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Augustus 3.4.0
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This is the complete list of members for Gene, including all inherited members.
| addSampleCount(int k) (defined in Transcript) | Transcript | |
| addStatePostProbs(float p) (defined in Transcript) | Transcript | |
| addSupportedStates(HintGroup *group) (defined in Gene) | Gene | |
| addUTR(State *mrnaRanges, bool complete_l=true, bool complete_r=true) (defined in Gene) | Gene | |
| almostIdenticalTo(Gene *other) (defined in Gene) | Gene | virtual |
| almostIdenticalTo(Transcript *other) (defined in Gene) | Gene | virtual |
| apostprob (defined in Transcript) | Transcript | |
| bc (defined in Gene) | Gene | |
| CDSexonEvidence (defined in Gene) | Gene | |
| CDSintronEvidence (defined in Gene) | Gene | |
| clength | Gene | |
| clone() (defined in Gene) | Gene | inlinevirtual |
| cloneGeneSequence() (defined in Transcript) | Transcript | inline |
| codingend (defined in Gene) | Gene | |
| codingstart (defined in Gene) | Gene | |
| compileExtrinsicEvidence(list< HintGroup > *groupList) (defined in Gene) | Gene | |
| complete (defined in Transcript) | Transcript | |
| complete3utr (defined in Gene) | Gene | |
| complete5utr (defined in Gene) | Gene | |
| completeCDS() const (defined in Gene) | Gene | |
| destroyGeneSequence(Transcript *head) (defined in Transcript) | Transcript | inlinestatic |
| exons (defined in Transcript) | Transcript | |
| filterTranscriptsByMaxTracks(list< Transcript * > &gl, int maxTracks) (defined in Transcript) | Transcript | static |
| frame | Gene | |
| Gene() (defined in Gene) | Gene | inline |
| Gene(const Gene &other) (defined in Gene) | Gene | |
| geneBegin() const (defined in Gene) | Gene | inlinevirtual |
| geneEnd() const (defined in Gene) | Gene | inlinevirtual |
| geneid (defined in Transcript) | Transcript | |
| getCDSCoord(long loc, bool comp) const (defined in Gene) | Gene | |
| getExInHeads() const (defined in Gene) | Gene | inlinevirtual |
| getExInInHeads() const (defined in Gene) | Gene | inlinevirtual |
| getExonicSequence(AnnoSequence *annoseq=NULL, bool noOffset=false) const (defined in Transcript) | Transcript | |
| getGenesOnStrand(Transcript *genes, Strand strand) (defined in Transcript) | Transcript | static |
| getPercentSupported() const (defined in Gene) | Gene | |
| gff3 (defined in Transcript) | Transcript | static |
| hasInFrameStop(AnnoSequence *annoseq) const (defined in Gene) | Gene | |
| hasProbs (defined in Transcript) | Transcript | |
| id (defined in Transcript) | Transcript | |
| identicalCDS(Gene *other) (defined in Gene) | Gene | |
| incompatibleEvidence (defined in Gene) | Gene | |
| init() (defined in Gene) | Gene | static |
| introns (defined in Transcript) | Transcript | |
| isCoding() const (defined in Gene) | Gene | inlinevirtual |
| lastExon() const (defined in Gene) | Gene | |
| length | Gene | |
| meanStateProb() (defined in Transcript) | Transcript | |
| next (defined in Transcript) | Transcript | |
| normPostProb(float n) (defined in Transcript) | Transcript | |
| numExons() const (defined in Gene) | Gene | |
| operator<(const Transcript &other) const (defined in Transcript) | Transcript | |
| operator=(const Transcript &other) (defined in Transcript) | Transcript | |
| operator==(const Transcript &other) const (defined in Transcript) | Transcript | |
| print() (defined in Gene) | Gene | |
| print_blocks (defined in Gene) | Gene | static |
| print_cds (defined in Gene) | Gene | static |
| print_exonnames (defined in Gene) | Gene | static |
| print_introns (defined in Gene) | Gene | static |
| print_start | Gene | static |
| print_stop (defined in Gene) | Gene | static |
| print_tss (defined in Transcript) | Transcript | static |
| print_tts (defined in Transcript) | Transcript | static |
| print_utr (defined in Gene) | Gene | static |
| printBlockSequences(AnnoSequence *annoseq) const (defined in Gene) | Gene | virtual |
| printCodingSeq(AnnoSequence *annoseq) const (defined in Gene) | Gene | virtual |
| printEvidence() const (defined in Gene) | Gene | virtual |
| printGFF() const (defined in Gene) | Gene | virtual |
| printProteinSeq(AnnoSequence *annoseq) const (defined in Gene) | Gene | virtual |
| proteinMatches (defined in Gene) | Gene | |
| seqname (defined in Transcript) | Transcript | |
| setSampleCount(int k) (defined in Transcript) | Transcript | |
| setStateHasScore(bool has) (defined in Transcript) | Transcript | |
| setStatePostProbs(float p) (defined in Transcript) | Transcript | |
| shiftCoordinates(long d) (defined in Gene) | Gene | virtual |
| source (defined in Transcript) | Transcript | |
| stopCodonExcludedFromCDS (defined in Gene) | Gene | static |
| strand (defined in Transcript) | Transcript | |
| supportingEvidence (defined in Gene) | Gene | |
| supportingFraction(HintGroup *group) (defined in Gene) | Gene | virtual |
| throwaway (defined in Transcript) | Transcript | |
| Transcript() (defined in Transcript) | Transcript | inline |
| Transcript(const Transcript &other) (defined in Transcript) | Transcript | |
| transend (defined in Transcript) | Transcript | |
| transstart (defined in Transcript) | Transcript | |
| truncateMaskedUTR(AnnoSequence *annoseq) (defined in Gene) | Gene | |
| updatePostProb(Transcript *other) (defined in Transcript) | Transcript | |
| utr3exons (defined in Gene) | Gene | |
| utr3introns (defined in Gene) | Gene | |
| UTR3stateEvidence (defined in Gene) | Gene | |
| utr5exons | Gene | |
| utr5introns (defined in Gene) | Gene | |
| UTR5stateEvidence (defined in Gene) | Gene | |
| viterbi (defined in Transcript) | Transcript | |
| weight (defined in Gene) | Gene | |
| ~Gene() (defined in Gene) | Gene | inline |
| ~Transcript() (defined in Transcript) | Transcript | inlinevirtual |
1.9.8