htsjdk.variant.vcf

Class VCFSimpleHeaderLine

java.lang.Object

htsjdk.variant.vcf.VCFHeaderLine

htsjdk.variant.vcf.VCFSimpleHeaderLine

All Implemented Interfaces:

VCFIDHeaderLine, java.io.Serializable, java.lang.Comparable

Direct Known Subclasses:

VCFAltHeaderLine, VCFContigHeaderLine, VCFFilterHeaderLine, VCFMetaHeaderLine, VCFPedigreeHeaderLine, VCFSampleHeaderLine

public class VCFSimpleHeaderLine
extends VCFHeaderLine
implements VCFIDHeaderLine

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	DESCRIPTION_ATTRIBUTE
static java.lang.String	ID_ATTRIBUTE

Fields inherited from class htsjdk.variant.vcf.VCFHeaderLine

ALLOW_UNBOUND_DESCRIPTIONS, serialVersionUID, UNBOUND_DESCRIPTION

Constructor Summary

Constructors

Constructor and Description
VCFSimpleHeaderLine(java.lang.String key, java.util.Map<java.lang.String,java.lang.String> mapping)
VCFSimpleHeaderLine(java.lang.String key, java.lang.String name, java.lang.String description) create a VCF filter header line
VCFSimpleHeaderLine(java.lang.String line, VCFHeaderVersion version, java.lang.String key, java.util.List<java.lang.String> expectedTagOrdering) create a VCF info header line
VCFSimpleHeaderLine(java.lang.String line, VCFHeaderVersion version, java.lang.String key, java.util.List<java.lang.String> expectedTagOrdering, java.util.List<java.lang.String> recommendedTags) create a VCF info header line

Method Summary

Modifier and Type	Method and Description
boolean	equals(java.lang.Object o)
java.util.Map<java.lang.String,java.lang.String>	getGenericFields()
java.lang.String	getID()
int	hashCode()
protected void	initialize(java.lang.String name, java.util.Map<java.lang.String,java.lang.String> genericFields)
protected java.lang.String	toStringEncoding() Should be overloaded in sub classes to do subclass specific

Methods inherited from class htsjdk.variant.vcf.VCFHeaderLine

compareTo, getKey, getValue, isHeaderLine, shouldBeAddedToDictionary, toString, toStringEncoding

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

ID_ATTRIBUTE

public static final java.lang.String ID_ATTRIBUTE

See Also:

Constant Field Values

DESCRIPTION_ATTRIBUTE

public static final java.lang.String DESCRIPTION_ATTRIBUTE

See Also:

Constant Field Values

Constructor Detail

VCFSimpleHeaderLine

public VCFSimpleHeaderLine(java.lang.String key,
                           java.lang.String name,
                           java.lang.String description)

create a VCF filter header line

Parameters:

key - the key for this header line

name - the name for this header line

description - description for this header line

VCFSimpleHeaderLine

public VCFSimpleHeaderLine(java.lang.String line,
                           VCFHeaderVersion version,
                           java.lang.String key,
                           java.util.List<java.lang.String> expectedTagOrdering)

create a VCF info header line

Parameters:

line - the header line

version - the vcf header version

key - the key for this header line

expectedTagOrdering - the tag ordering expected for this header line

See Also:

VCFv4.2+ recommended tags support

VCFSimpleHeaderLine

public VCFSimpleHeaderLine(java.lang.String line,
                           VCFHeaderVersion version,
                           java.lang.String key,
                           java.util.List<java.lang.String> expectedTagOrdering,
                           java.util.List<java.lang.String> recommendedTags)

create a VCF info header line

Parameters:

line - the header line

version - the vcf header version

key - the key for this header line

expectedTagOrdering - the tag ordering expected for this header line

recommendedTags - tags that are optional for this header line

VCFSimpleHeaderLine

public VCFSimpleHeaderLine(java.lang.String key,
                           java.util.Map<java.lang.String,java.lang.String> mapping)

Method Detail

initialize

protected void initialize(java.lang.String name,
                          java.util.Map<java.lang.String,java.lang.String> genericFields)

toStringEncoding

protected java.lang.String toStringEncoding()

Description copied from class: VCFHeaderLine

Should be overloaded in sub classes to do subclass specific

Overrides:

toStringEncoding in class VCFHeaderLine

Returns:

the string encoding

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class VCFHeaderLine

hashCode

public int hashCode()

Overrides:

hashCode in class VCFHeaderLine

getID

public java.lang.String getID()

Specified by:

getID in interface VCFIDHeaderLine

getGenericFields

public java.util.Map<java.lang.String,java.lang.String> getGenericFields()

Returns:

a map of all pairs of fields and values in this header line