import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
-import jalview.analysis.AlignmentUtils.DnaVariant;
+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.SortedMap;
+import java.util.TreeMap;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.GeneLociI;
import jalview.datamodel.Mapping;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SeqDistanceContactMatrix;
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.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.Arrays;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
public class AlignmentUtilsTests
{
SequenceI s1 = ts.deriveSequence().getSubSequence(i, i + 7);
al.addSequence(s1);
}
- System.out.println(new AppletFormatAdapter().formatSequences(
- FileFormat.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(
- FileFormat.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,
protected AlignmentI loadAlignment(final String data, FileFormatI format)
throws IOException
{
- AlignmentI a = new FormatAdapter().readFile(data,
- DataSourceType.PASTE, format);
+ AlignmentI a = new FormatAdapter().readFile(data, DataSourceType.PASTE,
+ format);
a.setDataset(null);
return a;
}
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);
"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()));
}
/**
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
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
assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
// now the other way round
- seq1.setDBRefs(null);
+ seq1.setDBRefs(null);
seq2.addDBRef(new DBRefEntry("EMBL", "1", "A12345"));
assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
* put a variant feature on dna2 base 8
* - should transfer to cds2 base 5
*/
- dna2.addSequenceFeature(new SequenceFeature("variant", "hgmd", 8, 8,
- 0f, null));
+ dna2.addSequenceFeature(
+ new SequenceFeature("variant", "hgmd", 8, 8, 0f, null));
/*
* need a sourceDbRef if we are to construct dbrefs to the CDS
* 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);
+ 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);
+ new int[]
+ { 1, 3 }, 3, 1);
acf = new AlignedCodonFrame();
acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(),
mapfordna2);
/*
* 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
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());
/*
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);
+ 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);
+ new int[]
+ { 1, 9 }, 1, 1);
assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap());
/*
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);
+ 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);
+ cdsToDnaMapping = new MapList(new int[] { 1, 9 },
+ new int[]
+ { 1, 3, 7, 9, 13, 15 }, 1, 1);
assertEquals(cdsToDnaMapping, dbRefEntry.getMap().getMap());
/*
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
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));
+ 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" })
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);
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
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");
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");
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());
pep1CdsMappings);
assertEquals(1, sr.getResults().size());
SearchResultMatchI m = sr.getResults().get(0);
- assertEquals(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
+ assertEquals(cds.getSequenceAt(0).getDatasetSequence(),
+ m.getSequence());
assertEquals(1, m.getStart());
assertEquals(3, m.getEnd());
sr = MappingUtils.buildSearchResults(pep1, 2, pep1CdsMappings);
sr = MappingUtils.buildSearchResults(pep2, 1, pep2CdsMappings);
assertEquals(1, sr.getResults().size());
m = sr.getResults().get(0);
- assertEquals(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
+ assertEquals(cds.getSequenceAt(1).getDatasetSequence(),
+ m.getSequence());
assertEquals(1, m.getStart());
assertEquals(3, m.getEnd());
sr = MappingUtils.buildSearchResults(pep2, 2, pep2CdsMappings);
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);
}
/**
- * 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
- * TAA -> STOP source: dnSNP
- * 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";
-
- /*
- * NB setting "id" (as returned by Ensembl for features in JSON format);
- * previously "ID" (as returned for GFF3 format)
- */
- SequenceFeature sf1 = new SequenceFeature("sequence_variant", "", 1, 1,
- 0f, ensembl);
- sf1.setValue("alleles", "A,G"); // AAA -> GAA -> K/E
- sf1.setValue("id", "var1.125A>G");
-
- SequenceFeature sf2 = new SequenceFeature("sequence_variant", "", 1, 1,
- 0f, dbSnp);
- sf2.setValue("alleles", "A,C"); // AAA -> CAA -> K/Q
- sf2.setValue("id", "var2");
- sf2.setValue("clinical_significance", "Dodgy");
-
- SequenceFeature sf3 = new SequenceFeature("sequence_variant", "", 1, 1,
- 0f, dbSnp);
- sf3.setValue("alleles", "A,T"); // AAA -> TAA -> stop codon
- sf3.setValue("id", "var3");
- sf3.setValue("clinical_significance", "Bad");
-
- SequenceFeature sf4 = new SequenceFeature("sequence_variant", "", 3, 3,
- 0f, cosmic);
- sf4.setValue("alleles", "A,G"); // AAA -> AAG synonymous
- sf4.setValue("id", "var4");
- sf4.setValue("clinical_significance", "None");
-
- SequenceFeature sf5 = new SequenceFeature("sequence_variant", "", 3, 3,
- 0f, ensembl);
- sf5.setValue("alleles", "A,T"); // AAA -> AAT -> K/N
- sf5.setValue("id", "sequence_variant:var5"); // prefix gets stripped off
- sf5.setValue("clinical_significance", "Benign");
-
- SequenceFeature sf6 = new SequenceFeature("sequence_variant", "", 6, 6,
- 0f, dbSnp);
- sf6.setValue("alleles", "T,C"); // TTT -> TTC synonymous
- sf6.setValue("id", "var6");
-
- SequenceFeature sf7 = new SequenceFeature("sequence_variant", "", 8, 8,
- 0f, cosmic);
- sf7.setValue("alleles", "C,A,G"); // CCC -> CAC,CGC -> P/H/R
- sf7.setValue("id", "var7");
- sf7.setValue("clinical_significance", "Good");
-
- List<DnaVariant> codon1Variants = new ArrayList<>();
- List<DnaVariant> codon2Variants = new ArrayList<>();
- List<DnaVariant> codon3Variants = new ArrayList<>();
-
- 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));
- codon1Variants.add(new DnaVariant("A", sf3));
- codon2Variants.add(new DnaVariant("A"));
- // codon2Variants.add(new DnaVariant("A"));
- codon3Variants.add(new DnaVariant("A", sf4));
- codon3Variants.add(new DnaVariant("A", sf5));
- 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", sf6));
- 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", sf7));
- codon3Variants.add(new DnaVariant("C"));
- AlignmentUtils.computePeptideVariants(peptide, 3, codonVariants);
-
- /*
- * verify added sequence features for
- * var1 K -> E Ensembl
- * var2 K -> Q dbSNP
- * var3 K -> stop
- * var4 synonymous
- * var5 K -> N Ensembl
- * var6 synonymous
- * var7 P -> H COSMIC
- * var8 P -> R COSMIC
- */
- List<SequenceFeature> sfs = peptide.getSequenceFeatures();
- SequenceFeatures.sortFeatures(sfs, true);
- assertEquals(8, sfs.size());
-
- /*
- * features are sorted by start position ascending, but in no
- * particular order where start positions match; asserts here
- * simply match the data returned (the order is not important)
- */
- // AAA -> AAT -> K/N
- SequenceFeature sf = sfs.get(0);
- assertEquals(1, sf.getBegin());
- assertEquals(1, sf.getEnd());
- assertEquals("nonsynonymous_variant", sf.getType());
- assertEquals("p.Lys1Asn", sf.getDescription());
- assertEquals("var5", sf.getValue("id"));
- assertEquals("Benign", sf.getValue("clinical_significance"));
- assertEquals("id=var5;clinical_significance=Benign",
- sf.getAttributes());
- assertEquals(1, sf.links.size());
- assertEquals(
- "p.Lys1Asn var5|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var5",
- sf.links.get(0));
- assertEquals(ensembl, sf.getFeatureGroup());
-
- // AAA -> CAA -> K/Q
- sf = sfs.get(1);
- assertEquals(1, sf.getBegin());
- assertEquals(1, sf.getEnd());
- assertEquals("nonsynonymous_variant", sf.getType());
- 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());
-
- // AAA -> GAA -> K/E
- sf = sfs.get(2);
- assertEquals(1, sf.getBegin());
- assertEquals(1, sf.getEnd());
- assertEquals("nonsynonymous_variant", sf.getType());
- 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());
-
- // AAA -> TAA -> stop codon
- sf = sfs.get(3);
- assertEquals(1, sf.getBegin());
- assertEquals(1, sf.getEnd());
- assertEquals("stop_gained", sf.getType());
- assertEquals("Aaa/Taa", sf.getDescription());
- assertEquals("var3", sf.getValue("id"));
- assertEquals("Bad", sf.getValue("clinical_significance"));
- assertEquals("id=var3;clinical_significance=Bad", sf.getAttributes());
- assertEquals(1, sf.links.size());
- assertEquals(
- "Aaa/Taa var3|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var3",
- sf.links.get(0));
- assertEquals(dbSnp, sf.getFeatureGroup());
-
- // AAA -> AAG synonymous
- sf = sfs.get(4);
- assertEquals(1, sf.getBegin());
- assertEquals(1, sf.getEnd());
- assertEquals("synonymous_variant", sf.getType());
- assertEquals("aaA/aaG", sf.getDescription());
- assertEquals("var4", sf.getValue("id"));
- assertEquals("None", sf.getValue("clinical_significance"));
- assertEquals("id=var4;clinical_significance=None", sf.getAttributes());
- assertEquals(1, sf.links.size());
- assertEquals(
- "aaA/aaG var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
- sf.links.get(0));
- assertEquals(cosmic, sf.getFeatureGroup());
-
- // TTT -> TTC synonymous
- sf = sfs.get(5);
- assertEquals(2, sf.getBegin());
- assertEquals(2, sf.getEnd());
- assertEquals("synonymous_variant", sf.getType());
- assertEquals("ttT/ttC", sf.getDescription());
- assertEquals("var6", sf.getValue("id"));
- assertNull(sf.getValue("clinical_significance"));
- assertEquals("id=var6", sf.getAttributes());
- assertEquals(1, sf.links.size());
- assertEquals(
- "ttT/ttC var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
- sf.links.get(0));
- assertEquals(dbSnp, sf.getFeatureGroup());
-
- // var7 generates two distinct protein variant features (two alleles)
- // CCC -> CGC -> P/R
- sf = sfs.get(6);
- assertEquals(3, sf.getBegin());
- assertEquals(3, sf.getEnd());
- assertEquals("nonsynonymous_variant", sf.getType());
- assertEquals("p.Pro3Arg", sf.getDescription());
- assertEquals("var7", sf.getValue("id"));
- assertEquals("Good", sf.getValue("clinical_significance"));
- assertEquals("id=var7;clinical_significance=Good", sf.getAttributes());
- assertEquals(1, sf.links.size());
- assertEquals(
- "p.Pro3Arg var7|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var7",
- sf.links.get(0));
- assertEquals(cosmic, sf.getFeatureGroup());
-
- // CCC -> CAC -> P/H
- sf = sfs.get(7);
- assertEquals(3, sf.getBegin());
- assertEquals(3, sf.getEnd());
- assertEquals("nonsynonymous_variant", sf.getType());
- assertEquals("p.Pro3His", sf.getDescription());
- assertEquals("var7", sf.getValue("id"));
- assertEquals("Good", sf.getValue("clinical_significance"));
- assertEquals("id=var7;clinical_significance=Good", sf.getAttributes());
- assertEquals(1, sf.links.size());
- assertEquals(
- "p.Pro3His var7|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var7",
- 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)
*/
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));
+ 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));
+ 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);
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);
/*
* 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());
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 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();
+ 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 ?
SequenceI uas1 = dna1.deriveSequence();
SequenceI uas2 = dna1.deriveSequence().getSubSequence(3, 7);
SequenceI uas3 = dna2.deriveSequence();
- AlignmentI tobealigned = new Alignment(new SequenceI[] { uas1, uas2,
- uas3 });
+ 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" })
* 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
+ @Test(groups = "Functional")
public void testFindCdsForProtein()
{
List<AlignedCodonFrame> mappings = new ArrayList<>();
SequenceI pep1 = new Sequence("pep1", "MLS");
pep1.createDatasetSequence();
List<AlignedCodonFrame> seqMappings = new ArrayList<>();
- MapList mapList = new MapList(
+ MapList mapList = new MapList(new int[] { 5, 6, 9, 15 },
new int[]
- { 5, 6, 9, 15 }, new int[] { 1, 3 }, 3, 1);
+ { 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(),
// 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);
+ 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,
* 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
+ @Test(groups = "Functional")
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);
+ 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)
// 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);
+ 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!
*/
dnaToPeptide);
assertSame(seq, cds1.getDatasetSequence());
}
+
+ @Test(groups = "Functional")
+ public void testAddReferenceContactMap()
+ {
+ SequenceI sq = new Sequence("a", "SSSQ");
+ ContactMatrixI cm = new SeqDistanceContactMatrix(4);
+ AlignmentAnnotation cm_aan = sq.addContactList(cm);
+ cm_aan.description = cm_aan.description + " cm1";
+ SequenceI dssq = sq.createDatasetSequence();
+
+ // remove annotation on our non-dataset sequence
+ sq.removeAlignmentAnnotation(sq.getAnnotation()[0]);
+ // test transfer
+ Alignment al = new Alignment(new SequenceI[] { sq });
+ SortedMap<String, String> tipEntries = new TreeMap<>();
+ Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
+
+ AlignmentUtils.findAddableReferenceAnnotations(al.getSequences(),
+ tipEntries, candidates, al);
+ AlignmentUtils.addReferenceAnnotations(candidates, al, null);
+ assertTrue("No contact map annotation transferred",
+ al.getAlignmentAnnotation() != null
+ && al.getAlignmentAnnotation().length == 1);
+ AlignmentAnnotation alan = al.findAnnotations(sq, null, cm_aan.label)
+ .iterator().next();
+ ContactListI cl = al.getContactListFor(alan, 1);
+ assertNotNull(
+ "No contact matrix recovered after reference annotation transfer",
+ cl);
+ // semantics of sequence associated contact list is slightly tricky - column 3 in alignment should have data
+ cl = al.getContactListFor(alan, 3);
+ assertNotNull(
+ "Contact matrix should have data for last position in sequence",
+ cl);
+
+ ContactMatrixI cm2 = new SeqDistanceContactMatrix(4);
+ dssq.addContactList(cm2);
+ tipEntries = new TreeMap<>();
+ candidates = new LinkedHashMap<>();
+
+ AlignmentUtils.findAddableReferenceAnnotations(al.getSequences(),
+ tipEntries, candidates, al);
+ AlignmentUtils.addReferenceAnnotations(candidates, al, null);
+ assertTrue("Expected two contact map annotation transferred",
+ al.getAlignmentAnnotation() != null
+ && al.getAlignmentAnnotation().length == 2);
+
+ }
}