htsjdk.variant.variantcontext.writer

Class BCF2FieldEncoder.StringOrCharacter

java.lang.Object

htsjdk.variant.variantcontext.writer.BCF2FieldEncoder

htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.StringOrCharacter

Enclosing class:

BCF2FieldEncoder

public static class BCF2FieldEncoder.StringOrCharacter
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
StringOrCharacter(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.
boolean	hasConstantNumElements()
boolean	hasContextDeterminedNumElements()
boolean	hasValueDeterminedNumElements()
protected int	numElementsFromValue(java.lang.Object value) Given a value, return the number of elements we will encode for it.

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

getCountType, getDynamicType, getField, getStaticType, getType, isDynamicallyTyped, isStaticallyTyped, numElements, numElements, numElements, numElements, toString, writeFieldKey

Methods inherited from class java.lang.Object

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

Constructor Detail

StringOrCharacter

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

Method Detail

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

hasConstantNumElements

public boolean hasConstantNumElements()

Overrides:

hasConstantNumElements in class BCF2FieldEncoder

Returns:

True if this field has a constant, fixed number of elements (such as 1 for an atomic integer)

hasContextDeterminedNumElements

public boolean hasContextDeterminedNumElements()

Overrides:

hasContextDeterminedNumElements in class BCF2FieldEncoder

Returns:

True if this field has a non-fixed number of elements that depends only on the properties of the current VariantContext, such as one value per Allele or per genotype configuration.

hasValueDeterminedNumElements

public boolean hasValueDeterminedNumElements()

Overrides:

hasValueDeterminedNumElements in class BCF2FieldEncoder

Returns:

True if the only way to determine how many elements this field contains is by inspecting the actual value directly, such as when the number of elements is a variable length list per site or per genotype.

numElementsFromValue

protected int numElementsFromValue(java.lang.Object value)

Description copied from class: BCF2FieldEncoder

Given a value, return the number of elements we will encode for it. Assumes the value is encoded as a List

Overrides:

numElementsFromValue in class BCF2FieldEncoder

Returns:

the number of elements we will encode for .