(a.getAbsoluteHeight(), height - 2); + assertEquals(a.getHiddenSequences().getSize(), 1); + } + + @Test( + groups = "Functional", + expectedExceptions = + { IllegalArgumentException.class }) + public void testSetDataset_selfReference() + { + SequenceI seq = new Sequence("a", "a"); + AlignmentI alignment = new Alignment(new SequenceI[] { seq }); + alignment.setDataset(alignment); + } + + @Test(groups = "Functional") + public void testAppend() + { + SequenceI seq = new Sequence("seq1", "FRMLPSRT-A--L-"); + AlignmentI alignment = new Alignment(new SequenceI[] { seq }); + alignment.setGapCharacter('-'); + SequenceI seq2 = new Sequence("seq1", "KP..L.FQII."); + AlignmentI alignment2 = new Alignment(new SequenceI[] { seq2 }); + alignment2.setGapCharacter('.'); + + alignment.append(alignment2); + + assertEquals('-', alignment.getGapCharacter()); + assertSame(seq, alignment.getSequenceAt(0)); + assertEquals("KP--L-FQII-", + alignment.getSequenceAt(1).getSequenceAsString()); + + // todo test coverage for annotations, mappings, groups, + // hidden sequences, properties + } + + /** + * test that calcId == null on findOrCreate doesn't raise an NPE, and yields + * an annotation with a null calcId + * + */ + @Test(groups = "Functional") + public void testFindOrCreateForNullCalcId() + { + SequenceI seq = new Sequence("seq1", "FRMLPSRT-A--L-"); + AlignmentI alignment = new Alignment(new SequenceI[] { seq }); + + AlignmentAnnotation ala = alignment.findOrCreateAnnotation( + "Temperature Factor", null, false, seq, null); + assertNotNull(ala); + assertEquals(seq, ala.sequenceRef); + assertEquals("", ala.calcId); + } + + @Test(groups = "Functional") + public void testPropagateInsertions() + { + // create an alignment with no gaps - this will be the profile seq and other + // JPRED seqs + AlignmentGenerator gen = new AlignmentGenerator(false); + AlignmentI al = gen.generate(25, 10, 1234, 0, 0); + + // get the profileseq + SequenceI profileseq = al.getSequenceAt(0); + SequenceI gappedseq = new Sequence(profileseq); + gappedseq.insertCharAt(5, al.getGapCharacter()); + gappedseq.insertCharAt(6, al.getGapCharacter()); + gappedseq.insertCharAt(7, al.getGapCharacter()); + gappedseq.insertCharAt(8, al.getGapCharacter()); + + // force different kinds of padding + al.getSequenceAt(3).deleteChars(2, 23); + al.getSequenceAt(4).deleteChars(2, 27); + al.getSequenceAt(5).deleteChars(10, 27); + + // create an alignment view with the gapped sequence + SequenceI[] seqs = new SequenceI[1]; + seqs[0] = gappedseq; + AlignmentI newal = new Alignment(seqs); + HiddenColumns hidden = new HiddenColumns(); + hidden.hideColumns(15, 17); + + AlignmentView view = new AlignmentView(newal, hidden, null, true, false, + false); + + // confirm that original contigs are as expected + Iterator visible = hidden.getVisContigsIterator(0, 25, false); + int[] region = visible.next(); + assertEquals("[0, 14]", Arrays.toString(region)); + region = visible.next(); + assertEquals("[18, 24]", Arrays.toString(region)); + + // propagate insertions + HiddenColumns result = al.propagateInsertions(profileseq, view); + + // confirm that the contigs have changed to account for the gaps + visible = result.getVisContigsIterator(0, 25, false); + region = visible.next(); + assertEquals("[0, 10]", Arrays.toString(region)); + region = visible.next(); + assertEquals("[14, 24]", Arrays.toString(region)); + + // confirm the alignment has been changed so that the other sequences have + // gaps inserted where the columns are hidden + assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[10])); + assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[11])); + assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[12])); + assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[13])); + assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[14])); + + } + + @Test(groups = "Functional") + public void testPropagateInsertionsOverlap() + { + // test propagateInsertions where gaps and hiddenColumns overlap + + // create an alignment with no gaps - this will be the profile seq and other + // JPRED seqs + AlignmentGenerator gen = new AlignmentGenerator(false); + AlignmentI al = gen.generate(20, 10, 1234, 0, 0); + + // get the profileseq + SequenceI profileseq = al.getSequenceAt(0); + SequenceI gappedseq = new Sequence(profileseq); + gappedseq.insertCharAt(5, al.getGapCharacter()); + gappedseq.insertCharAt(6, al.getGapCharacter()); + gappedseq.insertCharAt(7, al.getGapCharacter()); + gappedseq.insertCharAt(8, al.getGapCharacter()); + + // create an alignment view with the gapped sequence + SequenceI[] seqs = new SequenceI[1]; + seqs[0] = gappedseq; + AlignmentI newal = new Alignment(seqs); + + // hide columns so that some overlap with the gaps + HiddenColumns hidden = new HiddenColumns(); + hidden.hideColumns(7, 10); + + AlignmentView view = new AlignmentView(newal, hidden, null, true, false, + false); + + // confirm that original contigs are as expected + Iterator visible = hidden.getVisContigsIterator(0, 20, false); + int[] region = visible.next(); + assertEquals("[0, 6]", Arrays.toString(region)); + region = visible.next(); + assertEquals("[11, 19]", Arrays.toString(region)); + assertFalse(visible.hasNext()); + + // propagate insertions + HiddenColumns result = al.propagateInsertions(profileseq, view); + + // confirm that the contigs have changed to account for the gaps + visible = result.getVisContigsIterator(0, 20, false); + region = visible.next(); + assertEquals("[0, 4]", Arrays.toString(region)); + region = visible.next(); + assertEquals("[7, 19]", Arrays.toString(region)); + assertFalse(visible.hasNext()); + + // confirm the alignment has been changed so that the other sequences have + // gaps inserted where the columns are hidden + assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[4])); + assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[5])); + assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[6])); + assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[7])); + } + + @Test(groups = { "Functional" }) + public void testPadGaps() + { + SequenceI seq1 = new Sequence("seq1", "ABCDEF--"); + SequenceI seq2 = new Sequence("seq2", "-JKLMNO--"); + SequenceI seq3 = new Sequence("seq2", "-PQR"); + AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 }); + a.setGapCharacter('.'); // this replaces existing gaps + assertEquals("ABCDEF..", seq1.getSequenceAsString()); + a.padGaps(); + // trailing gaps are pruned, short sequences padded with gap character + assertEquals("ABCDEF.", seq1.getSequenceAsString()); + assertEquals(".JKLMNO", seq2.getSequenceAsString()); + assertEquals(".PQR...", seq3.getSequenceAsString()); + } + + /** + * Test for setHiddenColumns, to check it returns true if the hidden columns + * have changed, else false + */ + @Test(groups = { "Functional" }) + public void testSetHiddenColumns() + { + AlignmentI al = new Alignment(new SequenceI[] {}); + assertFalse(al.getHiddenColumns().hasHiddenColumns()); + + HiddenColumns hc = new HiddenColumns(); + assertFalse(al.setHiddenColumns(hc)); // no change + assertSame(hc, al.getHiddenColumns()); + + hc.hideColumns(2, 4); + assertTrue(al.getHiddenColumns().hasHiddenColumns()); + + /* + * set a different object but with the same columns hidden + */ + HiddenColumns hc2 = new HiddenColumns(); + hc2.hideColumns(2, 4); + assertFalse(al.setHiddenColumns(hc2)); // no change + assertSame(hc2, al.getHiddenColumns()); + + assertTrue(al.setHiddenColumns(null)); + assertNull(al.getHiddenColumns()); + assertTrue(al.setHiddenColumns(hc)); + assertSame(hc, al.getHiddenColumns()); + + al.getHiddenColumns().hideColumns(10, 12); + hc2.hideColumns(10, 12); + assertFalse(al.setHiddenColumns(hc2)); // no change + + /* + * hide columns 15-16 then 17-18 in hc + * hide columns 15-18 in hc2 + * these are not now 'equal' objects even though they + * represent the same set of columns + */ + assertSame(hc2, al.getHiddenColumns()); + hc.hideColumns(15, 16); + hc.hideColumns(17, 18); + hc2.hideColumns(15, 18); + assertFalse(hc.equals(hc2)); + assertTrue(al.setHiddenColumns(hc)); // 'changed' + } + + @Test(groups = { "Functional" }) + public void testGetWidth() + { + SequenceI seq1 = new Sequence("seq1", "ABCDEF--"); + SequenceI seq2 = new Sequence("seq2", "-JKLMNO--"); + SequenceI seq3 = new Sequence("seq2", "-PQR"); + AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 }); + + assertEquals(9, a.getWidth()); + + // width includes hidden columns + a.getHiddenColumns().hideColumns(2, 5); + assertEquals(9, a.getWidth()); + } + + @Test(groups = { "Functional" }) + public void testGetVisibleWidth() + { + SequenceI seq1 = new Sequence("seq1", "ABCDEF--"); + SequenceI seq2 = new Sequence("seq2", "-JKLMNO--"); + SequenceI seq3 = new Sequence("seq2", "-PQR"); + AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 }); + + assertEquals(9, a.getVisibleWidth()); + + // width excludes hidden columns + a.getHiddenColumns().hideColumns(2, 5); + assertEquals(5, a.getVisibleWidth()); + } + + @Test(groups = { "Functional" }) + public void testGetContactMap() + { + // TODO + // 1. test adding/removing/manipulating contact maps with/without associated + // sequence(s) or groups + // 2. For sequence associated - ensure that inserting a gap in sequence + // results in the contact map being relocated accordingly + // 3. RENDERER QUESTION - should contact maps reflect gaps in the alignment + // ? + } }