PrimerDesign Class Reference

#include <PRD_Design.hxx>

Inheritance diagram for PrimerDesign:

Collaboration diagram for PrimerDesign:

Public Member Functions
	PrimerDesign (const char *sequence_, long int seqLength_, Range pos1_, Range pos2_, Range length_, Range distance_, Range ratio_, Range temperature_, int min_dist_to_next_, bool expand_IUPAC_Codes_, int max_count_primerpairs_, double GC_factor_, double temp_factor_)
	PrimerDesign (const char *sequence_, long int seqLength_, Range pos1_, Range pos2_, Range length_, Range distance_, int max_count_primerpairs_, double GC_factor_, double temp_factor_)
	PrimerDesign (const char *sequence_, long int seqLength_)
	~PrimerDesign ()
void	setPositionalParameters (Range pos1_, Range pos2_, Range length_, Range distance_)
void	setConditionalParameters (Range ratio_, Range temperature_, int min_dist_to_next_, bool expand_IUPAC_Codes_, int max_count_primerpairs_, double GC_factor_, double temp_factor_)
void	buildPrimerTrees ()
void	matchSequenceAgainstPrimerTrees ()
void	convertTreesToLists ()
void	evaluatePrimerPairs ()
void	run ()
GB_ERROR	get_error () const
PRD_Sequence_Pos	get_max_primer_length () const
PRD_Sequence_Pos	get_max_primer_pos () const
const char *	get_result (int num, const char *&primers, int max_primer_length, int max_position_length, int max_length_length) const

Static Public Attributes
static const int	PRINT_RAW_TREES = 1
static const int	PRINT_MATCHED_TREES = 2
static const int	PRINT_PRIMER_LISTS = 4
static const int	PRINT_PRIMER_PAIRS = 8

Detailed Description

Definition at line 29 of file PRD_Design.hxx.

Constructor & Destructor Documentation

PrimerDesign::PrimerDesign	(	const char *	sequence_,
		long int	seqLength_,
		Range	pos1_,
		Range	pos2_,
		Range	length_,
		Range	distance_,
		Range	ratio_,
		Range	temperature_,
		int	min_dist_to_next_,
		bool	expand_IUPAC_Codes_,
		int	max_count_primerpairs_,
		double	GC_factor_,
		double	temp_factor_
	)

Definition at line 50 of file PRD_Design.cxx.

PrimerDesign::PrimerDesign	(	const char *	sequence_,
		long int	seqLength_,
		Range	pos1_,
		Range	pos2_,
		Range	length_,
		Range	distance_,
		int	max_count_primerpairs_,
		double	GC_factor_,
		double	temp_factor_
	)

Definition at line 59 of file PRD_Design.cxx.

PrimerDesign::PrimerDesign	(	const char *	sequence_,
		long int	seqLength_
	)

Definition at line 66 of file PRD_Design.cxx.

PrimerDesign::~PrimerDesign

(

)

Definition at line 74 of file PRD_Design.cxx.

Member Function Documentation

void PrimerDesign::setPositionalParameters	(	Range	pos1_,
		Range	pos2_,
		Range	length_,
		Range	distance_
	)

Definition at line 83 of file PRD_Design.cxx.

References SequenceIterator::EOS, SequenceIterator::FORWARD, SequenceIterator::IGNORE, Range::max(), Range::min(), SequenceIterator::nextBase(), SequenceIterator::pos, and SequenceIterator::restart().

void PrimerDesign::setConditionalParameters	(	Range	ratio_,
		Range	temperature_,
		int	min_dist_to_next_,
		bool	expand_IUPAC_Codes_,
		int	max_count_primerpairs_,
		double	GC_factor_,
		double	temp_factor_
	)

Definition at line 126 of file PRD_Design.cxx.

References Range::max(), and Range::min().

void PrimerDesign::buildPrimerTrees

(

)

Definition at line 274 of file PRD_Design.cxx.

References Node::child, SequenceIterator::delivered, SequenceIterator::EOS, SequenceIterator::FORWARD, SequenceIterator::IGNORE, Range::max(), Range::min(), SequenceIterator::nextBase(), offset, SequenceIterator::pos, Range::print(), and SequenceIterator::restart().

Referenced by run().

void PrimerDesign::matchSequenceAgainstPrimerTrees

(

)

Definition at line 471 of file PRD_Design.cxx.

References SequenceIterator::BACKWARD, Node::child, arb_progress::done(), SequenceIterator::EOS, SearchFIFO::flush(), SequenceIterator::FORWARD, SequenceIterator::IGNORE, arb_progress::inc(), Range::includes(), INVERT, SearchFIFO::iterateWith(), SequenceIterator::nextBase(), SequenceIterator::pos, SearchFIFO::push(), SequenceIterator::restart(), and arb_progress::subtitle().

Referenced by run().

void PrimerDesign::convertTreesToLists

(

)

Definition at line 590 of file PRD_Design.cxx.

References Node::child, Range::includes(), Node::isValidPrimer(), Node::last_base_index, Range::min(), Item::next, NULp, Item::offset, Node::offset, PRD_MAX_SEQUENCE_POS, and Range::print().

Referenced by run().

void PrimerDesign::evaluatePrimerPairs

(

)

Definition at line 894 of file PRD_Design.cxx.

References arb_progress::inc(), and Item::next.

Referenced by run().

void PrimerDesign::run

(

)

Definition at line 151 of file PRD_Design.cxx.

References buildPrimerTrees(), convertTreesToLists(), evaluatePrimerPairs(), matchSequenceAgainstPrimerTrees(), Range::print(), and arb_progress::show_comment().

Referenced by primer_design_event_go().

GB_ERROR PrimerDesign::get_error ( ) const

inline

Definition at line 145 of file PRD_Design.hxx.

Referenced by primer_design_event_go().

PRD_Sequence_Pos PrimerDesign::get_max_primer_length ( ) const

inline

Definition at line 147 of file PRD_Design.hxx.

References Range::max().

Referenced by primer_design_event_go().

PRD_Sequence_Pos PrimerDesign::get_max_primer_pos ( ) const

inline

Definition at line 148 of file PRD_Design.hxx.

References Range::max().

Referenced by primer_design_event_go().

const char * PrimerDesign::get_result	(	int	num,
		const char *&	primers,
		int	max_primer_length,
		int	max_position_length,
		int	max_length_length
	)		const

Definition at line 953 of file PRD_Design.cxx.

References Pair::get_primers(), Pair::get_result(), and NULp.

Referenced by primer_design_event_go().

Member Data Documentation

const int PrimerDesign::PRINT_RAW_TREES = 1

static

Definition at line 152 of file PRD_Design.hxx.

const int PrimerDesign::PRINT_MATCHED_TREES = 2

static

Definition at line 153 of file PRD_Design.hxx.

const int PrimerDesign::PRINT_PRIMER_LISTS = 4

static

Definition at line 154 of file PRD_Design.hxx.

const int PrimerDesign::PRINT_PRIMER_PAIRS = 8

static

Definition at line 155 of file PRD_Design.hxx.

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

• PRIMER_DESIGN/PRD_Design.hxx
• PRIMER_DESIGN/PRD_Design.cxx