bbq Implementation Documentation

bbq::weighted_bit_multi_set Class Reference

This class provides the most advanced (but also most inefficient) way of handling sets, which is a major part of the algorithms underlying bbq. More...

#include <weighted_bit_multi_set.h>

List of all members.

Public Types

typedef unsigned char c_uint

Public Member Functions

weighted_bit_multi_set (const weighted_bit_multi_set &)

copy constructor

weighted_bit_multi_set & operator= (const weighted_bit_multi_set &vb)

assignment operator

weighted_bit_multi_set ()

default constructor

~weighted_bit_multi_set ()

destrcutor

bool subseteq (const weighted_bit_multi_set &) const

bool subseteq (const weighted_bit_multi_set &, const unsigned int &J) const

bool operator< (const weighted_bit_multi_set &) const

We obtain a canonical order on subsets of [1:k] by considering such a set as a number between 0 and 2^k-1.

bool operator== (const weighted_bit_multi_set &) const

Two sets are considered equivalent iff they contain the same elements, not regarding their weights.

int cardinality ()

returns the number of elements contained in the multiset

float weight ()

in the simple form implemented here, the weight is equal to the number of elements contained in the multiset.

void intersect (const weighted_bit_multi_set &b)

standard multiset intersection

void set (const int &j, const float &w)

add one element j to the multiset.

void reset (const int &j, const float &w)

change the weight of element j; only needed for sets, not for multisets.

void decrease (const int &j, const float &w)

remove ONE element j from the multiset.

void remove (const int &j, const float &w)

remove ALL elements j from the multiset.

bool contains (const int &)

is there at least one element with the index passed by the parameter?

Public Attributes

c_uint * counts

float * weights

Static Public Attributes

int k = 128

k corresponds to the number of bits and hence the number of sequence fragments in footprint_detector

bool weighted = true

left for compatibility reasons with other set types

int k_ = 4

Friends

std::ostream & operator<< (std::ostream &o, const weighted_bit_multi_set &)

Detailed Description

This class provides the most advanced (but also most inefficient) way of handling sets, which is a major part of the algorithms underlying bbq.

This class particularly supports weighted sets whose cardinality is unlimited. It supports weighing as well as multiset capabilities, but is far less memory efficient than the unweighted and simple-set versions.

Member Typedef Documentation

typedef unsigned char bbq::weighted_bit_multi_set::c_uint

Constructor & Destructor Documentation

bbq::weighted_bit_multi_set::weighted_bit_multi_set ( const weighted_bit_multi_set & )

copy constructor

bbq::weighted_bit_multi_set::weighted_bit_multi_set ( )

default constructor

bbq::weighted_bit_multi_set::~weighted_bit_multi_set ( ) [inline]

destrcutor

Member Function Documentation

int bbq::weighted_bit_multi_set::cardinality ( )

returns the number of elements contained in the multiset

bool bbq::weighted_bit_multi_set::contains ( const int & )

is there at least one element with the index passed by the parameter?

void bbq::weighted_bit_multi_set::decrease ( const int & j,

const float & w

)

remove ONE element j from the multiset.

void bbq::weighted_bit_multi_set::intersect ( const weighted_bit_multi_set & b )

standard multiset intersection

bool bbq::weighted_bit_multi_set::operator< ( const weighted_bit_multi_set & ) const

We obtain a canonical order on subsets of [1:k] by considering such a set as a number between 0 and 2^k-1.
This order is needed for inserting weighted sets into (multi-)sets for the enumerate_differences() method. Note that weightings are not taken into account; two sets containing the same elements but different weights are considered equivalent (which is the reason why they are stored in a multiset rather than a set).

weighted_bit_multi_set & bbq::weighted_bit_multi_set::operator= ( const weighted_bit_multi_set & vb )

assignment operator

bool bbq::weighted_bit_multi_set::operator== ( const weighted_bit_multi_set & ) const

Two sets are considered equivalent iff they contain the same elements, not regarding their weights.
this is needed for inserting weighted sets into (multi-)sets for the enumerate_differences() method. Note that weightings are not taken into account; two sets containing the same elements but different weights are considered equivalent (which is the reason why they are stored in a multiset rather than a set).

void bbq::weighted_bit_multi_set::remove ( const int & j,

const float & w

)

remove ALL elements j from the multiset.
Can actually be ignored for multisets, since the remove job is taken by decrease.

void bbq::weighted_bit_multi_set::reset ( const int & j,

const float & w

)

change the weight of element j; only needed for sets, not for multisets.

void bbq::weighted_bit_multi_set::set ( const int & j,

const float & w

)

add one element j to the multiset.
The weight is (currently) neglected.

bool bbq::weighted_bit_multi_set::subseteq ( const weighted_bit_multi_set & ,

const unsigned int & J

) const

bool bbq::weighted_bit_multi_set::subseteq ( const weighted_bit_multi_set & ) const

float bbq::weighted_bit_multi_set::weight ( )

in the simple form implemented here, the weight is equal to the number of elements contained in the multiset.

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream & o,

const weighted_bit_multi_set & I

) [friend]

Member Data Documentation

c_uint* bbq::weighted_bit_multi_set::counts

int bbq::weighted_bit_multi_set::k = 128 [static]

k corresponds to the number of bits and hence the number of sequence fragments in footprint_detector

int bbq::weighted_bit_multi_set::k_ = 4 [static]

bool bbq::weighted_bit_multi_set::weighted = true [static]

left for compatibility reasons with other set types

float* bbq::weighted_bit_multi_set::weights

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

bbq Implementation Documentation
Axel Mosig, Bioinformatics, University of Leipzig


Public Types
typedef unsigned char	c_uint
Public Member Functions
	weighted_bit_multi_set (const weighted_bit_multi_set &)
	copy constructor
weighted_bit_multi_set &	operator= (const weighted_bit_multi_set &vb)
	assignment operator
	weighted_bit_multi_set ()
	default constructor
	~weighted_bit_multi_set ()
	destrcutor
bool	subseteq (const weighted_bit_multi_set &) const
bool	subseteq (const weighted_bit_multi_set &, const unsigned int &J) const
bool	operator< (const weighted_bit_multi_set &) const
	We obtain a canonical order on subsets of [1:k] by considering such a set as a number between 0 and 2^k-1.
bool	operator== (const weighted_bit_multi_set &) const
	Two sets are considered equivalent iff they contain the same elements, not regarding their weights.
int	cardinality ()
	returns the number of elements contained in the multiset
float	weight ()
	in the simple form implemented here, the weight is equal to the number of elements contained in the multiset.
void	intersect (const weighted_bit_multi_set &b)
	standard multiset intersection
void	set (const int &j, const float &w)
	add one element j to the multiset.
void	reset (const int &j, const float &w)
	change the weight of element j; only needed for sets, not for multisets.
void	decrease (const int &j, const float &w)
	remove ONE element j from the multiset.
void	remove (const int &j, const float &w)
	remove ALL elements j from the multiset.
bool	contains (const int &)
	is there at least one element with the index passed by the parameter?
Public Attributes
c_uint *	counts
float *	weights
Static Public Attributes
int	k = 128
	k corresponds to the number of bits and hence the number of sequence fragments in footprint_detector
bool	weighted = true
	left for compatibility reasons with other set types
int	k_ = 4
Friends
std::ostream &	operator<< (std::ostream &o, const weighted_bit_multi_set &)