OrthoExon Member List
This is the complete list of members for OrthoExon, including all inherited members.
| exonExists(int pos) const (defined in OrthoExon) | OrthoExon | |
| firstAlignedPos (defined in OrthoExon) | OrthoExon | |
| getAliEnd() const (defined in OrthoExon) | OrthoExon | inline |
| getAliLen() const (defined in OrthoExon) | OrthoExon | inline |
| getAliStart() const (defined in OrthoExon) | OrthoExon | inline |
| getBV() const (defined in OrthoExon) | OrthoExon | inline |
| getClamsaProb() const (defined in OrthoExon) | OrthoExon | inline |
| getClamsaScore() const (defined in OrthoExon) | OrthoExon | inline |
| getConsScore() const (defined in OrthoExon) | OrthoExon | inline |
| getContainment() const (defined in OrthoExon) | OrthoExon | inline |
| getDiversity() const (defined in OrthoExon) | OrthoExon | inline |
| getEndInWindow(int s) const (defined in OrthoExon) | OrthoExon | inline |
| getEomega() const (defined in OrthoExon) | OrthoExon | inline |
| getLeftConsScore() const (defined in OrthoExon) | OrthoExon | inline |
| getLeftExtOmega() const (defined in OrthoExon) | OrthoExon | inline |
| getLeftIntOmega() const (defined in OrthoExon) | OrthoExon | inline |
| getLogRegScore() const (defined in OrthoExon) | OrthoExon | |
| getOmega() const (defined in OrthoExon) | OrthoExon | inline |
| getPhyleticPattern() const (defined in OrthoExon) | OrthoExon | |
| getRFC(vector< int > offsets) const (defined in OrthoExon) | OrthoExon | inline |
| getRFC(vector< int > offsets) (defined in OrthoExon) | OrthoExon | |
| getRightConsScore() const (defined in OrthoExon) | OrthoExon | inline |
| getRightExtOmega() const (defined in OrthoExon) | OrthoExon | inline |
| getRightIntOmega() const (defined in OrthoExon) | OrthoExon | inline |
| getStartInWindow(int s) const (defined in OrthoExon) | OrthoExon | inline |
| getStateType() const (defined in OrthoExon) | OrthoExon | |
| getSubst() const (defined in OrthoExon) | OrthoExon | inline |
| getTree() const (defined in OrthoExon) | OrthoExon | inline |
| getVarOmega() const (defined in OrthoExon) | OrthoExon | inline |
| hasConservation() const (defined in OrthoExon) | OrthoExon | inline |
| hasContainment() const (defined in OrthoExon) | OrthoExon | inline |
| hasDiversity() const (defined in OrthoExon) | OrthoExon | inline |
| hasOmega() const (defined in OrthoExon) | OrthoExon | inline |
| hasVarOmega() const (defined in OrthoExon) | OrthoExon | inline |
| ID (defined in OrthoExon) | OrthoExon | |
| isAbsent(int i) const (defined in OrthoExon) | OrthoExon | inline |
| isUnaligned(int i) const (defined in OrthoExon) | OrthoExon | inline |
| labels (defined in OrthoExon) | OrthoExon | |
| lastAlignedPos (defined in OrthoExon) | OrthoExon | |
| numExons() const (defined in OrthoExon) | OrthoExon | |
| orthoex (defined in OrthoExon) | OrthoExon | |
| OrthoExon(int_fast64_t k, size_t numSpecies) (defined in OrthoExon) | OrthoExon | |
| orthonode (defined in OrthoExon) | OrthoExon | |
| setAbsent(bit_vector v) (defined in OrthoExon) | OrthoExon | |
| setBV(bit_vector b) (defined in OrthoExon) | OrthoExon | inline |
| setClamsa(const cumValues &cv, CodonEvoDiscr *codonevo, bool oeStart) (defined in OrthoExon) | OrthoExon | |
| setClamsa2(const cumValues &cv, CodonEvoDiscr *codonevo) (defined in OrthoExon) | OrthoExon | |
| setConsScore(double c) (defined in OrthoExon) | OrthoExon | inline |
| setContainment(int c) (defined in OrthoExon) | OrthoExon | inline |
| setDiversity(double d) (defined in OrthoExon) | OrthoExon | inline |
| setLeftConsScore(double c) (defined in OrthoExon) | OrthoExon | inline |
| setOmega(double o) (defined in OrthoExon) | OrthoExon | inline |
| setOmega(vector< double > *llo, CodonEvo *codonevo, bool oeStart) (defined in OrthoExon) | OrthoExon | |
| setPhyleticPattern(map< int, list< int > > &pp_init, map< int, list< int > > &pp_opt) (defined in OrthoExon) | OrthoExon | |
| setPresent(bit_vector v) (defined in OrthoExon) | OrthoExon | |
| setRightConsScore(double c) (defined in OrthoExon) | OrthoExon | inline |
| setSubst(int s) (defined in OrthoExon) | OrthoExon | inline |
| setSubst(int subs, bool oeStart) (defined in OrthoExon) | OrthoExon | |
| setTree(PhyloTree *t) (defined in OrthoExon) | OrthoExon | |
| storeClamsa(double currClamsa) (defined in OrthoExon) | OrthoExon | |
| storeOmega(double currOmega, double currVarOmega) (defined in OrthoExon) | OrthoExon | |
| weights (defined in OrthoExon) | OrthoExon | |
| ~OrthoExon() (defined in OrthoExon) | OrthoExon | inline |
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