Package org.snpeff.serializer

Class MarkerSerializer

java.lang.Object

org.snpeff.serializer.MarkerSerializer

public class MarkerSerializer
extends java.lang.Object

Serialize markers to (and from) file

Note: Marker's children are serialized first (e.g. a transcript get all exons serialized first).

Note: Since Marker is a tree-like structure, we first load all the markers and then assign parents. Markers are assigned a fake parent object (MarkerParentId) which is later replaced by the 'real' parent.

Note: All 'IDs' used have not meaning outside this serialization process.

Author:

pcingola

Constructor Summary

Constructors

Constructor	Description
MarkerSerializer(Genome genome)

Method Summary

Modifier and Type	Method	Description
void	doNotSave(Marker m)
protected TxtSerializable	getById(int id)
int	getIdByMarker(Marker m)
protected Marker	getMarkerById(int id)
java.lang.String	getNextField()
boolean	getNextFieldBoolean()
int	getNextFieldInt()
Marker	getNextFieldMarker()
Markers	getNextFieldMarkers()
protected int	getNextId()
Markers	load(java.lang.String fileName)	Load data from file
java.lang.String	save(java.lang.Iterable<Marker> markersCollection)	Save all markers
void	save(java.lang.String fileName, Markers markers)	Save data to file
int	save(Marker m)	Save a marker

Methods inherited from class java.lang.Object

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

Constructor Detail

MarkerSerializer

public MarkerSerializer(Genome genome)

Method Detail

doNotSave

public void doNotSave(Marker m)

getById

protected TxtSerializable getById(int id)

getIdByMarker

public int getIdByMarker(Marker m)

getMarkerById

protected Marker getMarkerById(int id)

getNextField

public java.lang.String getNextField()

getNextFieldBoolean

public boolean getNextFieldBoolean()

getNextFieldInt

public int getNextFieldInt()

getNextFieldMarker

public Marker getNextFieldMarker()

getNextFieldMarkers

public Markers getNextFieldMarkers()

getNextId

protected int getNextId()

load

public Markers load(java.lang.String fileName)

Load data from file

save

public java.lang.String save(java.lang.Iterable<Marker> markersCollection)

Save all markers

save

public int save(Marker m)

Save a marker

save

public void save(java.lang.String fileName,
                 Markers markers)

Save data to file