// -----------------------------------------------------------------
//
// Master routine to look at the header, a specific line, and
// build an appropriate Genotypes for that header element
//
// -----------------------------------------------------------------
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: private BCF2FieldWriter.GenotypesWriter createGenotypesWriter(final VCFHeader header, final VCFFormatHeaderLine line, final BCF2Encoder encoder, final java.util.Map<String, Integer> dict)
private BCF2FieldWriter.GenotypesWriter createGenotypesWriter(VCFHeader header, VCFFormatHeaderLine line, BCF2Encoder encoder, IDictionary <string, int?> dict)
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final String field = line.getID();
string field = line.ID;
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final BCF2FieldEncoder fieldEncoder = createFieldEncoder(line, encoder, dict, true);
BCF2FieldEncoder fieldEncoder = createFieldEncoder(line, encoder, dict, true);
if (field.Equals(VCFConstants.GENOTYPE_KEY))
{
return(new BCF2FieldWriter.GTWriter(header, fieldEncoder));
}
else if (line.ID.Equals(VCFConstants.GENOTYPE_FILTER_KEY))
{
return(new BCF2FieldWriter.FTGenotypesWriter(header, fieldEncoder));
}
else if (intGenotypeFieldAccessors.getAccessor(field) != null)
{
return(new BCF2FieldWriter.IGFGenotypesWriter(header, fieldEncoder, intGenotypeFieldAccessors.getAccessor(field)));
}
else if (line.Type == VCFHeaderLineType.Integer)
{
return(new BCF2FieldWriter.IntegerTypeGenotypesWriter(header, fieldEncoder));
}
else
{
return(new BCF2FieldWriter.StaticallyTypeGenotypesWriter(header, fieldEncoder));
}
}
//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 WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public IGFGenotypesWriter(final Bio.VCF.VCFHeader header, final BCF2FieldEncoder fieldEncoder, final IntGenotypeFieldAccessors.Accessor ige)
public IGFGenotypesWriter(VCFHeader header, BCF2FieldEncoder fieldEncoder, IntGenotypeFieldAccessors.Accessor ige) : base(header, fieldEncoder)
{
this.ige = ige;
if (!(fieldEncoder is BCF2FieldEncoder.IntArray))
{
throw new System.ArgumentException("BUG: IntGenotypesWriter requires IntArray encoder for field " + Field);
}
}
//JAVA TO C# CONVERTER TODO TASK: Most Java annotations will not have direct .NET equivalent attributes:
//ORIGINAL LINE: @Requires({"header != null", "fieldEncoder != null"}) protected BCF2FieldWriter(final Bio.VCF.VCFHeader header, final BCF2FieldEncoder fieldEncoder)
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
protected internal BCF2FieldWriter(VCFHeader header, BCF2FieldEncoder fieldEncoder)
{
this.header = header;
this.fieldEncoder = fieldEncoder;
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public GTWriter(final Bio.VCF.VCFHeader header, final BCF2FieldEncoder fieldEncoder)
public GTWriter(VCFHeader header, BCF2FieldEncoder fieldEncoder) : base(header, fieldEncoder)
{
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public FTGenotypesWriter(final Bio.VCF.VCFHeader header, final BCF2FieldEncoder fieldEncoder)
public FTGenotypesWriter(VCFHeader header, BCF2FieldEncoder fieldEncoder) : base(header, fieldEncoder)
{
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public IntegerTypeGenotypesWriter(final Bio.VCF.VCFHeader header, final BCF2FieldEncoder fieldEncoder)
public IntegerTypeGenotypesWriter(VCFHeader header, BCF2FieldEncoder fieldEncoder) : base(header, fieldEncoder)
{
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public StaticallyTypeGenotypesWriter(final Bio.VCF.VCFHeader header, final BCF2FieldEncoder fieldEncoder)
public StaticallyTypeGenotypesWriter(VCFHeader header, BCF2FieldEncoder fieldEncoder) : base(header, fieldEncoder)
{
encodingType = FieldEncoder.StaticType;
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public GenericSiteWriter(final Bio.VCF.VCFHeader header, final BCF2FieldEncoder fieldEncoder)
public GenericSiteWriter(VCFHeader header, BCF2FieldEncoder fieldEncoder) : base(header, fieldEncoder)
{
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: protected SiteWriter(final Bio.VCF.VCFHeader header, final BCF2FieldEncoder fieldEncoder)
protected internal SiteWriter(VCFHeader header, BCF2FieldEncoder fieldEncoder) : base(header, fieldEncoder)
{
}