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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/PCRPrimerSeq_8cpp_source.html below:

NCBI C++ ToolKit: src/objects/seqfeat/PCRPrimerSeq.cpp Source File

57 bool

in_brackets =

false

;

58

string::iterator ch_iter =

.begin();

59 while

(ch_iter !=

.end()) {

60 const char

ch = *ch_iter;

180

string::iterator sit =

.begin();

181 while

(sit !=

.end()) {

184 if

(pos2 == string::npos) {

188 string match

=

.substr(pos + 1, pos2 - pos - 1);

189 if

(find(list_begin, list_end,

) == list_end) {

193

sit += pos2 - pos + 1;

196 if

(*sit !=

'('

&& *sit !=

')'

&& *sit !=

','

&& *sit !=

':'

) {

202 if

(strchr (

"ABCDGHKMNRSTVWY"

, ch) ==

) {

217 const char

* starts[] = {

"5'-"

,

"5`-"

,

"5-"

,

"5'"

,

"5`"

,

"-"

,

};

218 const char

* ends[] = {

"-3'"

,

"-3`"

,

"-3"

,

"3'"

,

"3`"

,

"-"

,

};

222 for

(

int i

=0; starts[

i

] !=

;

i

++) {

223 size_t len

= strlen(starts[

i

]);

224 size_t

pos = seq.find(starts[

i

]);

225 if

(pos == 0 &&

< seq.length())

226

seq = seq.substr(

);

229 for

(

int i

=0; ends[

i

] !=

;

i

++) {

230 size_t len

= strlen(ends[

i

]);

231 size_t

pos = seq.rfind(ends[

i

]);

232 if

(

< seq.length() && pos == seq.length()-

)

233

seq = seq.substr(0,seq.length()-

);

235 return

(

!= seq);

241 for

(

size_t i

= 0;

i

< seq.size(); ++

i

) {

242 if

(seq[

i

] ==

'I'

)

248 while

(pos !=

&& pos < seq.length()) {

249

pos = seq.find(

'i'

, pos);

253 if

(pos==0 || seq[pos-1]!=

'<'

)

258 if

(pos==seq.length()-1 || seq[pos+1]!=

'>'

)

261

seq = seq.substr(0, pos) + repl + seq.substr(pos + 1,

);

262

pos += repl.length();

266 return

(

!= seq);

const char * sm_ValidModifiedPrimerBases[]

static void s_EraseSpacesOutsideBrackets(string &str)

User-defined methods of the data storage class.

static bool TrimJunk(string &seq)

static bool IsValid(const string &seq, char &bad_ch)

static bool Fixi(string &seq)

static void Clean(string &seq)

static const char * str(char *buf, int n)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

NCBI_NS_STD::string::size_type SIZE_TYPE

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

static string & ToLower(string &str)

Convert string to lower case â string& version.

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is orig

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)

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