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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/find__pattern_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/sequence/find_pattern.cpp Source File

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42

vector<TSeqPos>& starts, vector<TSeqPos>& ends) {

56

starts.push_back(res[0]);

57

ends.push_back(res[1] - 1);

69

vector<TSeqPos>& starts,

70

vector<TSeqPos>& ends)

73

total_pattern =

"("

+ pattern +

")\\1{" 75  Find

(seq, total_pattern, starts, ends);

84  int n

,

int

min_repeats,

85

vector<TSeqPos>& starts,

86

vector<TSeqPos>& ends)

89  for

(

int i

= 0;

i

<

n

; ++

i

) {

static void Find(const string &seq, const string &pattern, vector< TSeqPos > &starts, vector< TSeqPos > &ends)

Find non-overlapping matches of regular expression in sequence.

static void FindNucNmerRepeats(const string &seq, int n, int min_repeats, vector< TSeqPos > &starts, vector< TSeqPos > &ends)

Find all cases of at least min_repeats consecutive occurrences of any n-mer consisting of unambiguous...

static void FindRepeatsOf(const string &seq, const string &pattern, int min_repeats, vector< TSeqPos > &starts, vector< TSeqPos > &ends)

Find cases of at least min_repeats consecutive occurrences of any *particular* match to pattern.

const TOffset * GetResults(size_t idx) const

Get location of pattern/subpattern for the last GetMatch().

CTempString GetMatch(CTempString str, size_t offset=0, size_t idx=0, TMatch flags=fMatch_default, bool noreturn=false)

Get matching pattern and subpatterns.

size_t TOffset

Element type for GetResults().

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

bool empty(void) const

Return true if the represented string is empty (i.e., the length is zero)

C++ wrappers for the Perl-compatible regular expression (PCRE) library.

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