EggLib
EggLib version 2.1 is archived.

Table Of Contents

Previous topic

Python module

Next topic

Top-level Egglib components

This Page

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
Hosted by  Get seqlib at SourceForge.net. Fast, secure and Free Open Source software downloads