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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/gi2taxid_8cpp_source.html below:

NCBI C++ ToolKit: src/app/gi2taxid/gi2taxid.cpp Source File

49 virtual void Init

(

void

);

50 virtual int Run

(

void

);

60

arg_desc->AddDefaultKey(

"gi"

"GI"

65

arg_desc->AddOptionalKey(

"file"

"InputFile"

66 "Input file to test, one gi or accession per line"

69

arg_desc->AddFlag(

"show_acc"

70 "Show the passed accession as well as the gi"

);

82 bool

show = args[

"show_acc"

];

84

vector<string> id_list;

85 if

( args[

"gi"

].AsInteger() ) {

86

id_list.push_back( args[

"gi"

].AsString() );

93

id_list.push_back(acc);

101 static const char

* sc_ValidChars =

102 "abcdefghijklmnopqrstuvwxyz" 103 "ABCDEFGHIJKLMNOPQRSTUVWXYZ" 107 ITERATE

(vector<string>, iter, id_list) {

108 string

id_str = *iter;

110

string::size_type pos = id_str.find_first_not_of(sc_ValidChars);

111 if

(pos != string::npos) {

114 if

( id_str.empty() ) {

122

gi = NStr::StringToNumeric<TGi>(id_str);

126

cout <<

"trying: "

<< *iter <<

" -> "

<< id_str << endl;

135 ERR_POST

(

Error

"don't know anything about accession/id: " 144

cout << id_str <<

" "

;

146

cout << gi <<

" "

<< tax_id << endl;

153 int main

(

int

argc,

const char

* argv[])

virtual int Run(void)

Run the application.

virtual void Init(void)

Initialize the application.

bool GetTaxId4GI(TGi gi, TTaxId &tax_id_out)

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

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.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

SStrictId_Tax::TId TTaxId

Taxon id type.

@ eInputFile

Name of file (must exist and be readable)

@ eInteger

Convertible into an integer number (int or Int8)

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

@ eDS_Default

Try standard log file (app.name + ".log") in /log/, use stderr on failure.

void Error(CExceptionArgs_Base &args)

void Info(CExceptionArgs_Base &args)

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

static string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

virtual NCBI_NS_NCBI::TGi AskGetgi(const CSeq_id &req, TReply *reply=0)

Magic spell ;-) needed for some weird compilers... very empiric.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

Process information in the NCBI Registry, including working with configuration files.

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