Sequence::SimData Class Reference
[Classes Related to Polymorphism tables, Classes and functions related to simulating data under coalescent models]

Data from coalescent simulations. More...

#include <Sequence/SimData.hpp>

Inheritance diagram for Sequence::SimData:

Public Types
typedef std::string &	reference
typedef const std::string &	const_reference
typedef std::vector < std::string >::size_type	size_type
typedef std::vector < std::string >::iterator	data_iterator
typedef std::vector < std::string > ::const_iterator	const_data_iterator
typedef std::vector< double > ::iterator	pos_iterator
typedef std::vector< double > ::const_iterator	const_pos_iterator
typedef Sequence::polySiteVector::const_iterator	const_site_iterator
Public Member Functions
	SimData (const size_t &nsam=0, const size_t &nsnps=0)
	SimData (double pos, char *sample, int nsam, int S)
	SimData (const std::vector< double > &pos, const std::vector< std::string > &data)
	SimData (const SimData::const_site_iterator beg, const SimData::const_site_iterator end)
virtual std::istream &	read (std::istream &s) throw ()
virtual std::ostream &	print (std::ostream &o) const
void	Binary (bool haveOutgroup=false, unsigned outgroup=0, bool strictInfSites=true)
virtual int	fromfile (FILE *openedfile)
int	segsites (void) const
data_iterator	begin ()
const_data_iterator	begin () const
data_iterator	end ()
const_data_iterator	end () const
pos_iterator	pbegin ()
const_pos_iterator	pbegin () const
pos_iterator	pend ()
const_pos_iterator	pend () const
const_site_iterator	sbegin () const
const_site_iterator	send () const
std::vector< double >	GetPositions (void) const
std::vector< std::string >	GetData (void) const
virtual void	ApplyFreqFilter (unsigned mincount, bool haveOutgroup=false, unsigned outgroup=0)
virtual void	RemoveMultiHits (bool skipOutgroup=false, unsigned outgroup=0)
virtual void	RemoveMissing (bool skipOutgroup=false, unsigned outgroup=0)
virtual void	RemoveAmbiguous (bool skipOutgroup=false, unsigned outgroup=0)
virtual bool	operator== (const PolyTable &rhs) const
virtual bool	operator!= (const PolyTable &rhs) const
	operator Sequence::polySiteVector () const
const_reference	operator[] (const size_type &i) const
reference	operator[] (const size_type &i)
bool	empty () const
bool	assign (PolyTable::const_site_iterator beg, PolyTable::const_site_iterator end)
template<typename numeric_type , typename string_type >
bool	assign (const numeric_type _positions, const size_t &_num_positions, const string_type _data, const size_t &_num_individuals)
size_type	size (void) const
double	position (const std::vector< double >::size_type &i) const
unsigned	numsites (void) const

Detailed Description

Data from coalescent simulations.

A class for reading in data from ms. ms is Dick Hudson's coalescent simulation program, available from http://home.uchicago.edu/~rhudson1/. This class reads in the data one record at a time. As of the time this document was written, the output of Hudon's program for one run looks like:

segsites: 10
positions: 0.2512 0.3212 0.3449 0.4386 0.4571 0.4842 0.5745 0.6333 0.7042 0.9928
0100010010
0000000100
0100010011
0000000000
0100010010
0101010010
0100010011
0110010010
1100111010
0000000000

Look at the example program tajd.cc for an example of how to pipe simulated data into a C++ program using these libraries.

Note:: Be sure that you notice that the positions of the segregating sites fall in the interval (0,1].

Author:: Kevin Thornton

Examples:: bottleneck.cc, fragments.cc, ms--.cc, and msstats.cc.

Definition at line 69 of file SimData.hpp.

Member Typedef Documentation

typedef std::vector<std::string>::const_iterator Sequence::PolyTable::const_data_iterator [inherited]

const iterator to the data

Definition at line 90 of file PolyTable.hpp.

typedef std::vector<double>::const_iterator Sequence::PolyTable::const_pos_iterator [inherited]

const iterator to the positions

Definition at line 98 of file PolyTable.hpp.

typedef Sequence::polySiteVector::const_iterator Sequence::PolyTable::const_site_iterator [inherited]

Const iterator to segregating sites. The value type of this iterator is const std::pair<double,std::string>, where the double is the position of the segregating site, and the string the list of states at the site. The first character in the string corresponds to the state of the first character in the PolyTable (i.e. (*this)[0]), etc.

Examples:: PolyTableIterators.cc.

Definition at line 107 of file PolyTable.hpp.

typedef std::vector<std::string>::iterator Sequence::PolyTable::data_iterator [inherited]

non-const iterator to the data

Definition at line 86 of file PolyTable.hpp.

typedef std::vector<double>::iterator Sequence::PolyTable::pos_iterator [inherited]

non-const iterator to the positions

Definition at line 94 of file PolyTable.hpp.

Constructor & Destructor Documentation

Sequence::SimData::SimData	(	const size_t &	nsam = `0`,
		const size_t &	nsnps = `0`
	)			`[explicit]`

The constructor needs to know the sample size simulated. This is easily obtainted using Sequence::SimParams. An example of this is found in the example file tajd.cc

Definition at line 32 of file SimData.cc.

Member Function Documentation

void Sequence::PolyTable::ApplyFreqFilter	(	unsigned	mincount,
		bool	haveOutgroup = `false`,
		unsigned	outgroup = `0`
	)			`[virtual, inherited]`

go through the data and remove all positions where there is a variant at count (# of occurences in the sample) < minfreq

Parameters:

	mincount	minimum count of a variant in the data. Variants that occur < mincount times are thrown out.
	haveOutgroup	`true` if an outgroup is present in the data, `false` otherwise
	outgroup	the index in the data array containing the outgroup (if present)

Definition at line 256 of file PolyTable.cc.

template<typename numeric_type , typename string_type >

bool Sequence::PolyTable::assign	(	const numeric_type *	_positions,
		const size_t &	_num_positions,
		const string_type *	_data,
		const size_t &	_num_individuals
	)			`[inline, inherited]`

Assign SNP data to the polymorphism table from a vector/array.

Parameters:

	_positions	an array representing the positions of the SNPs
	_num_positions	the number of elements in _positions
	_data	an array containing the characters for each SNP in each individual
	_num_individuals	the number of elements in _data

Note:

If the length of the elements in _data does not equal _num_positions, the assignment will fail and you will be left with an empty polymorphism table. The following piece of code shows how to assign from a std::vector:

      Sequence::PolySites snpTable;
      std::vector<double> positions;
      std::vector<std::string> data;
      //fill positions and data...
      if ( snpTable.assign(&positions[0],positions.size(),&data[0],data.size()) == true )
      {
      //ok
      }
      else
      {
      //assignment failed for some reason...
      }

Definition at line 34 of file PolyTable.tcc.

bool Sequence::PolyTable::assign	(	PolyTable::const_site_iterator	beg,
		PolyTable::const_site_iterator	end
	)			`[inherited]`

Assignment operation, allowing a range of polymorphic sites to be assigned to a polymorphism table. This exists mainly for two purposes. One is the ability to assign tables from "slices" of other tables. Second is to facilitate the writing of "sliding window" routines.

Returns:: true if the assignment was successful, false otherwise. The only case where false is returned is if the number of individuals at each site is not the constan from beg to end.

Definition at line 71 of file PolyTable.cc.

PolyTable::const_data_iterator Sequence::PolyTable::begin ( ) const [inherited]

Returns:: a const iterator pointing to the beginning of the std::vector<string> containing the data

Definition at line 173 of file PolyTable.cc.

PolyTable::data_iterator Sequence::PolyTable::begin ( ) [inherited]

Returns:: an iterator pointing to the beginning of the std::vector<string> containing the data

Examples:: PolyTableIterators.cc.

Definition at line 153 of file PolyTable.cc.

void Sequence::SimData::Binary	(	bool	haveOutgroup = `false`,
		unsigned	outgroup = `0`,
		bool	strictInfSites = `true`
	)			`[inline, virtual]`

Recode the polymorphism table in 0,1 (binary notation)

Parameters:

	haveOutgroup	use `true` if an outgroup is present, `false` otherwise
	outgroup	the index of the outgroup in the data vector used to construct the object
	strictInfSites	if `true`, throw out all sites with > 2 character states (including outgroup!)

Note:: if haveOutgroup== true, then 0 means an ancestral state and 1 a derived state in the resulting. /note If haveOutgroup == true, and there are sites with missing data in the outrgroup sequence, those sites are removed from the data, since its assumed you actually want to know ancestral/derived for every site

Reimplemented from Sequence::PolyTable.

Definition at line 89 of file SimData.hpp.

bool Sequence::PolyTable::empty ( ) const [inherited]

Returns:: true if object contains no data, false otherwise

Examples:: slidingWindow.cc.

Definition at line 66 of file PolyTable.cc.

PolyTable::const_data_iterator Sequence::PolyTable::end ( ) const [inherited]

Returns:: a const iterator pointing to the end of the std::vector<string> containing the data

Definition at line 182 of file PolyTable.cc.

PolyTable::data_iterator Sequence::PolyTable::end ( ) [inherited]

Returns:: an iterator pointing to the end of the std::vector<string> containing the data

Examples:: PolyTableIterators.cc.

Definition at line 163 of file PolyTable.cc.

int Sequence::SimData::fromfile ( FILE * openedfile ) [virtual]

In practice, simulation analysis is I/O intensive. This method provies a routine to read in objects of type Sequence::SimData using C-style I/O routines, rather than the C++ operator>>. This can result in huge efficiency gains

Returns:: an integer that is the the return value from fscanf, so that you can check for EOF, etc...

Definition at line 134 of file SimData.cc.

std::vector< std::string > Sequence::PolyTable::GetData ( void ) const [inherited]

Returns PolyTable::data, a vector of std::strings containing polymorphic sites. Assuming the vector is returned to a vector<string> called data, accessing data[i][j] accesses the j-th site of the i-th sequence

Definition at line 527 of file PolyTable.cc.

std::vector< double > Sequence::PolyTable::GetPositions ( void ) const [inherited]

Returns PolyTable::positions.

Definition at line 519 of file PolyTable.cc.

unsigned Sequence::PolyTable::numsites ( void ) const [inline, inherited]

Return how many positions are stored in PolyTable::positions

Examples:: bottleneck.cc.

Definition at line 233 of file PolyTable.hpp.

Sequence::PolyTable::operator Sequence::polySiteVector ( ) const [inherited]

allow (implicit) typecast of Sequence::PolyTable to Sequence::polySiteVector

Definition at line 140 of file PolyTable.cc.

reference Sequence::PolyTable::operator[] ( const size_type & i ) [inline, inherited]

Return the i-th element of PolyTable::data.

Note:: range-checking done by assert()

Definition at line 160 of file PolyTable.hpp.

const_reference Sequence::PolyTable::operator[] ( const size_type & i ) const [inline, inherited]

Return the i-th element of PolyTable::data.

Note:: range-checking done by assert()

Definition at line 150 of file PolyTable.hpp.

PolyTable::const_pos_iterator Sequence::PolyTable::pbegin ( ) const [inherited]

Returns:: a const iterator pointing to the beginning of the list of positions

Definition at line 209 of file PolyTable.cc.

PolyTable::pos_iterator Sequence::PolyTable::pbegin ( ) [inherited]

Returns:: an iterator pointing to the beginning of the list of positions

Examples:: PolyTableIterators.cc.

Definition at line 191 of file PolyTable.cc.

PolyTable::const_pos_iterator Sequence::PolyTable::pend ( ) const [inherited]

Returns:: a const iterator pointing to the beginning of the list of positions

Definition at line 217 of file PolyTable.cc.

PolyTable::pos_iterator Sequence::PolyTable::pend ( ) [inherited]

Returns:: an iterator pointing to the end of the list of positions

Examples:: PolyTableIterators.cc.

Definition at line 200 of file PolyTable.cc.

double Sequence::PolyTable::position ( const std::vector< double >::size_type & i ) const [inline, inherited]

Return the i-th position from the PolyTable::positions.

Note:: range-checking done by assert()

Definition at line 223 of file PolyTable.hpp.

std::ostream & Sequence::SimData::print ( std::ostream & o ) const [virtual]

print the data to o

Implements Sequence::PolyTable.

Definition at line 108 of file SimData.cc.

std::istream & Sequence::SimData::read ( std::istream & stream ) throw () [virtual]

A call to istream Sequence::operator>> on a object of type SimData results in a call to this function. NOTE: This is the C++ way to read in SimData, but it's the slow way

Implements Sequence::PolyTable.

Definition at line 48 of file SimData.cc.

void Sequence::PolyTable::RemoveAmbiguous	(	bool	skipOutgroup = `false`,
		unsigned	outgroup = `0`
	)			`[virtual, inherited]`

go through the data and remove all the sites with states other than {A,G,C,T,N,-}

Parameters:

	skipOutgroup	default is `false`. If `true`, the character state of the outgroup is ignored.
	outgroup	the index of the outgroup in the data vector

Definition at line 402 of file PolyTable.cc.

void Sequence::PolyTable::RemoveMissing	(	bool	skipOutgroup = `false`,
		unsigned	outgroup = `0`
	)			`[virtual, inherited]`

go through the data and remove all the sites with missing data (the character N).

Parameters:

	skipOutgroup	default is `false`. If `true`, the character state of the outgroup is ignored.
	outgroup	the index of the outgroup in the data vector

Definition at line 360 of file PolyTable.cc.

void Sequence::PolyTable::RemoveMultiHits	(	bool	skipOutgroup = `false`,
		unsigned	outgroup = `0`
	)			`[virtual, inherited]`

go through the data and remove all the sites with more than 2 states segregating. By default, this routine also removes sites where there are 2 states segregating in the ingroup. and the outgroup (if present) has a 3rd state.

Parameters:

	skipOutgroup	default is `false`. If `true`, the character state of the outgroup is ignored.
	outgroup	the index of the outgroup in the data vector

Definition at line 321 of file PolyTable.cc.

PolyTable::const_site_iterator Sequence::PolyTable::sbegin ( ) const [inherited]

Returns:: an object of type Sequence::PolyTable::const_site_iterator These iterators allow access to the columns (segregating sites) of polymorphism tables

Examples:: PolyTableIterators.cc, slidingWindow.cc, and slidingWindow2.cc.

Definition at line 226 of file PolyTable.cc.

int Sequence::SimData::segsites ( void ) const [inline]

Returns the number of segregating sites in the data block.

Definition at line 97 of file SimData.hpp.

PolyTable::const_site_iterator Sequence::PolyTable::send ( ) const [inherited]

Returns:: an object of type Sequence::PolyTable::const_site_iterator These iterators allow access to the columns (segregating sites) of polymorphism tables

Examples:: PolyTableIterators.cc, slidingWindow.cc, and slidingWindow2.cc.

Definition at line 241 of file PolyTable.cc.

size_type Sequence::PolyTable::size ( void ) const [inline, inherited]

Return how many std::strings are stored in PolyTable::data.

Definition at line 214 of file PolyTable.hpp.

The documentation for this class was generated from the following files:

Sequence::SimData Class Reference [Classes Related to Polymorphism tables, Classes and functions related to simulating data under coalescent models]

Public Types

Public Member Functions

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Sequence::SimData Class Reference
[Classes Related to Polymorphism tables, Classes and functions related to simulating data under coalescent models]