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Augustus 3.4.0
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maintains orthologous exons for comparative gene prediction More...
#include <orthoexon.hh>
Public Member Functions | |
| OrthoExon (int_fast64_t k, size_t numSpecies) | |
| StateType | getStateType () const |
| int | numExons () const |
| double | getOmega () const |
| double | getEomega () const |
| double | getVarOmega () const |
| double | getLeftExtOmega () const |
| double | getRightExtOmega () const |
| double | getLeftIntOmega () const |
| double | getRightIntOmega () const |
| double | getClamsaProb () const |
| double | getClamsaScore () const |
| double | getSubst () const |
| double | getConsScore () const |
| double | getLeftConsScore () const |
| double | getRightConsScore () const |
| double | getDiversity () const |
| size_t | getContainment () const |
| bool | hasOmega () const |
| bool | hasVarOmega () const |
| bool | hasConservation () const |
| bool | hasContainment () const |
| bool | hasDiversity () const |
| bit_vector | getBV () const |
| vector< int > | getRFC (vector< int > offsets) const |
| PhyloTree * | getTree () const |
| int | getAliStart () const |
| int | getAliLen () const |
| int | getAliEnd () const |
| int | getStartInWindow (int s) const |
| int | getEndInWindow (int s) const |
| bool | exonExists (int pos) const |
| bool | isUnaligned (int i) const |
| bool | isAbsent (int i) const |
| void | setPresent (bit_vector v) |
| void | setAbsent (bit_vector v) |
| void | setOmega (double o) |
| void | setOmega (vector< double > *llo, CodonEvo *codonevo, bool oeStart) |
| void | storeOmega (double currOmega, double currVarOmega) |
| void | setClamsa (const cumValues &cv, CodonEvoDiscr *codonevo, bool oeStart) |
| void | setClamsa2 (const cumValues &cv, CodonEvoDiscr *codonevo) |
| void | storeClamsa (double currClamsa) |
| void | setSubst (int s) |
| void | setSubst (int subs, bool oeStart) |
| void | setConsScore (double c) |
| void | setLeftConsScore (double c) |
| void | setRightConsScore (double c) |
| void | setDiversity (double d) |
| void | setContainment (int c) |
| void | setTree (PhyloTree *t) |
| void | setBV (bit_vector b) |
| string | getPhyleticPattern () const |
| void | setPhyleticPattern (map< int, list< int > > &pp_init, map< int, list< int > > &pp_opt) |
| vector< int > | getRFC (vector< int > offsets) |
| double | getLogRegScore () const |
Public Attributes | |
| vector< ExonCandidate * > | orthoex |
| vector< Node * > | orthonode |
| vector< double > | weights |
| vector< int > | labels |
| int | ID |
| vector< int > | firstAlignedPos |
| vector< int > | lastAlignedPos |
maintains orthologous exons for comparative gene prediction
1.9.8