htsjdk.variant.vcf
Class VCFSimpleHeaderLine

java.lang.Object
  htsjdk.variant.vcf.VCFHeaderLine
      htsjdk.variant.vcf.VCFSimpleHeaderLine

All Implemented Interfaces:

VCFIDHeaderLine, java.lang.Comparable

Direct Known Subclasses:

VCFContigHeaderLine, VCFFilterHeaderLine

public class VCFSimpleHeaderLine
extends VCFHeaderLine
implements VCFIDHeaderLine

Field Summary

Fields inherited from class htsjdk.variant.vcf.VCFHeaderLine

ALLOW_UNBOUND_DESCRIPTIONS, UNBOUND_DESCRIPTION

Constructor Summary

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

Method Summary

boolean	equals(java.lang.Object o)
java.lang.String	getID()
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, hashCode, notify, notifyAll, wait, wait, wait

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

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

getID

public java.lang.String getID()

Specified by:

getID in interface VCFIDHeaderLine