import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.GeneLociI;
import jalview.datamodel.Mapping;
-import jalview.datamodel.SearchResults;
-import jalview.datamodel.SearchResults.Match;
+import jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeatures;
+import jalview.gui.JvOptionPane;
import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
import jalview.io.FormatAdapter;
+import jalview.io.gff.SequenceOntologyI;
import jalview.util.MapList;
import jalview.util.MappingUtils;
+import jalview.ws.params.InvalidArgumentException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Map;
import java.util.TreeMap;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class AlignmentUtilsTests
{
- public static Sequence ts = new Sequence("short",
+ private static Sequence ts = new Sequence("short",
"ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testExpandContext()
{
SequenceI s1 = ts.deriveSequence().getSubSequence(i, i + 7);
al.addSequence(s1);
}
- System.out.println(new AppletFormatAdapter().formatSequences("Clustal",
- al, true));
+ System.out.println(new AppletFormatAdapter()
+ .formatSequences(FileFormat.Clustal, al, true));
for (int flnk = -1; flnk < 25; flnk++)
{
AlignmentI exp = AlignmentUtils.expandContext(al, flnk);
System.out.println("\nFlank size: " + flnk);
- System.out.println(new AppletFormatAdapter().formatSequences(
- "Clustal", exp, true));
+ System.out.println(new AppletFormatAdapter()
+ .formatSequences(FileFormat.Clustal, exp, true));
if (flnk == -1)
{
/*
{
String ung = sq.getSequenceAsString().replaceAll("-+", "");
final String errorMsg = "Flanking sequence not the same as original dataset sequence.\n"
- + ung
- + "\n"
+ + ung + "\n"
+ sq.getDatasetSequence().getSequenceAsString();
- assertTrue(errorMsg, ung.equalsIgnoreCase(sq.getDatasetSequence()
- .getSequenceAsString()));
+ assertTrue(errorMsg, ung.equalsIgnoreCase(
+ sq.getDatasetSequence().getSequenceAsString()));
}
}
else if (flnk == 24)
* Expand the subsequence to the full sequence abcDEFghi
*/
AlignmentI expanded = AlignmentUtils.expandContext(al, -1);
- assertEquals("abcDEFghi", expanded.getSequenceAt(0)
- .getSequenceAsString());
+ assertEquals("abcDEFghi",
+ expanded.getSequenceAt(0).getSequenceAsString());
/*
* Confirm the alignment and sequence have the same SS annotation,
{
final String data = ">Seq1Name\nKQYL\n" + ">Seq2Name\nRFPW\n"
+ ">Seq1Name\nABCD\n";
- AlignmentI al = loadAlignment(data, "FASTA");
+ AlignmentI al = loadAlignment(data, FileFormat.Fasta);
Map<String, List<SequenceI>> map = AlignmentUtils
.getSequencesByName(al);
assertEquals(2, map.keySet().size());
* @return
* @throws IOException
*/
- protected AlignmentI loadAlignment(final String data, String format)
+ protected AlignmentI loadAlignment(final String data, FileFormatI format)
throws IOException
{
- AlignmentI a = new FormatAdapter().readFile(data,
- AppletFormatAdapter.PASTE, format);
+ AlignmentI a = new FormatAdapter().readFile(data, DataSourceType.PASTE,
+ format);
a.setDataset(null);
return a;
}
@Test(groups = { "Functional" })
public void testMapProteinAlignmentToCdna_noXrefs() throws IOException
{
- List<SequenceI> protseqs = new ArrayList<SequenceI>();
+ List<SequenceI> protseqs = new ArrayList<>();
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>();
+ List<SequenceI> dnaseqs = new ArrayList<>();
dnaseqs.add(new Sequence("EMBL|A11111", "TCAGCACGC")); // = SAR
dnaseqs.add(new Sequence("EMBL|A22222", "GAGATACAA")); // = EIQ
dnaseqs.add(new Sequence("EMBL|A33333", "GAAATCCAG")); // = EIQ
MapList mapList = protMappings[0].getMap();
assertEquals(3, mapList.getFromRatio());
assertEquals(1, mapList.getToRatio());
- assertTrue(Arrays.equals(new int[] { 1, 9 }, mapList.getFromRanges()
- .get(0)));
+ assertTrue(
+ Arrays.equals(new int[]
+ { 1, 9 }, mapList.getFromRanges().get(0)));
assertEquals(1, mapList.getFromRanges().size());
- assertTrue(Arrays.equals(new int[] { 1, 3 },
- mapList.getToRanges().get(0)));
+ assertTrue(
+ Arrays.equals(new int[]
+ { 1, 3 }, mapList.getToRanges().get(0)));
assertEquals(1, mapList.getToRanges().size());
// V12346 mapped to A33333
* Exons at codon 2 (AAA) and 4 (TTT)
*/
MapList map = new MapList(new int[] { 4, 6, 10, 12 },
- new int[] { 1, 2 }, 3, 1);
+ new int[]
+ { 1, 2 }, 3, 1);
/*
* Simple case: no gaps in dna
/*
* 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");
+ 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");
+ 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.
/*
* 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-");
+ 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-");
+ 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-");
}
/**
/*
* Exons at codon 2 (AAA) and 4 (TTT) mapped to A and P
*/
- final MapList map = new MapList(new int[] { 4, 6, 10, 12 }, new int[] {
- 1, 1, 3, 3 }, 3, 1);
+ final MapList map = new MapList(new int[] { 4, 6, 10, 12 },
+ new int[]
+ { 1, 1, 3, 3 }, 3, 1);
/*
* -L- 'aligns' ccc------
SequenceI alignFrom = new Sequence("Seq2", alignModel);
alignFrom.createDatasetSequence();
AlignedCodonFrame acf = new AlignedCodonFrame();
- acf.addMap(alignMe.getDatasetSequence(), alignFrom.getDatasetSequence(), map);
+ acf.addMap(alignMe.getDatasetSequence(), alignFrom.getDatasetSequence(),
+ map);
AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "---", '-',
preserveMappedGaps, preserveUnmappedGaps);
/*
* Intron GGGAAA followed by exon CCCTTT
*/
- MapList map = new MapList(new int[] { 7, 12 }, new int[] { 1, 2 }, 3, 1);
+ 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");
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 });
+ AlignmentI protein = new Alignment(
+ new SequenceI[]
+ { prot1, prot2, prot3, prot4 });
protein.setDataset(null);
- MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1);
+ MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3,
+ 1);
AlignedCodonFrame acf = new AlignedCodonFrame();
acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map);
acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map);
- ArrayList<AlignedCodonFrame> acfs = new ArrayList<AlignedCodonFrame>();
+ ArrayList<AlignedCodonFrame> acfs = new ArrayList<>();
acfs.add(acf);
protein.setCodonFrames(acfs);
"F*PK*G".toCharArray()));
// wrong protein
- assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
- 0, "FPMG".toCharArray()));
+ 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()));
+ assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
+ "FPK".toCharArray()));
// overlong dna (doesn't end in stop codon)
- assertFalse(AlignmentUtils.translatesAs(
- "tttcccaaagggttt".toCharArray(), 0, "FPKG".toCharArray()));
+ 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()));
+ assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
+ "FPKGQ".toCharArray()));
}
/**
public void testMapProteinAlignmentToCdna_withStartAndStopCodons()
throws IOException
{
- List<SequenceI> protseqs = new ArrayList<SequenceI>();
+ List<SequenceI> protseqs = new ArrayList<>();
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>();
+ List<SequenceI> dnaseqs = new ArrayList<>();
// start + SAR:
dnaseqs.add(new Sequence("EMBL|A11111", "ATGTCAGCACGC"));
// = EIQ + stop
MapList mapList = protMappings[0].getMap();
assertEquals(3, mapList.getFromRatio());
assertEquals(1, mapList.getToRatio());
- assertTrue(Arrays.equals(new int[] { 1, 9 }, mapList.getFromRanges()
- .get(0)));
+ assertTrue(
+ Arrays.equals(new int[]
+ { 1, 9 }, mapList.getFromRanges().get(0)));
assertEquals(1, mapList.getFromRanges().size());
- assertTrue(Arrays.equals(new int[] { 1, 3 },
- mapList.getToRanges().get(0)));
+ assertTrue(
+ Arrays.equals(new int[]
+ { 1, 3 }, mapList.getToRanges().get(0)));
assertEquals(1, mapList.getToRanges().size());
// V12346 mapped from A33333 starting position 4
mapList = protMappings[0].getMap();
assertEquals(3, mapList.getFromRatio());
assertEquals(1, mapList.getToRatio());
- assertTrue(Arrays.equals(new int[] { 4, 12 }, mapList.getFromRanges()
- .get(0)));
+ assertTrue(
+ Arrays.equals(new int[]
+ { 4, 12 }, mapList.getFromRanges().get(0)));
assertEquals(1, mapList.getFromRanges().size());
- assertTrue(Arrays.equals(new int[] { 1, 3 },
- mapList.getToRanges().get(0)));
+ assertTrue(
+ Arrays.equals(new int[]
+ { 1, 3 }, mapList.getToRanges().get(0)));
assertEquals(1, mapList.getToRanges().size());
// V12347 mapped to A11111 starting position 4
mapList = protMappings[0].getMap();
assertEquals(3, mapList.getFromRatio());
assertEquals(1, mapList.getToRatio());
- assertTrue(Arrays.equals(new int[] { 4, 12 }, mapList.getFromRanges()
- .get(0)));
+ assertTrue(
+ Arrays.equals(new int[]
+ { 4, 12 }, mapList.getFromRanges().get(0)));
assertEquals(1, mapList.getFromRanges().size());
- assertTrue(Arrays.equals(new int[] { 1, 3 },
- mapList.getToRanges().get(0)));
+ assertTrue(
+ Arrays.equals(new int[]
+ { 1, 3 }, mapList.getToRanges().get(0)));
assertEquals(1, mapList.getToRanges().size());
// no mapping involving the 'extra' A44444
@Test(groups = { "Functional" })
public void testMapProteinAlignmentToCdna_withXrefs() throws IOException
{
- List<SequenceI> protseqs = new ArrayList<SequenceI>();
+ List<SequenceI> protseqs = new ArrayList<>();
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>();
+ List<SequenceI> dnaseqs = new ArrayList<>();
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
public void testMapProteinAlignmentToCdna_prioritiseXrefs()
throws IOException
{
- List<SequenceI> protseqs = new ArrayList<SequenceI>();
+ List<SequenceI> protseqs = new ArrayList<>();
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>();
+ List<SequenceI> dnaseqs = new ArrayList<>();
dnaseqs.add(new Sequence("EMBL|A11111", "GAAATCCAG")); // = EIQ
dnaseqs.add(new Sequence("EMBL|A22222", "GAAATTCAG")); // = EIQ
- AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[dnaseqs
- .size()]));
+ AlignmentI cdna = new Alignment(
+ dnaseqs.toArray(new SequenceI[dnaseqs.size()]));
cdna.setDataset(null);
// Xref A22222 to V12345 (should get mapped)
ann2.setSequenceRef(seq2);
AlignmentAnnotation ann3 = new AlignmentAnnotation("Structure", "ann3",
anns);
- AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "ann4", anns);
+ AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "ann4",
+ anns);
ann4.setSequenceRef(seq1);
- AlignmentAnnotation ann5 = new AlignmentAnnotation("Temp", "ann5", anns);
+ AlignmentAnnotation ann5 = new AlignmentAnnotation("Temp", "ann5",
+ anns);
ann5.setSequenceRef(seq2);
- AlignmentAnnotation ann6 = new AlignmentAnnotation("Temp", "ann6", anns);
+ 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(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>();
+ List<String> types = new ArrayList<>();
+ List<SequenceI> scope = new ArrayList<>();
/*
* Set all sequence related Structure to hidden (ann1, ann2)
/*
* scenario:
* dna1 --> [4, 6] [10,12] --> pep1
- * dna2 --> [1, 3] [7, 9] [13,15] --> pep1
+ * dna2 --> [1, 3] [7, 9] [13,15] --> pep2
*/
SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
SequenceI dna2 = new Sequence("dna2", "GGGcccTTTaaaCCC");
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
+ * sequence from the dna contig sequences
*/
DBRefEntry dbref = new DBRefEntry("ENSEMBL", "0", "dna1");
- dna1.getDatasetSequence().setSourceDBRef(dbref);
+ dna1.getDatasetSequence().addDBRef(dbref);
+ org.testng.Assert.assertEquals(dbref, dna1.getPrimaryDBRefs().get(0));
dbref = new DBRefEntry("ENSEMBL", "0", "dna2");
- dna2.getDatasetSequence().setSourceDBRef(dbref);
+ 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 map = new MapList(new int[] { 4, 6, 10, 12 },
- new int[] { 1, 2 }, 3, 1);
+ 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(), map);
+ acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
+ mapfordna1);
dna.addCodonFrame(acf);
- map = new MapList(new int[] { 1, 3, 7, 9, 13, 15 }, new int[] { 1, 3 },
- 3, 1);
+ 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(), map);
+ 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.addDBRef(dna1xref);
+ assertEquals(2, dna1.getDBRefs().size()); // to self and to pep1
+ DBRefEntry dna2xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep2",
+ new Mapping(mapfordna2));
+ dna2.addDBRef(dna2xref);
+ assertEquals(2, dna2.getDBRefs().size()); // to self and to pep2
+
+ /*
* execute method under test:
*/
- AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
- dna1, dna2 }, dna.getDataset(), null);
+ AlignmentI cds = AlignmentUtils
+ .makeCdsAlignment(new SequenceI[]
+ { dna1, dna2 }, dna.getDataset(), null);
/*
* verify cds sequences
* verify CDS has a dbref with mapping to peptide
*/
assertNotNull(cds1Dss.getDBRefs());
- assertEquals(1, cds1Dss.getDBRefs().length);
- dbref = cds1Dss.getDBRefs()[0];
- assertEquals("UNIPROT", dbref.getSource());
- assertEquals("0", dbref.getVersion());
- assertEquals("pep1", dbref.getAccessionId());
+ assertEquals(2, cds1Dss.getDBRefs().size());
+ dbref = cds1Dss.getDBRefs().get(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);
+ 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());
- assertEquals(2, pep1.getDBRefs().length);
- dbref = pep1.getDBRefs()[1];
+ // FIXME pep1.getDBRefs() is 1 - is that the correct behaviour ?
+ assertEquals(2, pep1.getDBRefs().size());
+ dbref = pep1.getDBRefs().get(1);
assertEquals("ENSEMBL", dbref.getSource());
assertEquals("0", dbref.getVersion());
assertEquals("CDS|dna1", dbref.getAccessionId());
assertEquals(cdsMapping.getInverse(), dbref.getMap().getMap());
/*
+ * verify cDNA has added a dbref with mapping to CDS
+ */
+ assertEquals(3, dna1.getDBRefs().size());
+ DBRefEntry dbRefEntry = dna1.getDBRefs().get(2);
+ assertSame(cds1Dss, dbRefEntry.getMap().getTo());
+ MapList dnaToCdsMapping = new MapList(new int[] { 4, 6, 10, 12 },
+ new int[]
+ { 1, 6 }, 1, 1);
+ assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap());
+ assertEquals(3, dna2.getDBRefs().size());
+ dbRefEntry = dna2.getDBRefs().get(2);
+ assertSame(cds2Dss, dbRefEntry.getMap().getTo());
+ dnaToCdsMapping = new MapList(new int[] { 1, 3, 7, 9, 13, 15 },
+ new int[]
+ { 1, 9 }, 1, 1);
+ assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap());
+
+ /*
+ * verify CDS has added a dbref with mapping to cDNA
+ */
+ assertEquals(2, cds1Dss.getDBRefs().size());
+ dbRefEntry = cds1Dss.getDBRefs().get(1);
+ assertSame(dna1.getDatasetSequence(), dbRefEntry.getMap().getTo());
+ MapList cdsToDnaMapping = new MapList(new int[] { 1, 6 },
+ new int[]
+ { 4, 6, 10, 12 }, 1, 1);
+ assertEquals(cdsToDnaMapping, dbRefEntry.getMap().getMap());
+ assertEquals(2, cds2Dss.getDBRefs().size());
+ dbRefEntry = cds2Dss.getDBRefs().get(1);
+ assertSame(dna2.getDatasetSequence(), dbRefEntry.getMap().getTo());
+ cdsToDnaMapping = new MapList(new int[] { 1, 9 },
+ new int[]
+ { 1, 3, 7, 9, 13, 15 }, 1, 1);
+ assertEquals(cdsToDnaMapping, dbRefEntry.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)
assertEquals(1, mappings.size());
// map G to GGG
- SearchResults sr = MappingUtils.buildSearchResults(pep1, 1, mappings);
+ SearchResultsI sr = MappingUtils.buildSearchResults(pep1, 1, mappings);
assertEquals(1, sr.getResults().size());
- Match m = sr.getResults().get(0);
+ SearchResultMatchI m = sr.getResults().get(0);
assertSame(cds1Dss, m.getSequence());
assertEquals(1, m.getStart());
assertEquals(3, m.getEnd());
assertSame(cds2Dss, m.getSequence());
assertEquals(7, m.getStart());
assertEquals(9, m.getEnd());
+
+ /*
+ * check cds2 acquired a variant feature in position 5
+ */
+ List<SequenceFeature> sfs = cds2Dss.getSequenceFeatures();
+ assertNotNull(sfs);
+ assertEquals(1, sfs.size());
+ assertEquals("variant", sfs.get(0).type);
+ assertEquals(5, sfs.get(0).begin);
+ assertEquals(5, sfs.get(0).end);
}
/**
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"));
+ 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
*/
// map ...GGG...TTT to GF
MapList map = new MapList(new int[] { 4, 6, 10, 12 },
- new int[] { 1, 2 }, 3, 1);
+ new int[]
+ { 1, 2 }, 3, 1);
AlignedCodonFrame acf = new AlignedCodonFrame();
acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
dna.addCodonFrame(acf);
/*
* execute method under test
*/
- AlignmentI cdsal = AlignmentUtils.makeCdsAlignment(
- new SequenceI[] { dna1 }, dna.getDataset(), null);
+ AlignmentI cdsal = AlignmentUtils
+ .makeCdsAlignment(new SequenceI[]
+ { dna1 }, dna.getDataset(), null);
/*
* Verify we have 3 cds sequences, mapped to pep1/2/3 respectively
.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());
+ assertSame(pep1.getDatasetSequence(),
+ mappings.get(0).getMappings().get(0).getMapping().getTo());
/*
* dna1 to cds1
.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));
+ 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());
+ assertSame(pep2.getDatasetSequence(),
+ mappings.get(0).getMappings().get(0).getMapping().getTo());
/*
* dna1 to cds2
.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));
+ 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());
+ assertSame(pep3.getDatasetSequence(),
+ mappings.get(0).getMappings().get(0).getMapping().getTo());
/*
* dna1 to cds3
.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));
+ assertEquals("T(4) in CDS should map to T(10) in DNA", 10,
+ mapping.getMap().getToPosition(4));
}
@Test(groups = { "Functional" })
* @throws IOException
*/
@Test(groups = { "Functional" })
- public void testMapCdnaToProtein_forSubsequence()
- throws IOException
+ public void testMapCdnaToProtein_forSubsequence() throws IOException
{
SequenceI prot = new Sequence("UNIPROT|V12345", "E-I--Q", 10, 12);
prot.createDatasetSequence();
@Test(groups = { "Functional" })
public void testAlignSequenceAs_mappedProteinProtein()
{
-
+
SequenceI alignMe = new Sequence("Match", "MGAASEV");
alignMe.createDatasetSequence();
SequenceI alignFrom = new Sequence("Query", "LQTGYMGAASEVMFSPTRR");
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);
-
+ 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());
{
// 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---");
}
SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
// no overlap
- dna.addSequenceFeature(new SequenceFeature("type1", "desc1", 1, 2, 1f,
- null));
+ 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));
+ 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));
+ 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));
+ 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));
+ dna.addSequenceFeature(
+ new SequenceFeature("type5", "desc5", 4, 12, 5f, null));
// no overlap (internal)
- dna.addSequenceFeature(new SequenceFeature("type6", "desc6", 7, 9, 6f,
- null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type6", "desc6", 7, 9, 6f, null));
// no overlap (3' end)
- dna.addSequenceFeature(new SequenceFeature("type7", "desc7", 13, 15,
- 7f, null));
+ 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));
+ dna.addSequenceFeature(
+ new SequenceFeature("type8", "desc8", 12, 12, 8f, null));
// extended overlap - to [6, +]
- dna.addSequenceFeature(new SequenceFeature("type9", "desc9", 12, 13,
- 9f, null));
+ 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);
+ 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);
+ List<SequenceFeature> sfs = cds.getSequenceFeatures();
+ assertEquals(6, sfs.size());
- SequenceFeature sf = sfs[0];
+ SequenceFeature sf = sfs.get(0);
assertEquals("type2", sf.getType());
assertEquals("desc2", sf.getDescription());
assertEquals(2f, sf.getScore());
assertEquals(1, sf.getBegin());
assertEquals(1, sf.getEnd());
- sf = sfs[1];
+ sf = sfs.get(1);
assertEquals("type3", sf.getType());
assertEquals("desc3", sf.getDescription());
assertEquals(3f, sf.getScore());
assertEquals(1, sf.getBegin());
assertEquals(3, sf.getEnd());
- sf = sfs[2];
+ sf = sfs.get(2);
assertEquals("type4", sf.getType());
assertEquals(2, sf.getBegin());
assertEquals(5, sf.getEnd());
- sf = sfs[3];
+ sf = sfs.get(3);
assertEquals("type5", sf.getType());
assertEquals(1, sf.getBegin());
assertEquals(6, sf.getEnd());
- sf = sfs[4];
+ sf = sfs.get(4);
assertEquals("type8", sf.getType());
assertEquals(6, sf.getBegin());
assertEquals(6, sf.getEnd());
- sf = sfs[5];
+ sf = sfs.get(5);
assertEquals("type9", sf.getType());
assertEquals(6, sf.getBegin());
assertEquals(6, sf.getEnd());
SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
MapList map = new MapList(new int[] { 4, 6, 10, 12 },
- new int[] { 1, 6 }, 1, 1);
-
+ new int[]
+ { 1, 6 }, 1, 1);
+
// [5, 11] maps to [2, 5]
- dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f,
- null));
+ 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));
+ 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));
-
+ 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];
+ List<SequenceFeature> sfs = cds.getSequenceFeatures();
+ assertEquals(1, sfs.size());
+
+ SequenceFeature sf = sfs.get(0);
assertEquals("type5", sf.getType());
assertEquals(1, sf.getBegin());
assertEquals(6, sf.getEnd());
{
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);
-
+ new int[]
+ { 1, 6 }, 1, 1);
+
// [5, 11] maps to [2, 5]
- dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f,
- null));
+ 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));
+ 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));
-
+ 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];
+ List<SequenceFeature> sfs = cds.getSequenceFeatures();
+ assertEquals(1, sfs.size());
+
+ SequenceFeature sf = sfs.get(0);
assertEquals("type5", sf.getType());
assertEquals(1, sf.getBegin());
assertEquals(6, sf.getEnd());
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);
+ 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);
+ 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);
+
+ 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
*/
*/
List<AlignedCodonFrame> mappings = cds.getCodonFrames();
assertEquals(6, mappings.size());
-
+
/*
* 2 mappings involve pep1
*/
List<AlignedCodonFrame> pep1CdsMappings = MappingUtils
.findMappingsForSequence(cds.getSequenceAt(0), pep1Mappings);
assertEquals(1, pep1CdsMappings.size());
- SearchResults sr = MappingUtils.buildSearchResults(pep1, 1,
+ SearchResultsI sr = MappingUtils.buildSearchResults(pep1, 1,
pep1CdsMappings);
assertEquals(1, sr.getResults().size());
- Match m = sr.getResults().get(0);
+ SearchResultMatchI m = sr.getResults().get(0);
assertEquals(cds.getSequenceAt(0).getDatasetSequence(),
m.getSequence());
assertEquals(1, m.getStart());
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
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 });
+ 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);
+ 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 = 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>();
+ ArrayList<AlignedCodonFrame> acfs = new ArrayList<>();
acfs.add(acf);
protein.setCodonFrames(acfs);
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
// 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
*/
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);
// 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] }
}
/**
- * 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, with variants
- * GAA -> E
- * CAA -> Q
- * AAG synonymous
- * AAT -> N
- * TTC synonymous
- * CAC,CGC -> H,R (as one variant)
- */
- SequenceI peptide = new Sequence("pep/10-12", "KFP");
-
- /*
- * two distinct variants for codon 1 position 1
- * second one has clinical significance
- */
- SequenceFeature sf1 = new SequenceFeature("sequence_variant", "", 1, 1,
- 0f, null);
- sf1.setValue("alleles", "A,G"); // GAA -> E
- sf1.setValue("ID", "var1.125A>G");
- SequenceFeature sf2 = new SequenceFeature("sequence_variant", "", 1, 1,
- 0f, null);
- 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, null);
- sf3.setValue("alleles", "A,G"); // synonymous
- sf3.setValue("ID", "var3");
- sf3.setValue("clinical_significance", "None");
- SequenceFeature sf4 = new SequenceFeature("sequence_variant", "", 3, 3,
- 0f, null);
- 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, null);
- sf5.setValue("alleles", "T,C"); // synonymous
- sf5.setValue("ID", "var5");
- sf5.setValue("clinical_significance", "Bad");
- SequenceFeature sf6 = new SequenceFeature("sequence_variant", "", 8, 8,
- 0f, null);
- 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
- * var2 K -> Q
- * var4 K -> N
- * var6 P -> H
- * var6 P -> R
- */
- 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("Jalview", 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("Jalview", 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("Jalview", sf.getFeatureGroup());
- 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));
- // var5 generates two distinct protein variant features
- assertEquals("Jalview", 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("Jalview", sf.getFeatureGroup());
- }
-
- /**
* Tests for the method that maps the subset of a dna sequence that has CDS
* (or subtype) feature, with CDS strand = '-' (reverse)
*/
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("-");
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] }
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("-");
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]
dna.addCodonFrame(acf);
AlignmentUtils.alignAs(cds, dna);
assertEquals("---GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
- assertEquals("CCC------AAA", cds.getSequenceAt(1).getSequenceAsString());
+ assertEquals("CCC------AAA",
+ cds.getSequenceAt(1).getSequenceAsString());
}
@Test(groups = { "Functional" })
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>>();
+ 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<>();
AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
/*
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>>();
+ 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<>();
AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
-
+
/*
* verify map has seq1 residues in columns 3,4,6,7,11,12
*/
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);
+ new int[]
+ { 1, 2 }, 3, 1);
acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map);
dna.addCodonFrame(acf);
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());
-
+ 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
*/
.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
* 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]
// 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> mappings = MappingUtils
.findMappingsForSequence(cds.getSequenceAt(0), pep3Mappings);
assertEquals(1, mappings.size());
-
+
// map G to GGG
- SearchResults sr = MappingUtils.buildSearchResults(pep3, 1, mappings);
+ SearchResultsI sr = MappingUtils.buildSearchResults(pep3, 1, mappings);
assertEquals(1, sr.getResults().size());
- Match m = sr.getResults().get(0);
+ SearchResultMatchI m = sr.getResults().get(0);
assertSame(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
assertEquals(1, m.getStart());
assertEquals(3, m.getEnd());
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
dna4.setSequence(seq2);
AlignmentI al2 = new Alignment(new SequenceI[] { dna3, dna4 });
((Alignment) al2).createDatasetAlignment();
-
+
+ /*
+ * alignment removes gapped columns (two internal, two trailing)
+ */
assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
- assertEquals(seq1, al1.getSequenceAt(0).getSequenceAsString());
- assertEquals(seq2, al1.getSequenceAt(1).getSequenceAsString());
+ String aligned1 = "-cc-GG-GTTT-aaa";
+ assertEquals(aligned1, al1.getSequenceAt(0).getSequenceAsString());
+ String aligned2 = "C--C-Cgg-gtttAAA";
+ assertEquals(aligned2, al1.getSequenceAt(1).getSequenceAsString());
/*
* add another sequence to 'aligned' - should still succeed, since
dna5.createDatasetSequence();
al2.addSequence(dna5);
assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
- assertEquals(seq1, al1.getSequenceAt(0).getSequenceAsString());
- assertEquals(seq2, al1.getSequenceAt(1).getSequenceAsString());
+ assertEquals(aligned1, al1.getSequenceAt(0).getSequenceAsString());
+ assertEquals(aligned2, al1.getSequenceAt(1).getSequenceAsString());
/*
* add another sequence to 'unaligned' - should fail, since now not
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));
}
{
SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
- SequenceI as1 = dna1.deriveSequence(), as2 = dna1.deriveSequence()
- .getSubSequence(3, 7), as3 = dna2.deriveSequence();
+ SequenceI as1 = dna1.deriveSequence(); // cccGGGTTTaaa/1-12
+ SequenceI as2 = dna1.deriveSequence().getSubSequence(3, 7); // GGGT/4-7
+ SequenceI as3 = dna2.deriveSequence(); // CCCgggtttAAA/1-12
as1.insertCharAt(6, 5, '-');
- String s_as1 = as1.getSequenceAsString();
+ assertEquals("cccGGG-----TTTaaa", as1.getSequenceAsString());
as2.insertCharAt(6, 5, '-');
- String s_as2 = as2.getSequenceAsString();
- as3.insertCharAt(6, 5, '-');
- String s_as3 = as3.getSequenceAsString();
+ assertEquals("GGGT-----", as2.getSequenceAsString());
+ as3.insertCharAt(3, 5, '-');
+ assertEquals("CCC-----gggtttAAA", 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(), uas2 = dna1.deriveSequence()
- .getSubSequence(3, 7), uas3 = dna2.deriveSequence();
- AlignmentI tobealigned = new Alignment(new SequenceI[] { uas1, uas2,
- uas3 });
+ 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();
+ /*
+ * alignAs lines up dataset sequences and removes empty columns (two)
+ */
assertTrue(AlignmentUtils.alignAsSameSequences(tobealigned, aligned));
- assertEquals(s_as1, uas1.getSequenceAsString());
- assertEquals(s_as2, uas2.getSequenceAsString());
- assertEquals(s_as3, uas3.getSequenceAsString());
+ assertEquals("cccGGG---TTTaaa", uas1.getSequenceAsString());
+ assertEquals("GGGT", uas2.getSequenceAsString());
+ assertEquals("CCC---gggtttAAA", uas3.getSequenceAsString());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testTransferGeneLoci()
+ {
+ SequenceI from = new Sequence("transcript",
+ "aaacccgggTTTAAACCCGGGtttaaacccgggttt");
+ SequenceI to = new Sequence("CDS", "TTTAAACCCGGG");
+ MapList map = new MapList(new int[] { 1, 12 }, new int[] { 10, 21 }, 1,
+ 1);
+
+ /*
+ * first with nothing to transfer
+ */
+ AlignmentUtils.transferGeneLoci(from, map, to);
+ assertNull(to.getGeneLoci());
+
+ /*
+ * next with gene loci set on 'from' sequence
+ */
+ int[] exons = new int[] { 100, 105, 155, 164, 210, 229 };
+ MapList geneMap = new MapList(new int[] { 1, 36 }, exons, 1, 1);
+ from.setGeneLoci("human", "GRCh38", "7", geneMap);
+ AlignmentUtils.transferGeneLoci(from, map, to);
+
+ GeneLociI toLoci = to.getGeneLoci();
+ assertNotNull(toLoci);
+ // DBRefEntry constructor upper-cases 'source'
+ assertEquals("HUMAN", toLoci.getSpeciesId());
+ assertEquals("GRCh38", toLoci.getAssemblyId());
+ assertEquals("7", toLoci.getChromosomeId());
+
+ /*
+ * transcript 'exons' are 1-6, 7-16, 17-36
+ * CDS 1:12 is transcript 10-21
+ * transcript 'CDS' is 10-16, 17-21
+ * which is 'gene' 158-164, 210-214
+ */
+ MapList toMap = toLoci.getMapping();
+ assertEquals(1, toMap.getFromRanges().size());
+ assertEquals(2, toMap.getFromRanges().get(0).length);
+ assertEquals(1, toMap.getFromRanges().get(0)[0]);
+ assertEquals(12, toMap.getFromRanges().get(0)[1]);
+ assertEquals(2, toMap.getToRanges().size());
+ assertEquals(2, toMap.getToRanges().get(0).length);
+ assertEquals(158, toMap.getToRanges().get(0)[0]);
+ assertEquals(164, toMap.getToRanges().get(0)[1]);
+ assertEquals(210, toMap.getToRanges().get(1)[0]);
+ assertEquals(214, toMap.getToRanges().get(1)[1]);
+ // or summarised as (but toString might change in future):
+ assertEquals("[ [1, 12] ] 1:1 to [ [158, 164] [210, 214] ]",
+ toMap.toString());
+
+ /*
+ * an existing value is not overridden
+ */
+ geneMap = new MapList(new int[] { 1, 36 }, new int[] { 36, 1 }, 1, 1);
+ from.setGeneLoci("inhuman", "GRCh37", "6", geneMap);
+ AlignmentUtils.transferGeneLoci(from, map, to);
+ assertEquals("GRCh38", toLoci.getAssemblyId());
+ assertEquals("7", toLoci.getChromosomeId());
+ toMap = toLoci.getMapping();
+ assertEquals("[ [1, 12] ] 1:1 to [ [158, 164] [210, 214] ]",
+ toMap.toString());
+ }
+
+ /**
+ * Tests for the method that maps nucleotide to protein based on CDS features
+ */
+ @Test(groups = "Functional")
+ public void testMapCdsToProtein()
+ {
+ SequenceI peptide = new Sequence("pep", "KLQ");
+
+ /*
+ * Case 1: CDS 3 times length of peptide
+ * NB method only checks lengths match, not translation
+ */
+ SequenceI dna = new Sequence("dna", "AACGacgtCTCCT");
+ dna.createDatasetSequence();
+ dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
+ dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 13, null));
+ MapList ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
+ assertEquals(3, ml.getFromRatio());
+ assertEquals(1, ml.getToRatio());
+ assertEquals("[[1, 3]]",
+ Arrays.deepToString(ml.getToRanges().toArray()));
+ assertEquals("[[1, 4], [9, 13]]",
+ Arrays.deepToString(ml.getFromRanges().toArray()));
+
+ /*
+ * Case 2: CDS 3 times length of peptide + stop codon
+ * (note code does not currently check trailing codon is a stop codon)
+ */
+ dna = new Sequence("dna", "AACGacgtCTCCTCCC");
+ dna.createDatasetSequence();
+ dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
+ dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 16, null));
+ ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
+ assertEquals(3, ml.getFromRatio());
+ assertEquals(1, ml.getToRatio());
+ assertEquals("[[1, 3]]",
+ Arrays.deepToString(ml.getToRanges().toArray()));
+ assertEquals("[[1, 4], [9, 13]]",
+ Arrays.deepToString(ml.getFromRanges().toArray()));
+
+ /*
+ * Case 3: CDS longer than 3 * peptide + stop codon - no mapping is made
+ */
+ dna = new Sequence("dna", "AACGacgtCTCCTTGATCA");
+ dna.createDatasetSequence();
+ dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
+ dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 19, null));
+ ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
+ assertNull(ml);
+
+ /*
+ * Case 4: CDS shorter than 3 * peptide - no mapping is made
+ */
+ dna = new Sequence("dna", "AACGacgtCTCC");
+ dna.createDatasetSequence();
+ dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
+ dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 12, null));
+ ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
+ assertNull(ml);
+
+ /*
+ * Case 5: CDS 3 times length of peptide + part codon - mapping is truncated
+ */
+ dna = new Sequence("dna", "AACGacgtCTCCTTG");
+ dna.createDatasetSequence();
+ dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
+ dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 15, null));
+ ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
+ assertEquals(3, ml.getFromRatio());
+ assertEquals(1, ml.getToRatio());
+ assertEquals("[[1, 3]]",
+ Arrays.deepToString(ml.getToRanges().toArray()));
+ assertEquals("[[1, 4], [9, 13]]",
+ Arrays.deepToString(ml.getFromRanges().toArray()));
+
+ /*
+ * Case 6: incomplete start codon corresponding to X in peptide
+ */
+ dna = new Sequence("dna", "ACGacgtCTCCTTGG");
+ dna.createDatasetSequence();
+ SequenceFeature sf = new SequenceFeature("CDS", "", 1, 3, null);
+ sf.setPhase("2"); // skip 2 positions (AC) to start of next codon (GCT)
+ dna.addSequenceFeature(sf);
+ dna.addSequenceFeature(new SequenceFeature("CDS", "", 8, 15, null));
+ peptide = new Sequence("pep", "XLQ");
+ ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
+ assertEquals("[[2, 3]]",
+ Arrays.deepToString(ml.getToRanges().toArray()));
+ assertEquals("[[3, 3], [8, 12]]",
+ Arrays.deepToString(ml.getFromRanges().toArray()));
+ }
+
+ /**
+ * Tests for the method that locates the CDS sequence that has a mapping to
+ * the given protein. That is, given a transcript-to-peptide mapping, find the
+ * cds-to-peptide mapping that relates to both, and return the CDS sequence.
+ */
+ @Test
+ public void testFindCdsForProtein()
+ {
+ List<AlignedCodonFrame> mappings = new ArrayList<>();
+ AlignedCodonFrame acf1 = new AlignedCodonFrame();
+ mappings.add(acf1);
+
+ SequenceI dna1 = new Sequence("dna1", "cgatATcgGCTATCTATGacg");
+ dna1.createDatasetSequence();
+
+ // NB we currently exclude STOP codon from CDS sequences
+ // the test would need to change if this changes in future
+ SequenceI cds1 = new Sequence("cds1", "ATGCTATCT");
+ cds1.createDatasetSequence();
+
+ SequenceI pep1 = new Sequence("pep1", "MLS");
+ pep1.createDatasetSequence();
+ List<AlignedCodonFrame> seqMappings = new ArrayList<>();
+ MapList mapList = new MapList(new int[] { 5, 6, 9, 15 },
+ new int[]
+ { 1, 3 }, 3, 1);
+ Mapping dnaToPeptide = new Mapping(pep1.getDatasetSequence(), mapList);
+
+ // add dna to peptide mapping
+ seqMappings.add(acf1);
+ acf1.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
+ mapList);
+
+ /*
+ * first case - no dna-to-CDS mapping exists - search fails
+ */
+ SequenceI seq = AlignmentUtils.findCdsForProtein(mappings, dna1,
+ seqMappings, dnaToPeptide);
+ assertNull(seq);
+
+ /*
+ * second case - CDS-to-peptide mapping exists but no dna-to-CDS
+ * - search fails
+ */
+ // todo this test fails if the mapping is added to acf1, not acf2
+ // need to tidy up use of lists of mappings in AlignedCodonFrame
+ AlignedCodonFrame acf2 = new AlignedCodonFrame();
+ mappings.add(acf2);
+ MapList cdsToPeptideMapping = new MapList(new int[] { 1, 9 },
+ new int[]
+ { 1, 3 }, 3, 1);
+ acf2.addMap(cds1.getDatasetSequence(), pep1.getDatasetSequence(),
+ cdsToPeptideMapping);
+ assertNull(AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
+ dnaToPeptide));
+
+ /*
+ * third case - add dna-to-CDS mapping - CDS is now found!
+ */
+ MapList dnaToCdsMapping = new MapList(new int[] { 5, 6, 9, 15 },
+ new int[]
+ { 1, 9 }, 1, 1);
+ acf1.addMap(dna1.getDatasetSequence(), cds1.getDatasetSequence(),
+ dnaToCdsMapping);
+ seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
+ dnaToPeptide);
+ assertSame(seq, cds1.getDatasetSequence());
+ }
+
+ /**
+ * Tests for the method that locates the CDS sequence that has a mapping to
+ * the given protein. That is, given a transcript-to-peptide mapping, find the
+ * cds-to-peptide mapping that relates to both, and return the CDS sequence.
+ * This test is for the case where transcript and CDS are the same length.
+ */
+ @Test
+ public void testFindCdsForProtein_noUTR()
+ {
+ List<AlignedCodonFrame> mappings = new ArrayList<>();
+ AlignedCodonFrame acf1 = new AlignedCodonFrame();
+ mappings.add(acf1);
+
+ SequenceI dna1 = new Sequence("dna1", "ATGCTATCTTAA");
+ dna1.createDatasetSequence();
+
+ // NB we currently exclude STOP codon from CDS sequences
+ // the test would need to change if this changes in future
+ SequenceI cds1 = new Sequence("cds1", "ATGCTATCT");
+ cds1.createDatasetSequence();
+
+ SequenceI pep1 = new Sequence("pep1", "MLS");
+ pep1.createDatasetSequence();
+ List<AlignedCodonFrame> seqMappings = new ArrayList<>();
+ MapList mapList = new MapList(new int[] { 1, 9 }, new int[] { 1, 3 }, 3,
+ 1);
+ Mapping dnaToPeptide = new Mapping(pep1.getDatasetSequence(), mapList);
+
+ // add dna to peptide mapping
+ seqMappings.add(acf1);
+ acf1.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
+ mapList);
+
+ /*
+ * first case - transcript lacks CDS features - it appears to be
+ * the CDS sequence and is returned
+ */
+ SequenceI seq = AlignmentUtils.findCdsForProtein(mappings, dna1,
+ seqMappings, dnaToPeptide);
+ assertSame(seq, dna1.getDatasetSequence());
+
+ /*
+ * second case - transcript has CDS feature - this means it is
+ * not returned as a match for CDS (CDS sequences don't have CDS features)
+ */
+ dna1.addSequenceFeature(
+ new SequenceFeature(SequenceOntologyI.CDS, "cds", 1, 12, null));
+ seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
+ dnaToPeptide);
+ assertNull(seq);
+
+ /*
+ * third case - CDS-to-peptide mapping exists but no dna-to-CDS
+ * - search fails
+ */
+ // todo this test fails if the mapping is added to acf1, not acf2
+ // need to tidy up use of lists of mappings in AlignedCodonFrame
+ AlignedCodonFrame acf2 = new AlignedCodonFrame();
+ mappings.add(acf2);
+ MapList cdsToPeptideMapping = new MapList(new int[] { 1, 9 },
+ new int[]
+ { 1, 3 }, 3, 1);
+ acf2.addMap(cds1.getDatasetSequence(), pep1.getDatasetSequence(),
+ cdsToPeptideMapping);
+ assertNull(AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
+ dnaToPeptide));
+
+ /*
+ * fourth case - add dna-to-CDS mapping - CDS is now found!
+ */
+ MapList dnaToCdsMapping = new MapList(new int[] { 1, 9 },
+ new int[]
+ { 1, 9 }, 1, 1);
+ acf1.addMap(dna1.getDatasetSequence(), cds1.getDatasetSequence(),
+ dnaToCdsMapping);
+ seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
+ dnaToPeptide);
+ assertSame(seq, cds1.getDatasetSequence());
}
-
}
git://source.jalview.org / jalview.git / blobdiff