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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/pubmed__citmatch_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/edit/pubmed_citmatch/pubmed_citmatch.cpp Source File

47 void

dump_cm_list(

CNcbiOstream

& os,

const

vector<SCitMatch>& cm_list)

49 for

(

const auto

& cm : cm_list) {

50 if

(! cm.Journal.empty()) {

51

os <<

"Journal="

<< cm.Journal << endl;

53 if

(! cm.Volume.empty()) {

54

os <<

"Volume="

<< cm.Volume << endl;

56 if

(! cm.Page.empty()) {

57

os <<

"Page="

<< cm.Page << endl;

59 if

(! cm.Year.empty()) {

60

os <<

"Year="

<< cm.Year << endl;

62 if

(! cm.Author.empty()) {

63

os <<

"Author="

<< cm.Author << endl;

65 if

(! cm.Issue.empty()) {

66

os <<

"Issue="

<< cm.Issue << endl;

68 if

(! cm.Title.empty()) {

69

os <<

"Title="

<< cm.Title << endl;

72

os <<

"InPress="

<< cm.InPress << endl;

78 void

read_cm_list(

CNcbiIstream

& is, vector<SCitMatch>& cm_list)

81

unique_ptr<SCitMatch> cm;

87

cm_list.push_back(*cm);

148

arg_desc->SetUsageContext(

""

"Match publications from PubMed and print Ids"

);

151

arg_desc->AddOptionalKey(

"url"

"eutils base URL (http://eutils.ncbi.nlm.nih.gov/entrez/eutils/ by default)"

CArgDescriptions::eString

);

153

arg_desc->AddFlag(

"stats"

"Also print execution statistics"

);

161

vector<SCitMatch> cm_list;

163

read_cm_list(is, cm_list);

165 if

(cm_list.empty()) {

166

cerr <<

"Warning: No input data"

<< endl;

170

ostream*

output

nullptr

;

172 output

= &args[

"o"

].AsOutputFile();

180 string

url = args[

"url"

].AsString();

181

upd->SetBaseURL(url);

184 bool

bstats = args[

"stats"

];

188 results

.reserve(cm_list.size());

196 TEntrezId

pmid = upd->CitMatch(cm, &err);

202

oss <<

"Error: "

<< err;

216

output

" * Number of runs: "

<< nruns << endl;

217

output

" * successful: "

<< ngood << endl;

218

output

" * Elapsed time: "

<< endl;

222

args[

"o"

].CloseFile();

229 int main

(

int

argc,

const char

* argv[])

int Run() override

Run the application.

void Init() override

Initialize the application.

CPubmedFetchApplication()

static SQLCHAR output[256]

SStrictId_Entrez::TId TEntrezId

TEntrezId type for entrez ids which require the same strictness as TGi.

#define ENTREZ_ID_TO(T, entrez_id)

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

int AppMain(int argc, const char *const *argv, const char *const *envp=0, EAppDiagStream diag=eDS_Default, const char *conf=NcbiEmptyCStr, const string &name=NcbiEmptyString)

Main function (entry point) for the NCBI application.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

void SetVersion(const CVersionInfo &version)

Set the version number for the program.

@ fHidden

Hide it in Usage.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

CNcbiIstream & NcbiGetlineEOL(CNcbiIstream &is, string &str, string::size_type *count=NULL)

Read from "is" to "str" the next line (taking into account platform specifics of End-of-Line)

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

static string Sanitize(CTempString str, TSS_Flags flags=fSS_print)

Sanitize a string, allowing only specified classes of characters.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

void Stop(void)

Suspend the timer.

void Start(void)

Start the timer.

const struct ncbi::grid::netcache::search::fields::KEY key

#define NCBI_SC_VERSION_PROXY

#define NCBI_TEAMCITY_BUILD_NUMBER_PROXY

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

int main(int argc, const char *argv[])

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