X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FAlignmentUtilsTests.java;h=75cc18b40c086c314e902eb93323358124b4122e;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=d44a6bc092261ffa2a2d4f508c732eb141d64334;hpb=44e5428356c618d139354d02bbfc2f9008ae50b6;p=jalview.git diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java index d44a6bc..75cc18b 100644 --- a/test/jalview/analysis/AlignmentUtilsTests.java +++ b/test/jalview/analysis/AlignmentUtilsTests.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -20,7 +20,6 @@ */ package jalview.analysis; - import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertFalse; import static org.testng.AssertJUnit.assertNull; @@ -96,17 +95,18 @@ public class AlignmentUtilsTests public static Sequence ts = new Sequence("short", "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm"); - @Test + @Test(groups = { "Functional" }) public void testExpandContext() { AlignmentI al = new Alignment(new Sequence[] {}); for (int i = 4; i < 14; i += 2) { - SequenceI s1=ts.deriveSequence().getSubSequence(i, i+7); + SequenceI s1 = ts.deriveSequence().getSubSequence(i, i + 7); al.addSequence(s1); } - System.out.println(new AppletFormatAdapter().formatSequences("Clustal", al, true)); - for (int flnk=-1;flnk<25; flnk++) + System.out.println(new AppletFormatAdapter().formatSequences("Clustal", + al, true)); + for (int flnk = -1; flnk < 25; flnk++) { AlignmentI exp = AlignmentUtils.expandContext(al, flnk); System.out.println("\nFlank size: " + flnk); @@ -150,11 +150,10 @@ public class AlignmentUtilsTests /** * Test that annotations are correctly adjusted by expandContext */ - @Test + @Test(groups = { "Functional" }) public void testExpandContext_annotation() { - AlignmentI al = new Alignment(new Sequence[] - {}); + AlignmentI al = new Alignment(new Sequence[] {}); SequenceI ds = new Sequence("Seq1", "ABCDEFGHI"); // subsequence DEF: SequenceI seq1 = ds.deriveSequence().getSubSequence(3, 6); @@ -163,8 +162,8 @@ public class AlignmentUtilsTests /* * Annotate DEF with 4/5/6 respectively */ - Annotation[] anns = new Annotation[] - { new Annotation(4), new Annotation(5), new Annotation(6) }; + Annotation[] anns = new Annotation[] { new Annotation(4), + new Annotation(5), new Annotation(6) }; AlignmentAnnotation ann = new AlignmentAnnotation("SS", "secondary structure", anns); seq1.addAlignmentAnnotation(ann); @@ -240,7 +239,7 @@ public class AlignmentUtilsTests * * @throws IOException */ - @Test + @Test(groups = { "Functional" }) public void testGetSequencesByName() throws IOException { final String data = ">Seq1Name\nKQYL\n" + ">Seq2Name\nRFPW\n" @@ -255,22 +254,25 @@ public class AlignmentUtilsTests assertEquals(1, map.get("Seq2Name").size()); assertEquals("RFPW", map.get("Seq2Name").get(0).getSequenceAsString()); } + /** * Helper method to load an alignment and ensure dataset sequences are set up. * * @param data - * @param format TODO + * @param format + * TODO * @return * @throws IOException */ - protected AlignmentI loadAlignment(final String data, String format) throws IOException + protected AlignmentI loadAlignment(final String data, String format) + throws IOException { AlignmentI a = new FormatAdapter().readFile(data, AppletFormatAdapter.PASTE, format); a.setDataset(null); return a; } - + /** * Test mapping of protein to cDNA, for the case where we have no sequence * cross-references, so mappings are made first-served 1-1 where sequences @@ -278,7 +280,7 @@ public class AlignmentUtilsTests * * @throws IOException */ - @Test + @Test(groups = { "Functional" }) public void testMapProteinToCdna_noXrefs() throws IOException { List protseqs = new ArrayList(); @@ -305,8 +307,8 @@ public class AlignmentUtilsTests assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size()); // V12345 mapped to A22222 - AlignedCodonFrame acf = protein.getCodonFrame( - protein.getSequenceAt(0)).get(0); + AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0)) + .get(0); assertEquals(1, acf.getdnaSeqs().length); assertEquals(cdna.getSequenceAt(1).getDatasetSequence(), acf.getdnaSeqs()[0]); @@ -315,11 +317,11 @@ public class AlignmentUtilsTests MapList mapList = protMappings[0].getMap(); assertEquals(3, mapList.getFromRatio()); assertEquals(1, mapList.getToRatio()); - assertTrue(Arrays.equals(new int[] - { 1, 9 }, mapList.getFromRanges().get(0))); + assertTrue(Arrays.equals(new int[] { 1, 9 }, mapList.getFromRanges() + .get(0))); assertEquals(1, mapList.getFromRanges().size()); - assertTrue(Arrays.equals(new int[] - { 1, 3 }, mapList.getToRanges().get(0))); + assertTrue(Arrays.equals(new int[] { 1, 3 }, + mapList.getToRanges().get(0))); assertEquals(1, mapList.getToRanges().size()); // V12346 mapped to A33333 @@ -341,12 +343,10 @@ public class AlignmentUtilsTests /** * Test for the alignSequenceAs method that takes two sequences and a mapping. */ - @Test + @Test(groups = { "Functional" }) public void testAlignSequenceAs_withMapping_noIntrons() { - MapList map = new MapList(new int[] - { 1, 6 }, new int[] - { 1, 2 }, 3, 1); + MapList map = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 }, 3, 1); /* * No existing gaps in dna: @@ -387,15 +387,14 @@ public class AlignmentUtilsTests /** * Test for the alignSequenceAs method that takes two sequences and a mapping. */ - @Test + @Test(groups = { "Functional" }) public void testAlignSequenceAs_withMapping_withIntrons() { /* * Exons at codon 2 (AAA) and 4 (TTT) */ - MapList map = new MapList(new int[] - { 4, 6, 10, 12 }, new int[] - { 1, 2 }, 3, 1); + MapList map = new MapList(new int[] { 4, 6, 10, 12 }, + new int[] { 1, 2 }, 3, 1); /* * Simple case: no gaps in dna @@ -437,24 +436,22 @@ public class AlignmentUtilsTests /** * Test for the case where not all of the protein sequence is mapped to cDNA. */ - @Test + @Test(groups = { "Functional" }) public void testAlignSequenceAs_withMapping_withUnmappedProtein() { - + /* * Exons at codon 2 (AAA) and 4 (TTT) mapped to A and P */ - final MapList map = new MapList(new int[] - { 4, 6, 10, 12 }, new int[] - { 1, 1, 3, 3 }, 3, 1); - + final MapList map = new MapList(new int[] { 4, 6, 10, 12 }, new int[] { + 1, 1, 3, 3 }, 3, 1); /* * Expect alignment does nothing (aborts realignment). Change this test * first if different behaviour wanted. */ - checkAlignSequenceAs("GGGAAACCCTTTGGG", "-A-L-P-", false, - false, map, "GGGAAACCCTTTGGG"); + checkAlignSequenceAs("GGGAAACCCTTTGGG", "-A-L-P-", false, false, map, + "GGGAAACCCTTTGGG"); } /** @@ -487,26 +484,24 @@ public class AlignmentUtilsTests /** * Test for the alignSequenceAs method where we preserve gaps in introns only. */ - @Test + @Test(groups = { "Functional" }) public void testAlignSequenceAs_keepIntronGapsOnly() { /* * Intron GGGAAA followed by exon CCCTTT */ - MapList map = new MapList(new int[] - { 7, 12 }, new int[] - { 1, 2 }, 3, 1); - - checkAlignSequenceAs("GG-G-AA-A-C-CC-T-TT", "AL", - false, true, map, "GG-G-AA-ACCCTTT"); + MapList map = new MapList(new int[] { 7, 12 }, new int[] { 1, 2 }, 3, 1); + + checkAlignSequenceAs("GG-G-AA-A-C-CC-T-TT", "AL", false, true, map, + "GG-G-AA-ACCCTTT"); } /** * Test for the method that generates an aligned translated sequence from one * mapping. */ - @Test + @Test(groups = { "Functional" }) public void testGetAlignedTranslation_dnaLikeProtein() { // dna alignment will be replaced @@ -515,22 +510,21 @@ public class AlignmentUtilsTests // protein alignment will be 'applied' to dna SequenceI protein = new Sequence("Seq1", "-CH-Y--Q-"); protein.createDatasetSequence(); - MapList map = new MapList(new int[] - { 1, 12 }, new int[] - { 1, 4 }, 3, 1); + MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1); AlignedCodonFrame acf = new AlignedCodonFrame(); acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map); - final SequenceI aligned = AlignmentUtils - .getAlignedTranslation(protein, '-', acf); - assertEquals("---TGCCAT---TAC------CAG---", aligned.getSequenceAsString()); + final SequenceI aligned = AlignmentUtils.getAlignedTranslation(protein, + '-', acf); + assertEquals("---TGCCAT---TAC------CAG---", + aligned.getSequenceAsString()); assertSame(aligned.getDatasetSequence(), dna.getDatasetSequence()); } /** * Test the method that realigns protein to match mapped codon alignment. */ - @Test + @Test(groups = { "Functional" }) public void testAlignProteinAsDna() { // seq1 codons are [1,2,3] [4,5,6] [7,8,9] [10,11,12] @@ -539,21 +533,19 @@ public class AlignmentUtilsTests SequenceI dna2 = new Sequence("Seq2", "T-GCCATTACCAG"); // seq3 codons are [1,2,3] [4,5,7] [8,9,10] [11,12,13] SequenceI dna3 = new Sequence("Seq3", "TGCCA-TTACCAG"); - AlignmentI dna = new Alignment(new SequenceI[] - { dna1, dna2, dna3 }); + AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 }); dna.setDataset(null); // protein alignment will be realigned like dna SequenceI prot1 = new Sequence("Seq1", "CHYQ"); SequenceI prot2 = new Sequence("Seq2", "CHYQ"); SequenceI prot3 = new Sequence("Seq3", "CHYQ"); - AlignmentI protein = new Alignment(new SequenceI[] - { prot1, prot2, prot3 }); + SequenceI prot4 = new Sequence("Seq4", "R-QSV"); // unmapped, unchanged + AlignmentI protein = new Alignment(new SequenceI[] { prot1, prot2, + prot3, prot4 }); protein.setDataset(null); - MapList map = new MapList(new int[] - { 1, 12 }, new int[] - { 1, 4 }, 3, 1); + MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1); AlignedCodonFrame acf = new AlignedCodonFrame(); acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map); acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map); @@ -568,43 +560,54 @@ public class AlignmentUtilsTests assertEquals("C-H--Y-Q-", prot1.getSequenceAsString()); assertEquals("-C--H-Y-Q", prot2.getSequenceAsString()); assertEquals("C--H--Y-Q", prot3.getSequenceAsString()); + assertEquals("R-QSV", prot4.getSequenceAsString()); } /** * Test the method that tests whether a CDNA sequence translates to a protein * sequence */ - @Test + @Test(groups = { "Functional" }) public void testTranslatesAs() { assertTrue(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0, "FPKG".toCharArray())); - // with start codon + // with start codon (not in protein) assertTrue(AlignmentUtils.translatesAs("atgtttcccaaaggg".toCharArray(), 3, "FPKG".toCharArray())); - // with stop codon1 + // with stop codon1 (not in protein) assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtaa".toCharArray(), 0, "FPKG".toCharArray())); - // with stop codon2 + // with stop codon1 (in protein as *) + assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtaa".toCharArray(), + 0, "FPKG*".toCharArray())); + // with stop codon2 (not in protein) assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtag".toCharArray(), 0, "FPKG".toCharArray())); - // with stop codon3 + // with stop codon3 (not in protein) assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtga".toCharArray(), 0, "FPKG".toCharArray())); // with start and stop codon1 assertTrue(AlignmentUtils.translatesAs( - "atgtttcccaaaggtaa".toCharArray(), 3, "FPKG".toCharArray())); + "atgtttcccaaagggtaa".toCharArray(), 3, "FPKG".toCharArray())); + // with start and stop codon1 (in protein as *) + assertTrue(AlignmentUtils.translatesAs( + "atgtttcccaaagggtaa".toCharArray(), 3, "FPKG*".toCharArray())); // with start and stop codon2 assertTrue(AlignmentUtils.translatesAs( - "atgtttcccaaaggtag".toCharArray(), 3, "FPKG".toCharArray())); + "atgtttcccaaagggtag".toCharArray(), 3, "FPKG".toCharArray())); // with start and stop codon3 assertTrue(AlignmentUtils.translatesAs( - "atgtttcccaaaggtga".toCharArray(), 3, "FPKG".toCharArray())); + "atgtttcccaaagggtga".toCharArray(), 3, "FPKG".toCharArray())); + + // with embedded stop codon + assertTrue(AlignmentUtils.translatesAs( + "atgtttTAGcccaaaTAAgggtga".toCharArray(), 3, + "F*PK*G".toCharArray())); // wrong protein assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), - 0, - "FPMG".toCharArray())); + 0, "FPMG".toCharArray())); } /** @@ -613,7 +616,7 @@ public class AlignmentUtilsTests * * @throws IOException */ - @Test + @Test(groups = { "Functional" }) public void testMapProteinToCdna_withStartAndStopCodons() throws IOException { @@ -623,7 +626,7 @@ public class AlignmentUtilsTests protseqs.add(new Sequence("UNIPROT|V12347", "SAR")); AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3])); protein.setDataset(null); - + List dnaseqs = new ArrayList(); // start + SAR: dnaseqs.add(new Sequence("EMBL|A11111", "ATGTCAGCACGC")); @@ -634,7 +637,7 @@ public class AlignmentUtilsTests dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG")); AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4])); cdna.setDataset(null); - + assertTrue(AlignmentUtils.mapProteinToCdna(protein, cdna)); // 3 mappings made, each from 1 to 1 sequence @@ -642,10 +645,10 @@ public class AlignmentUtilsTests assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size()); assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size()); assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size()); - + // V12345 mapped from A22222 - AlignedCodonFrame acf = protein.getCodonFrame( - protein.getSequenceAt(0)).get(0); + AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0)) + .get(0); assertEquals(1, acf.getdnaSeqs().length); assertEquals(cdna.getSequenceAt(1).getDatasetSequence(), acf.getdnaSeqs()[0]); @@ -654,11 +657,11 @@ public class AlignmentUtilsTests MapList mapList = protMappings[0].getMap(); assertEquals(3, mapList.getFromRatio()); assertEquals(1, mapList.getToRatio()); - assertTrue(Arrays.equals(new int[] - { 1, 9 }, mapList.getFromRanges().get(0))); + assertTrue(Arrays.equals(new int[] { 1, 9 }, mapList.getFromRanges() + .get(0))); assertEquals(1, mapList.getFromRanges().size()); - assertTrue(Arrays.equals(new int[] - { 1, 3 }, mapList.getToRanges().get(0))); + assertTrue(Arrays.equals(new int[] { 1, 3 }, + mapList.getToRanges().get(0))); assertEquals(1, mapList.getToRanges().size()); // V12346 mapped from A33333 starting position 4 @@ -671,13 +674,13 @@ public class AlignmentUtilsTests mapList = protMappings[0].getMap(); assertEquals(3, mapList.getFromRatio()); assertEquals(1, mapList.getToRatio()); - assertTrue(Arrays.equals(new int[] - { 4, 12 }, mapList.getFromRanges().get(0))); + assertTrue(Arrays.equals(new int[] { 4, 12 }, mapList.getFromRanges() + .get(0))); assertEquals(1, mapList.getFromRanges().size()); - assertTrue(Arrays.equals(new int[] - { 1, 3 }, mapList.getToRanges().get(0))); + assertTrue(Arrays.equals(new int[] { 1, 3 }, + mapList.getToRanges().get(0))); assertEquals(1, mapList.getToRanges().size()); - + // V12347 mapped to A11111 starting position 4 acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0); assertEquals(1, acf.getdnaSeqs().length); @@ -688,13 +691,13 @@ public class AlignmentUtilsTests mapList = protMappings[0].getMap(); assertEquals(3, mapList.getFromRatio()); assertEquals(1, mapList.getToRatio()); - assertTrue(Arrays.equals(new int[] - { 4, 12 }, mapList.getFromRanges().get(0))); + assertTrue(Arrays.equals(new int[] { 4, 12 }, mapList.getFromRanges() + .get(0))); assertEquals(1, mapList.getFromRanges().size()); - assertTrue(Arrays.equals(new int[] - { 1, 3 }, mapList.getToRanges().get(0))); + assertTrue(Arrays.equals(new int[] { 1, 3 }, + mapList.getToRanges().get(0))); assertEquals(1, mapList.getToRanges().size()); - + // no mapping involving the 'extra' A44444 assertTrue(protein.getCodonFrame(cdna.getSequenceAt(3)).isEmpty()); } @@ -706,7 +709,7 @@ public class AlignmentUtilsTests * * @throws IOException */ - @Test + @Test(groups = { "Functional" }) public void testMapProteinToCdna_withXrefs() throws IOException { List protseqs = new ArrayList(); @@ -715,7 +718,7 @@ public class AlignmentUtilsTests protseqs.add(new Sequence("UNIPROT|V12347", "SAR")); AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3])); protein.setDataset(null); - + List dnaseqs = new ArrayList(); dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR dnaseqs.add(new Sequence("EMBL|A22222", "ATGGAGATACAA")); // = start + EIQ @@ -724,7 +727,7 @@ public class AlignmentUtilsTests dnaseqs.add(new Sequence("EMBL|A55555", "GAGATTCAG")); // = EIQ AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[5])); cdna.setDataset(null); - + // Xref A22222 to V12345 (should get mapped) dnaseqs.get(1).addDBRef(new DBRefEntry("UNIPROT", "1", "V12345")); // Xref V12345 to A44444 (should get mapped) @@ -749,28 +752,28 @@ public class AlignmentUtilsTests assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(1)).size()); assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(2)).size()); assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(3)).size()); - + // V12345 mapped to A22222 and A44444 - AlignedCodonFrame acf = protein.getCodonFrame( - protein.getSequenceAt(0)).get(0); + AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0)) + .get(0); assertEquals(2, acf.getdnaSeqs().length); assertEquals(cdna.getSequenceAt(1).getDatasetSequence(), acf.getdnaSeqs()[0]); assertEquals(cdna.getSequenceAt(3).getDatasetSequence(), acf.getdnaSeqs()[1]); - + // V12346 mapped to A33333 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0); assertEquals(1, acf.getdnaSeqs().length); assertEquals(cdna.getSequenceAt(2).getDatasetSequence(), acf.getdnaSeqs()[0]); - + // V12347 mapped to A11111 acf = protein.getCodonFrame(protein.getSequenceAt(2)).get(0); assertEquals(1, acf.getdnaSeqs().length); assertEquals(cdna.getSequenceAt(0).getDatasetSequence(), acf.getdnaSeqs()[0]); - + // no mapping involving the 'extra' A55555 assertTrue(protein.getCodonFrame(cdna.getSequenceAt(4)).isEmpty()); } @@ -782,7 +785,7 @@ public class AlignmentUtilsTests * * @throws IOException */ - @Test + @Test(groups = { "Functional" }) public void testMapProteinToCdna_prioritiseXrefs() throws IOException { List protseqs = new ArrayList(); @@ -791,36 +794,36 @@ public class AlignmentUtilsTests AlignmentI protein = new Alignment( protseqs.toArray(new SequenceI[protseqs.size()])); protein.setDataset(null); - + List dnaseqs = new ArrayList(); dnaseqs.add(new Sequence("EMBL|A11111", "GAAATCCAG")); // = EIQ dnaseqs.add(new Sequence("EMBL|A22222", "GAAATTCAG")); // = EIQ AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[dnaseqs .size()])); cdna.setDataset(null); - + // Xref A22222 to V12345 (should get mapped) // A11111 should then be mapped to the unmapped V12346 dnaseqs.get(1).addDBRef(new DBRefEntry("UNIPROT", "1", "V12345")); - + assertTrue(AlignmentUtils.mapProteinToCdna(protein, cdna)); - + // 2 protein mappings made assertEquals(2, protein.getCodonFrames().size()); assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size()); assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size()); - + // one mapping for each of the cDNA sequences assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(0)).size()); assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(1)).size()); - + // V12345 mapped to A22222 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0)) .get(0); assertEquals(1, acf.getdnaSeqs().length); assertEquals(cdna.getSequenceAt(1).getDatasetSequence(), acf.getdnaSeqs()[0]); - + // V12346 mapped to A11111 acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0); assertEquals(1, acf.getdnaSeqs().length); @@ -832,14 +835,13 @@ public class AlignmentUtilsTests * Test the method that shows or hides sequence annotations by type(s) and * selection group. */ - @Test + @Test(groups = { "Functional" }) public void testShowOrHideSequenceAnnotations() { SequenceI seq1 = new Sequence("Seq1", "AAA"); SequenceI seq2 = new Sequence("Seq2", "BBB"); SequenceI seq3 = new Sequence("Seq3", "CCC"); - Annotation[] anns = new Annotation[] - { new Annotation(2f) }; + Annotation[] anns = new Annotation[] { new Annotation(2f) }; AlignmentAnnotation ann1 = new AlignmentAnnotation("Structure", "ann1", anns); ann1.setSequenceRef(seq1); @@ -853,7 +855,7 @@ public class AlignmentUtilsTests AlignmentAnnotation ann5 = new AlignmentAnnotation("Temp", "ann5", anns); ann5.setSequenceRef(seq2); AlignmentAnnotation ann6 = new AlignmentAnnotation("Temp", "ann6", anns); - AlignmentI al = new Alignment(new SequenceI[] {seq1, seq2, seq3}); + AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2, seq3 }); al.addAnnotation(ann1); // Structure for Seq1 al.addAnnotation(ann2); // Structure for Seq2 al.addAnnotation(ann3); // Structure for no sequence @@ -940,7 +942,7 @@ public class AlignmentUtilsTests /** * Tests for the method that checks if one sequence cross-references another */ - @Test + @Test(groups = { "Functional" }) public void testHasCrossRef() { assertFalse(AlignmentUtils.hasCrossRef(null, null)); @@ -949,15 +951,15 @@ public class AlignmentUtilsTests assertFalse(AlignmentUtils.hasCrossRef(null, seq1)); SequenceI seq2 = new Sequence("UNIPROT|V20192", "ABCDEF"); assertFalse(AlignmentUtils.hasCrossRef(seq1, seq2)); - + // different ref seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "v20193")); assertFalse(AlignmentUtils.hasCrossRef(seq1, seq2)); - + // case-insensitive; version number is ignored seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "v20192")); assertTrue(AlignmentUtils.hasCrossRef(seq1, seq2)); - + // right case! seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192")); assertTrue(AlignmentUtils.hasCrossRef(seq1, seq2)); @@ -969,7 +971,7 @@ public class AlignmentUtilsTests * Tests for the method that checks if either sequence cross-references the * other */ - @Test + @Test(groups = { "Functional" }) public void testHaveCrossRef() { assertFalse(AlignmentUtils.hasCrossRef(null, null)); @@ -978,18 +980,18 @@ public class AlignmentUtilsTests assertFalse(AlignmentUtils.haveCrossRef(null, seq1)); SequenceI seq2 = new Sequence("UNIPROT|V20192", "ABCDEF"); assertFalse(AlignmentUtils.haveCrossRef(seq1, seq2)); - + seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192")); assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2)); // next is true for haveCrossRef, false for hasCrossRef assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1)); - + // now the other way round seq1.setDBRef(null); seq2.addDBRef(new DBRefEntry("EMBL", "1", "A12345")); assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2)); assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1)); - + // now both ways seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192")); assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2)); @@ -999,7 +1001,7 @@ public class AlignmentUtilsTests /** * Test the method that extracts the exon-only part of a dna alignment. */ - @Test + @Test(groups = { "Functional" }) public void testMakeExonAlignment() { SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa"); @@ -1012,21 +1014,19 @@ public class AlignmentUtilsTests pep2.createDatasetSequence(); Set mappings = new HashSet(); - MapList map = new MapList(new int[] - { 4, 6, 10, 12 }, new int[] - { 1, 2 }, 3, 1); + MapList map = new MapList(new int[] { 4, 6, 10, 12 }, + new int[] { 1, 2 }, 3, 1); AlignedCodonFrame acf = new AlignedCodonFrame(); acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map); mappings.add(acf); - map = new MapList(new int[] - { 1, 3, 7, 9, 13, 15 }, new int[] - { 1, 3 }, 3, 1); + map = new MapList(new int[] { 1, 3, 7, 9, 13, 15 }, new int[] { 1, 3 }, + 3, 1); acf = new AlignedCodonFrame(); acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map); mappings.add(acf); - - AlignmentI exons = AlignmentUtils.makeExonAlignment(new SequenceI[] - { dna1, dna2 }, mappings); + + AlignmentI exons = AlignmentUtils.makeExonAlignment(new SequenceI[] { + dna1, dna2 }, mappings); assertEquals(2, exons.getSequences().size()); assertEquals("GGGTTT", exons.getSequenceAt(0).getSequenceAsString()); assertEquals("GGGTTTCCC", exons.getSequenceAt(1).getSequenceAsString()); @@ -1094,7 +1094,7 @@ public class AlignmentUtilsTests * already has a protein product (Uniprot translation) which in turn has an * x-ref to the EMBLCDS record. */ - @Test + @Test(groups = { "Functional" }) public void testMakeExonSequences() { SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa"); @@ -1109,9 +1109,8 @@ public class AlignmentUtilsTests * EMBLCDS|A12345. */ Set mappings = new HashSet(); - MapList map = new MapList(new int[] - { 4, 6, 10, 12 }, new int[] - { 1, 2 }, 3, 1); + MapList map = new MapList(new int[] { 4, 6, 10, 12 }, + new int[] { 1, 2 }, 3, 1); AlignedCodonFrame acf = new AlignedCodonFrame(); acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map); mappings.add(acf); @@ -1136,7 +1135,7 @@ public class AlignmentUtilsTests * its product mappings, for the case where there are multiple exon mappings * to different protein products. */ - @Test + @Test(groups = { "Functional" }) public void testMakeExonAlignment_multipleProteins() { SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa"); @@ -1161,25 +1160,20 @@ public class AlignmentUtilsTests */ Set mappings = new LinkedHashSet(); // map ...GGG...TTT to GF - MapList map = new MapList(new int[] - { 4, 6, 10, 12 }, new int[] - { 1, 2 }, 3, 1); + MapList map = new MapList(new int[] { 4, 6, 10, 12 }, + new int[] { 1, 2 }, 3, 1); AlignedCodonFrame acf = new AlignedCodonFrame(); acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map); mappings.add(acf); // map aaa...ccc to KP - map = new MapList(new int[] - { 1, 3, 7, 9 }, new int[] - { 1, 2 }, 3, 1); + map = new MapList(new int[] { 1, 3, 7, 9 }, new int[] { 1, 2 }, 3, 1); acf = new AlignedCodonFrame(); acf.addMap(dna1.getDatasetSequence(), pep2.getDatasetSequence(), map); mappings.add(acf); // map aaa......TTT to KF - map = new MapList(new int[] - { 1, 3, 10, 12 }, new int[] - { 1, 2 }, 3, 1); + map = new MapList(new int[] { 1, 3, 10, 12 }, new int[] { 1, 2 }, 3, 1); acf = new AlignedCodonFrame(); acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map); mappings.add(acf); @@ -1188,8 +1182,8 @@ public class AlignmentUtilsTests * Create the Exon alignment; also replaces the dna-to-protein mappings with * exon-to-protein and exon-to-dna mappings */ - AlignmentI exal = AlignmentUtils.makeExonAlignment(new SequenceI[] - { dna1 }, mappings); + AlignmentI exal = AlignmentUtils.makeExonAlignment( + new SequenceI[] { dna1 }, mappings); /* * Verify we have 3 exon sequences, mapped to pep1/2/3 respectively @@ -1267,4 +1261,22 @@ public class AlignmentUtilsTests assertEquals(1, peptideMappings.size()); assertSame(pep3.getDatasetSequence(), peptideMappings.get(0).getTo()); } + + @Test(groups = { "Functional" }) + public void testIsMappable() + { + SequenceI dna1 = new Sequence("dna1", "cgCAGtgGT"); + SequenceI aa1 = new Sequence("aa1", "RSG"); + AlignmentI al1 = new Alignment(new SequenceI[] { dna1 }); + AlignmentI al2 = new Alignment(new SequenceI[] { aa1 }); + + assertFalse(AlignmentUtils.isMappable(null, null)); + assertFalse(AlignmentUtils.isMappable(al1, null)); + assertFalse(AlignmentUtils.isMappable(null, al1)); + assertFalse(AlignmentUtils.isMappable(al1, al1)); + assertFalse(AlignmentUtils.isMappable(al2, al2)); + + assertTrue(AlignmentUtils.isMappable(al1, al2)); + assertTrue(AlignmentUtils.isMappable(al2, al1)); + } }