htsjdk.variant.variantcontext.writer

Class BCF2FieldEncoder.Flag

java.lang.Object

htsjdk.variant.variantcontext.writer.BCF2FieldEncoder

htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.Flag

Enclosing class:

BCF2FieldEncoder

public static class BCF2FieldEncoder.Flag
extends BCF2FieldEncoder

Nested Class Summary

Nested classes/interfaces inherited from class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder

BCF2FieldEncoder.AtomicInt, BCF2FieldEncoder.Flag, BCF2FieldEncoder.Float, BCF2FieldEncoder.GenericInts, BCF2FieldEncoder.IntArray, BCF2FieldEncoder.StringOrCharacter

Constructor Summary

Constructors

Constructor and Description
Flag(VCFCompoundHeaderLine headerLine, java.util.Map<java.lang.String,java.lang.Integer> dict)

Method Summary

Modifier and Type	Method and Description
void	encodeValue(BCF2Encoder encoder, java.lang.Object value, BCF2Type type, int minValues) Key abstract method that should encode a value of the given type into the encoder.
int	numElements() Get the number of elements, assuming this field has a constant number of elements.

Methods inherited from class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder

getCountType, getDynamicType, getField, getStaticType, getType, hasConstantNumElements, hasContextDeterminedNumElements, hasValueDeterminedNumElements, isDynamicallyTyped, isStaticallyTyped, numElements, numElements, numElements, numElementsFromValue, toString, writeFieldKey

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Flag

public Flag(VCFCompoundHeaderLine headerLine,
            java.util.Map<java.lang.String,java.lang.Integer> dict)

Method Detail

numElements

public int numElements()

Description copied from class: BCF2FieldEncoder

Get the number of elements, assuming this field has a constant number of elements.

Overrides:

numElements in class BCF2FieldEncoder

Returns:

encodeValue

public void encodeValue(BCF2Encoder encoder,
                        java.lang.Object value,
                        BCF2Type type,
                        int minValues)
                 throws java.io.IOException

Description copied from class: BCF2FieldEncoder

Key abstract method that should encode a value of the given type into the encoder. Value will be of a type appropriate to the underlying encoder. If the genotype field is represented as an int[], this will be value, and the encoder needs to handle encoding all of the values in the int[]. The argument should be used, not the getType() method in the superclass as an outer loop might have decided a more general type (int16) to use, even through this encoder could have been done with int8. If minValues > 0, then encodeValue must write in at least minValues items from value. If value is atomic, this means that minValues - 1 MISSING values should be added to the encoder. If minValues is a collection type (int[]) then minValues - values.length should be added. This argument is intended to handle padding of values in genotype fields.

Specified by:

encodeValue in class BCF2FieldEncoder

Throws:

java.io.IOException