NucleotideDiversity Member List

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

aaMapping	BaseDiversity	static
analyzeSite(CharMatrix &data, unsigned int index, double maxMissingData, bool ignoreOutgroup) (defined in BaseDiversity)	BaseDiversity	protected
average_Pi()	NucleotideDiversity
b_analysisSites (defined in NucleotideDiversity)	NucleotideDiversity	protected
b_differentiation (defined in NucleotideDiversity)	NucleotideDiversity	protected
b_diversity (defined in NucleotideDiversity)	NucleotideDiversity	protected
b_outgroupDiversity (defined in NucleotideDiversity)	NucleotideDiversity	protected
b_triConfigurations (defined in NucleotideDiversity)	NucleotideDiversity	protected
BaseDiversity()	BaseDiversity
clear() (defined in NucleotideDiversity)	NucleotideDiversity	protectedvirtual
CommonAlleles()	NucleotideDiversity
CommonAlleles(unsigned int pop1, unsigned int pop2)	NucleotideDiversity
D()	NucleotideDiversity
differentiation() (defined in NucleotideDiversity)	NucleotideDiversity	protected
diversity() (defined in NucleotideDiversity)	NucleotideDiversity	protected
dnaMapping	BaseDiversity	static
E()	NucleotideDiversity
eta() const	NucleotideDiversity
FixedDifferences()	NucleotideDiversity
FixedDifferences(unsigned int pop1, unsigned int pop2)	NucleotideDiversity
get_position(unsigned int index) const	BaseDiversity
get_site(unsigned int index) const	BaseDiversity
getPopIndex(unsigned int label) const (defined in BaseDiversity)	BaseDiversity	protected
H()	NucleotideDiversity
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 NucleotideDiversity)	NucleotideDiversity	protectedvirtual
load(CharMatrix &data, bool allowMultipleMutations=false, double minimumExploitableData=1., unsigned int ignoreFrequency=0, std::string characterMapping=dnaMapping, bool useZeroAsAncestral=false)	NucleotideDiversity	virtual
lseff() const	NucleotideDiversity
lseffo() const	NucleotideDiversity
npop() const	NucleotideDiversity
nseff() const	NucleotideDiversity
nseffo() const	NucleotideDiversity
NucleotideDiversity()	NucleotideDiversity
NucleotideDiversity(const NucleotideDiversity &source)	NucleotideDiversity	inlineprotected
operator=(const NucleotideDiversity &source)	NucleotideDiversity	inlineprotected
outgroupDiversity() (defined in NucleotideDiversity)	NucleotideDiversity	protected
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
Pi()	NucleotideDiversity
polymorphic_positions() const	NucleotideDiversity
Polymorphisms(unsigned int pop)	NucleotideDiversity
pop_Pi(unsigned int popIndex)	NucleotideDiversity
popLabel(unsigned int popIndex) const	NucleotideDiversity
reserve(unsigned int numberOfSites)	BaseDiversity	virtual
reset()	BaseDiversity	virtual
rnaMapping	BaseDiversity	static
S() const	NucleotideDiversity
SharedAlleles()	NucleotideDiversity
SharedAlleles(unsigned int pop1, unsigned int pop2)	NucleotideDiversity
singleton_positions() const	NucleotideDiversity
So() const	NucleotideDiversity
SpecificAlleles()	NucleotideDiversity
SpecificAlleles(unsigned int pop)	NucleotideDiversity
SpecificDerivedAlleles()	NucleotideDiversity
SpecificDerivedAlleles(unsigned int pop)	NucleotideDiversity
thetaH()	NucleotideDiversity
thetaL()	NucleotideDiversity
thetaW()	NucleotideDiversity
triConfiguration(unsigned int index)	NucleotideDiversity
triConfigurations() (defined in NucleotideDiversity)	NucleotideDiversity	protected
v_average_Pi (defined in NucleotideDiversity)	NucleotideDiversity	protected
v_countCommonAlleles (defined in NucleotideDiversity)	NucleotideDiversity	protected
v_countFixedDifferences (defined in NucleotideDiversity)	NucleotideDiversity	protected
v_countSharedAlleles (defined in NucleotideDiversity)	NucleotideDiversity	protected
v_countSpecificAlleles (defined in NucleotideDiversity)	NucleotideDiversity	protected
v_countSpecificDerivedAlleles (defined in NucleotideDiversity)	NucleotideDiversity	protected
v_D (defined in NucleotideDiversity)	NucleotideDiversity	protected
v_E (defined in NucleotideDiversity)	NucleotideDiversity	protected
v_eta (defined in BaseDiversity)	BaseDiversity	protected
v_H (defined in NucleotideDiversity)	NucleotideDiversity	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_pairwiseCommonAlleles (defined in NucleotideDiversity)	NucleotideDiversity	protected
v_pairwiseFixedDifferences (defined in NucleotideDiversity)	NucleotideDiversity	protected
v_pairwiseSharedAlleles (defined in NucleotideDiversity)	NucleotideDiversity	protected
v_Pi (defined in NucleotideDiversity)	NucleotideDiversity	protected
v_pop_Pi (defined in NucleotideDiversity)	NucleotideDiversity	protected
v_popLabel (defined in BaseDiversity)	BaseDiversity	protected
v_popPolymorphic (defined in NucleotideDiversity)	NucleotideDiversity	protected
v_popSpecific (defined in NucleotideDiversity)	NucleotideDiversity	protected
v_popSpecificDerived (defined in NucleotideDiversity)	NucleotideDiversity	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
v_thetaH (defined in NucleotideDiversity)	NucleotideDiversity	protected
v_thetaL (defined in NucleotideDiversity)	NucleotideDiversity	protected
v_thetaW (defined in NucleotideDiversity)	NucleotideDiversity	protected
v_triConfigurations (defined in NucleotideDiversity)	NucleotideDiversity	protected
v_Z (defined in NucleotideDiversity)	NucleotideDiversity	protected
Z()	NucleotideDiversity
~BaseDiversity()	BaseDiversity	virtual
~NucleotideDiversity()	NucleotideDiversity	virtual