Package org.snpsift.lang.expression

Class Field

java.lang.Object

org.snpsift.lang.expression.Expression

org.snpsift.lang.expression.Field

Direct Known Subclasses:

FieldConstant, FieldSub

public class Field
extends Expression

A field: E.g.: 'DP', 'CHROM'

Author:

pablocingolani

Field Summary

Fields

Modifier and Type	Field	Description
protected boolean	exceptionIfNotFound
protected java.lang.String	name
protected int	number
protected org.snpeff.vcf.VcfInfoType	returnType
static int	TYPE_ALL
static int	TYPE_ANY
protected org.snpeff.vcf.VcfHeaderInfo	vcfInfo
protected org.snpeff.vcf.VcfHeaderInfo.VcfInfoNumber	vcfInfoNumber

Fields inherited from class org.snpsift.lang.expression.Expression

debug, negated, operator

Constructor Summary

Constructors

Constructor	Description
Field(java.lang.String name)

Method Summary

Modifier and Type	Method	Description
Value	eval(org.snpeff.vcf.VcfEntry vcfEntry)	Evaluate expression using VcfEntry
Value	eval(org.snpeff.vcf.VcfGenotype vcfGenotype)	Evaluate expression using genotype
protected java.lang.Object	fieldHeaderNotFound(org.snpeff.vcf.VcfEntry vcfEntry)
protected java.lang.Object	fieldNotFound(org.snpeff.vcf.VcfEntry vcfEntry)
java.lang.String	getFieldString(org.snpeff.vcf.VcfGenotype vcfGenotype)
java.lang.String	getName()
org.snpeff.vcf.VcfInfoType	getReturnType(org.snpeff.vcf.VcfGenotype vcfGenotype)
protected int	getSampleNum(org.snpeff.vcf.VcfEntry vcfEntry, java.lang.String name)
protected java.lang.Object	gtFieldNotFound(org.snpeff.vcf.VcfGenotype vcfGenotype)
java.lang.String	indexStr(int index)	Convert and index to a string
protected boolean	isSampleName(org.snpeff.vcf.VcfEntry vcfEntry, java.lang.String name)
protected boolean	isSub()
org.snpeff.vcf.VcfInfoType	returnType(org.snpeff.vcf.VcfEntry vcfEntry)
org.snpeff.vcf.VcfInfoType	returnType(org.snpeff.vcf.VcfGenotype vcfGenotype)
void	setExceptionIfNotFound(boolean exceptionIfNotFound)
java.lang.String	toString()

Methods inherited from class org.snpsift.lang.expression.Expression

setNegated

Methods inherited from class java.lang.Object

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

Field Detail

TYPE_ALL

public static final int TYPE_ALL

See Also:

Constant Field Values

TYPE_ANY

public static final int TYPE_ANY

See Also:

Constant Field Values

name

protected java.lang.String name

returnType

protected org.snpeff.vcf.VcfInfoType returnType

exceptionIfNotFound

protected boolean exceptionIfNotFound

vcfInfo

protected org.snpeff.vcf.VcfHeaderInfo vcfInfo

number

protected int number

vcfInfoNumber

protected org.snpeff.vcf.VcfHeaderInfo.VcfInfoNumber vcfInfoNumber

Constructor Detail

Field

public Field(java.lang.String name)

Method Detail

eval

public Value eval(org.snpeff.vcf.VcfEntry vcfEntry)

Description copied from class: Expression

Evaluate expression using VcfEntry

Specified by:

eval in class Expression

eval

public Value eval(org.snpeff.vcf.VcfGenotype vcfGenotype)

Description copied from class: Expression

Evaluate expression using genotype

Specified by:

eval in class Expression

fieldHeaderNotFound

protected java.lang.Object fieldHeaderNotFound(org.snpeff.vcf.VcfEntry vcfEntry)

fieldNotFound

protected java.lang.Object fieldNotFound(org.snpeff.vcf.VcfEntry vcfEntry)

getFieldString

public java.lang.String getFieldString(org.snpeff.vcf.VcfGenotype vcfGenotype)

getName

public java.lang.String getName()

getReturnType

public org.snpeff.vcf.VcfInfoType getReturnType(org.snpeff.vcf.VcfGenotype vcfGenotype)

getSampleNum

protected int getSampleNum(org.snpeff.vcf.VcfEntry vcfEntry,
                           java.lang.String name)

gtFieldNotFound

protected java.lang.Object gtFieldNotFound(org.snpeff.vcf.VcfGenotype vcfGenotype)

indexStr

public java.lang.String indexStr(int index)

Convert and index to a string

isSampleName

protected boolean isSampleName(org.snpeff.vcf.VcfEntry vcfEntry,
                               java.lang.String name)

isSub

protected boolean isSub()

returnType

public org.snpeff.vcf.VcfInfoType returnType(org.snpeff.vcf.VcfEntry vcfEntry)

returnType

public org.snpeff.vcf.VcfInfoType returnType(org.snpeff.vcf.VcfGenotype vcfGenotype)

setExceptionIfNotFound

public void setExceptionIfNotFound(boolean exceptionIfNotFound)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object