ARB
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#include <PRD_Design.hxx>
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 |
Definition at line 29 of file PRD_Design.hxx.
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.
Definition at line 66 of file PRD_Design.cxx.
PrimerDesign::~PrimerDesign | ( | ) |
Definition at line 74 of file PRD_Design.cxx.
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().
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inline |
Definition at line 145 of file PRD_Design.hxx.
Referenced by primer_design_event_go().
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inline |
Definition at line 147 of file PRD_Design.hxx.
References Range::max().
Referenced by primer_design_event_go().
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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().
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Definition at line 152 of file PRD_Design.hxx.
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Definition at line 153 of file PRD_Design.hxx.
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Definition at line 154 of file PRD_Design.hxx.
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Definition at line 155 of file PRD_Design.hxx.