ARB
Public Member Functions | Static Public Attributes | List of all members
PrimerDesign Class Reference

#include <PRD_Design.hxx>

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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 charget_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_ 
)
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().

Referenced by main().

void PrimerDesign::buildPrimerTrees ( )
void PrimerDesign::matchSequenceAgainstPrimerTrees ( )
void PrimerDesign::convertTreesToLists ( )
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 ( )
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.

Referenced by main().


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