X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FAlignmentUtilsTests.java;h=a82a881f91586833ac48c228f684689888797fdb;hb=c6c67aaa8e2d236305a3495f4edfc8cc88e22b79;hp=10fb81fe573e6e709a4b7c578d04d595c263e042;hpb=6dd554fdbf34db6b79595d5027159d20225f4894;p=jalview.git diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java index 10fb81f..a82a881 100644 --- a/test/jalview/analysis/AlignmentUtilsTests.java +++ b/test/jalview/analysis/AlignmentUtilsTests.java @@ -20,11 +20,12 @@ */ package jalview.analysis; -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertFalse; -import static org.junit.Assert.assertNull; -import static org.junit.Assert.assertSame; -import static org.junit.Assert.assertTrue; +import static org.testng.AssertJUnit.assertEquals; +import static org.testng.AssertJUnit.assertFalse; +import static org.testng.AssertJUnit.assertNull; +import static org.testng.AssertJUnit.assertSame; +import static org.testng.AssertJUnit.assertTrue; + import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; @@ -35,6 +36,7 @@ import jalview.datamodel.Mapping; import jalview.datamodel.SearchResults; import jalview.datamodel.SearchResults.Match; import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.io.AppletFormatAdapter; import jalview.io.FormatAdapter; @@ -44,17 +46,15 @@ import jalview.util.MappingUtils; import java.io.IOException; import java.util.ArrayList; import java.util.Arrays; -import java.util.Collections; import java.util.HashSet; import java.util.Iterator; -import java.util.LinkedHashSet; import java.util.List; import java.util.Map; import java.util.Set; -import org.junit.Test; +import org.testng.annotations.Test; -public class AlignmentUtilsTests +public class AlignmentUtilsTests { // @formatter:off private static final String TEST_DATA = @@ -94,17 +94,18 @@ 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); @@ -148,11 +149,10 @@ 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); @@ -161,8 +161,8 @@ 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); @@ -238,7 +238,7 @@ public class AlignmentUtilsTests * * @throws IOException */ - @Test + @Test(groups = { "Functional" }) public void testGetSequencesByName() throws IOException { final String data = ">Seq1Name\nKQYL\n" + ">Seq2Name\nRFPW\n" @@ -253,22 +253,25 @@ 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 @@ -276,8 +279,8 @@ public class AlignmentUtilsTests * * @throws IOException */ - @Test - public void testMapProteinToCdna_noXrefs() throws IOException + @Test(groups = { "Functional" }) + public void testMapProteinAlignmentToCdna_noXrefs() throws IOException { List protseqs = new ArrayList(); protseqs.add(new Sequence("UNIPROT|V12345", "EIQ")); @@ -294,7 +297,7 @@ public class AlignmentUtilsTests AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4])); cdna.setDataset(null); - assertTrue(AlignmentUtils.mapProteinToCdna(protein, cdna)); + assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna)); // 3 mappings made, each from 1 to 1 sequence assertEquals(3, protein.getCodonFrames().size()); @@ -303,8 +306,8 @@ 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]); @@ -313,11 +316,11 @@ 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 @@ -339,12 +342,10 @@ 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: @@ -370,8 +371,8 @@ public class AlignmentUtilsTests * region). The leading gap, and the gaps between codons, are subsumed by * the protein alignment gap. */ - checkAlignSequenceAs("-G-GG--AA-A-", "-A-L-", true, true, map, - "---G-GG---AA-A-"); + checkAlignSequenceAs("-G-GG--AA-A---", "-A-L-", true, true, map, + "---G-GG---AA-A---"); /* * Include only unmapped gaps in dna when realigning (outside the exon @@ -379,21 +380,20 @@ public class AlignmentUtilsTests * the protein alignment gap. */ checkAlignSequenceAs("-G-GG--AA-A-", "-A-L-", false, true, map, - "---GGG---AAA-"); + "---GGG---AAA---"); } /** * 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 @@ -435,76 +435,72 @@ 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. + * -L- 'aligns' ccc------ */ - checkAlignSequenceAs("GGGAAACCCTTTGGG", "-A-L-P-", false, - false, map, "GGGAAACCCTTTGGG"); + checkAlignSequenceAs("gggAAAcccTTTggg", "-A-L-P-", false, false, map, + "gggAAAccc------TTTggg"); } /** * Helper method that performs and verifies the method under test. * - * @param dnaSeq - * @param proteinSeq + * @param alignee + * the sequence to be realigned + * @param alignModel + * the sequence whose alignment is to be copied * @param preserveMappedGaps * @param preserveUnmappedGaps * @param map * @param expected */ - protected void checkAlignSequenceAs(final String dnaSeq, - final String proteinSeq, final boolean preserveMappedGaps, + protected void checkAlignSequenceAs(final String alignee, + final String alignModel, final boolean preserveMappedGaps, final boolean preserveUnmappedGaps, MapList map, final String expected) { - SequenceI dna = new Sequence("Seq1", dnaSeq); - dna.createDatasetSequence(); - SequenceI protein = new Sequence("Seq1", proteinSeq); - protein.createDatasetSequence(); + SequenceI alignMe = new Sequence("Seq1", alignee); + alignMe.createDatasetSequence(); + SequenceI alignFrom = new Sequence("Seq2", alignModel); + alignFrom.createDatasetSequence(); AlignedCodonFrame acf = new AlignedCodonFrame(); - acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map); + acf.addMap(alignMe.getDatasetSequence(), alignFrom.getDatasetSequence(), map); - AlignmentUtils.alignSequenceAs(dna, protein, acf, "---", '-', + AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "---", '-', preserveMappedGaps, preserveUnmappedGaps); - assertEquals(expected, dna.getSequenceAsString()); + assertEquals(expected, alignMe.getSequenceAsString()); } /** * 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 @@ -513,22 +509,21 @@ 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] @@ -537,26 +532,26 @@ 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); acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map); - protein.setCodonFrames(Collections.singleton(acf)); + ArrayList acfs = new ArrayList(); + acfs.add(acf); + protein.setCodonFrames(acfs); /* * Translated codon order is [1,2,3] [1,3,4] [4,5,6] [4,5,7] [5,6,7] [7,8,9] @@ -566,43 +561,54 @@ 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())); } /** @@ -611,8 +617,8 @@ public class AlignmentUtilsTests * * @throws IOException */ - @Test - public void testMapProteinToCdna_withStartAndStopCodons() + @Test(groups = { "Functional" }) + public void testMapProteinAlignmentToCdna_withStartAndStopCodons() throws IOException { List protseqs = new ArrayList(); @@ -621,7 +627,7 @@ 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")); @@ -632,18 +638,18 @@ 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)); + + assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna)); // 3 mappings made, each from 1 to 1 sequence assertEquals(3, protein.getCodonFrames().size()); 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]); @@ -652,11 +658,11 @@ 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 @@ -669,13 +675,13 @@ 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); @@ -686,13 +692,13 @@ 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()); } @@ -704,8 +710,8 @@ public class AlignmentUtilsTests * * @throws IOException */ - @Test - public void testMapProteinToCdna_withXrefs() throws IOException + @Test(groups = { "Functional" }) + public void testMapProteinAlignmentToCdna_withXrefs() throws IOException { List protseqs = new ArrayList(); protseqs.add(new Sequence("UNIPROT|V12345", "EIQ")); @@ -713,7 +719,7 @@ 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 @@ -722,7 +728,7 @@ 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) @@ -734,7 +740,7 @@ public class AlignmentUtilsTests // A11111 should be mapped to V12347 // A55555 is spare and has no xref so is not mapped - assertTrue(AlignmentUtils.mapProteinToCdna(protein, cdna)); + assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna)); // 4 protein mappings made for 3 proteins, 2 to V12345, 1 each to V12346/7 assertEquals(3, protein.getCodonFrames().size()); @@ -747,28 +753,28 @@ 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()); } @@ -780,8 +786,9 @@ public class AlignmentUtilsTests * * @throws IOException */ - @Test - public void testMapProteinToCdna_prioritiseXrefs() throws IOException + @Test(groups = { "Functional" }) + public void testMapProteinAlignmentToCdna_prioritiseXrefs() + throws IOException { List protseqs = new ArrayList(); protseqs.add(new Sequence("UNIPROT|V12345", "EIQ")); @@ -789,36 +796,36 @@ 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)); - + + assertTrue(AlignmentUtils.mapProteinAlignmentToCdna(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); @@ -830,14 +837,13 @@ 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); @@ -851,7 +857,7 @@ 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 @@ -938,7 +944,7 @@ 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)); @@ -947,15 +953,15 @@ 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)); @@ -967,7 +973,7 @@ 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)); @@ -976,18 +982,18 @@ 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); + seq1.setDBRefs(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)); @@ -995,10 +1001,10 @@ public class AlignmentUtilsTests } /** - * Test the method that extracts the exon-only part of a dna alignment. + * Test the method that extracts the cds-only part of a dna alignment. */ - @Test - public void testMakeExonAlignment() + @Test(groups = { "Functional" }) + public void testMakeCdsAlignment() { SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa"); SequenceI dna2 = new Sequence("dna2", "GGGcccTTTaaaCCC"); @@ -1009,25 +1015,23 @@ public class AlignmentUtilsTests pep1.createDatasetSequence(); pep2.createDatasetSequence(); - Set mappings = new HashSet(); - MapList map = new MapList(new int[] - { 4, 6, 10, 12 }, new int[] - { 1, 2 }, 3, 1); + List mappings = new ArrayList(); + 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); - assertEquals(2, exons.getSequences().size()); - assertEquals("GGGTTT", exons.getSequenceAt(0).getSequenceAsString()); - assertEquals("GGGTTTCCC", exons.getSequenceAt(1).getSequenceAsString()); + + AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] { + dna1, dna2 }, mappings); + assertEquals(2, cds.getSequences().size()); + assertEquals("GGGTTT", cds.getSequenceAt(0).getSequenceAsString()); + assertEquals("GGGTTTCCC", cds.getSequenceAt(1).getSequenceAsString()); /* * Verify updated mappings @@ -1044,14 +1048,14 @@ public class AlignmentUtilsTests SearchResults sr = MappingUtils.buildSearchResults(pep1, 1, mappings); assertEquals(1, sr.getResults().size()); Match m = sr.getResults().get(0); - assertEquals(exons.getSequenceAt(0).getDatasetSequence(), + assertEquals(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence()); assertEquals(1, m.getStart()); assertEquals(3, m.getEnd()); // map F to TTT sr = MappingUtils.buildSearchResults(pep1, 2, mappings); m = sr.getResults().get(0); - assertEquals(exons.getSequenceAt(0).getDatasetSequence(), + assertEquals(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence()); assertEquals(4, m.getStart()); assertEquals(6, m.getEnd()); @@ -1066,34 +1070,34 @@ public class AlignmentUtilsTests sr = MappingUtils.buildSearchResults(pep2, 1, mappings); assertEquals(1, sr.getResults().size()); m = sr.getResults().get(0); - assertEquals(exons.getSequenceAt(1).getDatasetSequence(), + assertEquals(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence()); assertEquals(1, m.getStart()); assertEquals(3, m.getEnd()); // map F to TTT sr = MappingUtils.buildSearchResults(pep2, 2, mappings); m = sr.getResults().get(0); - assertEquals(exons.getSequenceAt(1).getDatasetSequence(), + assertEquals(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence()); assertEquals(4, m.getStart()); assertEquals(6, m.getEnd()); // map P to CCC sr = MappingUtils.buildSearchResults(pep2, 3, mappings); m = sr.getResults().get(0); - assertEquals(exons.getSequenceAt(1).getDatasetSequence(), + assertEquals(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence()); assertEquals(7, m.getStart()); assertEquals(9, m.getEnd()); } /** - * Test the method that makes an exon-only sequence from a DNA sequence and - * its product mapping. Test includes the expected case that the DNA sequence + * Test the method that makes a cds-only sequence from a DNA sequence and its + * product mapping. Test includes the expected case that the DNA sequence * already has a protein product (Uniprot translation) which in turn has an * x-ref to the EMBLCDS record. */ - @Test - public void testMakeExonSequences() + @Test(groups = { "Functional" }) + public void testMakeCdsSequences() { SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa"); SequenceI pep1 = new Sequence("pep1", "GF"); @@ -1107,35 +1111,34 @@ 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); AlignedCodonFrame newMapping = new AlignedCodonFrame(); - List exons = AlignmentUtils.makeExonSequences(dna1, acf, + List cdsSeqs = AlignmentUtils.makeCdsSequences(dna1, acf, newMapping); - assertEquals(1, exons.size()); - SequenceI exon = exons.get(0); + assertEquals(1, cdsSeqs.size()); + SequenceI cdsSeq = cdsSeqs.get(0); - assertEquals("GGGTTT", exon.getSequenceAsString()); - assertEquals("dna1|A12345", exon.getName()); - assertEquals(1, exon.getDBRef().length); - DBRefEntry cdsRef = exon.getDBRef()[0]; + assertEquals("GGGTTT", cdsSeq.getSequenceAsString()); + assertEquals("dna1|A12345", cdsSeq.getName()); + assertEquals(1, cdsSeq.getDBRefs().length); + DBRefEntry cdsRef = cdsSeq.getDBRefs()[0]; assertEquals("EMBLCDS", cdsRef.getSource()); assertEquals("2", cdsRef.getVersion()); assertEquals("A12345", cdsRef.getAccessionId()); } /** - * Test the method that makes an exon-only alignment from a DNA sequence and - * its product mappings, for the case where there are multiple exon mappings - * to different protein products. + * Test the method that makes a cds-only alignment from a DNA sequence and its + * product mappings, for the case where there are multiple exon mappings to + * different protein products. */ - @Test - public void testMakeExonAlignment_multipleProteins() + @Test(groups = { "Functional" }) + public void testMakeCdsAlignment_multipleProteins() { SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa"); SequenceI pep1 = new Sequence("pep1", "GF"); // GGGTTT @@ -1157,27 +1160,22 @@ public class AlignmentUtilsTests * convenience so results are in the input order. There is no assertion that * the generated exon sequences are in any particular order. */ - Set mappings = new LinkedHashSet(); + List mappings = new ArrayList(); // 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); @@ -1186,83 +1184,310 @@ 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.makeCdsAlignment( + new SequenceI[] { dna1 }, mappings); /* - * Verify we have 3 exon sequences, mapped to pep1/2/3 respectively + * Verify we have 3 cds sequences, mapped to pep1/2/3 respectively */ - List exons = exal.getSequences(); - assertEquals(3, exons.size()); - - SequenceI exon = exons.get(0); - assertEquals("GGGTTT", exon.getSequenceAsString()); - assertEquals("dna1|A12345", exon.getName()); - assertEquals(1, exon.getDBRef().length); - DBRefEntry cdsRef = exon.getDBRef()[0]; + List cds = exal.getSequences(); + assertEquals(3, cds.size()); + + SequenceI cdsSeq = cds.get(0); + assertEquals("GGGTTT", cdsSeq.getSequenceAsString()); + assertEquals("dna1|A12345", cdsSeq.getName()); + assertEquals(1, cdsSeq.getDBRefs().length); + DBRefEntry cdsRef = cdsSeq.getDBRefs()[0]; assertEquals("EMBLCDS", cdsRef.getSource()); assertEquals("2", cdsRef.getVersion()); assertEquals("A12345", cdsRef.getAccessionId()); - exon = exons.get(1); - assertEquals("aaaccc", exon.getSequenceAsString()); - assertEquals("dna1|A12346", exon.getName()); - assertEquals(1, exon.getDBRef().length); - cdsRef = exon.getDBRef()[0]; + cdsSeq = cds.get(1); + assertEquals("aaaccc", cdsSeq.getSequenceAsString()); + assertEquals("dna1|A12346", cdsSeq.getName()); + assertEquals(1, cdsSeq.getDBRefs().length); + cdsRef = cdsSeq.getDBRefs()[0]; assertEquals("EMBLCDS", cdsRef.getSource()); assertEquals("3", cdsRef.getVersion()); assertEquals("A12346", cdsRef.getAccessionId()); - exon = exons.get(2); - assertEquals("aaaTTT", exon.getSequenceAsString()); - assertEquals("dna1|A12347", exon.getName()); - assertEquals(1, exon.getDBRef().length); - cdsRef = exon.getDBRef()[0]; + cdsSeq = cds.get(2); + assertEquals("aaaTTT", cdsSeq.getSequenceAsString()); + assertEquals("dna1|A12347", cdsSeq.getName()); + assertEquals(1, cdsSeq.getDBRefs().length); + cdsRef = cdsSeq.getDBRefs()[0]; assertEquals("EMBLCDS", cdsRef.getSource()); assertEquals("4", cdsRef.getVersion()); assertEquals("A12347", cdsRef.getAccessionId()); /* - * Verify there are mappings from each exon sequence to its protein product + * Verify there are mappings from each cds sequence to its protein product * and also to its dna source */ Iterator newMappingsIterator = mappings.iterator(); // mappings for dna1 - exon1 - pep1 - AlignedCodonFrame exonMapping = newMappingsIterator.next(); - List dnaMappings = exonMapping.getMappingsForSequence(dna1); + AlignedCodonFrame cdsMapping = newMappingsIterator.next(); + List dnaMappings = cdsMapping.getMappingsForSequence(dna1); assertEquals(1, dnaMappings.size()); - assertSame(exons.get(0).getDatasetSequence(), dnaMappings.get(0) + assertSame(cds.get(0).getDatasetSequence(), dnaMappings.get(0) .getTo()); assertEquals("G(1) in CDS should map to G(4) in DNA", 4, dnaMappings .get(0).getMap().getToPosition(1)); - List peptideMappings = exonMapping + List peptideMappings = cdsMapping .getMappingsForSequence(pep1); assertEquals(1, peptideMappings.size()); assertSame(pep1.getDatasetSequence(), peptideMappings.get(0).getTo()); - // mappings for dna1 - exon2 - pep2 - exonMapping = newMappingsIterator.next(); - dnaMappings = exonMapping.getMappingsForSequence(dna1); + // mappings for dna1 - cds2 - pep2 + cdsMapping = newMappingsIterator.next(); + dnaMappings = cdsMapping.getMappingsForSequence(dna1); assertEquals(1, dnaMappings.size()); - assertSame(exons.get(1).getDatasetSequence(), dnaMappings.get(0) + assertSame(cds.get(1).getDatasetSequence(), dnaMappings.get(0) .getTo()); assertEquals("c(4) in CDS should map to c(7) in DNA", 7, dnaMappings .get(0).getMap().getToPosition(4)); - peptideMappings = exonMapping.getMappingsForSequence(pep2); + peptideMappings = cdsMapping.getMappingsForSequence(pep2); assertEquals(1, peptideMappings.size()); assertSame(pep2.getDatasetSequence(), peptideMappings.get(0).getTo()); - // mappings for dna1 - exon3 - pep3 - exonMapping = newMappingsIterator.next(); - dnaMappings = exonMapping.getMappingsForSequence(dna1); + // mappings for dna1 - cds3 - pep3 + cdsMapping = newMappingsIterator.next(); + dnaMappings = cdsMapping.getMappingsForSequence(dna1); assertEquals(1, dnaMappings.size()); - assertSame(exons.get(2).getDatasetSequence(), dnaMappings.get(0) + assertSame(cds.get(2).getDatasetSequence(), dnaMappings.get(0) .getTo()); assertEquals("T(4) in CDS should map to T(10) in DNA", 10, dnaMappings .get(0).getMap().getToPosition(4)); - peptideMappings = exonMapping.getMappingsForSequence(pep3); + peptideMappings = cdsMapping.getMappingsForSequence(pep3); 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)); + } + + /** + * Test creating a mapping when the sequences involved do not start at residue + * 1 + * + * @throws IOException + */ + @Test(groups = { "Functional" }) + public void testMapProteinSequenceToCdna_forSubsequence() + throws IOException + { + SequenceI prot = new Sequence("UNIPROT|V12345", "E-I--Q", 10, 12); + prot.createDatasetSequence(); + + SequenceI dna = new Sequence("EMBL|A33333", "GAA--AT-C-CAG", 40, 48); + dna.createDatasetSequence(); + + MapList map = AlignmentUtils.mapProteinSequenceToCdna(prot, dna); + assertEquals(10, map.getToLowest()); + assertEquals(12, map.getToHighest()); + assertEquals(40, map.getFromLowest()); + assertEquals(48, map.getFromHighest()); + } + + /** + * Test for the alignSequenceAs method where we have protein mapped to protein + */ + @Test(groups = { "Functional" }) + public void testAlignSequenceAs_mappedProteinProtein() + { + + SequenceI alignMe = new Sequence("Match", "MGAASEV"); + alignMe.createDatasetSequence(); + SequenceI alignFrom = new Sequence("Query", "LQTGYMGAASEVMFSPTRR"); + alignFrom.createDatasetSequence(); + + AlignedCodonFrame acf = new AlignedCodonFrame(); + // this is like a domain or motif match of part of a peptide sequence + MapList map = new MapList(new int[] { 6, 12 }, new int[] { 1, 7 }, 1, 1); + acf.addMap(alignFrom.getDatasetSequence(), + alignMe.getDatasetSequence(), map); + + AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "-", '-', true, + true); + assertEquals("-----MGAASEV-------", alignMe.getSequenceAsString()); + } + + /** + * Test for the alignSequenceAs method where there are trailing unmapped + * residues in the model sequence + */ + @Test(groups = { "Functional" }) + public void testAlignSequenceAs_withTrailingPeptide() + { + // map first 3 codons to KPF; G is a trailing unmapped residue + MapList map = new MapList(new int[] { 1, 9 }, new int[] { 1, 3 }, 3, 1); + + checkAlignSequenceAs("AAACCCTTT", "K-PFG", true, true, map, + "AAA---CCCTTT---"); + } + + /** + * Tests for transferring features between mapped sequences + */ + @Test(groups = { "Functional" }) + public void testTransferFeatures() + { + SequenceI dna = new Sequence("dna/20-34", "acgTAGcaaGCCcgt"); + SequenceI cds = new Sequence("cds/10-15", "TAGGCC"); + + // no overlap + dna.addSequenceFeature(new SequenceFeature("type1", "desc1", 1, 2, 1f, + null)); + // partial overlap - to [1, 1] + dna.addSequenceFeature(new SequenceFeature("type2", "desc2", 3, 4, 2f, + null)); + // exact overlap - to [1, 3] + dna.addSequenceFeature(new SequenceFeature("type3", "desc3", 4, 6, 3f, + null)); + // spanning overlap - to [2, 5] + dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f, + null)); + // exactly overlaps whole mapped range [1, 6] + dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f, + null)); + // no overlap (internal) + dna.addSequenceFeature(new SequenceFeature("type6", "desc6", 7, 9, 6f, + null)); + // no overlap (3' end) + dna.addSequenceFeature(new SequenceFeature("type7", "desc7", 13, 15, + 7f, null)); + // overlap (3' end) - to [6, 6] + dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12, + 8f, null)); + // extended overlap - to [6, +] + dna.addSequenceFeature(new SequenceFeature("type9", "desc9", 12, 13, + 9f, null)); + + MapList map = new MapList(new int[] { 4, 6, 10, 12 }, + new int[] { 1, 6 }, 1, 1); + + /* + * transferFeatures() will build 'partial overlap' for regions + * that partially overlap 5' or 3' (start or end) of target sequence + */ + AlignmentUtils.transferFeatures(dna, cds, map, null); + SequenceFeature[] sfs = cds.getSequenceFeatures(); + assertEquals(6, sfs.length); + + SequenceFeature sf = sfs[0]; + assertEquals("type2", sf.getType()); + assertEquals("desc2", sf.getDescription()); + assertEquals(2f, sf.getScore()); + assertEquals(1, sf.getBegin()); + assertEquals(1, sf.getEnd()); + + sf = sfs[1]; + assertEquals("type3", sf.getType()); + assertEquals("desc3", sf.getDescription()); + assertEquals(3f, sf.getScore()); + assertEquals(1, sf.getBegin()); + assertEquals(3, sf.getEnd()); + + sf = sfs[2]; + assertEquals("type4", sf.getType()); + assertEquals(2, sf.getBegin()); + assertEquals(5, sf.getEnd()); + + sf = sfs[3]; + assertEquals("type5", sf.getType()); + assertEquals(1, sf.getBegin()); + assertEquals(6, sf.getEnd()); + + sf = sfs[4]; + assertEquals("type8", sf.getType()); + assertEquals(6, sf.getBegin()); + assertEquals(6, sf.getEnd()); + + sf = sfs[5]; + assertEquals("type9", sf.getType()); + assertEquals(6, sf.getBegin()); + assertEquals(6, sf.getEnd()); + } + + /** + * Tests for transferring features between mapped sequences + */ + @Test(groups = { "Functional" }) + public void testTransferFeatures_withOmit() + { + SequenceI dna = new Sequence("dna/20-34", "acgTAGcaaGCCcgt"); + SequenceI cds = new Sequence("cds/10-15", "TAGGCC"); + + MapList map = new MapList(new int[] { 4, 6, 10, 12 }, + new int[] { 1, 6 }, 1, 1); + + // [5, 11] maps to [2, 5] + dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f, + null)); + // [4, 12] maps to [1, 6] + dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f, + null)); + // [12, 12] maps to [6, 6] + dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12, + 8f, null)); + + // desc4 and desc8 are the 'omit these' varargs + AlignmentUtils.transferFeatures(dna, cds, map, null, "type4", "type8"); + SequenceFeature[] sfs = cds.getSequenceFeatures(); + assertEquals(1, sfs.length); + + SequenceFeature sf = sfs[0]; + assertEquals("type5", sf.getType()); + assertEquals(1, sf.getBegin()); + assertEquals(6, sf.getEnd()); + } + + /** + * Tests for transferring features between mapped sequences + */ + @Test(groups = { "Functional" }) + public void testTransferFeatures_withSelect() + { + SequenceI dna = new Sequence("dna/20-34", "acgTAGcaaGCCcgt"); + SequenceI cds = new Sequence("cds/10-15", "TAGGCC"); + + MapList map = new MapList(new int[] { 4, 6, 10, 12 }, + new int[] { 1, 6 }, 1, 1); + + // [5, 11] maps to [2, 5] + dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f, + null)); + // [4, 12] maps to [1, 6] + dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f, + null)); + // [12, 12] maps to [6, 6] + dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12, + 8f, null)); + + // "type5" is the 'select this type' argument + AlignmentUtils.transferFeatures(dna, cds, map, "type5"); + SequenceFeature[] sfs = cds.getSequenceFeatures(); + assertEquals(1, sfs.length); + + SequenceFeature sf = sfs[0]; + assertEquals("type5", sf.getType()); + assertEquals(1, sf.getBegin()); + assertEquals(6, sf.getEnd()); + } }