+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.analysis;
-import org.junit.Test;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
+import jalview.analysis.AlignmentUtils.DnaVariant;
+import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.DBRefEntry;
+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;
+import jalview.util.MapList;
+import jalview.util.MappingUtils;
-public class AlignmentUtilsTests
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+
+import org.testng.annotations.Test;
+
+public class AlignmentUtilsTests
{
- public static Sequence ts=new Sequence("short","ASDASDASDASDASDASDASDASDASDASDASDASDASD");
- @Test
- public void testExpandFlanks()
+ public static Sequence ts = new Sequence("short",
+ "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
+
+ @Test(groups = { "Functional" })
+ public void testExpandContext()
{
AlignmentI al = new Alignment(new Sequence[] {});
- for (int i=4;i<14;i+=3)
+ 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++)
{
- System.out.println("\nFlank size: "+flnk);
- System.out.println(new AppletFormatAdapter().formatSequences("Clustal", AlignmentUtils.expandContext(al, flnk), true));
- }
+ AlignmentI exp = AlignmentUtils.expandContext(al, flnk);
+ System.out.println("\nFlank size: " + flnk);
+ System.out.println(new AppletFormatAdapter().formatSequences(
+ "Clustal", exp, true));
+ if (flnk == -1)
+ {
+ /*
+ * Full expansion to complete sequences
+ */
+ for (SequenceI sq : exp.getSequences())
+ {
+ String ung = sq.getSequenceAsString().replaceAll("-+", "");
+ final String errorMsg = "Flanking sequence not the same as original dataset sequence.\n"
+ + ung
+ + "\n"
+ + sq.getDatasetSequence().getSequenceAsString();
+ assertTrue(errorMsg, ung.equalsIgnoreCase(sq.getDatasetSequence()
+ .getSequenceAsString()));
+ }
+ }
+ else if (flnk == 24)
+ {
+ /*
+ * Last sequence is fully expanded, others have leading gaps to match
+ */
+ assertTrue(exp.getSequenceAt(4).getSequenceAsString()
+ .startsWith("abc"));
+ assertTrue(exp.getSequenceAt(3).getSequenceAsString()
+ .startsWith("--abc"));
+ assertTrue(exp.getSequenceAt(2).getSequenceAsString()
+ .startsWith("----abc"));
+ assertTrue(exp.getSequenceAt(1).getSequenceAsString()
+ .startsWith("------abc"));
+ assertTrue(exp.getSequenceAt(0).getSequenceAsString()
+ .startsWith("--------abc"));
+ }
+ }
+ }
+
+ /**
+ * Test that annotations are correctly adjusted by expandContext
+ */
+ @Test(groups = { "Functional" })
+ public void testExpandContext_annotation()
+ {
+ AlignmentI al = new Alignment(new Sequence[] {});
+ SequenceI ds = new Sequence("Seq1", "ABCDEFGHI");
+ // subsequence DEF:
+ SequenceI seq1 = ds.deriveSequence().getSubSequence(3, 6);
+ al.addSequence(seq1);
+
+ /*
+ * Annotate DEF with 4/5/6 respectively
+ */
+ Annotation[] anns = new Annotation[] { new Annotation(4),
+ new Annotation(5), new Annotation(6) };
+ AlignmentAnnotation ann = new AlignmentAnnotation("SS",
+ "secondary structure", anns);
+ seq1.addAlignmentAnnotation(ann);
+
+ /*
+ * The annotations array should match aligned positions
+ */
+ assertEquals(3, ann.annotations.length);
+ assertEquals(4, ann.annotations[0].value, 0.001);
+ assertEquals(5, ann.annotations[1].value, 0.001);
+ assertEquals(6, ann.annotations[2].value, 0.001);
+
+ /*
+ * Check annotation to sequence position mappings before expanding the
+ * sequence; these are set up in Sequence.addAlignmentAnnotation ->
+ * Annotation.setSequenceRef -> createSequenceMappings
+ */
+ assertNull(ann.getAnnotationForPosition(1));
+ assertNull(ann.getAnnotationForPosition(2));
+ assertNull(ann.getAnnotationForPosition(3));
+ assertEquals(4, ann.getAnnotationForPosition(4).value, 0.001);
+ assertEquals(5, ann.getAnnotationForPosition(5).value, 0.001);
+ assertEquals(6, ann.getAnnotationForPosition(6).value, 0.001);
+ assertNull(ann.getAnnotationForPosition(7));
+ assertNull(ann.getAnnotationForPosition(8));
+ assertNull(ann.getAnnotationForPosition(9));
+
+ /*
+ * Expand the subsequence to the full sequence abcDEFghi
+ */
+ AlignmentI expanded = AlignmentUtils.expandContext(al, -1);
+ assertEquals("abcDEFghi", expanded.getSequenceAt(0)
+ .getSequenceAsString());
+
+ /*
+ * Confirm the alignment and sequence have the same SS annotation,
+ * referencing the expanded sequence
+ */
+ ann = expanded.getSequenceAt(0).getAnnotation()[0];
+ assertSame(ann, expanded.getAlignmentAnnotation()[0]);
+ assertSame(expanded.getSequenceAt(0), ann.sequenceRef);
+
+ /*
+ * The annotations array should have null values except for annotated
+ * positions
+ */
+ assertNull(ann.annotations[0]);
+ assertNull(ann.annotations[1]);
+ assertNull(ann.annotations[2]);
+ assertEquals(4, ann.annotations[3].value, 0.001);
+ assertEquals(5, ann.annotations[4].value, 0.001);
+ assertEquals(6, ann.annotations[5].value, 0.001);
+ assertNull(ann.annotations[6]);
+ assertNull(ann.annotations[7]);
+ assertNull(ann.annotations[8]);
+
+ /*
+ * sequence position mappings should be unchanged
+ */
+ assertNull(ann.getAnnotationForPosition(1));
+ assertNull(ann.getAnnotationForPosition(2));
+ assertNull(ann.getAnnotationForPosition(3));
+ assertEquals(4, ann.getAnnotationForPosition(4).value, 0.001);
+ assertEquals(5, ann.getAnnotationForPosition(5).value, 0.001);
+ assertEquals(6, ann.getAnnotationForPosition(6).value, 0.001);
+ assertNull(ann.getAnnotationForPosition(7));
+ assertNull(ann.getAnnotationForPosition(8));
+ assertNull(ann.getAnnotationForPosition(9));
+ }
+
+ /**
+ * Test method that returns a map of lists of sequences by sequence name.
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" })
+ public void testGetSequencesByName() throws IOException
+ {
+ final String data = ">Seq1Name\nKQYL\n" + ">Seq2Name\nRFPW\n"
+ + ">Seq1Name\nABCD\n";
+ AlignmentI al = loadAlignment(data, "FASTA");
+ Map<String, List<SequenceI>> map = AlignmentUtils
+ .getSequencesByName(al);
+ assertEquals(2, map.keySet().size());
+ assertEquals(2, map.get("Seq1Name").size());
+ assertEquals("KQYL", map.get("Seq1Name").get(0).getSequenceAsString());
+ assertEquals("ABCD", map.get("Seq1Name").get(1).getSequenceAsString());
+ 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
+ * @return
+ * @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
+ * translate.
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" })
+ public void testMapProteinAlignmentToCdna_noXrefs() throws IOException
+ {
+ List<SequenceI> protseqs = new ArrayList<SequenceI>();
+ protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
+ protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
+ protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
+ AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
+ protein.setDataset(null);
+
+ List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
+ dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR
+ dnaseqs.add(new Sequence("EMBL|A22222", "GAGATACAA")); // = EIQ
+ dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ
+ dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG")); // = EIQ
+ AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
+ cdna.setDataset(null);
+
+ 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 to A22222
+ AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0))
+ .get(0);
+ assertEquals(1, acf.getdnaSeqs().length);
+ assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
+ acf.getdnaSeqs()[0]);
+ Mapping[] protMappings = acf.getProtMappings();
+ assertEquals(1, protMappings.length);
+ MapList mapList = protMappings[0].getMap();
+ assertEquals(3, mapList.getFromRatio());
+ assertEquals(1, mapList.getToRatio());
+ 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)));
+ assertEquals(1, mapList.getToRanges().size());
+
+ // 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' A44444
+ assertTrue(protein.getCodonFrame(cdna.getSequenceAt(3)).isEmpty());
+ }
+
+ /**
+ * Test for the alignSequenceAs method that takes two sequences and a mapping.
+ */
+ @Test(groups = { "Functional" })
+ public void testAlignSequenceAs_withMapping_noIntrons()
+ {
+ MapList map = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 }, 3, 1);
+
+ /*
+ * No existing gaps in dna:
+ */
+ checkAlignSequenceAs("GGGAAA", "-A-L-", false, false, map,
+ "---GGG---AAA");
+
+ /*
+ * Now introduce gaps in dna but ignore them when realigning.
+ */
+ checkAlignSequenceAs("-G-G-G-A-A-A-", "-A-L-", false, false, map,
+ "---GGG---AAA");
+
+ /*
+ * Now include gaps in dna when realigning. First retaining 'mapped' gaps
+ * only, i.e. those within the exon region.
+ */
+ checkAlignSequenceAs("-G-G--G-A--A-A-", "-A-L-", true, false, map,
+ "---G-G--G---A--A-A");
+
+ /*
+ * Include all gaps in dna when realigning (within and without the exon
+ * 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---");
+
+ /*
+ * Include only unmapped gaps in dna when realigning (outside the exon
+ * region). The leading gap, and the gaps between codons, are subsumed by
+ * the protein alignment gap.
+ */
+ checkAlignSequenceAs("-G-GG--AA-A-", "-A-L-", false, true, map,
+ "---GGG---AAA---");
+ }
+
+ /**
+ * Test for the alignSequenceAs method that takes two sequences and a mapping.
+ */
+ @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);
+
+ /*
+ * Simple case: no gaps in dna
+ */
+ checkAlignSequenceAs("GGGAAACCCTTTGGG", "--A-L-", false, false, map,
+ "GGG---AAACCCTTTGGG");
+
+ /*
+ * Add gaps to dna - but ignore when realigning.
+ */
+ checkAlignSequenceAs("-G-G-G--A--A---AC-CC-T-TT-GG-G-", "--A-L-",
+ false, false, map, "GGG---AAACCCTTTGGG");
+
+ /*
+ * Add gaps to dna - include within exons only when realigning.
+ */
+ checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
+ true, false, map, "GGG---A--A---ACCCT-TTGGG");
+
+ /*
+ * Include gaps outside exons only when realigning.
+ */
+ checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
+ false, true, map, "-G-G-GAAAC-CCTTT-GG-G-");
+
+ /*
+ * Include gaps following first intron if we are 'preserving mapped gaps'
+ */
+ checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
+ true, true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
+
+ /*
+ * Include all gaps in dna when realigning.
+ */
+ checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
+ true, true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
+ }
+
+ /**
+ * Test for the case where not all of the protein sequence is mapped to cDNA.
+ */
+ @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);
+
+ /*
+ * -L- 'aligns' ccc------
+ */
+ checkAlignSequenceAs("gggAAAcccTTTggg", "-A-L-P-", false, false, map,
+ "gggAAAccc------TTTggg");
}
+
+ /**
+ * Helper method that performs and verifies the method under test.
+ *
+ * @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 alignee,
+ final String alignModel, final boolean preserveMappedGaps,
+ final boolean preserveUnmappedGaps, MapList map,
+ final String expected)
+ {
+ SequenceI alignMe = new Sequence("Seq1", alignee);
+ alignMe.createDatasetSequence();
+ SequenceI alignFrom = new Sequence("Seq2", alignModel);
+ alignFrom.createDatasetSequence();
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ acf.addMap(alignMe.getDatasetSequence(),
+ alignFrom.getDatasetSequence(), map);
+
+ AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "---", '-',
+ preserveMappedGaps, preserveUnmappedGaps);
+ assertEquals(expected, alignMe.getSequenceAsString());
+ }
+
+ /**
+ * Test for the alignSequenceAs method where we preserve gaps in introns only.
+ */
+ @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");
+ }
+
+ /**
+ * Test the method that realigns protein to match mapped codon alignment.
+ */
+ @Test(groups = { "Functional" })
+ public void testAlignProteinAsDna()
+ {
+ // seq1 codons are [1,2,3] [4,5,6] [7,8,9] [10,11,12]
+ SequenceI dna1 = new Sequence("Seq1", "TGCCATTACCAG-");
+ // seq2 codons are [1,3,4] [5,6,7] [8,9,10] [11,12,13]
+ 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 });
+ 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");
+ 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);
+ 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);
+ ArrayList<AlignedCodonFrame> acfs = new ArrayList<AlignedCodonFrame>();
+ 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]
+ * [8,9,10] [10,11,12] [11,12,13]
+ */
+ AlignmentUtils.alignProteinAsDna(protein, dna);
+ 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(groups = { "Functional" })
+ public void testTranslatesAs()
+ {
+ // null arguments check
+ assertFalse(AlignmentUtils.translatesAs(null, 0, null));
+ assertFalse(AlignmentUtils.translatesAs(new char[] { 't' }, 0, null));
+ assertFalse(AlignmentUtils.translatesAs(null, 0, new char[] { 'a' }));
+
+ // straight translation
+ assertTrue(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
+ "FPKG".toCharArray()));
+ // with extra start codon (not in protein)
+ assertTrue(AlignmentUtils.translatesAs("atgtttcccaaaggg".toCharArray(),
+ 3, "FPKG".toCharArray()));
+ // with stop codon1 (not in protein)
+ assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtaa".toCharArray(),
+ 0, "FPKG".toCharArray()));
+ // 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 (not in protein)
+ assertTrue(AlignmentUtils.translatesAs("tttcccaaagggtga".toCharArray(),
+ 0, "FPKG".toCharArray()));
+ // with start and stop codon1
+ assertTrue(AlignmentUtils.translatesAs(
+ "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(
+ "atgtttcccaaagggtag".toCharArray(), 3, "FPKG".toCharArray()));
+ // with start and stop codon3
+ assertTrue(AlignmentUtils.translatesAs(
+ "atgtttcccaaagggtga".toCharArray(), 3, "FPKG".toCharArray()));
+
+ // with embedded stop codons
+ assertTrue(AlignmentUtils.translatesAs(
+ "atgtttTAGcccaaaTAAgggtga".toCharArray(), 3,
+ "F*PK*G".toCharArray()));
+
+ // wrong protein
+ assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
+ 0, "FPMG".toCharArray()));
+
+ // truncated dna
+ assertFalse(AlignmentUtils.translatesAs("tttcccaaagg".toCharArray(), 0,
+ "FPKG".toCharArray()));
+
+ // truncated protein
+ assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
+ 0, "FPK".toCharArray()));
+
+ // overlong dna (doesn't end in stop codon)
+ assertFalse(AlignmentUtils.translatesAs(
+ "tttcccaaagggttt".toCharArray(), 0, "FPKG".toCharArray()));
+
+ // dna + stop codon + more
+ assertFalse(AlignmentUtils.translatesAs(
+ "tttcccaaagggttaga".toCharArray(), 0, "FPKG".toCharArray()));
+
+ // overlong protein
+ assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
+ 0, "FPKGQ".toCharArray()));
+ }
+
+ /**
+ * Test mapping of protein to cDNA, for cases where the cDNA has start and/or
+ * stop codons in addition to the protein coding sequence.
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" })
+ public void testMapProteinAlignmentToCdna_withStartAndStopCodons()
+ throws IOException
+ {
+ List<SequenceI> protseqs = new ArrayList<SequenceI>();
+ protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
+ protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
+ protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
+ AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
+ protein.setDataset(null);
+
+ List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
+ // start + SAR:
+ dnaseqs.add(new Sequence("EMBL|A11111", "ATGTCAGCACGC"));
+ // = EIQ + stop
+ dnaseqs.add(new Sequence("EMBL|A22222", "GAGATACAATAA"));
+ // = start +EIQ + stop
+ dnaseqs.add(new Sequence("EMBL|A33333", "ATGGAAATCCAGTAG"));
+ dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG"));
+ AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[4]));
+ cdna.setDataset(null);
+
+ 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);
+ assertEquals(1, acf.getdnaSeqs().length);
+ assertEquals(cdna.getSequenceAt(1).getDatasetSequence(),
+ acf.getdnaSeqs()[0]);
+ Mapping[] protMappings = acf.getProtMappings();
+ assertEquals(1, protMappings.length);
+ MapList mapList = protMappings[0].getMap();
+ assertEquals(3, mapList.getFromRatio());
+ assertEquals(1, mapList.getToRatio());
+ 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)));
+ assertEquals(1, mapList.getToRanges().size());
+
+ // V12346 mapped from A33333 starting position 4
+ acf = protein.getCodonFrame(protein.getSequenceAt(1)).get(0);
+ assertEquals(1, acf.getdnaSeqs().length);
+ assertEquals(cdna.getSequenceAt(2).getDatasetSequence(),
+ acf.getdnaSeqs()[0]);
+ protMappings = acf.getProtMappings();
+ assertEquals(1, protMappings.length);
+ mapList = protMappings[0].getMap();
+ assertEquals(3, mapList.getFromRatio());
+ assertEquals(1, mapList.getToRatio());
+ 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)));
+ 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);
+ assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
+ acf.getdnaSeqs()[0]);
+ protMappings = acf.getProtMappings();
+ assertEquals(1, protMappings.length);
+ mapList = protMappings[0].getMap();
+ assertEquals(3, mapList.getFromRatio());
+ assertEquals(1, mapList.getToRatio());
+ 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)));
+ assertEquals(1, mapList.getToRanges().size());
+
+ // no mapping involving the 'extra' A44444
+ assertTrue(protein.getCodonFrame(cdna.getSequenceAt(3)).isEmpty());
+ }
+
+ /**
+ * Test mapping of protein to cDNA, for the case where we have some sequence
+ * cross-references. Verify that 1-to-many mappings are made where
+ * cross-references exist and sequences are mappable.
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" })
+ public void testMapProteinAlignmentToCdna_withXrefs() throws IOException
+ {
+ List<SequenceI> protseqs = new ArrayList<SequenceI>();
+ protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
+ protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
+ protseqs.add(new Sequence("UNIPROT|V12347", "SAR"));
+ AlignmentI protein = new Alignment(protseqs.toArray(new SequenceI[3]));
+ protein.setDataset(null);
+
+ List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
+ dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR
+ dnaseqs.add(new Sequence("EMBL|A22222", "ATGGAGATACAA")); // = start + EIQ
+ dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ
+ dnaseqs.add(new Sequence("EMBL|A44444", "GAAATTCAG")); // = EIQ
+ 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)
+ protseqs.get(0).addDBRef(new DBRefEntry("EMBL", "1", "A44444"));
+ // Xref A33333 to V12347 (sequence mismatch - should not get mapped)
+ dnaseqs.get(2).addDBRef(new DBRefEntry("UNIPROT", "1", "V12347"));
+ // as V12345 is mapped to A22222 and A44444, this leaves V12346 unmapped.
+ // it should get paired up with the unmapped A33333
+ // A11111 should be mapped to V12347
+ // A55555 is spare and has no xref so is not mapped
+
+ 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());
+ assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(0)).size());
+ assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(1)).size());
+ assertEquals(1, protein.getCodonFrame(protein.getSequenceAt(2)).size());
+
+ // one mapping for each of the first 4 cDNA sequences
+ assertEquals(1, protein.getCodonFrame(cdna.getSequenceAt(0)).size());
+ 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);
+ 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());
+ }
+
+ /**
+ * Test mapping of protein to cDNA, for the case where we have some sequence
+ * cross-references. Verify that once we have made an xref mapping we don't
+ * also map un-xrefd sequeces.
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" })
+ public void testMapProteinAlignmentToCdna_prioritiseXrefs()
+ throws IOException
+ {
+ List<SequenceI> protseqs = new ArrayList<SequenceI>();
+ protseqs.add(new Sequence("UNIPROT|V12345", "EIQ"));
+ protseqs.add(new Sequence("UNIPROT|V12346", "EIQ"));
+ AlignmentI protein = new Alignment(
+ protseqs.toArray(new SequenceI[protseqs.size()]));
+ protein.setDataset(null);
+
+ List<SequenceI> dnaseqs = new ArrayList<SequenceI>();
+ 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.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);
+ assertEquals(cdna.getSequenceAt(0).getDatasetSequence(),
+ acf.getdnaSeqs()[0]);
+ }
+
+ /**
+ * Test the method that shows or hides sequence annotations by type(s) and
+ * selection group.
+ */
+ @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) };
+ AlignmentAnnotation ann1 = new AlignmentAnnotation("Structure", "ann1",
+ anns);
+ ann1.setSequenceRef(seq1);
+ AlignmentAnnotation ann2 = new AlignmentAnnotation("Structure", "ann2",
+ anns);
+ ann2.setSequenceRef(seq2);
+ AlignmentAnnotation ann3 = new AlignmentAnnotation("Structure", "ann3",
+ anns);
+ AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "ann4", anns);
+ ann4.setSequenceRef(seq1);
+ 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 });
+ al.addAnnotation(ann1); // Structure for Seq1
+ al.addAnnotation(ann2); // Structure for Seq2
+ al.addAnnotation(ann3); // Structure for no sequence
+ al.addAnnotation(ann4); // Temp for seq1
+ al.addAnnotation(ann5); // Temp for seq2
+ al.addAnnotation(ann6); // Temp for no sequence
+ List<String> types = new ArrayList<String>();
+ List<SequenceI> scope = new ArrayList<SequenceI>();
+
+ /*
+ * Set all sequence related Structure to hidden (ann1, ann2)
+ */
+ types.add("Structure");
+ AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, false,
+ false);
+ assertFalse(ann1.visible);
+ assertFalse(ann2.visible);
+ assertTrue(ann3.visible); // not sequence-related, not affected
+ assertTrue(ann4.visible); // not Structure, not affected
+ assertTrue(ann5.visible); // "
+ assertTrue(ann6.visible); // not sequence-related, not affected
+
+ /*
+ * Set Temp in {seq1, seq3} to hidden
+ */
+ types.clear();
+ types.add("Temp");
+ scope.add(seq1);
+ scope.add(seq3);
+ AlignmentUtils.showOrHideSequenceAnnotations(al, types, scope, false,
+ false);
+ assertFalse(ann1.visible); // unchanged
+ assertFalse(ann2.visible); // unchanged
+ assertTrue(ann3.visible); // not sequence-related, not affected
+ assertFalse(ann4.visible); // Temp for seq1 hidden
+ assertTrue(ann5.visible); // not in scope, not affected
+ assertTrue(ann6.visible); // not sequence-related, not affected
+
+ /*
+ * Set Temp in all sequences to hidden
+ */
+ types.clear();
+ types.add("Temp");
+ scope.add(seq1);
+ scope.add(seq3);
+ AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, false,
+ false);
+ assertFalse(ann1.visible); // unchanged
+ assertFalse(ann2.visible); // unchanged
+ assertTrue(ann3.visible); // not sequence-related, not affected
+ assertFalse(ann4.visible); // Temp for seq1 hidden
+ assertFalse(ann5.visible); // Temp for seq2 hidden
+ assertTrue(ann6.visible); // not sequence-related, not affected
+
+ /*
+ * Set all types in {seq1, seq3} to visible
+ */
+ types.clear();
+ scope.clear();
+ scope.add(seq1);
+ scope.add(seq3);
+ AlignmentUtils.showOrHideSequenceAnnotations(al, types, scope, true,
+ true);
+ assertTrue(ann1.visible); // Structure for seq1 set visible
+ assertFalse(ann2.visible); // not in scope, unchanged
+ assertTrue(ann3.visible); // not sequence-related, not affected
+ assertTrue(ann4.visible); // Temp for seq1 set visible
+ assertFalse(ann5.visible); // not in scope, unchanged
+ assertTrue(ann6.visible); // not sequence-related, not affected
+
+ /*
+ * Set all types in all scope to hidden
+ */
+ AlignmentUtils.showOrHideSequenceAnnotations(al, types, null, true,
+ false);
+ assertFalse(ann1.visible);
+ assertFalse(ann2.visible);
+ assertTrue(ann3.visible); // not sequence-related, not affected
+ assertFalse(ann4.visible);
+ assertFalse(ann5.visible);
+ assertTrue(ann6.visible); // not sequence-related, not affected
+ }
+
+ /**
+ * Tests for the method that checks if one sequence cross-references another
+ */
+ @Test(groups = { "Functional" })
+ public void testHasCrossRef()
+ {
+ assertFalse(AlignmentUtils.hasCrossRef(null, null));
+ SequenceI seq1 = new Sequence("EMBL|A12345", "ABCDEF");
+ assertFalse(AlignmentUtils.hasCrossRef(seq1, null));
+ 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));
+ // test is one-way only
+ assertFalse(AlignmentUtils.hasCrossRef(seq2, seq1));
+ }
+
+ /**
+ * Tests for the method that checks if either sequence cross-references the
+ * other
+ */
+ @Test(groups = { "Functional" })
+ public void testHaveCrossRef()
+ {
+ assertFalse(AlignmentUtils.hasCrossRef(null, null));
+ SequenceI seq1 = new Sequence("EMBL|A12345", "ABCDEF");
+ assertFalse(AlignmentUtils.haveCrossRef(seq1, null));
+ 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.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));
+ assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
+ }
+
+ /**
+ * Test the method that extracts the cds-only part of a dna alignment.
+ */
+ @Test(groups = { "Functional" })
+ public void testMakeCdsAlignment()
+ {
+ /*
+ * scenario:
+ * dna1 --> [4, 6] [10,12] --> pep1
+ * dna2 --> [1, 3] [7, 9] [13,15] --> pep2
+ */
+ SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
+ SequenceI dna2 = new Sequence("dna2", "GGGcccTTTaaaCCC");
+ SequenceI pep1 = new Sequence("pep1", "GF");
+ SequenceI pep2 = new Sequence("pep2", "GFP");
+ pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "pep1"));
+ pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "pep2"));
+ dna1.createDatasetSequence();
+ dna2.createDatasetSequence();
+ pep1.createDatasetSequence();
+ pep2.createDatasetSequence();
+ AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
+ dna.setDataset(null);
+
+ /*
+ * put a variant feature on dna2 base 8
+ * - should transfer to cds2 base 5
+ */
+ dna2.addSequenceFeature(new SequenceFeature("variant", "hgmd", 8, 8,
+ 0f, null));
+
+ /*
+ * need a sourceDbRef if we are to construct dbrefs to the CDS
+ * sequence from the dna contig sequences
+ */
+ DBRefEntry dbref = new DBRefEntry("ENSEMBL", "0", "dna1");
+ dna1.getDatasetSequence().addDBRef(dbref);
+ org.testng.Assert.assertEquals(dbref, dna1.getPrimaryDBRefs().get(0));
+ dbref = new DBRefEntry("ENSEMBL", "0", "dna2");
+ dna2.getDatasetSequence().addDBRef(dbref);
+ org.testng.Assert.assertEquals(dbref, dna2.getPrimaryDBRefs().get(0));
+
+ /*
+ * CDS sequences are 'discovered' from dna-to-protein mappings on the alignment
+ * dataset (e.g. added from dbrefs by CrossRef.findXrefSequences)
+ */
+ MapList mapfordna1 = new MapList(new int[] { 4, 6, 10, 12 }, new int[] {
+ 1, 2 }, 3, 1);
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
+ mapfordna1);
+ dna.addCodonFrame(acf);
+ MapList mapfordna2 = 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(),
+ mapfordna2);
+ dna.addCodonFrame(acf);
+
+ /*
+ * In this case, mappings originally came from matching Uniprot accessions - so need an xref on dna involving those regions. These are normally constructed from CDS annotation
+ */
+ DBRefEntry dna1xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep1",
+ new Mapping(mapfordna1));
+ dna1.getDatasetSequence().addDBRef(dna1xref);
+ DBRefEntry dna2xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep2",
+ new Mapping(mapfordna2));
+ dna2.getDatasetSequence().addDBRef(dna2xref);
+
+ /*
+ * execute method under test:
+ */
+ AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
+ dna1, dna2 }, dna.getDataset(), null);
+
+ /*
+ * verify cds sequences
+ */
+ assertEquals(2, cds.getSequences().size());
+ assertEquals("GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
+ assertEquals("GGGTTTCCC", cds.getSequenceAt(1).getSequenceAsString());
+
+ /*
+ * verify shared, extended alignment dataset
+ */
+ assertSame(dna.getDataset(), cds.getDataset());
+ SequenceI cds1Dss = cds.getSequenceAt(0).getDatasetSequence();
+ SequenceI cds2Dss = cds.getSequenceAt(1).getDatasetSequence();
+ assertTrue(dna.getDataset().getSequences().contains(cds1Dss));
+ assertTrue(dna.getDataset().getSequences().contains(cds2Dss));
+
+ /*
+ * verify CDS has a dbref with mapping to peptide
+ */
+ assertNotNull(cds1Dss.getDBRefs());
+ assertEquals(2, cds1Dss.getDBRefs().length);
+ dbref = cds1Dss.getDBRefs()[0];
+ assertEquals(dna1xref.getSource(), dbref.getSource());
+ // version is via ensembl's primary ref
+ assertEquals(dna1xref.getVersion(), dbref.getVersion());
+ assertEquals(dna1xref.getAccessionId(), dbref.getAccessionId());
+ assertNotNull(dbref.getMap());
+ assertSame(pep1.getDatasetSequence(), dbref.getMap().getTo());
+ MapList cdsMapping = new MapList(new int[] { 1, 6 },
+ new int[] { 1, 2 }, 3, 1);
+ assertEquals(cdsMapping, dbref.getMap().getMap());
+
+ /*
+ * verify peptide has added a dbref with reverse mapping to CDS
+ */
+ assertNotNull(pep1.getDBRefs());
+ // FIXME pep1.getDBRefs() is 1 - is that the correct behaviour ?
+ assertEquals(2, pep1.getDBRefs().length);
+ dbref = pep1.getDBRefs()[1];
+ assertEquals("ENSEMBL", dbref.getSource());
+ assertEquals("0", dbref.getVersion());
+ assertEquals("CDS|dna1", dbref.getAccessionId());
+ assertNotNull(dbref.getMap());
+ assertSame(cds1Dss, dbref.getMap().getTo());
+ assertEquals(cdsMapping.getInverse(), dbref.getMap().getMap());
+
+ /*
+ * Verify mappings from CDS to peptide, cDNA to CDS, and cDNA to peptide
+ * the mappings are on the shared alignment dataset
+ * 6 mappings, 2*(DNA->CDS), 2*(DNA->Pep), 2*(CDS->Pep)
+ */
+ List<AlignedCodonFrame> cdsMappings = cds.getDataset().getCodonFrames();
+ assertEquals(6, cdsMappings.size());
+
+ /*
+ * verify that mapping sets for dna and cds alignments are different
+ * [not current behaviour - all mappings are on the alignment dataset]
+ */
+ // select -> subselect type to test.
+ // Assert.assertNotSame(dna.getCodonFrames(), cds.getCodonFrames());
+ // assertEquals(4, dna.getCodonFrames().size());
+ // assertEquals(4, cds.getCodonFrames().size());
+
+ /*
+ * Two mappings involve pep1 (dna to pep1, cds to pep1)
+ * Mapping from pep1 to GGGTTT in first new exon sequence
+ */
+ List<AlignedCodonFrame> pep1Mappings = MappingUtils
+ .findMappingsForSequence(pep1, cdsMappings);
+ assertEquals(2, pep1Mappings.size());
+ List<AlignedCodonFrame> mappings = MappingUtils
+ .findMappingsForSequence(cds.getSequenceAt(0), pep1Mappings);
+ assertEquals(1, mappings.size());
+
+ // map G to GGG
+ SearchResults sr = MappingUtils.buildSearchResults(pep1, 1, mappings);
+ assertEquals(1, sr.getResults().size());
+ Match m = sr.getResults().get(0);
+ assertSame(cds1Dss, 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);
+ assertSame(cds1Dss, m.getSequence());
+ assertEquals(4, m.getStart());
+ assertEquals(6, m.getEnd());
+
+ /*
+ * Two mappings involve pep2 (dna to pep2, cds to pep2)
+ * Verify mapping from pep2 to GGGTTTCCC in second new exon sequence
+ */
+ List<AlignedCodonFrame> pep2Mappings = MappingUtils
+ .findMappingsForSequence(pep2, cdsMappings);
+ assertEquals(2, pep2Mappings.size());
+ mappings = MappingUtils.findMappingsForSequence(cds.getSequenceAt(1),
+ pep2Mappings);
+ assertEquals(1, mappings.size());
+ // map G to GGG
+ sr = MappingUtils.buildSearchResults(pep2, 1, mappings);
+ assertEquals(1, sr.getResults().size());
+ m = sr.getResults().get(0);
+ assertSame(cds2Dss, 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);
+ assertSame(cds2Dss, 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);
+ assertSame(cds2Dss, m.getSequence());
+ assertEquals(7, m.getStart());
+ assertEquals(9, m.getEnd());
+
+ /*
+ * check cds2 acquired a variant feature in position 5
+ */
+ SequenceFeature[] sfs = cds2Dss.getSequenceFeatures();
+ assertNotNull(sfs);
+ assertEquals(1, sfs.length);
+ assertEquals("variant", sfs[0].type);
+ assertEquals(5, sfs[0].begin);
+ assertEquals(5, sfs[0].end);
+ }
+
+ /**
+ * 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(groups = { "Functional" })
+ public void testMakeCdsAlignment_multipleProteins()
+ {
+ SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
+ SequenceI pep1 = new Sequence("pep1", "GF"); // GGGTTT
+ SequenceI pep2 = new Sequence("pep2", "KP"); // aaaccc
+ SequenceI pep3 = new Sequence("pep3", "KF"); // aaaTTT
+ dna1.createDatasetSequence();
+ pep1.createDatasetSequence();
+ pep2.createDatasetSequence();
+ pep3.createDatasetSequence();
+ pep1.getDatasetSequence().addDBRef(
+ new DBRefEntry("EMBLCDS", "2", "A12345"));
+ pep2.getDatasetSequence().addDBRef(
+ new DBRefEntry("EMBLCDS", "3", "A12346"));
+ pep3.getDatasetSequence().addDBRef(
+ new DBRefEntry("EMBLCDS", "4", "A12347"));
+
+ /*
+ * Create the CDS alignment
+ */
+ AlignmentI dna = new Alignment(new SequenceI[] { dna1 });
+ dna.setDataset(null);
+
+ /*
+ * Make the mappings from dna to protein
+ */
+ // map ...GGG...TTT to GF
+ 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);
+ dna.addCodonFrame(acf);
+
+ // map aaa...ccc to KP
+ 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);
+ dna.addCodonFrame(acf);
+
+ // map aaa......TTT to KF
+ 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);
+ dna.addCodonFrame(acf);
+
+ /*
+ * execute method under test
+ */
+ AlignmentI cdsal = AlignmentUtils.makeCdsAlignment(
+ new SequenceI[] { dna1 }, dna.getDataset(), null);
+
+ /*
+ * Verify we have 3 cds sequences, mapped to pep1/2/3 respectively
+ */
+ List<SequenceI> cds = cdsal.getSequences();
+ assertEquals(3, cds.size());
+
+ /*
+ * verify shared, extended alignment dataset
+ */
+ assertSame(cdsal.getDataset(), dna.getDataset());
+ assertTrue(dna.getDataset().getSequences()
+ .contains(cds.get(0).getDatasetSequence()));
+ assertTrue(dna.getDataset().getSequences()
+ .contains(cds.get(1).getDatasetSequence()));
+ assertTrue(dna.getDataset().getSequences()
+ .contains(cds.get(2).getDatasetSequence()));
+
+ /*
+ * verify aligned cds sequences and their xrefs
+ */
+ SequenceI cdsSeq = cds.get(0);
+ assertEquals("GGGTTT", cdsSeq.getSequenceAsString());
+ // assertEquals("dna1|A12345", cdsSeq.getName());
+ assertEquals("CDS|dna1", cdsSeq.getName());
+ // assertEquals(1, cdsSeq.getDBRefs().length);
+ // DBRefEntry cdsRef = cdsSeq.getDBRefs()[0];
+ // assertEquals("EMBLCDS", cdsRef.getSource());
+ // assertEquals("2", cdsRef.getVersion());
+ // assertEquals("A12345", cdsRef.getAccessionId());
+
+ cdsSeq = cds.get(1);
+ assertEquals("aaaccc", cdsSeq.getSequenceAsString());
+ // assertEquals("dna1|A12346", cdsSeq.getName());
+ assertEquals("CDS|dna1", cdsSeq.getName());
+ // assertEquals(1, cdsSeq.getDBRefs().length);
+ // cdsRef = cdsSeq.getDBRefs()[0];
+ // assertEquals("EMBLCDS", cdsRef.getSource());
+ // assertEquals("3", cdsRef.getVersion());
+ // assertEquals("A12346", cdsRef.getAccessionId());
+
+ cdsSeq = cds.get(2);
+ assertEquals("aaaTTT", cdsSeq.getSequenceAsString());
+ // assertEquals("dna1|A12347", cdsSeq.getName());
+ assertEquals("CDS|dna1", 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 cds sequence to its protein product
+ * and also to its dna source
+ */
+ List<AlignedCodonFrame> newMappings = cdsal.getCodonFrames();
+
+ /*
+ * 6 mappings involve dna1 (to pep1/2/3, cds1/2/3)
+ */
+ List<AlignedCodonFrame> dnaMappings = MappingUtils
+ .findMappingsForSequence(dna1, newMappings);
+ assertEquals(6, dnaMappings.size());
+
+ /*
+ * dna1 to pep1
+ */
+ List<AlignedCodonFrame> mappings = MappingUtils
+ .findMappingsForSequence(pep1, dnaMappings);
+ assertEquals(1, mappings.size());
+ assertEquals(1, mappings.get(0).getMappings().size());
+ assertSame(pep1.getDatasetSequence(), mappings.get(0).getMappings()
+ .get(0).getMapping().getTo());
+
+ /*
+ * dna1 to cds1
+ */
+ List<AlignedCodonFrame> dnaToCds1Mappings = MappingUtils
+ .findMappingsForSequence(cds.get(0), dnaMappings);
+ Mapping mapping = dnaToCds1Mappings.get(0).getMappings().get(0)
+ .getMapping();
+ assertSame(cds.get(0).getDatasetSequence(), mapping.getTo());
+ assertEquals("G(1) in CDS should map to G(4) in DNA", 4, mapping
+ .getMap().getToPosition(1));
+
+ /*
+ * dna1 to pep2
+ */
+ mappings = MappingUtils.findMappingsForSequence(pep2, dnaMappings);
+ assertEquals(1, mappings.size());
+ assertEquals(1, mappings.get(0).getMappings().size());
+ assertSame(pep2.getDatasetSequence(), mappings.get(0).getMappings()
+ .get(0).getMapping().getTo());
+
+ /*
+ * dna1 to cds2
+ */
+ List<AlignedCodonFrame> dnaToCds2Mappings = MappingUtils
+ .findMappingsForSequence(cds.get(1), dnaMappings);
+ mapping = dnaToCds2Mappings.get(0).getMappings().get(0).getMapping();
+ assertSame(cds.get(1).getDatasetSequence(), mapping.getTo());
+ assertEquals("c(4) in CDS should map to c(7) in DNA", 7, mapping
+ .getMap().getToPosition(4));
+
+ /*
+ * dna1 to pep3
+ */
+ mappings = MappingUtils.findMappingsForSequence(pep3, dnaMappings);
+ assertEquals(1, mappings.size());
+ assertEquals(1, mappings.get(0).getMappings().size());
+ assertSame(pep3.getDatasetSequence(), mappings.get(0).getMappings()
+ .get(0).getMapping().getTo());
+
+ /*
+ * dna1 to cds3
+ */
+ List<AlignedCodonFrame> dnaToCds3Mappings = MappingUtils
+ .findMappingsForSequence(cds.get(2), dnaMappings);
+ mapping = dnaToCds3Mappings.get(0).getMappings().get(0).getMapping();
+ assertSame(cds.get(2).getDatasetSequence(), mapping.getTo());
+ assertEquals("T(4) in CDS should map to T(10) in DNA", 10, mapping
+ .getMap().getToPosition(4));
+ }
+
+ @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 testMapCdnaToProtein_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.mapCdnaToProtein(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());
+ }
+
+ /**
+ * Test the method that extracts the cds-only part of a dna alignment, for the
+ * case where the cds should be aligned to match its nucleotide sequence.
+ */
+ @Test(groups = { "Functional" })
+ public void testMakeCdsAlignment_alternativeTranscripts()
+ {
+ SequenceI dna1 = new Sequence("dna1", "aaaGGGCC-----CTTTaaaGGG");
+ // alternative transcript of same dna skips CCC codon
+ SequenceI dna2 = new Sequence("dna2", "aaaGGGCC-----cttTaaaGGG");
+ // dna3 has no mapping (protein product) so should be ignored here
+ SequenceI dna3 = new Sequence("dna3", "aaaGGGCCCCCGGGcttTaaaGGG");
+ SequenceI pep1 = new Sequence("pep1", "GPFG");
+ SequenceI pep2 = new Sequence("pep2", "GPG");
+ dna1.createDatasetSequence();
+ dna2.createDatasetSequence();
+ dna3.createDatasetSequence();
+ pep1.createDatasetSequence();
+ pep2.createDatasetSequence();
+
+ AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
+ dna.setDataset(null);
+
+ MapList map = new MapList(new int[] { 4, 12, 16, 18 },
+ new int[] { 1, 4 }, 3, 1);
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
+ dna.addCodonFrame(acf);
+ map = new MapList(new int[] { 4, 8, 12, 12, 16, 18 },
+ new int[] { 1, 3 }, 3, 1);
+ acf = new AlignedCodonFrame();
+ acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
+ dna.addCodonFrame(acf);
+
+ AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
+ dna1, dna2, dna3 }, dna.getDataset(), null);
+ List<SequenceI> cdsSeqs = cds.getSequences();
+ assertEquals(2, cdsSeqs.size());
+ assertEquals("GGGCCCTTTGGG", cdsSeqs.get(0).getSequenceAsString());
+ assertEquals("GGGCCTGGG", cdsSeqs.get(1).getSequenceAsString());
+
+ /*
+ * verify shared, extended alignment dataset
+ */
+ assertSame(dna.getDataset(), cds.getDataset());
+ assertTrue(dna.getDataset().getSequences()
+ .contains(cdsSeqs.get(0).getDatasetSequence()));
+ assertTrue(dna.getDataset().getSequences()
+ .contains(cdsSeqs.get(1).getDatasetSequence()));
+
+ /*
+ * Verify 6 mappings: dna1 to cds1, cds1 to pep1, dna1 to pep1
+ * and the same for dna2/cds2/pep2
+ */
+ List<AlignedCodonFrame> mappings = cds.getCodonFrames();
+ assertEquals(6, mappings.size());
+
+ /*
+ * 2 mappings involve pep1
+ */
+ List<AlignedCodonFrame> pep1Mappings = MappingUtils
+ .findMappingsForSequence(pep1, mappings);
+ assertEquals(2, pep1Mappings.size());
+
+ /*
+ * Get mapping of pep1 to cds1 and verify it
+ * maps GPFG to 1-3,4-6,7-9,10-12
+ */
+ List<AlignedCodonFrame> pep1CdsMappings = MappingUtils
+ .findMappingsForSequence(cds.getSequenceAt(0), pep1Mappings);
+ assertEquals(1, pep1CdsMappings.size());
+ SearchResults sr = MappingUtils.buildSearchResults(pep1, 1,
+ pep1CdsMappings);
+ assertEquals(1, sr.getResults().size());
+ Match m = sr.getResults().get(0);
+ assertEquals(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
+ assertEquals(1, m.getStart());
+ assertEquals(3, m.getEnd());
+ sr = MappingUtils.buildSearchResults(pep1, 2, pep1CdsMappings);
+ m = sr.getResults().get(0);
+ assertEquals(4, m.getStart());
+ assertEquals(6, m.getEnd());
+ sr = MappingUtils.buildSearchResults(pep1, 3, pep1CdsMappings);
+ m = sr.getResults().get(0);
+ assertEquals(7, m.getStart());
+ assertEquals(9, m.getEnd());
+ sr = MappingUtils.buildSearchResults(pep1, 4, pep1CdsMappings);
+ m = sr.getResults().get(0);
+ assertEquals(10, m.getStart());
+ assertEquals(12, m.getEnd());
+
+ /*
+ * Get mapping of pep2 to cds2 and verify it
+ * maps GPG in pep2 to 1-3,4-6,7-9 in second CDS sequence
+ */
+ List<AlignedCodonFrame> pep2Mappings = MappingUtils
+ .findMappingsForSequence(pep2, mappings);
+ assertEquals(2, pep2Mappings.size());
+ List<AlignedCodonFrame> pep2CdsMappings = MappingUtils
+ .findMappingsForSequence(cds.getSequenceAt(1), pep2Mappings);
+ assertEquals(1, pep2CdsMappings.size());
+ sr = MappingUtils.buildSearchResults(pep2, 1, pep2CdsMappings);
+ assertEquals(1, sr.getResults().size());
+ m = sr.getResults().get(0);
+ assertEquals(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
+ assertEquals(1, m.getStart());
+ assertEquals(3, m.getEnd());
+ sr = MappingUtils.buildSearchResults(pep2, 2, pep2CdsMappings);
+ m = sr.getResults().get(0);
+ assertEquals(4, m.getStart());
+ assertEquals(6, m.getEnd());
+ sr = MappingUtils.buildSearchResults(pep2, 3, pep2CdsMappings);
+ m = sr.getResults().get(0);
+ assertEquals(7, m.getStart());
+ assertEquals(9, m.getEnd());
+ }
+
+ /**
+ * Test the method that realigns protein to match mapped codon alignment.
+ */
+ @Test(groups = { "Functional" })
+ public void testAlignProteinAsDna_incompleteStartCodon()
+ {
+ // seq1: incomplete start codon (not mapped), then [3, 11]
+ SequenceI dna1 = new Sequence("Seq1", "ccAAA-TTT-GGG-");
+ // seq2 codons are [4, 5], [8, 11]
+ SequenceI dna2 = new Sequence("Seq2", "ccaAA-ttT-GGG-");
+ // seq3 incomplete start codon at 'tt'
+ SequenceI dna3 = new Sequence("Seq3", "ccaaa-ttt-GGG-");
+ AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
+ dna.setDataset(null);
+
+ // prot1 has 'X' for incomplete start codon (not mapped)
+ SequenceI prot1 = new Sequence("Seq1", "XKFG"); // X for incomplete start
+ SequenceI prot2 = new Sequence("Seq2", "NG");
+ SequenceI prot3 = new Sequence("Seq3", "XG"); // X for incomplete start
+ AlignmentI protein = new Alignment(new SequenceI[] { prot1, prot2,
+ prot3 });
+ protein.setDataset(null);
+
+ // map dna1 [3, 11] to prot1 [2, 4] KFG
+ MapList map = new MapList(new int[] { 3, 11 }, new int[] { 2, 4 }, 3, 1);
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
+
+ // map dna2 [4, 5] [8, 11] to prot2 [1, 2] NG
+ map = new MapList(new int[] { 4, 5, 8, 11 }, new int[] { 1, 2 }, 3, 1);
+ acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map);
+
+ // map dna3 [9, 11] to prot3 [2, 2] G
+ map = new MapList(new int[] { 9, 11 }, new int[] { 2, 2 }, 3, 1);
+ acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map);
+
+ ArrayList<AlignedCodonFrame> acfs = new ArrayList<AlignedCodonFrame>();
+ acfs.add(acf);
+ protein.setCodonFrames(acfs);
+
+ /*
+ * verify X is included in the aligned proteins, and placed just
+ * before the first mapped residue
+ * CCT is between CCC and TTT
+ */
+ AlignmentUtils.alignProteinAsDna(protein, dna);
+ assertEquals("XK-FG", prot1.getSequenceAsString());
+ assertEquals("--N-G", prot2.getSequenceAsString());
+ assertEquals("---XG", prot3.getSequenceAsString());
+ }
+
+ /**
+ * Tests for the method that maps the subset of a dna sequence that has CDS
+ * (or subtype) feature - case where the start codon is incomplete.
+ */
+ @Test(groups = "Functional")
+ public void testFindCdsPositions_fivePrimeIncomplete()
+ {
+ SequenceI dnaSeq = new Sequence("dna", "aaagGGCCCaaaTTTttt");
+ dnaSeq.createDatasetSequence();
+ SequenceI ds = dnaSeq.getDatasetSequence();
+
+ // CDS for dna 5-6 (incomplete codon), 7-9
+ SequenceFeature sf = new SequenceFeature("CDS", "", 5, 9, 0f, null);
+ sf.setPhase("2"); // skip 2 bases to start of next codon
+ ds.addSequenceFeature(sf);
+ // CDS for dna 13-15
+ sf = new SequenceFeature("CDS_predicted", "", 13, 15, 0f, null);
+ ds.addSequenceFeature(sf);
+
+ List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
+
+ /*
+ * check the mapping starts with the first complete codon
+ */
+ assertEquals(6, MappingUtils.getLength(ranges));
+ assertEquals(2, ranges.size());
+ assertEquals(7, ranges.get(0)[0]);
+ assertEquals(9, ranges.get(0)[1]);
+ assertEquals(13, ranges.get(1)[0]);
+ assertEquals(15, ranges.get(1)[1]);
+ }
+
+ /**
+ * Tests for the method that maps the subset of a dna sequence that has CDS
+ * (or subtype) feature.
+ */
+ @Test(groups = "Functional")
+ public void testFindCdsPositions()
+ {
+ SequenceI dnaSeq = new Sequence("dna", "aaaGGGcccAAATTTttt");
+ dnaSeq.createDatasetSequence();
+ SequenceI ds = dnaSeq.getDatasetSequence();
+
+ // CDS for dna 10-12
+ SequenceFeature sf = new SequenceFeature("CDS_predicted", "", 10, 12,
+ 0f, null);
+ sf.setStrand("+");
+ ds.addSequenceFeature(sf);
+ // CDS for dna 4-6
+ sf = new SequenceFeature("CDS", "", 4, 6, 0f, null);
+ sf.setStrand("+");
+ ds.addSequenceFeature(sf);
+ // exon feature should be ignored here
+ sf = new SequenceFeature("exon", "", 7, 9, 0f, null);
+ ds.addSequenceFeature(sf);
+
+ List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
+ /*
+ * verify ranges { [4-6], [12-10] }
+ * note CDS ranges are ordered ascending even if the CDS
+ * features are not
+ */
+ assertEquals(6, MappingUtils.getLength(ranges));
+ assertEquals(2, ranges.size());
+ assertEquals(4, ranges.get(0)[0]);
+ assertEquals(6, ranges.get(0)[1]);
+ assertEquals(10, ranges.get(1)[0]);
+ assertEquals(12, ranges.get(1)[1]);
+ }
+
+ /**
+ * Test the method that computes a map of codon variants for each protein
+ * position from "sequence_variant" features on dna
+ */
+ @Test(groups = "Functional")
+ public void testBuildDnaVariantsMap()
+ {
+ SequenceI dna = new Sequence("dna", "atgAAATTTGGGCCCtag");
+ MapList map = new MapList(new int[] { 1, 18 }, new int[] { 1, 5 }, 3, 1);
+
+ /*
+ * first with no variants on dna
+ */
+ LinkedHashMap<Integer, List<DnaVariant>[]> variantsMap = AlignmentUtils
+ .buildDnaVariantsMap(dna, map);
+ assertTrue(variantsMap.isEmpty());
+
+ /*
+ * single allele codon 1, on base 1
+ */
+ SequenceFeature sf1 = new SequenceFeature("sequence_variant", "", 1, 1,
+ 0f, null);
+ sf1.setValue("alleles", "T");
+ sf1.setValue("ID", "sequence_variant:rs758803211");
+ dna.addSequenceFeature(sf1);
+
+ /*
+ * two alleles codon 2, on bases 2 and 3 (distinct variants)
+ */
+ SequenceFeature sf2 = new SequenceFeature("sequence_variant", "", 5, 5,
+ 0f, null);
+ sf2.setValue("alleles", "T");
+ sf2.setValue("ID", "sequence_variant:rs758803212");
+ dna.addSequenceFeature(sf2);
+ SequenceFeature sf3 = new SequenceFeature("sequence_variant", "", 6, 6,
+ 0f, null);
+ sf3.setValue("alleles", "G");
+ sf3.setValue("ID", "sequence_variant:rs758803213");
+ dna.addSequenceFeature(sf3);
+
+ /*
+ * two alleles codon 3, both on base 2 (one variant)
+ */
+ SequenceFeature sf4 = new SequenceFeature("sequence_variant", "", 8, 8,
+ 0f, null);
+ sf4.setValue("alleles", "C, G");
+ sf4.setValue("ID", "sequence_variant:rs758803214");
+ dna.addSequenceFeature(sf4);
+
+ // no alleles on codon 4
+
+ /*
+ * alleles on codon 5 on all 3 bases (distinct variants)
+ */
+ SequenceFeature sf5 = new SequenceFeature("sequence_variant", "", 13,
+ 13, 0f, null);
+ sf5.setValue("alleles", "C, G"); // (C duplicates given base value)
+ sf5.setValue("ID", "sequence_variant:rs758803215");
+ dna.addSequenceFeature(sf5);
+ SequenceFeature sf6 = new SequenceFeature("sequence_variant", "", 14,
+ 14, 0f, null);
+ sf6.setValue("alleles", "g, a"); // should force to upper-case
+ sf6.setValue("ID", "sequence_variant:rs758803216");
+ dna.addSequenceFeature(sf6);
+ SequenceFeature sf7 = new SequenceFeature("sequence_variant", "", 15,
+ 15, 0f, null);
+ sf7.setValue("alleles", "A, T");
+ sf7.setValue("ID", "sequence_variant:rs758803217");
+ dna.addSequenceFeature(sf7);
+
+ /*
+ * build map - expect variants on positions 1, 2, 3, 5
+ */
+ variantsMap = AlignmentUtils.buildDnaVariantsMap(dna, map);
+ assertEquals(4, variantsMap.size());
+
+ /*
+ * protein residue 1: variant on codon (ATG) base 1, not on 2 or 3
+ */
+ List<DnaVariant>[] pep1Variants = variantsMap.get(1);
+ assertEquals(3, pep1Variants.length);
+ assertEquals(1, pep1Variants[0].size());
+ assertEquals("A", pep1Variants[0].get(0).base); // codon[1] base
+ assertSame(sf1, pep1Variants[0].get(0).variant); // codon[1] variant
+ assertEquals(1, pep1Variants[1].size());
+ assertEquals("T", pep1Variants[1].get(0).base); // codon[2] base
+ assertNull(pep1Variants[1].get(0).variant); // no variant here
+ assertEquals(1, pep1Variants[2].size());
+ assertEquals("G", pep1Variants[2].get(0).base); // codon[3] base
+ assertNull(pep1Variants[2].get(0).variant); // no variant here
+
+ /*
+ * protein residue 2: variants on codon (AAA) bases 2 and 3
+ */
+ List<DnaVariant>[] pep2Variants = variantsMap.get(2);
+ assertEquals(3, pep2Variants.length);
+ assertEquals(1, pep2Variants[0].size());
+ // codon[1] base recorded while processing variant on codon[2]
+ assertEquals("A", pep2Variants[0].get(0).base);
+ assertNull(pep2Variants[0].get(0).variant); // no variant here
+ // codon[2] base and variant:
+ assertEquals(1, pep2Variants[1].size());
+ assertEquals("A", pep2Variants[1].get(0).base);
+ assertSame(sf2, pep2Variants[1].get(0).variant);
+ // codon[3] base was recorded when processing codon[2] variant
+ // and then the variant for codon[3] added to it
+ assertEquals(1, pep2Variants[2].size());
+ assertEquals("A", pep2Variants[2].get(0).base);
+ assertSame(sf3, pep2Variants[2].get(0).variant);
+
+ /*
+ * protein residue 3: variants on codon (TTT) base 2 only
+ */
+ List<DnaVariant>[] pep3Variants = variantsMap.get(3);
+ assertEquals(3, pep3Variants.length);
+ assertEquals(1, pep3Variants[0].size());
+ assertEquals("T", pep3Variants[0].get(0).base); // codon[1] base
+ assertNull(pep3Variants[0].get(0).variant); // no variant here
+ assertEquals(1, pep3Variants[1].size());
+ assertEquals("T", pep3Variants[1].get(0).base); // codon[2] base
+ assertSame(sf4, pep3Variants[1].get(0).variant); // codon[2] variant
+ assertEquals(1, pep3Variants[2].size());
+ assertEquals("T", pep3Variants[2].get(0).base); // codon[3] base
+ assertNull(pep3Variants[2].get(0).variant); // no variant here
+
+ /*
+ * three variants on protein position 5
+ */
+ List<DnaVariant>[] pep5Variants = variantsMap.get(5);
+ assertEquals(3, pep5Variants.length);
+ assertEquals(1, pep5Variants[0].size());
+ assertEquals("C", pep5Variants[0].get(0).base); // codon[1] base
+ assertSame(sf5, pep5Variants[0].get(0).variant); // codon[1] variant
+ assertEquals(1, pep5Variants[1].size());
+ assertEquals("C", pep5Variants[1].get(0).base); // codon[2] base
+ assertSame(sf6, pep5Variants[1].get(0).variant); // codon[2] variant
+ assertEquals(1, pep5Variants[2].size());
+ assertEquals("C", pep5Variants[2].get(0).base); // codon[3] base
+ assertSame(sf7, pep5Variants[2].get(0).variant); // codon[3] variant
+ }
+
+ /**
+ * Tests for the method that computes all peptide variants given codon
+ * variants
+ */
+ @Test(groups = "Functional")
+ public void testComputePeptideVariants()
+ {
+ /*
+ * scenario: AAATTTCCC codes for KFP
+ * variants:
+ * GAA -> E source: Ensembl
+ * CAA -> Q source: dbSNP
+ * AAG synonymous source: COSMIC
+ * AAT -> N source: Ensembl
+ * ...TTC synonymous source: dbSNP
+ * ......CAC,CGC -> H,R source: COSMIC
+ * (one variant with two alleles)
+ */
+ SequenceI peptide = new Sequence("pep/10-12", "KFP");
+
+ /*
+ * two distinct variants for codon 1 position 1
+ * second one has clinical significance
+ */
+ String ensembl = "Ensembl";
+ String dbSnp = "dbSNP";
+ String cosmic = "COSMIC";
+ SequenceFeature sf1 = new SequenceFeature("sequence_variant", "", 1, 1,
+ 0f, ensembl);
+ sf1.setValue("alleles", "A,G"); // GAA -> E
+ sf1.setValue("ID", "var1.125A>G");
+ SequenceFeature sf2 = new SequenceFeature("sequence_variant", "", 1, 1,
+ 0f, dbSnp);
+ sf2.setValue("alleles", "A,C"); // CAA -> Q
+ sf2.setValue("ID", "var2");
+ sf2.setValue("clinical_significance", "Dodgy");
+ SequenceFeature sf3 = new SequenceFeature("sequence_variant", "", 3, 3,
+ 0f, cosmic);
+ sf3.setValue("alleles", "A,G"); // synonymous
+ sf3.setValue("ID", "var3");
+ sf3.setValue("clinical_significance", "None");
+ SequenceFeature sf4 = new SequenceFeature("sequence_variant", "", 3, 3,
+ 0f, ensembl);
+ sf4.setValue("alleles", "A,T"); // AAT -> N
+ sf4.setValue("ID", "sequence_variant:var4"); // prefix gets stripped off
+ sf4.setValue("clinical_significance", "Benign");
+ SequenceFeature sf5 = new SequenceFeature("sequence_variant", "", 6, 6,
+ 0f, dbSnp);
+ sf5.setValue("alleles", "T,C"); // synonymous
+ sf5.setValue("ID", "var5");
+ sf5.setValue("clinical_significance", "Bad");
+ SequenceFeature sf6 = new SequenceFeature("sequence_variant", "", 8, 8,
+ 0f, cosmic);
+ sf6.setValue("alleles", "C,A,G"); // CAC,CGC -> H,R
+ sf6.setValue("ID", "var6");
+ sf6.setValue("clinical_significance", "Good");
+
+ List<DnaVariant> codon1Variants = new ArrayList<DnaVariant>();
+ List<DnaVariant> codon2Variants = new ArrayList<DnaVariant>();
+ List<DnaVariant> codon3Variants = new ArrayList<DnaVariant>();
+ List<DnaVariant> codonVariants[] = new ArrayList[3];
+ codonVariants[0] = codon1Variants;
+ codonVariants[1] = codon2Variants;
+ codonVariants[2] = codon3Variants;
+
+ /*
+ * compute variants for protein position 1
+ */
+ codon1Variants.add(new DnaVariant("A", sf1));
+ codon1Variants.add(new DnaVariant("A", sf2));
+ codon2Variants.add(new DnaVariant("A"));
+ codon2Variants.add(new DnaVariant("A"));
+ codon3Variants.add(new DnaVariant("A", sf3));
+ codon3Variants.add(new DnaVariant("A", sf4));
+ AlignmentUtils.computePeptideVariants(peptide, 1, codonVariants);
+
+ /*
+ * compute variants for protein position 2
+ */
+ codon1Variants.clear();
+ codon2Variants.clear();
+ codon3Variants.clear();
+ codon1Variants.add(new DnaVariant("T"));
+ codon2Variants.add(new DnaVariant("T"));
+ codon3Variants.add(new DnaVariant("T", sf5));
+ AlignmentUtils.computePeptideVariants(peptide, 2, codonVariants);
+
+ /*
+ * compute variants for protein position 3
+ */
+ codon1Variants.clear();
+ codon2Variants.clear();
+ codon3Variants.clear();
+ codon1Variants.add(new DnaVariant("C"));
+ codon2Variants.add(new DnaVariant("C", sf6));
+ codon3Variants.add(new DnaVariant("C"));
+ AlignmentUtils.computePeptideVariants(peptide, 3, codonVariants);
+
+ /*
+ * verify added sequence features for
+ * var1 K -> E Ensembl
+ * var2 K -> Q dbSNP
+ * var4 K -> N Ensembl
+ * var6 P -> H COSMIC
+ * var6 P -> R COSMIC
+ */
+ SequenceFeature[] sfs = peptide.getSequenceFeatures();
+ assertEquals(5, sfs.length);
+
+ SequenceFeature sf = sfs[0];
+ assertEquals(1, sf.getBegin());
+ assertEquals(1, sf.getEnd());
+ assertEquals("p.Lys1Glu", sf.getDescription());
+ assertEquals("var1.125A>G", sf.getValue("ID"));
+ assertNull(sf.getValue("clinical_significance"));
+ assertEquals("ID=var1.125A>G", sf.getAttributes());
+ assertEquals(1, sf.links.size());
+ // link to variation is urlencoded
+ assertEquals(
+ "p.Lys1Glu var1.125A>G|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var1.125A%3EG",
+ sf.links.get(0));
+ assertEquals(ensembl, sf.getFeatureGroup());
+
+ sf = sfs[1];
+ assertEquals(1, sf.getBegin());
+ assertEquals(1, sf.getEnd());
+ assertEquals("p.Lys1Gln", sf.getDescription());
+ assertEquals("var2", sf.getValue("ID"));
+ assertEquals("Dodgy", sf.getValue("clinical_significance"));
+ assertEquals("ID=var2;clinical_significance=Dodgy", sf.getAttributes());
+ assertEquals(1, sf.links.size());
+ assertEquals(
+ "p.Lys1Gln var2|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var2",
+ sf.links.get(0));
+ assertEquals(dbSnp, sf.getFeatureGroup());
+
+ sf = sfs[2];
+ assertEquals(1, sf.getBegin());
+ assertEquals(1, sf.getEnd());
+ assertEquals("p.Lys1Asn", sf.getDescription());
+ assertEquals("var4", sf.getValue("ID"));
+ assertEquals("Benign", sf.getValue("clinical_significance"));
+ assertEquals("ID=var4;clinical_significance=Benign", sf.getAttributes());
+ assertEquals(1, sf.links.size());
+ assertEquals(
+ "p.Lys1Asn var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
+ sf.links.get(0));
+ assertEquals(ensembl, sf.getFeatureGroup());
+
+ // var5 generates two distinct protein variant features
+ sf = sfs[3];
+ assertEquals(3, sf.getBegin());
+ assertEquals(3, sf.getEnd());
+ assertEquals("p.Pro3His", sf.getDescription());
+ assertEquals("var6", sf.getValue("ID"));
+ assertEquals("Good", sf.getValue("clinical_significance"));
+ assertEquals("ID=var6;clinical_significance=Good", sf.getAttributes());
+ assertEquals(1, sf.links.size());
+ assertEquals(
+ "p.Pro3His var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
+ sf.links.get(0));
+ assertEquals(cosmic, sf.getFeatureGroup());
+
+ sf = sfs[4];
+ assertEquals(3, sf.getBegin());
+ assertEquals(3, sf.getEnd());
+ assertEquals("p.Pro3Arg", sf.getDescription());
+ assertEquals("var6", sf.getValue("ID"));
+ assertEquals("Good", sf.getValue("clinical_significance"));
+ assertEquals("ID=var6;clinical_significance=Good", sf.getAttributes());
+ assertEquals(1, sf.links.size());
+ assertEquals(
+ "p.Pro3Arg var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
+ sf.links.get(0));
+ assertEquals(cosmic, sf.getFeatureGroup());
+ }
+
+ /**
+ * Tests for the method that maps the subset of a dna sequence that has CDS
+ * (or subtype) feature, with CDS strand = '-' (reverse)
+ */
+ // test turned off as currently findCdsPositions is not strand-dependent
+ // left in case it comes around again...
+ @Test(groups = "Functional", enabled = false)
+ public void testFindCdsPositions_reverseStrand()
+ {
+ SequenceI dnaSeq = new Sequence("dna", "aaaGGGcccAAATTTttt");
+ dnaSeq.createDatasetSequence();
+ SequenceI ds = dnaSeq.getDatasetSequence();
+
+ // CDS for dna 4-6
+ SequenceFeature sf = new SequenceFeature("CDS", "", 4, 6, 0f, null);
+ sf.setStrand("-");
+ ds.addSequenceFeature(sf);
+ // exon feature should be ignored here
+ sf = new SequenceFeature("exon", "", 7, 9, 0f, null);
+ ds.addSequenceFeature(sf);
+ // CDS for dna 10-12
+ sf = new SequenceFeature("CDS_predicted", "", 10, 12, 0f, null);
+ sf.setStrand("-");
+ ds.addSequenceFeature(sf);
+
+ List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
+ /*
+ * verify ranges { [12-10], [6-4] }
+ */
+ assertEquals(6, MappingUtils.getLength(ranges));
+ assertEquals(2, ranges.size());
+ assertEquals(12, ranges.get(0)[0]);
+ assertEquals(10, ranges.get(0)[1]);
+ assertEquals(6, ranges.get(1)[0]);
+ assertEquals(4, ranges.get(1)[1]);
+ }
+
+ /**
+ * Tests for the method that maps the subset of a dna sequence that has CDS
+ * (or subtype) feature - reverse strand case where the start codon is
+ * incomplete.
+ */
+ @Test(groups = "Functional", enabled = false)
+ // test turned off as currently findCdsPositions is not strand-dependent
+ // left in case it comes around again...
+ public void testFindCdsPositions_reverseStrandThreePrimeIncomplete()
+ {
+ SequenceI dnaSeq = new Sequence("dna", "aaagGGCCCaaaTTTttt");
+ dnaSeq.createDatasetSequence();
+ SequenceI ds = dnaSeq.getDatasetSequence();
+
+ // CDS for dna 5-9
+ SequenceFeature sf = new SequenceFeature("CDS", "", 5, 9, 0f, null);
+ sf.setStrand("-");
+ ds.addSequenceFeature(sf);
+ // CDS for dna 13-15
+ sf = new SequenceFeature("CDS_predicted", "", 13, 15, 0f, null);
+ sf.setStrand("-");
+ sf.setPhase("2"); // skip 2 bases to start of next codon
+ ds.addSequenceFeature(sf);
+
+ List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
+
+ /*
+ * check the mapping starts with the first complete codon
+ * expect ranges [13, 13], [9, 5]
+ */
+ assertEquals(6, MappingUtils.getLength(ranges));
+ assertEquals(2, ranges.size());
+ assertEquals(13, ranges.get(0)[0]);
+ assertEquals(13, ranges.get(0)[1]);
+ assertEquals(9, ranges.get(1)[0]);
+ assertEquals(5, ranges.get(1)[1]);
+ }
+
+ @Test(groups = "Functional")
+ public void testAlignAs_alternateTranscriptsUngapped()
+ {
+ SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
+ SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
+ AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
+ ((Alignment) dna).createDatasetAlignment();
+ SequenceI cds1 = new Sequence("cds1", "GGGTTT");
+ SequenceI cds2 = new Sequence("cds2", "CCCAAA");
+ AlignmentI cds = new Alignment(new SequenceI[] { cds1, cds2 });
+ ((Alignment) cds).createDatasetAlignment();
+
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ MapList map = new MapList(new int[] { 4, 9 }, new int[] { 1, 6 }, 1, 1);
+ acf.addMap(dna1.getDatasetSequence(), cds1.getDatasetSequence(), map);
+ map = new MapList(new int[] { 1, 3, 10, 12 }, new int[] { 1, 6 }, 1, 1);
+ acf.addMap(dna2.getDatasetSequence(), cds2.getDatasetSequence(), map);
+
+ /*
+ * verify CDS alignment is as:
+ * cccGGGTTTaaa (cdna)
+ * CCCgggtttAAA (cdna)
+ *
+ * ---GGGTTT--- (cds)
+ * CCC------AAA (cds)
+ */
+ dna.addCodonFrame(acf);
+ AlignmentUtils.alignAs(cds, dna);
+ assertEquals("---GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
+ assertEquals("CCC------AAA", cds.getSequenceAt(1).getSequenceAsString());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testAddMappedPositions()
+ {
+ SequenceI from = new Sequence("dna", "ggAA-ATcc-TT-g");
+ SequenceI seq1 = new Sequence("cds", "AAATTT");
+ from.createDatasetSequence();
+ seq1.createDatasetSequence();
+ Mapping mapping = new Mapping(seq1, new MapList(
+ new int[] { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1));
+ Map<Integer, Map<SequenceI, Character>> map = new TreeMap<Integer, Map<SequenceI, Character>>();
+ AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
+
+ /*
+ * verify map has seq1 residues in columns 3,4,6,7,11,12
+ */
+ assertEquals(6, map.size());
+ assertEquals('A', map.get(3).get(seq1).charValue());
+ assertEquals('A', map.get(4).get(seq1).charValue());
+ assertEquals('A', map.get(6).get(seq1).charValue());
+ assertEquals('T', map.get(7).get(seq1).charValue());
+ assertEquals('T', map.get(11).get(seq1).charValue());
+ assertEquals('T', map.get(12).get(seq1).charValue());
+
+ /*
+ *
+ */
+ }
+
+ /**
+ * Test case where the mapping 'from' range includes a stop codon which is
+ * absent in the 'to' range
+ */
+ @Test(groups = { "Functional" })
+ public void testAddMappedPositions_withStopCodon()
+ {
+ SequenceI from = new Sequence("dna", "ggAA-ATcc-TT-g");
+ SequenceI seq1 = new Sequence("cds", "AAATTT");
+ from.createDatasetSequence();
+ seq1.createDatasetSequence();
+ Mapping mapping = new Mapping(seq1, new MapList(
+ new int[] { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1));
+ Map<Integer, Map<SequenceI, Character>> map = new TreeMap<Integer, Map<SequenceI, Character>>();
+ AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
+
+ /*
+ * verify map has seq1 residues in columns 3,4,6,7,11,12
+ */
+ assertEquals(6, map.size());
+ assertEquals('A', map.get(3).get(seq1).charValue());
+ assertEquals('A', map.get(4).get(seq1).charValue());
+ assertEquals('A', map.get(6).get(seq1).charValue());
+ assertEquals('T', map.get(7).get(seq1).charValue());
+ assertEquals('T', map.get(11).get(seq1).charValue());
+ assertEquals('T', map.get(12).get(seq1).charValue());
+ }
+
+ /**
+ * Test for the case where the products for which we want CDS are specified.
+ * This is to represent the case where EMBL has CDS mappings to both Uniprot
+ * and EMBLCDSPROTEIN. makeCdsAlignment() should only return the mappings for
+ * the protein sequences specified.
+ */
+ @Test(groups = { "Functional" })
+ public void testMakeCdsAlignment_filterProducts()
+ {
+ SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
+ SequenceI dna2 = new Sequence("dna2", "GGGcccTTTaaaCCC");
+ SequenceI pep1 = new Sequence("Uniprot|pep1", "GF");
+ SequenceI pep2 = new Sequence("Uniprot|pep2", "GFP");
+ SequenceI pep3 = new Sequence("EMBL|pep3", "GF");
+ SequenceI pep4 = new Sequence("EMBL|pep4", "GFP");
+ dna1.createDatasetSequence();
+ dna2.createDatasetSequence();
+ pep1.createDatasetSequence();
+ pep2.createDatasetSequence();
+ pep3.createDatasetSequence();
+ pep4.createDatasetSequence();
+ AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
+ dna.setDataset(null);
+ AlignmentI emblPeptides = new Alignment(new SequenceI[] { pep3, pep4 });
+ emblPeptides.setDataset(null);
+
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ MapList map = new MapList(new int[] { 4, 6, 10, 12 },
+ new int[] { 1, 2 }, 3, 1);
+ acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
+ acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map);
+ dna.addCodonFrame(acf);
+
+ acf = new AlignedCodonFrame();
+ map = new MapList(new int[] { 1, 3, 7, 9, 13, 15 }, new int[] { 1, 3 },
+ 3, 1);
+ acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
+ acf.addMap(dna2.getDatasetSequence(), pep4.getDatasetSequence(), map);
+ dna.addCodonFrame(acf);
+
+ /*
+ * execute method under test to find CDS for EMBL peptides only
+ */
+ AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
+ dna1, dna2 }, dna.getDataset(), emblPeptides.getSequencesArray());
+
+ assertEquals(2, cds.getSequences().size());
+ assertEquals("GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
+ assertEquals("GGGTTTCCC", cds.getSequenceAt(1).getSequenceAsString());
+
+ /*
+ * verify shared, extended alignment dataset
+ */
+ assertSame(dna.getDataset(), cds.getDataset());
+ assertTrue(dna.getDataset().getSequences()
+ .contains(cds.getSequenceAt(0).getDatasetSequence()));
+ assertTrue(dna.getDataset().getSequences()
+ .contains(cds.getSequenceAt(1).getDatasetSequence()));
+
+ /*
+ * Verify mappings from CDS to peptide, cDNA to CDS, and cDNA to peptide
+ * the mappings are on the shared alignment dataset
+ */
+ List<AlignedCodonFrame> cdsMappings = cds.getDataset().getCodonFrames();
+ /*
+ * 6 mappings, 2*(DNA->CDS), 2*(DNA->Pep), 2*(CDS->Pep)
+ */
+ assertEquals(6, cdsMappings.size());
+
+ /*
+ * verify that mapping sets for dna and cds alignments are different
+ * [not current behaviour - all mappings are on the alignment dataset]
+ */
+ // select -> subselect type to test.
+ // Assert.assertNotSame(dna.getCodonFrames(), cds.getCodonFrames());
+ // assertEquals(4, dna.getCodonFrames().size());
+ // assertEquals(4, cds.getCodonFrames().size());
+
+ /*
+ * Two mappings involve pep3 (dna to pep3, cds to pep3)
+ * Mapping from pep3 to GGGTTT in first new exon sequence
+ */
+ List<AlignedCodonFrame> pep3Mappings = MappingUtils
+ .findMappingsForSequence(pep3, cdsMappings);
+ assertEquals(2, pep3Mappings.size());
+ List<AlignedCodonFrame> mappings = MappingUtils
+ .findMappingsForSequence(cds.getSequenceAt(0), pep3Mappings);
+ assertEquals(1, mappings.size());
+
+ // map G to GGG
+ SearchResults sr = MappingUtils.buildSearchResults(pep3, 1, mappings);
+ assertEquals(1, sr.getResults().size());
+ Match m = sr.getResults().get(0);
+ assertSame(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
+ assertEquals(1, m.getStart());
+ assertEquals(3, m.getEnd());
+ // map F to TTT
+ sr = MappingUtils.buildSearchResults(pep3, 2, mappings);
+ m = sr.getResults().get(0);
+ assertSame(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
+ assertEquals(4, m.getStart());
+ assertEquals(6, m.getEnd());
+
+ /*
+ * Two mappings involve pep4 (dna to pep4, cds to pep4)
+ * Verify mapping from pep4 to GGGTTTCCC in second new exon sequence
+ */
+ List<AlignedCodonFrame> pep4Mappings = MappingUtils
+ .findMappingsForSequence(pep4, cdsMappings);
+ assertEquals(2, pep4Mappings.size());
+ mappings = MappingUtils.findMappingsForSequence(cds.getSequenceAt(1),
+ pep4Mappings);
+ assertEquals(1, mappings.size());
+ // map G to GGG
+ sr = MappingUtils.buildSearchResults(pep4, 1, mappings);
+ assertEquals(1, sr.getResults().size());
+ m = sr.getResults().get(0);
+ assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
+ assertEquals(1, m.getStart());
+ assertEquals(3, m.getEnd());
+ // map F to TTT
+ sr = MappingUtils.buildSearchResults(pep4, 2, mappings);
+ m = sr.getResults().get(0);
+ assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
+ assertEquals(4, m.getStart());
+ assertEquals(6, m.getEnd());
+ // map P to CCC
+ sr = MappingUtils.buildSearchResults(pep4, 3, mappings);
+ m = sr.getResults().get(0);
+ assertSame(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
+ assertEquals(7, m.getStart());
+ assertEquals(9, m.getEnd());
+ }
+
+ /**
+ * Test the method that just copies aligned sequences, provided all sequences
+ * to be aligned share the aligned sequence's dataset
+ */
+ @Test(groups = "Functional")
+ public void testAlignAsSameSequences()
+ {
+ SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
+ SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
+ AlignmentI al1 = new Alignment(new SequenceI[] { dna1, dna2 });
+ ((Alignment) al1).createDatasetAlignment();
+
+ SequenceI dna3 = new Sequence(dna1);
+ SequenceI dna4 = new Sequence(dna2);
+ assertSame(dna3.getDatasetSequence(), dna1.getDatasetSequence());
+ assertSame(dna4.getDatasetSequence(), dna2.getDatasetSequence());
+ String seq1 = "-cc-GG-GT-TT--aaa";
+ dna3.setSequence(seq1);
+ String seq2 = "C--C-Cgg--gtt-tAA-A-";
+ dna4.setSequence(seq2);
+ AlignmentI al2 = new Alignment(new SequenceI[] { dna3, dna4 });
+ ((Alignment) al2).createDatasetAlignment();
+
+ assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
+ assertEquals(seq1, al1.getSequenceAt(0).getSequenceAsString());
+ assertEquals(seq2, al1.getSequenceAt(1).getSequenceAsString());
+
+ /*
+ * add another sequence to 'aligned' - should still succeed, since
+ * unaligned sequences still share a dataset with aligned sequences
+ */
+ SequenceI dna5 = new Sequence("dna5", "CCCgggtttAAA");
+ dna5.createDatasetSequence();
+ al2.addSequence(dna5);
+ assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
+ assertEquals(seq1, al1.getSequenceAt(0).getSequenceAsString());
+ assertEquals(seq2, al1.getSequenceAt(1).getSequenceAsString());
+
+ /*
+ * add another sequence to 'unaligned' - should fail, since now not
+ * all unaligned sequences share a dataset with aligned sequences
+ */
+ SequenceI dna6 = new Sequence("dna6", "CCCgggtttAAA");
+ dna6.createDatasetSequence();
+ al1.addSequence(dna6);
+ // JAL-2110 JBP Comment: what's the use case for this behaviour ?
+ assertFalse(AlignmentUtils.alignAsSameSequences(al1, al2));
+ }
+
+ @Test(groups = "Functional")
+ public void testAlignAsSameSequencesMultipleSubSeq()
+ {
+ SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
+ SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
+ SequenceI as1 = dna1.deriveSequence();
+ SequenceI as2 = dna1.deriveSequence().getSubSequence(3, 7);
+ SequenceI as3 = dna2.deriveSequence();
+ as1.insertCharAt(6, 5, '-');
+ String s_as1 = as1.getSequenceAsString();
+ as2.insertCharAt(6, 5, '-');
+ String s_as2 = as2.getSequenceAsString();
+ as3.insertCharAt(6, 5, '-');
+ String s_as3 = as3.getSequenceAsString();
+ AlignmentI aligned = new Alignment(new SequenceI[] { as1, as2, as3 });
+
+ // why do we need to cast this still ?
+ ((Alignment) aligned).createDatasetAlignment();
+ SequenceI uas1 = dna1.deriveSequence();
+ SequenceI uas2 = dna1.deriveSequence().getSubSequence(3, 7);
+ SequenceI uas3 = dna2.deriveSequence();
+ AlignmentI tobealigned = new Alignment(new SequenceI[] { uas1, uas2,
+ uas3 });
+ ((Alignment) tobealigned).createDatasetAlignment();
+
+ assertTrue(AlignmentUtils.alignAsSameSequences(tobealigned, aligned));
+ assertEquals(s_as1, uas1.getSequenceAsString());
+ assertEquals(s_as2, uas2.getSequenceAsString());
+ assertEquals(s_as3, uas3.getSequenceAsString());
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff