SequenceIterator Class Reference

#include <PRD_SequenceIterator.hxx>

Collaboration diagram for SequenceIterator:

Public Member Functions
	SequenceIterator (const char *sequence_, PRD_Sequence_Pos start_pos_, PRD_Sequence_Pos stop_pos_, int max_length_, int direction_)
	SequenceIterator (const char *sequence)
void	restart (PRD_Sequence_Pos start_pos_, PRD_Sequence_Pos stop_pos_, int max_length_, int direction_)
unsigned char	nextBase ()

Public Attributes
PRD_Sequence_Pos	pos
int	delivered

Static Public Attributes
static const int	IGNORE = -1
static const char	EOS = '\x00'
static const int	FORWARD = 1
static const int	BACKWARD = -1

Detailed Description

Definition at line 8 of file PRD_SequenceIterator.hxx.

Constructor & Destructor Documentation

SequenceIterator::SequenceIterator	(	const char *	sequence_,
		PRD_Sequence_Pos	start_pos_,
		PRD_Sequence_Pos	stop_pos_,
		int	max_length_,
		int	direction_
	)

Definition at line 12 of file PRD_SequenceIterator.cxx.

SequenceIterator::SequenceIterator

(

const char *

sequence

)

Definition at line 21 of file PRD_SequenceIterator.cxx.

Member Function Documentation

void SequenceIterator::restart	(	PRD_Sequence_Pos	start_pos_,
		PRD_Sequence_Pos	stop_pos_,
		int	max_length_,
		int	direction_
	)

Definition at line 34 of file PRD_SequenceIterator.cxx.

Referenced by PrimerDesign::buildPrimerTrees(), PrimerDesign::matchSequenceAgainstPrimerTrees(), primer_design_event_init(), and PrimerDesign::setPositionalParameters().

unsigned char SequenceIterator::nextBase

(

)

Definition at line 46 of file PRD_SequenceIterator.cxx.

Referenced by PrimerDesign::buildPrimerTrees(), Item::getPrimerSequence(), PrimerDesign::matchSequenceAgainstPrimerTrees(), primer_design_event_init(), and PrimerDesign::setPositionalParameters().

Member Data Documentation

const int SequenceIterator::IGNORE = -1

static

Definition at line 17 of file PRD_SequenceIterator.hxx.

Referenced by PrimerDesign::buildPrimerTrees(), Item::getPrimerSequence(), PrimerDesign::matchSequenceAgainstPrimerTrees(), primer_design_event_init(), and PrimerDesign::setPositionalParameters().

const char SequenceIterator::EOS = '\x00'

static

Definition at line 18 of file PRD_SequenceIterator.hxx.

Referenced by PrimerDesign::buildPrimerTrees(), PrimerDesign::matchSequenceAgainstPrimerTrees(), primer_design_event_init(), and PrimerDesign::setPositionalParameters().

const int SequenceIterator::FORWARD = 1

static

Definition at line 19 of file PRD_SequenceIterator.hxx.

Referenced by PrimerDesign::buildPrimerTrees(), PrimerDesign::matchSequenceAgainstPrimerTrees(), primer_design_event_init(), and PrimerDesign::setPositionalParameters().

const int SequenceIterator::BACKWARD = -1

static

Definition at line 20 of file PRD_SequenceIterator.hxx.

Referenced by Item::getPrimerSequence(), PrimerDesign::matchSequenceAgainstPrimerTrees(), and primer_design_event_init().

PRD_Sequence_Pos SequenceIterator::pos

Definition at line 22 of file PRD_SequenceIterator.hxx.

Referenced by PrimerDesign::buildPrimerTrees(), Item::getPrimerSequence(), PrimerDesign::matchSequenceAgainstPrimerTrees(), primer_design_event_init(), and PrimerDesign::setPositionalParameters().

int SequenceIterator::delivered

Definition at line 23 of file PRD_SequenceIterator.hxx.

Referenced by PrimerDesign::buildPrimerTrees().

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

• PRIMER_DESIGN/PRD_SequenceIterator.hxx
• PRIMER_DESIGN/PRD_SequenceIterator.cxx