LinkageDisequilibrium Member List

This is the complete list of members for LinkageDisequilibrium, including all inherited members.

_correl(unsigned int n, const int *x, const double *y, double &r, double &a) (defined in LinkageDisequilibrium)	LinkageDisequilibrium	protectedstatic
_D (defined in LinkageDisequilibrium)	LinkageDisequilibrium	protected
_d (defined in LinkageDisequilibrium)	LinkageDisequilibrium	protected
_Dp (defined in LinkageDisequilibrium)	LinkageDisequilibrium	protected
_n (defined in LinkageDisequilibrium)	LinkageDisequilibrium	protected
_r (defined in LinkageDisequilibrium)	LinkageDisequilibrium	protected
_r2 (defined in LinkageDisequilibrium)	LinkageDisequilibrium	protected
_site1 (defined in LinkageDisequilibrium)	LinkageDisequilibrium	protected
_site2 (defined in LinkageDisequilibrium)	LinkageDisequilibrium	protected
aaMapping	BaseDiversity	static
add(CharMatrix &data, unsigned int position1, unsigned int position2) (defined in LinkageDisequilibrium)	LinkageDisequilibrium	protected
analyzeSite(CharMatrix &data, unsigned int index, double maxMissingData, bool ignoreOutgroup) (defined in BaseDiversity)	BaseDiversity	protected
BaseDiversity()	BaseDiversity
check(unsigned int pos) (defined in LinkageDisequilibrium)	LinkageDisequilibrium	inlineprotected
clear() (defined in LinkageDisequilibrium)	LinkageDisequilibrium	protectedvirtual
correl() const	LinkageDisequilibrium
d(unsigned int pair_index)	LinkageDisequilibrium
D(unsigned int pair_index)	LinkageDisequilibrium
dnaMapping	BaseDiversity	static
Dp(unsigned int pair_index)	LinkageDisequilibrium
get_position(unsigned int index) const	BaseDiversity
get_site(unsigned int index) const	BaseDiversity
getPopIndex(unsigned int label) const (defined in BaseDiversity)	BaseDiversity	protected
importSites(CharMatrix &data, bool allowMultipleMutations, double minimumExploitableData, unsigned int ignoreFrequency, std::string characterMapping, bool useZeroAsAncestral, bool ignoreOutgroup) (defined in BaseDiversity)	BaseDiversity	protected
init() (defined in LinkageDisequilibrium)	LinkageDisequilibrium	protectedvirtual
LinkageDisequilibrium()	LinkageDisequilibrium
load(CharMatrix &data, double minimumExploitableData=1., unsigned int ignoreFrequency=0, std::string characterMapping=dnaMapping)	LinkageDisequilibrium
max(double a, double b) (defined in LinkageDisequilibrium)	LinkageDisequilibrium	inlineprotected
min(double a, double b) (defined in LinkageDisequilibrium)	LinkageDisequilibrium	inlineprotected
numberOfPairs() const	LinkageDisequilibrium
p_allowMultipleMutations (defined in BaseDiversity)	BaseDiversity	protected
p_characterMapping (defined in BaseDiversity)	BaseDiversity	protected
p_ignoreFrequency (defined in BaseDiversity)	BaseDiversity	protected
p_minimumExploitableData (defined in BaseDiversity)	BaseDiversity	protected
p_pos_sep_mapping (defined in BaseDiversity)	BaseDiversity	protected
p_useZeroAsAncestral (defined in BaseDiversity)	BaseDiversity	protected
r(unsigned int pair_index)	LinkageDisequilibrium
r2(unsigned int pair_index)	LinkageDisequilibrium
reserve(unsigned int numberOfSites)	BaseDiversity	virtual
reset()	LinkageDisequilibrium	protectedvirtual
Rmin(CharMatrix &data) const	LinkageDisequilibrium
rnaMapping	BaseDiversity	static
site1(unsigned int pair_index)	LinkageDisequilibrium
site2(unsigned int pair_index)	LinkageDisequilibrium
v_eta (defined in BaseDiversity)	BaseDiversity	protected
v_lseff (defined in BaseDiversity)	BaseDiversity	protected
v_lseffo (defined in BaseDiversity)	BaseDiversity	protected
v_npop (defined in BaseDiversity)	BaseDiversity	protected
v_ns (defined in BaseDiversity)	BaseDiversity	protected
v_nseff (defined in BaseDiversity)	BaseDiversity	protected
v_nseffo (defined in BaseDiversity)	BaseDiversity	protected
v_orientables (defined in BaseDiversity)	BaseDiversity	protected
v_popLabel (defined in BaseDiversity)	BaseDiversity	protected
v_reserved (defined in BaseDiversity)	BaseDiversity	protected
v_S (defined in BaseDiversity)	BaseDiversity	protected
v_sitePositions (defined in BaseDiversity)	BaseDiversity	protected
v_sites (defined in BaseDiversity)	BaseDiversity	protected
v_So (defined in BaseDiversity)	BaseDiversity	protected
~BaseDiversity()	BaseDiversity	virtual
~LinkageDisequilibrium()	LinkageDisequilibrium	virtual