Package org.snpeff.stats

Class VariantEffectStats

java.lang.Object

org.snpeff.stats.VariantEffectStats

All Implemented Interfaces:

SamplingStats<VariantEffect>

public class VariantEffectStats
extends java.lang.Object
implements SamplingStats<VariantEffect>

Variants effect statistics

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	CHANGE_SEPARATOR

Constructor Summary

Constructors

Constructor	Description
VariantEffectStats(Genome genome)

Method Summary

Modifier and Type	Method	Description
java.lang.String	getAaChangeColor(java.lang.String oldAa, java.lang.String newAa)	Background color used for AA change table
long	getAaChangeCount(java.lang.String oldAa, java.lang.String newAa)	How many changes from oldAa to newAa do we have?
java.util.List<java.lang.String>	getAaList()	Get list of all amino acisd involved
java.lang.String	getCodonChangeColor(java.lang.String oldCodon, java.lang.String newCodon)
long	getCodonChangeCount(java.lang.String oldCodon, java.lang.String newCodon)	How many changes from oldCodo to newCodon do we have?
java.util.List<java.lang.String>	getCodonList()	Get a list of all codons involved
CountByType	getCountByEffect()
CountByType	getCountByFunctionalClass()
CountByType	getCountByGeneRegion()
CountByType	getCountByImpact()
int	getCountErrors()
int	getCountWarnings()
GeneCountByTypeTable	getGeneCountByEffectTable()
GeneCountByTypeTable	getGeneCountByImpactTable()
GeneCountByTypeTable	getGeneCountByRegionTable()
java.lang.String	getPlotGene()	Barplot of different gene regions
double	getSilentRatio()
boolean	hasData()	Does this statistic have any data?
void	sample(VariantEffect variantEffect)	Analyze one sample
void	setUseSequenceOntology(boolean useSequenceOntology)

Methods inherited from class java.lang.Object

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

Field Detail

CHANGE_SEPARATOR

public static final java.lang.String CHANGE_SEPARATOR

See Also:

Constant Field Values

Constructor Detail

VariantEffectStats

public VariantEffectStats(Genome genome)

Method Detail

getAaChangeColor

public java.lang.String getAaChangeColor(java.lang.String oldAa,
                                         java.lang.String newAa)

Background color used for AA change table

getAaChangeCount

public long getAaChangeCount(java.lang.String oldAa,
                             java.lang.String newAa)

How many changes from oldAa to newAa do we have?

getAaList

public java.util.List<java.lang.String> getAaList()

Get list of all amino acisd involved

getCodonChangeColor

public java.lang.String getCodonChangeColor(java.lang.String oldCodon,
                                            java.lang.String newCodon)

getCodonChangeCount

public long getCodonChangeCount(java.lang.String oldCodon,
                                java.lang.String newCodon)

How many changes from oldCodo to newCodon do we have?

getCodonList

public java.util.List<java.lang.String> getCodonList()

Get a list of all codons involved

getCountByEffect

public CountByType getCountByEffect()

getCountByFunctionalClass

public CountByType getCountByFunctionalClass()

getCountByGeneRegion

public CountByType getCountByGeneRegion()

getCountByImpact

public CountByType getCountByImpact()

getCountErrors

public int getCountErrors()

getCountWarnings

public int getCountWarnings()

getGeneCountByEffectTable

public GeneCountByTypeTable getGeneCountByEffectTable()

getGeneCountByImpactTable

public GeneCountByTypeTable getGeneCountByImpactTable()

getGeneCountByRegionTable

public GeneCountByTypeTable getGeneCountByRegionTable()

getPlotGene

public java.lang.String getPlotGene()

Barplot of different gene regions

getSilentRatio

public double getSilentRatio()

hasData

public boolean hasData()

Description copied from interface: SamplingStats

Does this statistic have any data?

Specified by:

hasData in interface SamplingStats<VariantEffect>

Returns:

sample

public void sample(VariantEffect variantEffect)

Description copied from interface: SamplingStats

Analyze one sample

Specified by:

sample in interface SamplingStats<VariantEffect>

setUseSequenceOntology

public void setUseSequenceOntology(boolean useSequenceOntology)