Class TestCasesBase

    • Field Detail

      • debug

        protected boolean debug
      • verbose

        protected boolean verbose
      • randSeed

        protected int randSeed
      • genomeName

        protected java.lang.String genomeName
      • addUtrs

        protected boolean addUtrs
      • onlyPlusStrand

        protected boolean onlyPlusStrand
      • onlyMinusStrand

        protected boolean onlyMinusStrand
      • shiftHgvs

        protected boolean shiftHgvs
      • numGenes

        protected int numGenes
      • maxGeneLen

        protected int maxGeneLen
      • maxTranscripts

        protected int maxTranscripts
      • maxExons

        protected int maxExons
      • minExons

        protected int minExons
      • spliceRegionExonSize

        protected int spliceRegionExonSize
      • spliceRegionIntronMin

        protected int spliceRegionIntronMin
      • spliceRegionIntronMax

        protected int spliceRegionIntronMax
      • rand

        protected java.util.Random rand
      • config

        protected Config config
      • genome

        protected Genome genome
      • gene

        protected Gene gene
      • chromoSequence

        protected java.lang.String chromoSequence
      • chromoBases

        protected char[] chromoBases
    • Constructor Detail

      • TestCasesBase

        public TestCasesBase()
    • Method Detail

      • after

        public void after()
      • before

        public void before()
      • checkApply

        public void checkApply​(Variant variant,
                               Variant.VariantType varType,
                               java.lang.String expectedCds,
                               java.lang.String expectedProtein,
                               int exonRank,
                               int expectedExon1Start,
                               int expectedExon1End)
        Apply a variant to a transcript and check resulting CDS sequence, protein sequence and exon coordinates
      • checkApplyDel

        public void checkApplyDel​(Variant variant,
                                  java.lang.String expectedCds,
                                  java.lang.String expectedProtein,
                                  int exonRank,
                                  int expectedExon1Start,
                                  int expectedExon1End)
      • checkApplyIns

        public void checkApplyIns​(Variant variant,
                                  java.lang.String expectedCds,
                                  java.lang.String expectedProtein,
                                  int exonRank,
                                  int expectedExon1Start,
                                  int expectedExon1End)
      • checkApplyMixed

        public void checkApplyMixed​(Variant variant,
                                    java.lang.String expectedCds,
                                    java.lang.String expectedProtein,
                                    int exonRank,
                                    int expectedExon1Start,
                                    int expectedExon1End)
      • checkApplyMnp

        public void checkApplyMnp​(Variant variant,
                                  java.lang.String expectedCds,
                                  java.lang.String expectedProtein,
                                  int exonRank,
                                  int expectedExon1Start,
                                  int expectedExon1End)
      • checkApplySnp

        public void checkApplySnp​(Variant variant,
                                  java.lang.String expectedCds,
                                  java.lang.String expectedProtein,
                                  int exonRank,
                                  int expectedExon1Start,
                                  int expectedExon1End)
      • checkEffect

        protected void checkEffect​(Variant variant,
                                   EffectType effectExpected)
      • formatVersion

        protected EffFormatVersion formatVersion​(java.lang.String vcfFileName)
        Get file's format version
      • hasEffect

        protected boolean hasEffect​(java.lang.String effectExpected,
                                    java.lang.String effStr)
        Is effectExpected included in effStr (many effects delimited by '&'
      • init

        protected void init()
      • initRand

        protected void initRand()
      • initSnpEffPredictor

        protected void initSnpEffPredictor()
      • initSnpEffPredictor

        protected void initSnpEffPredictor​(Gene[] genesToAdd)
        Create a predictor For the default parameters the first predictor created has only one transcript: 1:880-1001, strand: +, id:transcript_0, Protein Exons: 1:880-1001 'exon_0_0', rank: 1, frame: ., sequence: taaccccatatgattagtacggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgatgaccgatttatttgattccccacatttatttcatcggga CDS : taaccccatatgattagtacggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgatgaccgatttatttgattccccacatttatttcatcgggac Protein : *PHMISTVEEKHLTPIEQDLFRNTLYR*PIYLIPHIYFIG?
      • prependSequenceToFirstExon

        protected void prependSequenceToFirstExon​(java.lang.String prepend)
        Prepend first's exons sequence with a given one
      • showTranscripts

        public java.lang.String showTranscripts​(Genome genome)
        Show a genome in a 'standard' way