//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: protected GenotypesWriter(final Bio.VCF.VCFHeader header, final BCF2FieldEncoder fieldEncoder)
protected internal GenotypesWriter(VCFHeader header, BCF2FieldEncoder fieldEncoder) : base(header, fieldEncoder)
{
if (fieldEncoder.hasConstantNumElements())
{
nValuesPerGenotype = FieldEncoder.numElements();
}
}
//JAVA TO C# CONVERTER TODO TASK: Most Java annotations will not have direct .NET equivalent attributes:
//ORIGINAL LINE: @Override @Requires({"encodingType != null", "nValuesPerGenotype >= 0 || ! getFieldEncoder().hasConstantNumElements()"}) @Ensures("nValuesPerGenotype >= 0") public void start(final BCF2Encoder encoder, final org.broadinstitute.variant.variantcontext.VariantContext vc) throws java.io.IOException
//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in .NET:
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
public override void start(BCF2Encoder encoder, VariantContext vc)
{
// writes the key information
base.start(encoder, vc);
// only update if we need to
if (!FieldEncoder.hasConstantNumElements())
{
if (FieldEncoder.hasContextDeterminedNumElements())
// we are cheap -- just depends on genotype of allele counts
{
nValuesPerGenotype = FieldEncoder.numElements(vc);
}
else
// we have to go fishing through the values themselves (expensive)
{
nValuesPerGenotype = computeMaxSizeOfGenotypeFieldFromValues(vc);
}
}
encoder.encodeType(nValuesPerGenotype, encodingType);
}
//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in .NET:
//ORIGINAL LINE: public void site(final BCF2Encoder encoder, final org.broadinstitute.variant.variantcontext.VariantContext vc) throws java.io.IOException
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
public override void site(BCF2Encoder encoder, VariantContext vc)
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final Object rawValue = vc.getAttribute(getField(), null);
object rawValue = vc.getAttribute(Field, null);
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final org.broadinstitute.variant.bcf2.BCF2Type type = getFieldEncoder().getType(rawValue);
BCF2Type type = FieldEncoder.getType(rawValue);
if (rawValue == null)
{
// the value is missing, just write in null
encoder.encodeType(0, type);
}
else
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final int valueCount = getFieldEncoder().numElements(vc, rawValue);
int valueCount = FieldEncoder.numElements(vc, rawValue);
encoder.encodeType(valueCount, type);
FieldEncoder.encodeValue(encoder, rawValue, type, valueCount);
}
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: protected int numElements(final org.broadinstitute.variant.variantcontext.VariantContext vc, final org.broadinstitute.variant.variantcontext.Genotype g)
protected internal override int numElements(VariantContext vc, Genotype g)
{
return(FieldEncoder.numElements(vc, g.Filters));
}
//JAVA TO C# CONVERTER TODO TASK: Most Java annotations will not have direct .NET equivalent attributes:
//ORIGINAL LINE: @Ensures({"result >= 0"}) protected int numElements(final org.broadinstitute.variant.variantcontext.VariantContext vc, final org.broadinstitute.variant.variantcontext.Genotype g)
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
protected internal virtual int numElements(VariantContext vc, Genotype g)
{
return(FieldEncoder.numElements(vc, g.getExtendedAttribute(Field)));
}
