X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FAlignmentTest.java;h=1f3dedd6321463790487de2e549dd920a29133c0;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=618bac5bd2129ace9366d24892581fc2b88c5698;hpb=976c518ffa15791c680156dd357d33f5a06c3a54;p=jalview.git diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java index 618bac5..1f3dedd 100644 --- a/test/jalview/datamodel/AlignmentTest.java +++ b/test/jalview/datamodel/AlignmentTest.java @@ -27,16 +27,17 @@ import static org.testng.AssertJUnit.assertNull; import static org.testng.AssertJUnit.assertSame; import static org.testng.AssertJUnit.assertTrue; +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; import java.io.IOException; -import java.util.ArrayList; import java.util.Arrays; import java.util.Iterator; import java.util.List; @@ -192,8 +193,8 @@ public class AlignmentTest return false; } } - return verifyAlignmentDatasetRefs(alignment.getDataset(), - raiseAssert, message); + return verifyAlignmentDatasetRefs(alignment.getDataset(), raiseAssert, + message); } else { @@ -246,8 +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; } @@ -332,7 +334,8 @@ 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), @@ -352,8 +355,9 @@ public class AlignmentTest } if (!assertRaised) { - Assert.fail("Invalid test alignment passed when raiseAsserts enabled:" - + msg); + Assert.fail( + "Invalid test alignment passed when raiseAsserts enabled:" + + msg); } // also check validation passes with asserts disabled Assert.assertFalse(verifyAlignmentDatasetRefs(al, false, null), @@ -365,8 +369,8 @@ public class AlignmentTest @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 }); @@ -379,9 +383,7 @@ public class AlignmentTest "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 @@ -393,27 +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); @@ -424,21 +426,18 @@ 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, @@ -467,7 +466,8 @@ public class AlignmentTest * @param message * - null or message prepended to exception message. */ - public static void assertDatasetIsNormalised(AlignmentI al, String message) + public static void assertDatasetIsNormalised(AlignmentI al, + String message) { if (al.getDataset() != null) { @@ -532,7 +532,8 @@ public class AlignmentTest assertDatasetIsNormalised(al); } catch (AssertionError ae) { - Assert.fail("Two different sequences should be valid normalised dataset."); + Assert.fail( + "Two different sequences should be valid normalised dataset."); } /* * now change sq2's name in the alignment. should still be valid @@ -543,7 +544,8 @@ public class AlignmentTest assertDatasetIsNormalised(al); } catch (AssertionError ae) { - Assert.fail("Two different sequences in dataset, but same name in alignment, should be valid normalised dataset."); + Assert.fail( + "Two different sequences in dataset, but same name in alignment, should be valid normalised dataset."); } al.addSequence(sq1seqd); @@ -552,7 +554,8 @@ public class AlignmentTest assertDatasetIsNormalised(al); } catch (AssertionError ae) { - Assert.fail("sq1 and sq1 with different sequence should be distinct."); + Assert.fail( + "sq1 and sq1 with different sequence should be distinct."); } al.addSequence(sq1shift); @@ -561,7 +564,8 @@ public class AlignmentTest assertDatasetIsNormalised(al); } catch (AssertionError ae) { - Assert.fail("sq1 and sq1 with different start/end should be distinct."); + Assert.fail( + "sq1 and sq1 with different start/end should be distinct."); } /* * finally, the failure case @@ -611,6 +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" }) @@ -666,10 +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()); } /** @@ -713,10 +795,10 @@ 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) - .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()); } /** @@ -790,9 +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); } @@ -819,18 +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", FileFormat.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", 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); @@ -838,11 +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 @@ -853,10 +940,10 @@ 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") @@ -866,8 +953,9 @@ public class AlignmentTest // 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); @@ -876,10 +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?? @@ -929,10 +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: @@ -955,19 +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 }); @@ -1030,7 +1121,8 @@ public class AlignmentTest Assert.assertEquals(align.getDataset().getHeight(), 1, "Dataset shouldn't have more than one sequence."); - Sequence seq2 = new Sequence("newtestSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ"); + Sequence seq2 = new Sequence("newtestSeq", + "ABCDEFGHIJKLMNOPQRSTUVWXYZ"); align.addSequence(seq2); Assert.assertEquals(align.getDataset().getHeight(), 2, "Dataset should now have two sequences."); @@ -1039,35 +1131,6 @@ public class AlignmentTest "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]); - } - /** * Tests that dbrefs with mappings to sequence get updated if the sequence * acquires a dataset sequence @@ -1081,26 +1144,30 @@ public class AlignmentTest // 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))); + 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))); + 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))); + 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))); + 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 }); @@ -1121,14 +1188,14 @@ public class AlignmentTest /* * 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); + 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" }) @@ -1190,4 +1257,353 @@ public class AlignmentTest 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.getCalcId()); + } + + @Test(groups = {"Functional"}) + public void testUpdateFromOrAddAnnotation() + { + 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.getCalcId()); + + // Assuming findOrCreateForNullCalcId passed then this should work + + assertTrue(ala == alignment.updateFromOrCopyAnnotation(ala)); + AlignmentAnnotation updatedAla = new AlignmentAnnotation(ala); + updatedAla.description = "updated Description"; + Assert.assertTrue( + ala == alignment.updateFromOrCopyAnnotation(updatedAla)); + Assert.assertEquals(ala.toString(), updatedAla.toString()); + updatedAla.calcId = "newCalcId"; + AlignmentAnnotation newUpdatedAla = alignment + .updateFromOrCopyAnnotation(updatedAla); + Assert.assertTrue(updatedAla != newUpdatedAla); + Assert.assertEquals(updatedAla.toString(), newUpdatedAla.toString()); + } + + @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()); + } }