Package org.snpeff.serializer
Class MarkerSerializer
- java.lang.Object
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- org.snpeff.serializer.MarkerSerializer
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public class MarkerSerializer extends java.lang.Object
Serialize markers to (and from) fileNote: 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
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Constructor Summary
Constructors Constructor Description MarkerSerializer(Genome genome)
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Method Summary
All Methods Instance Methods Concrete Methods 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 filejava.lang.String
save(java.lang.Iterable<Marker> markersCollection)
Save all markersvoid
save(java.lang.String fileName, Markers markers)
Save data to fileint
save(Marker m)
Save a marker
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Constructor Detail
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MarkerSerializer
public MarkerSerializer(Genome genome)
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Method Detail
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doNotSave
public void doNotSave(Marker m)
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getById
protected TxtSerializable getById(int id)
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getIdByMarker
public int getIdByMarker(Marker m)
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getMarkerById
protected Marker getMarkerById(int id)
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getNextField
public java.lang.String getNextField()
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getNextFieldBoolean
public boolean getNextFieldBoolean()
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getNextFieldInt
public int getNextFieldInt()
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getNextFieldMarker
public Marker getNextFieldMarker()
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getNextFieldMarkers
public Markers getNextFieldMarkers()
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getNextId
protected int getNextId()
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load
public Markers load(java.lang.String fileName)
Load data from file
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save
public java.lang.String save(java.lang.Iterable<Marker> markersCollection)
Save all markers
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save
public int save(Marker m)
Save a marker
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save
public void save(java.lang.String fileName, Markers markers)
Save data to file
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