public GVFVariantVariantEffectComponent copy(GVFVariant e) { GVFVariantVariantEffectComponent dst = e.new GVFVariantVariantEffectComponent(); dst.sequenceVariant = sequenceVariant == null ? null : sequenceVariant.copy(); dst.index = index == null ? null : index.copy(); dst.featureType = featureType == null ? null : featureType.copy(); dst.featureId = new ArrayList<String_>(); for (String_ i : featureId) dst.featureId.add(i.copy()); return dst; }
public GVFVariantSampleComponent copy(GVFVariant e) { GVFVariantSampleComponent dst = e.new GVFVariantSampleComponent(); dst.phased = new ArrayList<String_>(); for (String_ i : phased) dst.phased.add(i.copy()); dst.genotype = new ArrayList<String_>(); for (String_ i : genotype) dst.genotype.add(i.copy()); dst.variantReads = new ArrayList<Integer>(); for (Integer i : variantReads) dst.variantReads.add(i.copy()); dst.totalReads = totalReads == null ? null : totalReads.copy(); dst.zygosity = zygosity == null ? null : zygosity.copy(); return dst; }
public GVFVariantBreakpointDetailComponent copy(GVFVariant e) { GVFVariantBreakpointDetailComponent dst = e.new GVFVariantBreakpointDetailComponent(); dst.seqid = seqid == null ? null : seqid.copy(); dst.start = start == null ? null : start.copy(); dst.end = end == null ? null : end.copy(); dst.strand = strand == null ? null : strand.copy(); return dst; }
public String_ addGenotypeSimple(String value) { String_ t = new String_(); t.setValue(value); this.genotype.add(t); return t; }
public String_ addPhasedSimple(String value) { String_ t = new String_(); t.setValue(value); this.phased.add(t); return t; }
public GVFVariantSequenceContextComponent copy(GVFVariant e) { GVFVariantSequenceContextComponent dst = e.new GVFVariantSequenceContextComponent(); dst.fivePrime = fivePrime == null ? null : fivePrime.copy(); dst.threePrime = threePrime == null ? null : threePrime.copy(); return dst; }
public GVFVariantDbxrefComponent copy(GVFVariant e) { GVFVariantDbxrefComponent dst = e.new GVFVariantDbxrefComponent(); dst.database = database == null ? null : database.copy(); dst.identity = identity == null ? null : identity.copy(); return dst; }
public String_ addFeatureIdSimple(String value) { String_ t = new String_(); t.setValue(value); this.featureId.add(t); return t; }
public GVFVariantSubjectComponent copy(GVFVariant e) { GVFVariantSubjectComponent dst = e.new GVFVariantSubjectComponent(); dst.patient = patient == null ? null : patient.copy(); dst.fileId = fileId == null ? null : fileId.copy(); return dst; }
public GVFVariant copy() { GVFVariant dst = new GVFVariant(); dst.subject = subject == null ? null : subject.copy(dst); dst.meta = meta == null ? null : meta.copy(); dst.sourceFile = sourceFile == null ? null : sourceFile.copy(); dst.seqid = seqid == null ? null : seqid.copy(); dst.source = source == null ? null : source.copy(); dst.type = type == null ? null : type.copy(); dst.start = start == null ? null : start.copy(); dst.end = end == null ? null : end.copy(); dst.score = score == null ? null : score.copy(); dst.strand = strand == null ? null : strand.copy(); dst.featureId = featureId == null ? null : featureId.copy(); dst.alias = alias == null ? null : alias.copy(); dst.dbxref = dbxref == null ? null : dbxref.copy(dst); dst.variantSeq = new ArrayList<String_>(); for (String_ i : variantSeq) dst.variantSeq.add(i.copy()); dst.referenceSeq = referenceSeq == null ? null : referenceSeq.copy(); dst.variantFreq = new ArrayList<Decimal>(); for (Decimal i : variantFreq) dst.variantFreq.add(i.copy()); dst.variantEffect = new ArrayList<GVFVariantVariantEffectComponent>(); for (GVFVariantVariantEffectComponent i : variantEffect) dst.variantEffect.add(i.copy(dst)); dst.startRange = startRange == null ? null : startRange.copy(dst); dst.endRange = endRange == null ? null : endRange.copy(dst); dst.variantCodon = new ArrayList<String_>(); for (String_ i : variantCodon) dst.variantCodon.add(i.copy()); dst.referenceCodon = referenceCodon == null ? null : referenceCodon.copy(); dst.variantAA = new ArrayList<String_>(); for (String_ i : variantAA) dst.variantAA.add(i.copy()); dst.referenceAA = new ArrayList<String_>(); for (String_ i : referenceAA) dst.referenceAA.add(i.copy()); dst.breakpointDetail = breakpointDetail == null ? null : breakpointDetail.copy(dst); dst.sequenceContext = sequenceContext == null ? null : sequenceContext.copy(dst); dst.individual = new ArrayList<String_>(); for (String_ i : individual) dst.individual.add(i.copy()); dst.sample = new ArrayList<GVFVariantSampleComponent>(); for (GVFVariantSampleComponent i : sample) dst.sample.add(i.copy(dst)); return dst; }
public String_ addIndividualSimple(String value) { String_ t = new String_(); t.setValue(value); this.individual.add(t); return t; }
public String_ addReferenceAASimple(String value) { String_ t = new String_(); t.setValue(value); this.referenceAA.add(t); return t; }
public String_ addVariantAASimple(String value) { String_ t = new String_(); t.setValue(value); this.variantAA.add(t); return t; }