htsjdk.variant.vcf

Class VCFHeaderLine

java.lang.Object

htsjdk.variant.vcf.VCFHeaderLine

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable

Direct Known Subclasses:

VCFCompoundHeaderLine, VCFSimpleHeaderLine

public class VCFHeaderLine
extends java.lang.Object
implements java.lang.Comparable, java.io.Serializable

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected static boolean	ALLOW_UNBOUND_DESCRIPTIONS
static long	serialVersionUID
protected static java.lang.String	UNBOUND_DESCRIPTION

Constructor Summary

Constructors

Constructor and Description
VCFHeaderLine(java.lang.String key, java.lang.String value) create a VCF header line

Method Summary

Modifier and Type	Method and Description
int	compareTo(java.lang.Object other)
boolean	equals(java.lang.Object o)
java.lang.String	getKey() Get the key
java.lang.String	getValue() Get the value
int	hashCode()
static boolean	isHeaderLine(java.lang.String line)
boolean	shouldBeAddedToDictionary() By default the header lines won't be added to the dictionary, unless this method will be override (for example in FORMAT, INFO or FILTER header lines)
java.lang.String	toString()
protected java.lang.String	toStringEncoding() Should be overloaded in sub classes to do subclass specific
static java.lang.String	toStringEncoding(java.util.Map<java.lang.String,? extends java.lang.Object> keyValues) create a string of a mapping pair for the target VCF version

Methods inherited from class java.lang.Object

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

Field Detail

serialVersionUID

public static final long serialVersionUID

See Also:

Constant Field Values

ALLOW_UNBOUND_DESCRIPTIONS

protected static final boolean ALLOW_UNBOUND_DESCRIPTIONS

See Also:

Constant Field Values

UNBOUND_DESCRIPTION

protected static final java.lang.String UNBOUND_DESCRIPTION

See Also:

Constant Field Values

Constructor Detail

VCFHeaderLine

public VCFHeaderLine(java.lang.String key,
                     java.lang.String value)

create a VCF header line

Parameters:

key - the key for this header line

value - the value for this header line

Method Detail

getKey

public java.lang.String getKey()

Get the key

Returns:

the key

getValue

public java.lang.String getValue()

Get the value

Returns:

the value

shouldBeAddedToDictionary

public boolean shouldBeAddedToDictionary()

By default the header lines won't be added to the dictionary, unless this method will be override (for example in FORMAT, INFO or FILTER header lines)

Returns:

false

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

toStringEncoding

protected java.lang.String toStringEncoding()

Should be overloaded in sub classes to do subclass specific

Returns:

the string encoding

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

compareTo

public int compareTo(java.lang.Object other)

Specified by:

compareTo in interface java.lang.Comparable

isHeaderLine

public static boolean isHeaderLine(java.lang.String line)

Parameters:

line - the line

Returns:

true if the line is a VCF meta data line, or false if it is not

toStringEncoding

public static java.lang.String toStringEncoding(java.util.Map<java.lang.String,? extends java.lang.Object> keyValues)

create a string of a mapping pair for the target VCF version

Parameters:

keyValues - a mapping of the key->value pairs to output

Returns:

a string, correctly formatted