Location.cxx File Reference

#include "Location.h"
#include <arb_stdstr.h>
#include <adGene.h>
#include <arbdb.h>
#include <cctype>
#include <string>

Include dependency graph for Location.cxx:

Go to the source code of this file.

Classes
class	SimpleLocation
class	JoinedLocation
class	ComplementLocation

Typedefs
typedef SmartPtr< Location >	LocationPtr
typedef vector< LocationPtr >	LocationVector

Functions
	DEFINE_ITERATORS (LocationVector)
static size_t	parsePosition (const string &source, char &uncertain)
static void	parseLocationList (const string &source, size_t startPos, LocationVector &locvec)
static bool	parseInfix (const string &str, const string &prefix, const string &postfix, string &foundInfix)
LocationPtr	parseLocation (const string &source)
LocationPtr	part2SimpleLocation (const GEN_position *pos, int i, bool inverseComplement)
LocationPtr	to_Location (const GEN_position *gp)

Typedef Documentation

typedef SmartPtr<Location> LocationPtr

Definition at line 23 of file Location.cxx.

typedef vector<LocationPtr> LocationVector

Definition at line 24 of file Location.cxx.

Function Documentation

DEFINE_ITERATORS

(

LocationVector

)

static size_t parsePosition ( const string &  source, char &  uncertain  )

static

Definition at line 171 of file Location.cxx.

References s, and string().

Referenced by parseLocation().

static void parseLocationList ( const string &  source, size_t  startPos, LocationVector &  locvec  )

static

Definition at line 198 of file Location.cxx.

References arb_assert, GBS_global_string(), and parseLocation().

Referenced by parseLocation().

static bool parseInfix ( const string &  str, const string &  prefix, const string &  postfix, string &  foundInfix  )

static

Definition at line 228 of file Location.cxx.

References beginsWith(), and endsWith().

Referenced by parseLocation().

LocationPtr parseLocation

(

const string &

source

)

Definition at line 243 of file Location.cxx.

References LJT_JOIN, LJT_ORDER, LJT_UNDEF, parseInfix(), parseLocation(), parseLocationList(), parsePosition(), pos1, pos2, JoinedLocation::push_back(), and string().

Referenced by GLE_update_from_location(), parseLocation(), and parseLocationList().

LocationPtr part2SimpleLocation ( const GEN_position *  pos, int  i, bool  inverseComplement  )

inline

Definition at line 325 of file Location.cxx.

References GEN_position::complement, GEN_position::start_pos, GEN_position::start_uncertain, GEN_position::stop_pos, and GEN_position::stop_uncertain.

Referenced by to_Location().

LocationPtr to_Location

(

const GEN_position *

gp

)

Definition at line 333 of file Location.cxx.

References arb_assert, GEN_position::complement, GEN_position::joinable, LJT_JOIN, LJT_ORDER, part2SimpleLocation(), GEN_position::parts, GEN_position::start_uncertain, and GEN_position::stop_uncertain.

Referenced by update_location_from_GEN_position().