htsjdk.variant.variantcontext.writer

Class BCF2FieldEncoder.AtomicInt

java.lang.Object

htsjdk.variant.variantcontext.writer.BCF2FieldEncoder

htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.AtomicInt

Enclosing class:

BCF2FieldEncoder

public static class BCF2FieldEncoder.AtomicInt
extends BCF2FieldEncoder

Specialized int encoder for atomic (non-list) integers

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
BCF2FieldEncoder.AtomicInt(VCFCompoundHeaderLine headerLine, java.util.Map<java.lang.String,java.lang.Integer> dict)

Method Summary

Methods

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.
BCF2Type	getDynamicType(java.lang.Object value)

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

getCountType, getField, getStaticType, getType, hasConstantNumElements, hasContextDeterminedNumElements, hasValueDeterminedNumElements, isDynamicallyTyped, isStaticallyTyped, numElements, 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

BCF2FieldEncoder.AtomicInt

public BCF2FieldEncoder.AtomicInt(VCFCompoundHeaderLine headerLine,
                          java.util.Map<java.lang.String,java.lang.Integer> dict)

Method Detail

getDynamicType

public BCF2Type getDynamicType(java.lang.Object value)

Overrides:

getDynamicType in class BCF2FieldEncoder

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