Package org.snpeff.stats

Class VariantEffectStats

java.lang.Object
org.snpeff.stats.VariantEffectStats
All Implemented Interfaces:
SamplingStats<VariantEffect>
public class VariantEffectStats extends Object implements SamplingStats<VariantEffect>
Variants effect statistics

  • Field Details

  • Constructor Details

    • VariantEffectStats

      public VariantEffectStats(Genome genome)

  • Method Details

    • getAaChangeColor

      public String getAaChangeColor(String oldAa, String newAa)
      Background color used for AA change table

    • getAaChangeCount

      public long getAaChangeCount(String oldAa, String newAa)
      How many changes from oldAa to newAa do we have?

    • getAaList

      public List<String> getAaList()
      Get list of all amino acisd involved

    • getCodonChangeColor

      public String getCodonChangeColor(String oldCodon, String newCodon)

    • getCodonChangeCount

      public long getCodonChangeCount(String oldCodon, String newCodon)
      How many changes from oldCodo to newCodon do we have?

    • getCodonList

      public List<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 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)