X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FAlignmentTest.java;h=7af77f54f79623c7fc35a89bc185601a2e54d173;hb=06ce849ffedc7ab10a3c54cda96b9a7dec58c136;hp=fcf724a7d817b9416c5bfd7a406dfc8ec3632330;hpb=4660937a02602e6986e7c0753699b22afa26347e;p=jalview.git diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java index fcf724a..7af77f5 100644 --- a/test/jalview/datamodel/AlignmentTest.java +++ b/test/jalview/datamodel/AlignmentTest.java @@ -28,7 +28,10 @@ import static org.testng.AssertJUnit.assertSame; import static org.testng.AssertJUnit.assertTrue; import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping; -import jalview.io.AppletFormatAdapter; +import jalview.gui.JvOptionPane; +import jalview.io.DataSourceType; +import jalview.io.FileFormat; +import jalview.io.FileFormatI; import jalview.io.FormatAdapter; import jalview.util.MapList; @@ -39,6 +42,7 @@ 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; @@ -50,6 +54,14 @@ 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 +106,11 @@ 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 +146,23 @@ 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 +177,8 @@ 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; } @@ -169,12 +186,14 @@ 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 { @@ -187,7 +206,8 @@ public class AlignmentTest { 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; } @@ -216,7 +236,8 @@ 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; @@ -225,7 +246,8 @@ public class AlignmentTest { if (raiseAssert) { - Assert.fail(message+" DBRefEntry for sequence in alignment had map to sequence not in dataset"); + Assert.fail(message + + " DBRefEntry for sequence in alignment had map to sequence not in dataset"); } return false; } @@ -245,7 +267,8 @@ 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; } @@ -254,7 +277,8 @@ 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; } @@ -262,7 +286,8 @@ 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; } @@ -271,7 +296,8 @@ 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; } @@ -335,6 +361,7 @@ public class AlignmentTest + msg); } } + @Test(groups = { "Functional" }) public void testVerifyAlignmentDatasetRefs() { @@ -342,16 +369,13 @@ public class AlignmentTest "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); @@ -445,7 +469,7 @@ public class AlignmentTest */ public static void assertDatasetIsNormalised(AlignmentI al, String message) { - if (al.getDataset()!=null) + if (al.getDataset() != null) { assertDatasetIsNormalised(al.getDataset(), message); return; @@ -454,17 +478,17 @@ public class AlignmentTest * look for pairs of sequences with same ID, start, end, and sequence */ List seqSet = al.getSequences(); - for (int p=0;pDna1/6-17\n" + dna1 - + "\n>Dna2/20-31\n" + dna2 + "\n", "FASTA"); + + "\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 @@ -837,7 +868,7 @@ public class AlignmentTest @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(); @@ -874,7 +905,7 @@ 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 @@ -1013,6 +1044,7 @@ public class AlignmentTest assertAlignmentDatasetRefs(align, "addSequence broke dataset reference integrity"); } + @Test(groups = "Functional") public void getVisibleStartAndEndIndexTest() { @@ -1052,7 +1084,7 @@ public class AlignmentTest 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[] { @@ -1078,14 +1110,14 @@ public class AlignmentTest 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())); @@ -1105,4 +1137,63 @@ public class AlignmentTest assertSame(pep.getDatasetSequence(), cds.getDBRefs()[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)); + } + }