//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public Flag(final Bio.VCF.VCFCompoundHeaderLine headerLine, final java.util.Map<String, Integer> dict)
public Flag(VCFCompoundHeaderLine headerLine, IDictionary <string, int?> dict) : base(headerLine, dict, BCF2Type.INT8)
{
if (!headerLine.FixedCount || headerLine.Count != 0)
{
throw new IllegalStateException("Flag encoder only supports atomic flags for field " + Field);
}
}
// ----------------------------------------------------------------------
//
// Constructor
//
// ----------------------------------------------------------------------
//JAVA TO C# CONVERTER TODO TASK: Most Java annotations will not have direct .NET equivalent attributes:
//ORIGINAL LINE: @Requires({"headerLine != null", "dict != null"}) private BCF2FieldEncoder(final Bio.VCF.VCFCompoundHeaderLine headerLine, final java.util.Map<String, Integer> dict, final org.broadinstitute.variant.bcf2.BCF2Type staticType)
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
private BCF2FieldEncoder(VCFCompoundHeaderLine headerLine, IDictionary <string, int?> dict, BCF2Type staticType)
{
this.headerLine = headerLine;
this.staticType = staticType;
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final Integer offset = dict.get(getField());
int?offset = dict[Field];
if (offset == null)
{
throw new IllegalStateException("Format error: could not find string " + Field + " in header as required by BCF");
}
this.dictionaryOffset = offset;
dictionaryOffsetType = BCF2Utils.determineIntegerType(offset);
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: private BCF2FieldEncoder createFieldEncoder(final VCFCompoundHeaderLine line, final BCF2Encoder encoder, final java.util.Map<String, Integer> dict, final boolean createGenotypesEncoders)
private BCF2FieldEncoder createFieldEncoder(VCFCompoundHeaderLine line, BCF2Encoder encoder, IDictionary <string, int?> dict, bool createGenotypesEncoders)
{
if (createGenotypesEncoders && intGenotypeFieldAccessors.getAccessor(line.ID) != null)
{
if (GeneralUtils.DEBUG_MODE_ENABLED && line.Type != VCFHeaderLineType.Integer)
{
Console.Error.WriteLine("Warning: field " + line.ID + " expected to encode an integer but saw " + line.Type + " for record " + line);
}
return(new BCF2FieldEncoder.IntArray(line, dict));
}
else if (createGenotypesEncoders && line.ID.Equals(VCFConstants.GENOTYPE_KEY))
{
return(new BCF2FieldEncoder.GenericInts(line, dict));
}
else
{
switch (line.Type)
{
case char?:
case string:
return(new BCF2FieldEncoder.StringOrCharacter(line, dict));
case Flag:
return(new BCF2FieldEncoder.Flag(line, dict));
case float?:
return(new BCF2FieldEncoder.Float(line, dict));
case int?:
if (line.FixedCount && line.Count == 1)
{
return(new BCF2FieldEncoder.AtomicInt(line, dict));
}
else
{
return(new BCF2FieldEncoder.GenericInts(line, dict));
}
default:
throw new System.ArgumentException("Unexpected type for field " + line.ID);
}
}
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public GenericInts(final Bio.VCF.VCFCompoundHeaderLine headerLine, final java.util.Map<String, Integer> dict)
public GenericInts(VCFCompoundHeaderLine headerLine, IDictionary <string, int?> dict) : base(headerLine, dict, null)
{
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public Float(final Bio.VCF.VCFCompoundHeaderLine headerLine, final java.util.Map<String, Integer> dict)
public Float(VCFCompoundHeaderLine headerLine, IDictionary <string, int?> dict) : base(headerLine, dict, BCF2Type.FLOAT)
{
isAtomic = hasConstantNumElements() && numElements() == 1;
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public StringOrCharacter(final Bio.VCF.VCFCompoundHeaderLine headerLine, final java.util.Map<String, Integer> dict)
public StringOrCharacter(VCFCompoundHeaderLine headerLine, IDictionary <string, int?> dict) : base(headerLine, dict, BCF2Type.CHAR)
{
}
