bipartition.h File Reference

Unary/binary operators on arbitrarily-sized bitstrings (strings of zeros and ones) like split bipartitions. More...

#include "lowlevel.h"

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Data Structures
struct	bipartition_struct
	Bit-string representation of splits. More...
struct	bipsize_struct

Typedefs
typedef struct bipartition_struct *	bipartition
typedef struct bipsize_struct *	bipsize
typedef bipartition *	tripartition

Functions
bipartition	new_bipartition (int size)
	create a new bipartition (bitstring) capable of storing an arbitrary number of bits and initialize it to zero More...
bipsize	new_bipsize (int size)
	Create a new bipsize, which controls some bipartition sizes.
bipartition	new_bipartition_copy_from (const bipartition from)
	Create a new bipartition (allocate memory) and initialize it from another bipartition.
bipartition	new_bipartition_from_bipsize (bipsize n)
	create new bipartition that will share bipsize – useful for bipartition vectors
void	del_bipartition (bipartition bip)
	free memory allocated by bipartition
void	del_bipsize (bipsize n)
	free memory allocated by bipsize
void	bipsize_resize (bipsize n, int nbits)
	update the valid number of bits and mask – e.g. when replacing subtrees by leaves in reduced trees
void	bipartition_initialize (bipartition bip, int position)
	set all bits to zero except the one at position-th bit
void	bipartition_zero (bipartition bip)
	set all bits to zero
void	bipartition_set (bipartition bip, int position)
	simply set the bit at "position" to one, irrespective of other bits
void	bipartition_set_lowlevel (bipartition bip, int i, int j)
void	bipartition_unset (bipartition bip, int position)
	simply unset the bit at "position" (set to zero), irrespective of other bits
void	bipartition_unset_lowlevel (bipartition bip, int i, int j)
void	bipartition_copy (bipartition to, const bipartition from)
	Copy contents from one bipartition to another.
void	bipartition_OR (bipartition result, const bipartition b1, const bipartition b2, bool update_count)
	Binary logical OR ("|") between b1 and b2, where update_count should be true if you need to know the resulting size (slow) or false if you don't care or if b1 and b2 are disjoint (no common elements)
void	bipartition_AND (bipartition result, const bipartition b1, const bipartition b2, bool update_count)
	Binary logical AND ("&") between b1 and b2, update_count should be set to false only if you really don't need to know the number of active bits (e.g. sorting, bipartition comparison)
void	bipartition_ANDNOT (bipartition result, const bipartition b1, const bipartition b2, bool update_count)
	Binary logical AND ("&") between b1 and ~b2 (NOT b2), that is, apply mask b1 on the inverse of b2.
void	bipartition_XOR (bipartition result, const bipartition b1, const bipartition b2, bool update_count)
	Binary logical eXclusive OR ("^") between b1 and b2, update_count should be set to false only if you really don't need to know the number of active bits (e.g. sorting, bipartition comparison)
void	bipartition_XORNOT (bipartition result, const bipartition b1, const bipartition b2, bool update_count)
	Binary logical eXclusive OR ("^") between b1 and complement of b2 (that is, NOT b2: b1 ^ ~b2). Used when finding best disagreement (that in this case erases the complement –other side – of agreement edge)
void	bipartition_NOT (bipartition result, const bipartition bip)
	Unary complement ("~") of bipartition. Use with caution, since there is no mask for unused padded bits.
void	bipartition_count_n_ones (const bipartition bip)
	Count the number of active bits (equal to one). Used by bipartition_AND() and bipartition_XOR() when update_count = true. Please use it parsimoniously since it is as slow as without bitstring representation.
void	bipartition_to_int_vector (const bipartition b, int *id, int vecsize)
	fill vector id[] with positions of set bits, up to vecsize bits set
bool	bipartition_is_equal (const bipartition b1, const bipartition b2)
	Compare equality of two bipartitions.
bool	bipartition_is_equal_bothsides (const bipartition b1, const bipartition b2)
	Compare if two bipartitions represent the same splits (or they are equal or one is the complement of the other)
int	compare_bipartitions_increasing (const void *a1, const void *a2)
	Bipartitions comparison, to be used by sort() since returns integer and uses (void)
int	compare_bipartitions_decreasing (const void *a1, const void *a2)
	Bipartitions comparison, to be used by sort() since returns integer and uses (void)
bool	bipartition_is_larger (const bipartition b1, const bipartition b2)
	Compare sizes of two bipartitions, by number of active bits with ties broken by actual bitstrings.
void	bipartition_flip_to_smaller_set (bipartition bip)
	invert ones and zeroes in loco when necessary to assure bipartition has more zeroes than ones
bool	bipartition_is_bit_set (const bipartition bip, int position)
	Check if position-th bit is equal to one or not.
bool	bipartition_contains_bits (const bipartition b1, const bipartition b2)
	Check if first bipartition contains all elements of second bipartition (b2 is a subset of b1)
void	bipartition_print_to_stdout (const bipartition b1)
	Print to screen a bit representation of the bipartition (with number of ones at the end)
void	bipartition_replace_bit_in_vector (bipartition *bvec, int n_b, int to, int from, bool reduce)
	replace bit info, copying 'from' one position 'to' another; bool "update" indicates if afterwards size will be reduced
void	bipartition_resize_vector (bipartition *bvec, int n_b)
	apply mask to last element (useful after manipulations) and count number of bits
tripartition	new_tripartition (int nleaves)
	tripartition of a node (a vector with 3 bipartitions, that should not be 'flipped' to smaller set, however)
void	del_tripartition (tripartition trip)
	free tripartition space (just 3 bipartitions)
void	store_tripartition_from_bipartitions (tripartition tri, bipartition b1, bipartition b2)
	from node, create tripartition from node->left and node->right (assuming bipartitions were not 'flipped' yet)
void	sort_tripartition (tripartition tri)
	sort order of bipartitions s.t. smallest is first
int	align_tripartitions (tripartition tp1, tripartition tp2, hungarian h)
	match bipartitions between two nodes and return optimal score (min disagreement)
bool	tripartition_is_equal (tripartition tp1, tripartition tp2)
	assuming tripartitions are ordered, check if nodes (represented by tripartitions) are the same

Detailed Description

Unary/binary operators on arbitrarily-sized bitstrings (strings of zeros and ones) like split bipartitions.

Function Documentation

new_bipartition()

bipartition new_bipartition

(

int

size

)

create a new bipartition (bitstring) capable of storing an arbitrary number of bits and initialize it to zero

Parameters

[in]

size

number of bits of desired bipartition

Returns

bipartition (opaquely a vector of long long ints)