Low-level binding of C++ library

Besides sequence storage classes Container and Align, the wrapped C++ library available through the egglib egglib-py module contains several classes that might be of use for Python scripts. Still, they are a priori not intended to be used directly and this page only provides automated documentation. The user is prompted to refer to the doxygen documentation of the C++ library for a more comprehensive documentation of these tools.

Data holders

class egglib.egglib_binding.Align(egglib::Align self)

Proxy of C++ egglib::Align class

__init__(egglib::Align self, unsigned int number_of_sequences, unsigned int alignment_length) -> Align __init__(egglib::Align self, Container container) -> Align

append(Align self, char const * name, char const * sequence, unsigned int group=0) → unsigned int

append(Align self, char const * name, char const * sequence) -> unsigned int

appendSequence(Container self, unsigned int pos, char const * sequence)

binSwitch(Align self, unsigned int pos)

character(Align self, unsigned int s, unsigned int p) → char

clear(Align self)

equalize(Container self, char ch='?') → unsigned int

equalize(Container self) -> unsigned int

find(Container self, char const * string, bool strict=True) → int

find(Container self, char const * string) -> int

get(Align self, unsigned int sequence, unsigned int position) → char

group(Container self, unsigned int pos, unsigned int group)

group(Container self, unsigned int pos) -> unsigned int

hslice(Container self, unsigned int a, unsigned int b) → Container

isEqual(Container self) → bool

ls(Align self) → unsigned int

ls(Align self, unsigned int pos) -> unsigned int

name(Container self, unsigned int pos, char const * name)

name(Container self, unsigned int pos) -> char const *

ns(Container self) → unsigned int

numberOfSequences(Align self) → unsigned int

numberOfSites(Align self) → unsigned int

populationLabel(Align self, unsigned int sequenceIndex) → unsigned int

remove(Align self, unsigned int pos) → unsigned int

removePosition(Align self, unsigned int pos) → unsigned int

sequence(Align self, unsigned int pos) → char const

sequence(Align self, unsigned int pos, char const * sequence)

set(Align self, unsigned int sequence, unsigned int position, char ch)

sitePosition(Align self, unsigned int position) → double

vslice(Align self, vectorui list_of_sites) → Align

vslice(Align self, unsigned int a, unsigned int b) -> Align

class egglib.egglib_binding.CharMatrix(*args, **kwargs)

Proxy of C++ egglib::CharMatrix class

character(CharMatrix self, unsigned int sequence, unsigned int site) → char

numberOfSequences(CharMatrix self) → unsigned int

numberOfSites(CharMatrix self) → unsigned int

populationLabel(CharMatrix self, unsigned int row) → unsigned int

sitePosition(CharMatrix self, unsigned int column) → double

class egglib.egglib_binding.Container(egglib::Container self)

Proxy of C++ egglib::Container class

__init__(egglib::Container self, Container source) -> Container

append(Container self, char const * name, char const * sequence, unsigned int group=0) → unsigned int

append(Container self, char const * name, char const * sequence) -> unsigned int

appendSequence(Container self, unsigned int pos, char const * sequence)

clear(Container self)

equalize(Container self, char ch='?') → unsigned int

equalize(Container self) -> unsigned int

find(Container self, char const * string, bool strict=True) → int

find(Container self, char const * string) -> int

get(Container self, unsigned int s, unsigned int p) → char

group(Container self, unsigned int pos, unsigned int group)

group(Container self, unsigned int pos) -> unsigned int

hslice(Container self, unsigned int a, unsigned int b) → Container

isEqual(Container self) → bool

ls(Container self, unsigned int pos) → unsigned int

name(Container self, unsigned int pos, char const * name)

name(Container self, unsigned int pos) -> char const *

ns(Container self) → unsigned int

remove(Container self, unsigned int pos) → unsigned int

sequence(Container self, unsigned int pos, char const * sequence)

sequence(Container self, unsigned int pos) -> char const *

set(Container self, unsigned int sequence, unsigned int position, char ch)

class egglib.egglib_binding.DataMatrix(egglib::DataMatrix self)

Proxy of C++ egglib::DataMatrix class

__init__(egglib::DataMatrix self, unsigned int numberOfSequences, unsigned int numberOfSites) -> DataMatrix __init__(egglib::DataMatrix self, DataMatrix arg2) -> DataMatrix

character(DataMatrix self, unsigned int sequence, unsigned int site) → char

clear(DataMatrix self)

get(DataMatrix self, unsigned int sequence, unsigned int site) → int

numberOfSequences(DataMatrix self) → unsigned int

numberOfSites(DataMatrix self) → unsigned int

populationLabel(DataMatrix self, unsigned int sequence, unsigned int value)

populationLabel(DataMatrix self, unsigned int sequence) -> unsigned int

resize(DataMatrix self, unsigned int newNumberOfSequences, unsigned int newNumberOfSites)

set(DataMatrix self, unsigned int sequence, unsigned int site, int value)

shift(DataMatrix self, int minimum)

sitePosition(DataMatrix self, unsigned int site, double value)

sitePosition(DataMatrix self, unsigned int site) -> double

Conversion and parsing

class egglib.egglib_binding.Consensus(egglib::Consensus self)

Proxy of C++ egglib::Consensus class

ambiguousPositions(Consensus self) → vectori

atLeastPartiallyResolvedAmbiguities(Consensus self) → vectori

check_sequences(Consensus self, Align align) → bool

complementaryPositions(Consensus self) → vectori

consensus(Consensus self, Align align, char separator='_', bool rigorous=True) → Align

consensus(Consensus self, Align align, char separator=’_’) -> Align consensus(Consensus self, Align align) -> Align

consistentPositions(Consensus self) → vectori

firstSequenceNames(Consensus self) → vectors

inconsistentPositions(Consensus self) → vectorvi

roots(Consensus self) → vectors

secondSequenceNames(Consensus self) → vectors

setDisagreement(Consensus self, char arg2)

setMissing(Consensus self, char arg2)

uninformativePositions(Consensus self) → vectori

class egglib.egglib_binding.Convert(*args, **kwargs)

Proxy of C++ egglib::Convert class

static align(*args)

align(DataMatrix dataMatrix, unsigned int length=0, Random random=None, bool randomizePositions=False,

bool randomizeNonVaryingStates=False, bool randomizeAlleles=False, bool enforceLength=False, std::string mapping=”ACGT”, char unknown=’?’, char nonVaryingState=’A’) -> Align

align(DataMatrix dataMatrix, unsigned int length=0, Random random=None, bool randomizePositions=False,

bool randomizeNonVaryingStates=False, bool randomizeAlleles=False, bool enforceLength=False, std::string mapping=”ACGT”, char unknown=’?’) -> Align

align(DataMatrix dataMatrix, unsigned int length=0, Random random=None, bool randomizePositions=False,

bool randomizeNonVaryingStates=False, bool randomizeAlleles=False, bool enforceLength=False, std::string mapping=”ACGT”) -> Align

align(DataMatrix dataMatrix, unsigned int length=0, Random random=None, bool randomizePositions=False,

bool randomizeNonVaryingStates=False, bool randomizeAlleles=False, bool enforceLength=False) -> Align

align(DataMatrix dataMatrix, unsigned int length=0, Random random=None, bool randomizePositions=False,

bool randomizeNonVaryingStates=False, bool randomizeAlleles=False) -> Align

align(DataMatrix dataMatrix, unsigned int length=0, Random random=None, bool randomizePositions=False,

bool randomizeNonVaryingStates=False) -> Align

align(DataMatrix dataMatrix, unsigned int length=0, Random random=None, bool randomizePositions=False) -> Align align(DataMatrix dataMatrix, unsigned int length=0, Random random=None) -> Align align(DataMatrix dataMatrix, unsigned int length=0) -> Align align(DataMatrix dataMatrix) -> Align

class egglib.egglib_binding.Fasta(*args, **kwargs)

Proxy of C++ egglib::Fasta class

static format(Container container, bool exportGroupLabels=False, unsigned int lineLength=50) → std::string

format(Container container, bool exportGroupLabels=False) -> std::string format(Container container) -> std::string

static formatf(char const * fname, Container container, bool exportGroupLabels=False, unsigned int lineLength=50)

formatf(char const * fname, Container container, bool exportGroupLabels=False) formatf(char const * fname, Container container)

static parse(std::string const & str, bool importGroupLabels=False) → Container

parse(std::string const & str) -> Container parse(std::string const & str, Container container, bool importGroupLabels=False) parse(std::string const & str, Container container)

static parsef(char const * fname, bool importGroupLabels=False) → Container

parsef(char const * fname) -> Container parsef(char const * fname, Container container, bool importGroupLabels=False) parsef(char const * fname, Container container)

class egglib.egglib_binding.Ms(*args, **kwargs)

Proxy of C++ egglib::Ms class

static format(DataMatrix dataMatrix, bool separated=False) → std::string

format(DataMatrix dataMatrix) -> std::string

static get(std::string const arg1, unsigned int ns, bool separated=False) → DataMatrix

get(std::string const arg1, unsigned int ns) -> DataMatrix

static prob() → double

static tMRCA() → double

static trees() → std::string

class egglib.egglib_binding.Staden(*args, **kwargs)

Proxy of C++ egglib::Staden class

static parse(std::string const & string, bool deleteConsensus=True) → Align

parse(std::string const & string) -> Align

Analysis of polymorphism

class egglib.egglib_binding.BaseDiversity(egglib::BaseDiversity self)

Proxy of C++ egglib::BaseDiversity class

get_position(BaseDiversity self, unsigned int index) → unsigned int

get_site(BaseDiversity self, unsigned int index) → SitePolymorphism

reserve(BaseDiversity self, unsigned int numberOfSites)

reset(BaseDiversity self)

class egglib.egglib_binding.BppDiversity(egglib::BppDiversity self)

Proxy of C++ egglib::BppDiversity class

D(BppDiversity self) → double

Deta(BppDiversity self) → double

Dfl(BppDiversity self) → double

Dflstar(BppDiversity self) → double

F(BppDiversity self) → double

Fstar(BppDiversity self) → double

H(BppDiversity self) → double

He(BppDiversity self) → double

He2(BppDiversity self) → double

K(BppDiversity self) → unsigned int

MK(BppDiversity self) → vectorui

NI(BppDiversity self) → double

NSsites(BppDiversity self) → double

PiNS(BppDiversity self) → double

PiS(BppDiversity self) → double

S(BppDiversity self) → unsigned int

SNS(BppDiversity self) → unsigned int

SS(BppDiversity self) → unsigned int

Sext(BppDiversity self) → unsigned int

Sinf(BppDiversity self) → unsigned int

Ssin(BppDiversity self) → unsigned int

Ssites(BppDiversity self) → double

T83(BppDiversity self) → double

Ti(BppDiversity self) → unsigned int

TiTv(BppDiversity self) → double

Tv(BppDiversity self) → unsigned int

eta(BppDiversity self) → unsigned int

hasOutgroup(BppDiversity self) → bool

load(BppDiversity self, Align align, unsigned int dataType=1)

load(BppDiversity self, Align align)

ncodon1mut(BppDiversity self) → unsigned int

nstop(BppDiversity self) → unsigned int

nsyn(BppDiversity self) → unsigned int

rhoH(BppDiversity self) → double

tW(BppDiversity self) → double

tWNS(BppDiversity self) → double

tWS(BppDiversity self) → double

class egglib.egglib_binding.FStatistics(egglib::FStatistics self)

Proxy of C++ egglib::FStatistics class

F(FStatistics self) → double

Vallele(FStatistics self) → double

Vindividual(FStatistics self) → double

Vpopulation(FStatistics self) → double

alleleFrequencyPerPopulation(FStatistics self, unsigned int populationIndex, unsigned int alleleIndex) → unsigned int

alleleFrequencyTotal(FStatistics self, unsigned int alleleIndex) → unsigned int

alleleValue(FStatistics self, unsigned int alleleIndex) → unsigned int

f(FStatistics self) → double

genotypeFrequencyPerPopulation(FStatistics self, unsigned int populationIndex, unsigned int alleleIndex1, unsigned int alleleIndex2) → unsigned int

genotypeFrequencyTotal(FStatistics self, unsigned int alleleIndex1, unsigned int alleleIndex2) → unsigned int

loadIndividual(FStatistics self, unsigned int genotype1, unsigned int genotype2, unsigned int populationLabel)

numberOfAlleles(FStatistics self) → unsigned int

numberOfGenotypes(FStatistics self) → unsigned int

numberOfPopulations(FStatistics self) → unsigned int

populationFrequency(FStatistics self, unsigned int populationIndex) → unsigned int

populationLabel(FStatistics self, unsigned int populationIndex) → unsigned int

reserve(FStatistics self, unsigned int numberOfIndividuals)

theta(FStatistics self) → double

class egglib.egglib_binding.HFStatistics(egglib::HFStatistics self)

Proxy of C++ egglib::HFStatistics class

T1(HFStatistics self) → double

T2(HFStatistics self) → double

alleleFrequencyPerPopulation(HFStatistics self, unsigned int populationIndex, unsigned int alleleIndex) → unsigned int

alleleFrequencyTotal(HFStatistics self, unsigned int alleleIndex) → unsigned int

alleleValue(HFStatistics self, unsigned int alleleIndex) → unsigned int

loadIndividual(HFStatistics self, unsigned int genotype, unsigned int populationLabel)

numberOfAlleles(HFStatistics self) → unsigned int

numberOfGenotypes(HFStatistics self) → unsigned int

numberOfPopulations(HFStatistics self) → unsigned int

populationFrequency(HFStatistics self, unsigned int populationIndex) → unsigned int

populationLabel(HFStatistics self, unsigned int populationIndex) → unsigned int

reserve(HFStatistics self, unsigned int numberOfIndividuals)

theta(HFStatistics self) → double

class egglib.egglib_binding.HaplotypeDiversity(egglib::HaplotypeDiversity self)

Proxy of C++ egglib::HaplotypeDiversity class

Fst(HaplotypeDiversity self) → double

Gst(HaplotypeDiversity self) → double

He(HaplotypeDiversity self) → double

Hst(HaplotypeDiversity self) → double

K(HaplotypeDiversity self) → unsigned int

Kst(HaplotypeDiversity self) → double

Snn(HaplotypeDiversity self) → double

get_position(BaseDiversity self, unsigned int index) → unsigned int

get_site(BaseDiversity self, unsigned int index) → SitePolymorphism

haplotypeIndex(HaplotypeDiversity self, unsigned int arg2) → unsigned int

load(*args)

load(HaplotypeDiversity self, CharMatrix data, bool allowMultipleMutations=False, unsigned int ignoreFrequency=0,

std::string characterMapping=dnaMapping)

load(HaplotypeDiversity self, CharMatrix data, bool allowMultipleMutations=False, unsigned int ignoreFrequency=0) load(HaplotypeDiversity self, CharMatrix data, bool allowMultipleMutations=False) load(HaplotypeDiversity self, CharMatrix data)

reserve(BaseDiversity self, unsigned int numberOfSites)

reset(BaseDiversity self)

class egglib.egglib_binding.LinkageDisequilibrium(egglib::LinkageDisequilibrium self)

Proxy of C++ egglib::LinkageDisequilibrium class

D(LinkageDisequilibrium self, unsigned int pair_index) → double

Dp(LinkageDisequilibrium self, unsigned int pair_index) → double

Rmin(LinkageDisequilibrium self, CharMatrix data) → unsigned int

correl(LinkageDisequilibrium self) → double

d(LinkageDisequilibrium self, unsigned int pair_index) → int

get_position(BaseDiversity self, unsigned int index) → unsigned int

get_site(BaseDiversity self, unsigned int index) → SitePolymorphism

load(*args)

load(LinkageDisequilibrium self, CharMatrix data, double minimumExploitableData=1., unsigned int ignoreFrequency=0,

std::string characterMapping=dnaMapping)

load(LinkageDisequilibrium self, CharMatrix data, double minimumExploitableData=1., unsigned int ignoreFrequency=0) load(LinkageDisequilibrium self, CharMatrix data, double minimumExploitableData=1.) load(LinkageDisequilibrium self, CharMatrix data)

numberOfPairs(LinkageDisequilibrium self) → unsigned int

r(LinkageDisequilibrium self, unsigned int pair_index) → double

r2(LinkageDisequilibrium self, unsigned int pair_index) → double

reserve(BaseDiversity self, unsigned int numberOfSites)

reset(BaseDiversity self)

site1(LinkageDisequilibrium self, unsigned int pair_index) → unsigned int

site2(LinkageDisequilibrium self, unsigned int pair_index) → unsigned int

class egglib.egglib_binding.MicrosatelliteDiversity(egglib::MicrosatelliteDiversity self)

Proxy of C++ egglib::MicrosatelliteDiversity class

He(MicrosatelliteDiversity self, unsigned int siteIndex) → double

load(MicrosatelliteDiversity self, DataMatrix dataMatrix, int missingData=999, bool noMissingData=False)

load(MicrosatelliteDiversity self, DataMatrix dataMatrix, int missingData=999) load(MicrosatelliteDiversity self, DataMatrix dataMatrix)

numberOfAlleles(MicrosatelliteDiversity self, unsigned int siteIndex) → unsigned int

numberOfSites(MicrosatelliteDiversity self) → unsigned int

sizeVariance(MicrosatelliteDiversity self, unsigned int siteIndex) → double

thetaAssumingIAM(MicrosatelliteDiversity self, unsigned int siteIndex) → double

thetaAssumingSMMfromHe(MicrosatelliteDiversity self, unsigned int siteIndex) → double

thetaAssumingSMMfromSizeVariance(MicrosatelliteDiversity self, unsigned int siteIndex) → double

class egglib.egglib_binding.NucleotideDiversity(egglib::NucleotideDiversity self)

Proxy of C++ egglib::NucleotideDiversity class

CommonAlleles(NucleotideDiversity self) → unsigned int

CommonAlleles(NucleotideDiversity self, unsigned int pop1, unsigned int pop2) -> unsigned int

D(NucleotideDiversity self) → double

E(NucleotideDiversity self) → double

FixedDifferences(NucleotideDiversity self) → unsigned int

FixedDifferences(NucleotideDiversity self, unsigned int pop1, unsigned int pop2) -> unsigned int

H(NucleotideDiversity self) → double

Pi(NucleotideDiversity self) → double

Polymorphisms(NucleotideDiversity self, unsigned int pop) → unsigned int

S(NucleotideDiversity self) → unsigned int

SharedAlleles(NucleotideDiversity self) → unsigned int

SharedAlleles(NucleotideDiversity self, unsigned int pop1, unsigned int pop2) -> unsigned int

So(NucleotideDiversity self) → unsigned int

SpecificAlleles(NucleotideDiversity self) → unsigned int

SpecificAlleles(NucleotideDiversity self, unsigned int pop) -> unsigned int

SpecificDerivedAlleles(NucleotideDiversity self) → unsigned int

SpecificDerivedAlleles(NucleotideDiversity self, unsigned int pop) -> unsigned int

Z(NucleotideDiversity self) → double

average_Pi(NucleotideDiversity self) → double

eta(NucleotideDiversity self) → unsigned int

get_position(BaseDiversity self, unsigned int index) → unsigned int

get_site(BaseDiversity self, unsigned int index) → SitePolymorphism

load(*args)

load(NucleotideDiversity self, CharMatrix data, bool allowMultipleMutations=False, double minimumExploitableData=1.,

unsigned int ignoreFrequency=0, std::string characterMapping=dnaMapping, bool useZeroAsAncestral=False)

load(NucleotideDiversity self, CharMatrix data, bool allowMultipleMutations=False, double minimumExploitableData=1.,

unsigned int ignoreFrequency=0, std::string characterMapping=dnaMapping)

load(NucleotideDiversity self, CharMatrix data, bool allowMultipleMutations=False, double minimumExploitableData=1.,

unsigned int ignoreFrequency=0)

load(NucleotideDiversity self, CharMatrix data, bool allowMultipleMutations=False, double minimumExploitableData=1.) load(NucleotideDiversity self, CharMatrix data, bool allowMultipleMutations=False) load(NucleotideDiversity self, CharMatrix data)

lseff(NucleotideDiversity self) → unsigned int

lseffo(NucleotideDiversity self) → unsigned int

npop(NucleotideDiversity self) → unsigned int

nseff(NucleotideDiversity self) → double

nseffo(NucleotideDiversity self) → double

polymorphic_positions(NucleotideDiversity self) → vectorui

popLabel(NucleotideDiversity self, unsigned int popIndex) → unsigned int

pop_Pi(NucleotideDiversity self, unsigned int popIndex) → double

reserve(BaseDiversity self, unsigned int numberOfSites)

reset(BaseDiversity self)

singleton_positions(NucleotideDiversity self) → vectorui

thetaH(NucleotideDiversity self) → double

thetaL(NucleotideDiversity self) → double

thetaW(NucleotideDiversity self) → double

triConfiguration(NucleotideDiversity self, unsigned int index) → unsigned int

class egglib.egglib_binding.SitePolymorphism(egglib::SitePolymorphism self)

Proxy of C++ egglib::SitePolymorphism class

__init__(egglib::SitePolymorphism self, unsigned int npop) -> SitePolymorphism __init__(egglib::SitePolymorphism self, SitePolymorphism source) -> SitePolymorphism

allele(SitePolymorphism self, unsigned int index) → char

alleleFrequency(SitePolymorphism self, unsigned int alleleIndex) → unsigned int

alleleFrequency(SitePolymorphism self, unsigned int popIndex, unsigned int alleleIndex) -> unsigned int

derivedAlleleFrequency(SitePolymorphism self) → unsigned int

hasSpecificAllele(SitePolymorphism self, unsigned int popIndex, bool restrictToDerived) → bool

haveCommonAllele(SitePolymorphism self, unsigned int pop1, unsigned int pop2) → bool

haveFixedDifference(SitePolymorphism self, unsigned int pop1, unsigned int pop2) → bool

haveSharedAllele(SitePolymorphism self, unsigned int pop1, unsigned int pop2) → bool

isOrientable(SitePolymorphism self) → bool

isPolymorphic(SitePolymorphism self, unsigned int popIndex) → bool

load(SitePolymorphism self, unsigned int populationIndex, char character)

ns(SitePolymorphism self) → unsigned int

ns(SitePolymorphism self, unsigned int popIndex) -> unsigned int

numberOfAlleles(SitePolymorphism self) → unsigned int

numberOfPopulations(SitePolymorphism self, unsigned int npop)

outgroup(SitePolymorphism self, char state)

Coalescent simulator

class egglib.egglib_binding.AllMigrationRateChange(egglib::AllMigrationRateChange self, double date, double value)

Proxy of C++ egglib::AllMigrationRateChange class

apply(AllMigrationRateChange self, ParamSet paramSet, Controller controller)

date(Change self) → double

date(Change self, double value)

value(SingleParamChange self) → double

value(SingleParamChange self, double value)

class egglib.egglib_binding.AllPopulationSizeChange(egglib::AllPopulationSizeChange self, double date, double value)

Proxy of C++ egglib::AllPopulationSizeChange class

apply(AllPopulationSizeChange self, ParamSet paramSet, Controller controller)

date(Change self) → double

date(Change self, double value)

value(SingleParamChange self) → double

value(SingleParamChange self, double value)

class egglib.egglib_binding.Arg(egglib::Arg self, Current current, unsigned int numberOfSegments)

Proxy of C++ egglib::Arg class

MRCA(Arg self, unsigned int segmentIndex) → Edge

addTime(Arg self, double increment)

ageMRCA(Arg self, unsigned int segmentIndex) → double

ageUltimateMRCA(Arg self) → double

coalescence(Arg self, double incr, unsigned int pop, unsigned int index1, unsigned int index2)

coalescence(Arg self, double incr, unsigned int pop, Random random)

mute(Arg self, unsigned int segment, double treePosition) → Edge

newick(Arg self, unsigned int segment) → std::string

numberOfEdges

Arg_numberOfEdges_get(Arg self) -> unsigned int

numberOfRecombinationEvents

Arg_numberOfRecombinationEvents_get(Arg self) -> unsigned int

numberOfSamples

Arg_numberOfSamples_get(Arg self) -> unsigned int

numberOfSegments

Arg_numberOfSegments_get(Arg self) -> unsigned int

recombination(Arg self, double incr, Random random)

reset(Arg self, Current current)

segmentLengths

Arg_segmentLengths_get(Arg self) -> double *

set(Arg self, Current current, unsigned int numberOfSegments)

time(Arg self) → double

totalLength

Arg_totalLength_get(Arg self) -> double

class egglib.egglib_binding.Bottleneck(egglib::Bottleneck self, double date, double param)

Proxy of C++ egglib::Bottleneck class

apply(Bottleneck self, ParamSet paramSet, Controller controller)

date(Change self) → double

date(Change self, double value)

value(SingleParamChange self) → double

value(SingleParamChange self, double value)

class egglib.egglib_binding.Change(*args, **kwargs)

Proxy of C++ egglib::Change class

apply(Change self, ParamSet paramSet, Controller controller)

date(Change self) → double

date(Change self, double value)

class egglib.egglib_binding.Controller(egglib::Controller self)

Proxy of C++ egglib::Controller class

__init__(egglib::Controller self, ParamSet paramSet, Random random) -> Controller

bottleneck(Controller self, unsigned int populationIndex, double strength)

getArg(Controller self) → Arg

moveAllLineages(Controller self, unsigned int source, unsigned int dest)

moveSomeLineages(Controller self, unsigned int source, unsigned int dest, double probability)

reset(Controller self)

step(Controller self) → unsigned int

class egglib.egglib_binding.Current(egglib::Current self)

Proxy of C++ egglib::Current class

__init__(egglib::Current self, ParamSet paramSet) -> Current __init__(egglib::Current self, Current arg2) -> Current

addPopulation(Current self)

numberOfPopulations(Current self) → unsigned int

population(Current self, unsigned int populationIndex) → egglib::Population *

populationNumberOfLineages(Current self, unsigned int populationIndex) → unsigned int

reset(Current self, ParamSet paramSet)

totalNumberOfLineages(Current self) → unsigned int

class egglib.egglib_binding.Edge(egglib::Edge self, unsigned int numberOfSegments)

Proxy of C++ egglib::Edge class

bottom

Edge_bottom_get(Edge self) -> double

coalescence(*args)

coalescence(Edge self, double date, Edge son1, Edge son2, unsigned int * edgesPerSegments, egglib::Edge ** MRCA,

double & totalLength, double * segmentLengths)

coverage

Edge_coverage_get(Edge self) -> unsigned int

label(Edge self) → unsigned int

length

Edge_length_get(Edge self) -> double

numberOfSons

Edge_numberOfSons_get(Edge self) -> unsigned int

recombination(Edge self, double date, Edge dest1, Edge dest2, Random random, double & totalLength, double * segmentLengths)

reset(Edge self)

segment(Edge self, unsigned int segmentIndex) → bool

set_terminal(Edge self, unsigned int leaf_index)

son1

Edge_son1_get(Edge self) -> Edge

son2

Edge_son2_get(Edge self) -> Edge

top

Edge_top_get(Edge self) -> double

class egglib.egglib_binding.GrowthRateChange(egglib::GrowthRateChange self, double date, double value)

Proxy of C++ egglib::GrowthRateChange class

apply(GrowthRateChange self, ParamSet paramSet, Controller controller)

date(Change self) → double

date(Change self, double value)

value(SingleParamChange self) → double

value(SingleParamChange self, double value)

class egglib.egglib_binding.Mutator(egglib::Mutator self)

Proxy of C++ egglib::Mutator class

TPMparam(Mutator self) → double

TPMparam(Mutator self, double value)

TPMproba(Mutator self) → double

TPMproba(Mutator self, double value)

fixedNumberOfMutations(Mutator self) → unsigned int

fixedNumberOfMutations(Mutator self, unsigned int arg2)

mutationModel(Mutator self) → char

mutationModel(Mutator self, char arg2)

mutationRate(Mutator self) → double

mutationRate(Mutator self, double arg2)

mute(Mutator self, Arg arg, Random random) → DataMatrix

numberOfAlleles(Mutator self) → unsigned int

numberOfAlleles(Mutator self, unsigned int arg2)

numberOfMutations(Mutator self) → unsigned int

numberOfSites(Mutator self) → unsigned int

numberOfSites(Mutator self, unsigned int arg2)

randomAncestralAllele(Mutator self, bool flag)

randomAncestralAllele(Mutator self) -> bool

reset(Mutator self)

sitePosition(Mutator self, unsigned int siteIndex) → double

sitePosition(Mutator self, unsigned int siteIndex, double position)

siteWeight(Mutator self, unsigned int siteIndex) → double

siteWeight(Mutator self, unsigned int siteIndex, double weight)

transitionWeight(Mutator self, unsigned int i, unsigned int j, double value)

transitionWeight(Mutator self, unsigned int i, unsigned int j) -> double

class egglib.egglib_binding.ParamSet(egglib::ParamSet self)

Proxy of C++ egglib::ParamSet class

__init__(egglib::ParamSet self, ParamSet arg2) -> ParamSet

addChange(ParamSet self, Change change)

addPopulation(ParamSet self, double migr)

dateOfLastChange(ParamSet self, unsigned int populationIndex) → double

doubles(ParamSet self, unsigned int populationIndex) → unsigned int

doubles(ParamSet self, unsigned int populationIndex, unsigned int value)

growthRate(ParamSet self, unsigned int populationIndex) → double

growthRate(ParamSet self, unsigned int populationIndex, double value)

migrationRate(ParamSet self, double value)

nextChangeDate(ParamSet self) → double

nextChangeDo(ParamSet self, Controller controller)

numberOfPopulations(ParamSet self) → unsigned int

numberOfSamples(ParamSet self) → unsigned int

numberOfSegments(ParamSet self) → unsigned int

numberOfSegments(ParamSet self, unsigned int value)

pairwiseMigrationRate(ParamSet self, unsigned int source, unsigned int dest) → double

pairwiseMigrationRate(ParamSet self, unsigned int source, unsigned int dest, double value)

populationSize(ParamSet self, unsigned int populationIndex) → double

populationSize(ParamSet self, unsigned int populationIndex, double value)

recombinationRate(ParamSet self) → double

recombinationRate(ParamSet self, double value)

reset(ParamSet self)

selfingRate(ParamSet self) → double

selfingRate(ParamSet self, double value)

setGroups(ParamSet self, DataMatrix dataMatrix, bool labelIndividuals=False)

setGroups(ParamSet self, DataMatrix dataMatrix)

singles(ParamSet self, unsigned int populationIndex) → unsigned int

singles(ParamSet self, unsigned int populationIndex, unsigned int value)

class egglib.egglib_binding.PopulationBottleneck(egglib::PopulationBottleneck self, double date, unsigned int population, double value)

Proxy of C++ egglib::PopulationBottleneck class

apply(PopulationBottleneck self, ParamSet paramSet, Controller controller)

date(Change self) → double

date(Change self, double value)

population(PopulationParamChange self) → unsigned int

population(PopulationParamChange self, unsigned int value)

value(SingleParamChange self) → double

value(SingleParamChange self, double value)

class egglib.egglib_binding.PopulationFusion(egglib::PopulationFusion self)

Proxy of C++ egglib::PopulationFusion class

__init__(egglib::PopulationFusion self, double date, unsigned int mother, unsigned int daughter) -> PopulationFusion

apply(PopulationFusion self, ParamSet paramSet, Controller controller)

date(Change self) → double

date(Change self, double value)

daughter(PopulationFusion self, unsigned int arg2)

daughter(PopulationFusion self) -> unsigned int

mother(PopulationFusion self, unsigned int arg2)

mother(PopulationFusion self) -> unsigned int

class egglib.egglib_binding.PopulationGrowthRateChange(egglib::PopulationGrowthRateChange self, double date, unsigned int population, double value)

Proxy of C++ egglib::PopulationGrowthRateChange class

apply(PopulationGrowthRateChange self, ParamSet paramSet, Controller controller)

date(Change self) → double

date(Change self, double value)

population(PopulationParamChange self) → unsigned int

population(PopulationParamChange self, unsigned int value)

value(SingleParamChange self) → double

value(SingleParamChange self, double value)

class egglib.egglib_binding.PopulationParamChange(*args, **kwargs)

Proxy of C++ egglib::PopulationParamChange class

apply(Change self, ParamSet paramSet, Controller controller)

date(Change self) → double

date(Change self, double value)

population(PopulationParamChange self) → unsigned int

population(PopulationParamChange self, unsigned int value)

value(SingleParamChange self) → double

value(SingleParamChange self, double value)

class egglib.egglib_binding.PopulationSplit(egglib::PopulationSplit self)

Proxy of C++ egglib::PopulationSplit class

__init__(egglib::PopulationSplit self, double date, unsigned int pop, double proba) -> PopulationSplit

apply(PopulationSplit self, ParamSet paramSet, Controller controller)

date(Change self) → double

date(Change self, double value)

population(PopulationSplit self) → unsigned int

population(PopulationSplit self, unsigned int arg2)

probability(PopulationSplit self) → double

probability(PopulationSplit self, double arg2)

class egglib.egglib_binding.SelfingRateChange(egglib::SelfingRateChange self, double date, double value)

Proxy of C++ egglib::SelfingRateChange class

apply(SelfingRateChange self, ParamSet paramSet, Controller controller)

date(Change self) → double

date(Change self, double value)

value(SingleParamChange self) → double

value(SingleParamChange self, double value)

class egglib.egglib_binding.SingleMigrationRateChange(egglib::SingleMigrationRateChange self)

Proxy of C++ egglib::SingleMigrationRateChange class

__init__(egglib::SingleMigrationRateChange self, double date, unsigned int source, unsigned int dest, double migr) -> SingleMigrationRateChange

apply(SingleMigrationRateChange self, ParamSet paramSet, Controller controller)

date(Change self) → double

date(Change self, double value)

dest(SingleMigrationRateChange self) → unsigned int

dest(SingleMigrationRateChange self, unsigned int arg2)

source(SingleMigrationRateChange self) → unsigned int

source(SingleMigrationRateChange self, unsigned int arg2)

value(SingleParamChange self) → double

value(SingleParamChange self, double value)

class egglib.egglib_binding.SingleParamChange(*args, **kwargs)

Proxy of C++ egglib::SingleParamChange class

apply(Change self, ParamSet paramSet, Controller controller)

date(Change self) → double

date(Change self, double value)

value(SingleParamChange self) → double

value(SingleParamChange self, double value)

class egglib.egglib_binding.SinglePopulationSizeChange(egglib::SinglePopulationSizeChange self, double date, unsigned int population, double value)

Proxy of C++ egglib::SinglePopulationSizeChange class

apply(SinglePopulationSizeChange self, ParamSet paramSet, Controller controller)

date(Change self) → double

date(Change self, double value)

population(PopulationParamChange self) → unsigned int

population(PopulationParamChange self, unsigned int value)

value(SingleParamChange self) → double

value(SingleParamChange self, double value)

Approximate Bayesian Computation

class egglib.egglib_binding.ABC(egglib::ABC self)

Proxy of C++ egglib::ABC class

add_fname(ABC self, char const * arg2, int arg3)

get_threshold(ABC self, double tolerance)

number_of_samples(ABC self) → unsigned int

number_of_statistics(ABC self, unsigned int ns)

obs(ABC self, unsigned int index, double value)

regression(ABC self, char const * infname, char const * outfname, egglib::ABC::TransformMode mode, char const * header="") → unsigned int

regression(ABC self, char const * infname, char const * outfname, egglib::ABC::TransformMode mode) -> unsigned int

rejection(ABC self, char const * outfname, bool exportlabels=False) → unsigned int

rejection(ABC self, char const * outfname) -> unsigned int

sd(ABC self, unsigned int index) → double

threshold(ABC self) → double

Random number generator

class egglib.egglib_binding.Random(egglib::Random self)

Proxy of C++ egglib::Random class

__init__(egglib::Random self, double seed1, double seed2) -> Random

erand(Random self, double expectation) → double

grand(Random self, double arg2) → unsigned int

irand(Random self, unsigned int max) → unsigned int

nrand(Random self) → double

prand(Random self, double p) → unsigned int

seed1(Random self) → double

seed1(Random self, double arg2)

seed2(Random self) → double

seed2(Random self, double arg2)

uniform(Random self) → double