de.charite.compbio.jannovar.data

Class ReferenceDictionaryBuilder

java.lang.Object

de.charite.compbio.jannovar.data.ReferenceDictionaryBuilder

public final class ReferenceDictionaryBuilder
extends Object

Builder class for incremental building of immutable ReferenceDictionary objects.

Author:

Manuel Holtgrewe

Constructor Summary

Constructors

Constructor and Description
ReferenceDictionaryBuilder()

Method Summary

Modifier and Type	Method and Description
ReferenceDictionary	build()
Integer	getContigID(String name) Allows contig name to numeric ID translation before final construction of the ReferenceDictionary.
Integer	getContigLength(int id) Allows contig length retrieval before final construction of the ReferenceDictionary.
String	getContigName(Integer id) Allows get contig name from a contig id.
void	putContigID(String name, int id) Add a contig name to numeric ID mapping to builder.
void	putContigLength(int id, int length) Add a contig id to length mapping.
void	putContigName(int id, String name) Set primary contig ID to name mapping.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ReferenceDictionaryBuilder

public ReferenceDictionaryBuilder()

Method Detail

getContigLength

public Integer getContigLength(int id)

Allows contig length retrieval before final construction of the ReferenceDictionary.

Parameters:

id - id of the contig to get the length for

Returns:

length of the contig or null if it could not be found

putContigLength

public void putContigLength(int id,
                            int length)

Add a contig id to length mapping.

Parameters:

id - numeric contig ID

length - contig length

getContigName

public String getContigName(Integer id)

Allows get contig name from a contig id.

Parameters:

id - numeric contig ID

Returns:

primary contig name or null if none could be found

putContigName

public void putContigName(int id,
                          String name)

Set primary contig ID to name mapping.

Parameters:

id - numeric contig ID

name - contig name

getContigID

public Integer getContigID(String name)

Allows contig name to numeric ID translation before final construction of the ReferenceDictionary.

Parameters:

name - name of contig to get numeric ID for

Returns:

canonical numeric ID for the contig with given name or null if none.

putContigID

public void putContigID(String name,
                        int id)

Add a contig name to numeric ID mapping to builder.

Parameters:

name - contig name

id - numeric contig ID

build

public ReferenceDictionary build()

Returns:

instance of immutable ReferenceDictionary object