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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/seq__match_8hpp_source.html below:

NCBI C++ ToolKit: include/algo/sequence/seq_match.hpp Source File

33 #ifndef GUI_CORE_ALGO_BASIC___SEQ_MATCH__HPP 34 #define GUI_CORE_ALGO_BASIC___SEQ_MATCH__HPP 69  template

<

class

Seq,

class

Pat,

class

Compare_fun>

71  const

Compare_fun compare_fun)

79  for

(

unsigned int i

= 0;

i

< pat.size();

i

++) {

80  EMatch

res = compare_fun(seq[pos+

i

], pat[

i

]);

92  template

<

class

Seq,

class

Pat>

99  template

<

class

Seq,

class

Pat>

103  const

Pat& pat,

TSeqPos

pos)

const 110  template

<

class

Seq,

class

Pat,

class

Match_fun>

113

vector<TSeqPos>& definite_matches,

114

vector<TSeqPos>& possible_matches,

117  for

(

unsigned int i

= 0;

i

< seq.size() - pat.size() + 1;

i

++) {

123

definite_matches.push_back(

i

);

127

possible_matches.push_back(

i

);

131  template

<

class

Seq,

class

Pat>

134

vector<TSeqPos>& definite_matches,

135

vector<TSeqPos>& possible_matches)

138

definite_matches, possible_matches,

This class provides functions for determining where sequences, perhaps containing ambiguity codes,...

static void FindMatchesNcbi8na(const Seq &seq, const Pat &pat, vector< TSeqPos > &definite_matches, vector< TSeqPos > &possible_matches)

static char IupacToNcbi8na(char in)

stuff for dealing with ncbi8na.

static EMatch MatchNcbi8na(const Seq &seq, const Pat &pat, TSeqPos pos)

static void CompNcbi8na(string &seq8na)

complement an ncbi8na sequence in place

static EMatch CompareNcbi8na(char s, char q)

determine whether ncbi8na base s is a match to q.

static void FindMatches(const Seq &seq, const Pat &pat, vector< TSeqPos > &definite_matches, vector< TSeqPos > &possible_matches, Match_fun match)

find all places where seq must or might match pat

static EMatch Match(const Seq &seq, const Pat &pat, TSeqPos pos, const Compare_fun compare_fun)

determine whether seq matches pattern pat starting at position pos.

Include a standard set of the NCBI C++ Toolkit most basic headers.

std::ofstream out("events_result.xml")

main entry point for tests

unsigned int TSeqPos

Type for sequence locations and lengths.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_XALGOSEQ_EXPORT

std::istream & in(std::istream &in_, double &x_)

static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)

EMatch operator()(const Seq &seq, const Pat &pat, TSeqPos pos) const

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