GeneMSA Member List
This is the complete list of members for GeneMSA, including all inherited members.
| calcColumnScore(int a, int c, int t, int g) (defined in GeneMSA) | GeneMSA | |
| calcConsScore(list< OrthoExon > &orthoExonsList, vector< AnnoSequence * > const &seqRanges, string outdir) (defined in GeneMSA) | GeneMSA | |
| closeOutputFiles() (defined in GeneMSA) | GeneMSA | static |
| collect_features(int species, list< OrthoExon > *hects, SpeciesGraph *speciesgraph) (defined in GeneMSA) | GeneMSA | |
| comparativeSignalScoring(list< OrthoExon > &orthoExonsList) (defined in GeneMSA) | GeneMSA | |
| computeClamsa(list< OrthoExon > &orthoExonsList, vector< AnnoSequence * > const &seqRanges, PhyloTree *ctree, ofstream *codonAli) (defined in GeneMSA) | GeneMSA | |
| computeClamsaEff(list< OrthoExon > &orthoExonsList, vector< AnnoSequence * > const &seqRanges, PhyloTree *ctree, ofstream *codonAli) | GeneMSA | |
| computedCumValues (defined in GeneMSA) | GeneMSA | static |
| computeOmegas(list< OrthoExon > &orthoExonsList, vector< AnnoSequence * > const &seqRanges, PhyloTree *ctree) (defined in GeneMSA) | GeneMSA | |
| computeOmegasEff(list< OrthoExon > &orthoExonsList, vector< AnnoSequence * > const &seqRanges, PhyloTree *ctree, ofstream *codonAli) (defined in GeneMSA) | GeneMSA | |
| consToWig(vector< double > &consScore, string outdir) (defined in GeneMSA) | GeneMSA | |
| constructTree() (defined in GeneMSA) | GeneMSA | |
| createExonCands(int s, const char *dna, map< int_fast64_t, ExonCandidate * > &ecs, map< int_fast64_t, ExonCandidate * > &addECs) (defined in GeneMSA) | GeneMSA | |
| createOrthoExons(list< OrthoExon > &orthoExonsList, map< int_fast64_t, list< pair< int, ExonCandidate * > > > &alignedECs, Evo *evo, float consThres=0.0, int minAvLen=0) | GeneMSA | |
| exonCandID (defined in GeneMSA) | GeneMSA | static |
| exonCands_outfiles (defined in GeneMSA) | GeneMSA | static |
| GeneMSA(RandSeqAccess *rsa, Alignment *a) | GeneMSA | |
| geneRangeID (defined in GeneMSA) | GeneMSA | static |
| geneRanges_outfiles_bed (defined in GeneMSA) | GeneMSA | static |
| geneRanges_outfiles_gff (defined in GeneMSA) | GeneMSA | static |
| getAlignment() (defined in GeneMSA) | GeneMSA | inline |
| getAllOEMsas(int species, list< OrthoExon > *hects, unordered_map< string, int > *ref_class, vector< AnnoSequence * > const &seqRanges) | GeneMSA | |
| getECHash(list< ExonCandidate * > *ec) (defined in GeneMSA) | GeneMSA | |
| getEnd(int speciesIdx) (defined in GeneMSA) | GeneMSA | inline |
| getExonCands(int speciesIdx) (defined in GeneMSA) | GeneMSA | inline |
| getMsa(OrthoExon const &oe, vector< AnnoSequence * > const &seqRanges, size_t flanking=0) | GeneMSA | |
| getOffsets() (defined in GeneMSA) | GeneMSA | inline |
| getSeqID(int speciesIdx) (defined in GeneMSA) | GeneMSA | |
| getStart(int speciesIdx) (defined in GeneMSA) | GeneMSA | inline |
| getStrand(int speciesIdx) (defined in GeneMSA) | GeneMSA | |
| numSpecies() (defined in GeneMSA) | GeneMSA | inlinestatic |
| omega_outfiles (defined in GeneMSA) | GeneMSA | static |
| omegaForCodonTuple(vector< double > *loglik) (defined in GeneMSA) | GeneMSA | |
| openOutputFiles(string outdir) (defined in GeneMSA) | GeneMSA | static |
| orthoExonID (defined in GeneMSA) | GeneMSA | static |
| orthoExons_outfiles (defined in GeneMSA) | GeneMSA | static |
| padding (defined in GeneMSA) | GeneMSA | static |
| printCumOmega() (defined in GeneMSA) | GeneMSA | |
| printExonCands() (defined in GeneMSA) | GeneMSA | |
| printGeneRanges() (defined in GeneMSA) | GeneMSA | |
| printOmegaForCodon(string outdir) (defined in GeneMSA) | GeneMSA | |
| printOrthoExons(list< OrthoExon > &orthoExonsList) (defined in GeneMSA) | GeneMSA | |
| printSingleOrthoExon(OrthoExon const &oe, bool files=true) (defined in GeneMSA) | GeneMSA | |
| printStats() (defined in GeneMSA) | GeneMSA | |
| pruneToBV(vector< string > *cs, bit_vector bv) (defined in GeneMSA) | GeneMSA | |
| pruneToBV(vector< int > *rfc, bit_vector bv) (defined in GeneMSA) | GeneMSA | |
| setCodonEvo(CodonEvo *c) (defined in GeneMSA) | GeneMSA | inlinestatic |
| setCodonEvoDiscr(CodonEvoDiscr *c) (defined in GeneMSA) | GeneMSA | inlinestatic |
| setExonCands(vector< map< int_fast64_t, ExonCandidate * > > &ecs) (defined in GeneMSA) | GeneMSA | |
| setTree(PhyloTree *t) (defined in GeneMSA) | GeneMSA | inlinestatic |
| topologies (defined in GeneMSA) | GeneMSA | static |
| ~GeneMSA() (defined in GeneMSA) | GeneMSA |
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