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;
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));
DBRefEntry dna1xref = new DBRefEntry("UNIPROT", "ENSEMBL", "pep1",
new Mapping(mapfordna1));
dna1.addDBRef(dna1xref);
- assertEquals(2, dna1.getDBRefs().length); // to self and to pep1
+ 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().length); // to self and to pep2
+ assertEquals(2, dna2.getDBRefs().size()); // to self and to pep2
/*
* execute method under test:
* verify CDS has a dbref with mapping to peptide
*/
assertNotNull(cds1Dss.getDBRefs());
- assertEquals(2, cds1Dss.getDBRefs().length);
- dbref = cds1Dss.getDBRefs()[0];
+ 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());
*/
assertNotNull(pep1.getDBRefs());
// FIXME pep1.getDBRefs() is 1 - is that the correct behaviour ?
- assertEquals(2, pep1.getDBRefs().length);
- dbref = pep1.getDBRefs()[1];
+ assertEquals(2, pep1.getDBRefs().size());
+ dbref = pep1.getDBRefs().get(1);
assertEquals("ENSEMBL", dbref.getSource());
assertEquals("0", dbref.getVersion());
assertEquals("CDS|dna1", dbref.getAccessionId());
/*
* verify cDNA has added a dbref with mapping to CDS
*/
- assertEquals(3, dna1.getDBRefs().length);
- DBRefEntry dbRefEntry = dna1.getDBRefs()[2];
+ 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().length);
- dbRefEntry = dna2.getDBRefs()[2];
+ 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);
/*
* verify CDS has added a dbref with mapping to cDNA
*/
- assertEquals(2, cds1Dss.getDBRefs().length);
- dbRefEntry = cds1Dss.getDBRefs()[1];
+ 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().length);
- dbRefEntry = cds2Dss.getDBRefs()[1];
+ 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);
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");
+ 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("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("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("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("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");
+ 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("id", "var7");
sf7.setValue("clinical_significance", "Good");
List<DnaVariant> codon1Variants = new ArrayList<>();
assertEquals(1, sf.getEnd());
assertEquals("nonsynonymous_variant", sf.getType());
assertEquals("p.Lys1Asn", sf.getDescription());
- assertEquals("var5", sf.getValue("ID"));
+ assertEquals("var5", sf.getValue("id"));
assertEquals("Benign", sf.getValue("clinical_significance"));
- assertEquals("ID=var5;clinical_significance=Benign",
+ assertEquals("id=var5;clinical_significance=Benign",
sf.getAttributes());
assertEquals(1, sf.links.size());
assertEquals(
assertEquals(1, sf.getEnd());
assertEquals("nonsynonymous_variant", sf.getType());
assertEquals("p.Lys1Gln", sf.getDescription());
- assertEquals("var2", sf.getValue("ID"));
+ assertEquals("var2", sf.getValue("id"));
assertEquals("Dodgy", sf.getValue("clinical_significance"));
- assertEquals("ID=var2;clinical_significance=Dodgy", sf.getAttributes());
+ 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",
assertEquals(1, sf.getEnd());
assertEquals("nonsynonymous_variant", sf.getType());
assertEquals("p.Lys1Glu", sf.getDescription());
- assertEquals("var1.125A>G", sf.getValue("ID"));
+ assertEquals("var1.125A>G", sf.getValue("id"));
assertNull(sf.getValue("clinical_significance"));
- assertEquals("ID=var1.125A>G", sf.getAttributes());
+ assertEquals("id=var1.125A>G", sf.getAttributes());
assertEquals(1, sf.links.size());
// link to variation is urlencoded
assertEquals(
assertEquals(1, sf.getEnd());
assertEquals("stop_gained", sf.getType());
assertEquals("Aaa/Taa", sf.getDescription());
- assertEquals("var3", sf.getValue("ID"));
+ assertEquals("var3", sf.getValue("id"));
assertEquals("Bad", sf.getValue("clinical_significance"));
- assertEquals("ID=var3;clinical_significance=Bad", sf.getAttributes());
+ 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",
assertEquals(1, sf.getEnd());
assertEquals("synonymous_variant", sf.getType());
assertEquals("aaA/aaG", sf.getDescription());
- assertEquals("var4", sf.getValue("ID"));
+ assertEquals("var4", sf.getValue("id"));
assertEquals("None", sf.getValue("clinical_significance"));
- assertEquals("ID=var4;clinical_significance=None", sf.getAttributes());
+ 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",
assertEquals(2, sf.getEnd());
assertEquals("synonymous_variant", sf.getType());
assertEquals("ttT/ttC", sf.getDescription());
- assertEquals("var6", sf.getValue("ID"));
+ assertEquals("var6", sf.getValue("id"));
assertNull(sf.getValue("clinical_significance"));
- assertEquals("ID=var6", sf.getAttributes());
+ assertEquals("id=var6", sf.getAttributes());
assertEquals(1, sf.links.size());
assertEquals(
"ttT/ttC var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
assertEquals(3, sf.getEnd());
assertEquals("nonsynonymous_variant", sf.getType());
assertEquals("p.Pro3Arg", sf.getDescription());
- assertEquals("var7", sf.getValue("ID"));
+ assertEquals("var7", sf.getValue("id"));
assertEquals("Good", sf.getValue("clinical_significance"));
- assertEquals("ID=var7;clinical_significance=Good", sf.getAttributes());
+ 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",
assertEquals(3, sf.getEnd());
assertEquals("nonsynonymous_variant", sf.getType());
assertEquals("p.Pro3His", sf.getDescription());
- assertEquals("var7", sf.getValue("ID"));
+ assertEquals("var7", sf.getValue("id"));
assertEquals("Good", sf.getValue("clinical_significance"));
- assertEquals("ID=var7;clinical_significance=Good", sf.getAttributes());
+ 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",
* transcript 'CDS' is 10-16, 17-21
* which is 'gene' 158-164, 210-214
*/
- MapList toMap = toLoci.getMap();
+ MapList toMap = toLoci.getMapping();
assertEquals(1, toMap.getFromRanges().size());
assertEquals(2, toMap.getFromRanges().get(0).length);
assertEquals(1, toMap.getFromRanges().get(0)[0]);
AlignmentUtils.transferGeneLoci(from, map, to);
assertEquals("GRCh38", toLoci.getAssemblyId());
assertEquals("7", toLoci.getChromosomeId());
- toMap = toLoci.getMap();
+ toMap = toLoci.getMapping();
assertEquals("[ [1, 12] ] 1:1 to [ [158, 164] [210, 214] ]",
toMap.toString());
}
git://source.jalview.org / jalview.git / blobdiff