X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FAlignmentTest.java;h=3b3d9267b77ad239498aea6ac28bb5a8e1eb8b84;hb=c9f31322ad542be7fab91e0c9f2ff3638a25c5b1;hp=93170b7ef7ac9b2d0ffdbefda9080092e9ebd586;hpb=b12de4788f39931038a17ef1627e8cf77a6d84d2;p=jalview.git diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java index 93170b7..3b3d926 100644 --- a/test/jalview/datamodel/AlignmentTest.java +++ b/test/jalview/datamodel/AlignmentTest.java @@ -4,6 +4,8 @@ import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertFalse; import static org.junit.Assert.assertTrue; import jalview.io.AppletFormatAdapter; +import jalview.io.FormatAdapter; +import jalview.util.MapList; import java.io.IOException; import java.util.Iterator; @@ -32,10 +34,45 @@ public class AlignmentTest "D.melanogaster.3 G.UGGCGCU..UAUGACGCA\n" + "#=GR D.melanogaster.3 SS (.(((...(....(((((((\n" + "//"; + + private static final String AA_SEQS_1 = + ">Seq1Name\n" + + "K-QY--L\n" + + ">Seq2Name\n" + + "-R-FP-W-\n"; + + private static final String CDNA_SEQS_1 = + ">Seq1Name\n" + + "AC-GG--CUC-CAA-CT\n" + + ">Seq2Name\n" + + "-CG-TTA--ACG---AAGT\n"; + + private static final String CDNA_SEQS_2 = + ">Seq1Name\n" + + "GCTCGUCGTACT\n" + + ">Seq2Name\n" + + "GGGTCAGGCAGT\n"; // @formatter:on + private AlignmentI al; - private Alignment al; + /** + * Helper method to load an alignment and ensure dataset sequences are set up. + * + * @param data + * @param format + * TODO + * @return + * @throws IOException + */ + protected AlignmentI loadAlignment(final String data, String format) + throws IOException + { + Alignment a = new FormatAdapter().readFile(data, + AppletFormatAdapter.PASTE, format); + a.setDataset(null); + return a; + } /* * Read in Stockholm format test data including secondary structure @@ -44,13 +81,12 @@ public class AlignmentTest @Before public void setUp() throws IOException { - al = new jalview.io.FormatAdapter().readFile(TEST_DATA, - AppletFormatAdapter.PASTE, "STH"); - for (int i = 0; i < al.getSequencesArray().length; ++i) + al = loadAlignment(TEST_DATA, "STH"); + int i = 0; + for (AlignmentAnnotation ann : al.getAlignmentAnnotation()) { - al.addAnnotation(al.getSequenceAt(i).getAnnotation()[0]); - al.getSequenceAt(i).getAnnotation()[0].setCalcId("CalcIdFor" - + al.getSequenceAt(i).getName()); + ann.setCalcId("CalcIdFor" + al.getSequenceAt(i).getName()); + i++; } } @@ -68,4 +104,174 @@ public class AlignmentTest assertEquals("D.melanogaster.2", ann.sequenceRef.getName()); assertFalse(iter.hasNext()); } + + @Test + public void testDeleteAllAnnotations_includingAutocalculated() + { + AlignmentAnnotation aa = new AlignmentAnnotation("Consensus", + "Consensus", 0.5); + aa.autoCalculated = true; + al.addAnnotation(aa); + AlignmentAnnotation[] anns = al.getAlignmentAnnotation(); + assertEquals("Wrong number of annotations before deleting", 4, + anns.length); + al.deleteAllAnnotations(true); + assertEquals("Not all deleted", 0, al.getAlignmentAnnotation().length); + } + + @Test + public void testDeleteAllAnnotations_excludingAutocalculated() + { + AlignmentAnnotation aa = new AlignmentAnnotation("Consensus", + "Consensus", 0.5); + aa.autoCalculated = true; + al.addAnnotation(aa); + AlignmentAnnotation[] anns = al.getAlignmentAnnotation(); + assertEquals("Wrong number of annotations before deleting", 4, + anns.length); + al.deleteAllAnnotations(false); + assertEquals("Not just one annotation left", 1, + al.getAlignmentAnnotation().length); + } + + /** + * Tests for realigning as per a supplied alignment: Dna as Dna. + * + * Note: AlignedCodonFrame's state variables are named for protein-to-cDNA + * mapping, but can be exploited for a general 'sequence-to-sequence' mapping + * as here. + * + * @throws IOException + */ + @Test + public void testAlignAs_dnaAsDna() throws IOException + { + // aligned cDNA: + AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA"); + // unaligned cDNA: + AlignmentI al2 = loadAlignment(CDNA_SEQS_2, "FASTA"); + + /* + * Make mappings between sequences. The 'aligned cDNA' is playing the role + * of what would normally be protein here. + */ + AlignedCodonFrame acf = new AlignedCodonFrame(); + MapList ml = new MapList(new int[] + { 1, 12 }, new int[] + { 1, 12 }, 1, 1); + acf.addMap(al2.getSequenceAt(0), al1.getSequenceAt(0), ml); + acf.addMap(al2.getSequenceAt(1), al1.getSequenceAt(1), ml); + al1.addCodonFrame(acf); + + ((Alignment) al2).alignAs(al1, false, true); + assertEquals("GC-TC--GUC-GTA-CT", al2.getSequenceAt(0) + .getSequenceAsString()); + assertEquals("-GG-GTC--AGG---CAGT", al2.getSequenceAt(1) + .getSequenceAsString()); + } + + /** + * Aligning protein from cDNA yet to be implemented, does nothing. + * + * @throws IOException + */ + @Test + public void testAlignAs_proteinAsCdna() throws IOException + { + AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA"); + AlignmentI al2 = loadAlignment(AA_SEQS_1, "FASTA"); + String before0 = al2.getSequenceAt(0).getSequenceAsString(); + String before1 = al2.getSequenceAt(1).getSequenceAsString(); + + ((Alignment) al2).alignAs(al1, false, true); + assertEquals(before0, al2.getSequenceAt(0).getSequenceAsString()); + assertEquals(before1, al2.getSequenceAt(1).getSequenceAsString()); + } + + /** + * Test aligning cdna as per protein alignment. + * + * @throws IOException + */ + @Test + public void testAlignAs_cdnaAsProtein() throws IOException + { + /* + * Load alignments and add mappings for cDNA to protein + */ + AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA"); + AlignmentI al2 = loadAlignment(AA_SEQS_1, "FASTA"); + AlignedCodonFrame acf = new AlignedCodonFrame(); + MapList ml = new MapList(new int[] + { 1, 12 }, new int[] + { 1, 4 }, 3, 1); + acf.addMap(al1.getSequenceAt(0), al2.getSequenceAt(0), ml); + acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml); + al2.addCodonFrame(acf); + + /* + * 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()); + } + + /** + * Test aligning dna as per protein alignment, for the case where there are + * introns (i.e. some dna sites have no mapping from a peptide). + * + * @throws IOException + */ + @Test + public void testAlignAs_dnaAsProtein_withIntrons() throws IOException + { + /* + * Load alignments and add mappings for cDNA to protein + */ + String dna1 = "A-Aa-gG-GCC-cT-TT"; + String dna2 = "c--CCGgg-TT--T-AA-A"; + AlignmentI al1 = loadAlignment(">Seq1\n" + dna1 + "\n>Seq2\n" + dna2 + + "\n", "FASTA"); + AlignmentI al2 = loadAlignment(">Seq1\n-P--YK\n>Seq2\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 + MapList ml1 = new MapList(new int[] + { 1, 2, 5, 8, 10, 12 }, new int[] + { 1, 3 }, 3, 1); + acf.addMap(al1.getSequenceAt(0), al2.getSequenceAt(0), ml1); + MapList ml2 = new MapList(new int[] + { 2, 4, 7, 12 }, new int[] + { 1, 3 }, 3, 1); + acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml2); + al2.addCodonFrame(acf); + + /* + * Align ignoring gaps in dna introns and exons + */ + ((Alignment) al1).alignAs(al2, false, false); + 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()); + + /* + * Reset and realign, preserving gaps in dna introns and exons + */ + al1.getSequenceAt(0).setSequence(dna1); + al1.getSequenceAt(1).setSequence(dna2); + ((Alignment) al1).alignAs(al2, true, true); + // 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()); + } }