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

All Implemented Interfaces:

VCFIDHeaderLine, Serializable, 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 Description

static String DESCRIPTION_ATTRIBUTE

static String ID_ATTRIBUTE
- Fields inherited from class htsjdk.variant.vcf.VCFHeaderLine
  ALLOW_UNBOUND_DESCRIPTIONS, serialVersionUID, UNBOUND_DESCRIPTION

Constructor Summary

Constructors
Constructor	Description
`VCFSimpleHeaderLine(String line, VCFHeaderVersion version, String key, List<String> expectedTagOrdering)`	create a VCF info header line
`VCFSimpleHeaderLine(String line, VCFHeaderVersion version, String key, List<String> expectedTagOrdering, List<String> recommendedTags)`	create a VCF info header line
`VCFSimpleHeaderLine(String key, String name, String description)`	create a VCF filter header line
`VCFSimpleHeaderLine(String key, Map<String,String> mapping)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`boolean`	`equals(Object o)`
`Map<String,String>`	`getGenericFields()`
`String`	`getID()`
`int`	`hashCode()`
`protected void`	`initialize(String name, Map<String,String> genericFields)`
`protected 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 String ID_ATTRIBUTE
```
  See Also:
  
  Constant Field Values
- DESCRIPTION_ATTRIBUTE
```
public static final String DESCRIPTION_ATTRIBUTE
```
  See Also:
  
  Constant Field Values

Constructor Detail

VCFSimpleHeaderLine

public VCFSimpleHeaderLine(String key,
                           String name,
                           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(String line,
                           VCFHeaderVersion version,
                           String key,
                           List<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(String line,
                           VCFHeaderVersion version,
                           String key,
                           List<String> expectedTagOrdering,
                           List<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(String key,
                           Map<String,String> mapping)

Method Detail
- initialize
```
protected void initialize(String name,
                          Map<String,String> genericFields)
```
- toStringEncoding
```
protected 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(Object o)
```
  Overrides:
  
  equals in class VCFHeaderLine
- hashCode
```
public int hashCode()
```
  Overrides:
  
  hashCode in class VCFHeaderLine
- getID
```
public String getID()
```
  Specified by:
  
  getID in interface VCFIDHeaderLine
- getGenericFields
```
public Map<String,String> getGenericFields()
```
  Returns:
  
  a map of all pairs of fields and values in this header line

Modifier and Type	Field	Description
`static String`	`DESCRIPTION_ATTRIBUTE`
`static String`	`ID_ATTRIBUTE`

Class VCFSimpleHeaderLine

Field Summary

Fields inherited from class htsjdk.variant.vcf.VCFHeaderLine

Constructor Summary

Method Summary

Methods inherited from class htsjdk.variant.vcf.VCFHeaderLine

Methods inherited from class java.lang.Object

Field Detail

ID_ATTRIBUTE

DESCRIPTION_ATTRIBUTE

Constructor Detail

VCFSimpleHeaderLine

VCFSimpleHeaderLine

VCFSimpleHeaderLine

VCFSimpleHeaderLine

Method Detail

initialize

toStringEncoding

equals

hashCode

getID

getGenericFields