Class VariantEffectStats

    • 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()
      • getPlotGene

        public java.lang.String getPlotGene()
        Barplot of different gene regions
      • getSilentRatio

        public double getSilentRatio()
      • setUseSequenceOntology

        public void setUseSequenceOntology​(boolean useSequenceOntology)