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;
}
