Sonde Class Reference

#include <MultiProbe.hxx>

Inheritance diagram for Sonde:

Collaboration diagram for Sonde:

Public Member Functions
double	get_Allowed_Mismatch_no (int no)
double	get_Outside_Mismatch_no (int no)
const char *	get_name ()
Hit *	get_hitdata_by_number (long index)
Hit **	get_Hitliste ()
long	get_length_hitliste ()
long	get_minelem ()
long	get_maxelem ()
positiontype	get_far ()
positiontype	get_mor ()
Bitvector *	get_bitkennung ()
void	set_bitkennung (Bitvector *bv)
void	set_far (positiontype far)
void	set_mor (positiontype mor)
void	print ()
void	sink (long i, long t, MO_Mismatch **A)
void	heapsort (long feldlaenge, MO_Mismatch **Nr_Mm_Feld)
double	check_for_min (long k, MO_Mismatch **probebacts, long laenge)
MO_Mismatch **	get_matching_species (int ptserver_id, bool match_also_revcompl, int match_weight, int match_mis, const char *match_seq, MO_Liste *convert, long *number_of_species, GB_ERROR &error)
int	gen_Hitliste (MO_Liste *Bakterienliste)
	Sonde (const char *bezeichner, int num_probes, int allowed_mis, double outside_mis)
	~Sonde ()

Detailed Description

Definition at line 230 of file MultiProbe.hxx.

Constructor & Destructor Documentation

Sonde::Sonde	(	const char *	bezeichner,
		int	num_probes,
		int	allowed_mis,
		double	outside_mis
	)

Definition at line 21 of file MP_sonde.cxx.

References ARB_strdup(), mp_assert, and NULp.

Sonde::~Sonde

(

)

Definition at line 45 of file MP_sonde.cxx.

Member Function Documentation

double Sonde::get_Allowed_Mismatch_no ( int  no )

inline

Definition at line 242 of file MultiProbe.hxx.

Referenced by Sondentopf::fill_Stat_Arrays(), Sondentopf::gen_color_hash(), and gen_Hitliste().

double Sonde::get_Outside_Mismatch_no ( int  no )

inline

Definition at line 243 of file MultiProbe.hxx.

const char* Sonde::get_name ( )

inline

Definition at line 244 of file MultiProbe.hxx.

Hit * Sonde::get_hitdata_by_number

(

long

index

)

Definition at line 279 of file MP_sonde.cxx.

References NULp.

Referenced by Sondentopf::gen_Mergefeld().

Hit** Sonde::get_Hitliste ( )

inline

Definition at line 246 of file MultiProbe.hxx.

long Sonde::get_length_hitliste ( )

inline

Definition at line 247 of file MultiProbe.hxx.

Referenced by Sondentopf::gen_Mergefeld().

long Sonde::get_minelem ( )

inline

Definition at line 248 of file MultiProbe.hxx.

long Sonde::get_maxelem ( )

inline

Definition at line 249 of file MultiProbe.hxx.

positiontype Sonde::get_far ( )

inline

Definition at line 250 of file MultiProbe.hxx.

positiontype Sonde::get_mor ( )

inline

Definition at line 251 of file MultiProbe.hxx.

Bitvector* Sonde::get_bitkennung ( )

inline

Definition at line 252 of file MultiProbe.hxx.

void Sonde::set_bitkennung

(

Bitvector *

bv

)

Definition at line 325 of file MP_sonde.cxx.

void Sonde::set_far ( positiontype  far )

inline

Definition at line 255 of file MultiProbe.hxx.

void Sonde::set_mor ( positiontype  mor )

inline

Definition at line 256 of file MultiProbe.hxx.

void Sonde::print

(

)

Definition at line 60 of file MP_sonde.cxx.

References Bitvector::print().

void Sonde::sink	(	long	i,
		long	t,
		MO_Mismatch **	A
	)

Definition at line 307 of file MP_sonde.cxx.

Referenced by heapsort().

void Sonde::heapsort	(	long	feldlaenge,
		MO_Mismatch **	Nr_Mm_Feld
	)

Definition at line 290 of file MP_sonde.cxx.

References sink().

Referenced by gen_Hitliste().

double Sonde::check_for_min	(	long	k,
		MO_Mismatch **	probebacts,
		long	laenge
	)

Definition at line 166 of file MP_sonde.cxx.

References min, and MO_Mismatch::mismatch.

Referenced by gen_Hitliste().

MO_Mismatch ** Sonde::get_matching_species	(	int	ptserver_id,
		bool	match_also_revcompl,
		int	match_weight,
		int	match_mis,
		const char *	match_seq,
		MO_Liste *	convert,
		long *	number_of_species,
		GB_ERROR &	error
	)

Definition at line 68 of file MP_sonde.cxx.

References aisc_close(), aisc_get(), AISC_MAGIC_NUMBER, aisc_open(), aisc_put(), arb_look_and_start_ptserver(), mp_gl_struct::com, bytestring::data, GBS_static_string(), MO_Liste::get_index_by_entry(), MO_Liste::get_mo_liste(), mp_gl_struct::link, mp_gl_struct::locs, MO_Mismatch::mismatch, mp_assert, MP_init_local_com_struct(), NON_WEIGHTED, NULp, and MO_Mismatch::nummer.

Referenced by gen_Hitliste().

int Sonde::gen_Hitliste

(

MO_Liste *

Bakterienliste

)

Definition at line 183 of file MP_sonde.cxx.

References aw_message(), check_for_min(), awar_vars::complement, error(), get_Allowed_Mismatch_no(), get_matching_species(), MO_Liste::get_mo_liste(), awar_vars::greyzone, heapsort(), Bakt_Info::kill_flag(), MO_Mismatch::mismatch, mp_assert, mp_gl_awars, NULp, MO_Mismatch::nummer, awar_vars::outside_mismatches_difference, awar_vars::ptserver, Hit::set_mismatch_at_pos(), and awar_vars::weightedmismatches.

Referenced by ST_Container::cache_Sonde().

---

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

• MULTI_PROBE/MultiProbe.hxx
• MULTI_PROBE/MP_sonde.cxx