Package org.snpeff.stats
Class VariantEffectStats
- java.lang.Object
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- org.snpeff.stats.VariantEffectStats
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- All Implemented Interfaces:
SamplingStats<VariantEffect>
public class VariantEffectStats extends java.lang.Object implements SamplingStats<VariantEffect>
Variants effect statistics
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
CHANGE_SEPARATOR
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Constructor Summary
Constructors Constructor Description VariantEffectStats(Genome genome)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.lang.String
getAaChangeColor(java.lang.String oldAa, java.lang.String newAa)
Background color used for AA change tablelong
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 involvedjava.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 involvedCountByType
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 regionsdouble
getSilentRatio()
boolean
hasData()
Does this statistic have any data?void
sample(VariantEffect variantEffect)
Analyze one samplevoid
setUseSequenceOntology(boolean useSequenceOntology)
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Field Detail
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CHANGE_SEPARATOR
public static final java.lang.String CHANGE_SEPARATOR
- See Also:
- Constant Field Values
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Constructor Detail
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VariantEffectStats
public VariantEffectStats(Genome genome)
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Method Detail
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getAaChangeColor
public java.lang.String getAaChangeColor(java.lang.String oldAa, java.lang.String newAa)
Background color used for AA change table
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getAaChangeCount
public long getAaChangeCount(java.lang.String oldAa, java.lang.String newAa)
How many changes from oldAa to newAa do we have?
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getAaList
public java.util.List<java.lang.String> getAaList()
Get list of all amino acisd involved
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getCodonChangeColor
public java.lang.String getCodonChangeColor(java.lang.String oldCodon, java.lang.String newCodon)
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getCodonChangeCount
public long getCodonChangeCount(java.lang.String oldCodon, java.lang.String newCodon)
How many changes from oldCodo to newCodon do we have?
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getCodonList
public java.util.List<java.lang.String> getCodonList()
Get a list of all codons involved
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getCountByEffect
public CountByType getCountByEffect()
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getCountByFunctionalClass
public CountByType getCountByFunctionalClass()
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getCountByGeneRegion
public CountByType getCountByGeneRegion()
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getCountByImpact
public CountByType getCountByImpact()
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getCountErrors
public int getCountErrors()
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getCountWarnings
public int getCountWarnings()
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getGeneCountByEffectTable
public GeneCountByTypeTable getGeneCountByEffectTable()
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getGeneCountByImpactTable
public GeneCountByTypeTable getGeneCountByImpactTable()
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getGeneCountByRegionTable
public GeneCountByTypeTable getGeneCountByRegionTable()
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getPlotGene
public java.lang.String getPlotGene()
Barplot of different gene regions
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getSilentRatio
public double getSilentRatio()
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hasData
public boolean hasData()
Description copied from interface:SamplingStats
Does this statistic have any data?- Specified by:
hasData
in interfaceSamplingStats<VariantEffect>
- Returns:
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sample
public void sample(VariantEffect variantEffect)
Description copied from interface:SamplingStats
Analyze one sample- Specified by:
sample
in interfaceSamplingStats<VariantEffect>
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setUseSequenceOntology
public void setUseSequenceOntology(boolean useSequenceOntology)
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