PT_family.cxx File Reference

#include "PT_rangeCheck.h"
#include "pt_prototypes.h"
#include <struct_man.h>
#include <PT_server_prototypes.h>
#include "PT_global_defs.h"
#include "PT_complement.h"
#include <arbdbt.h>
#include <algorithm>
#include <vector>
#include <map>

Include dependency graph for PT_family.cxx:

Go to the source code of this file.

Classes
struct	TraversalHitLimit
class	HitCounter
class	FamilyStat
class	PT_Traversal
struct	oligo_cmp_abs
struct	oligo_cmp_rel
class	oligo_comparator
class	OligoRegistry

Typedefs
typedef std::map< const char *, int, oligo_comparator >	OligoMap
typedef OligoMap::const_iterator	OligoIter

Functions
void	aisc_link (dll_public *dll, PT_family_list *family)
static int	make_PT_family_list (PT_family *ffinder, const FamilyStat &famStat)
bool	contains_ambiguities (char *oligo, int oligo_len)
int	find_family (PT_family *ffinder, bytestring *species)

Typedef Documentation

typedef std::map<const char *, int, oligo_comparator> OligoMap

Definition at line 371 of file PT_family.cxx.

typedef OligoMap::const_iterator OligoIter

Definition at line 372 of file PT_family.cxx.

Function Documentation

void aisc_link ( dll_public *  dll, PT_family_list *  family  )

inline

Definition at line 26 of file PT_family.cxx.

Referenced by make_PT_family_list().

static int make_PT_family_list ( PT_family *  ffinder, const FamilyStat &  famStat  )

static

Make sorted list of family members

Definition at line 264 of file PT_family.cxx.

References aisc_link(), ARB_strdup(), probe_struct_global::data, probe_struct_global::data_count, HitCounter::get_match_count(), HitCounter::get_rel_match_count(), probe_input_data::get_shortname(), FamilyStat::hits(), and psg.

Referenced by find_family().

bool contains_ambiguities ( char *  oligo, int  oligo_len  )

inline

Check the oligo for ambiguities

Definition at line 345 of file PT_family.cxx.

References is_std_base().

Referenced by find_family().

int find_family	(	PT_family *	ffinder,
		bytestring *	species
	)

make sorted list of family members of species

Definition at line 389 of file PT_family.cxx.

References OligoRegistry::add(), OligoRegistry::begin(), FamilyStat::calc_rel_matches(), complement_probe(), contains_ambiguities(), bytestring::data, probe_struct_global::data_count, OligoRegistry::end(), FF_COMPLEMENT, FF_FORWARD, FF_REVERSE, FF_REVERSE_COMPLEMENT, FamilyStat::limit_hits_for_next_traversal(), make_PT_family_list(), PT_Traversal::mark_matching(), probe_compress_sequence(), psg, PT_A, PT_Traversal::restrictMatchesToRegion(), reverse_probe(), s, seq, bytestring::size, probe_struct_global::TREE_ROOT2(), and PT_Traversal::unrestrictMatchesToRegion().