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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/app_2idmapper_2idmapper_8cpp_source.html below:

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

88

std::vector< std::string >& );

108

arg_desc->SetUsageContext(

110 "Convert foreign ids to GI numbers"

115 "Map in opposite direction"

118

arg_desc->AddDefaultKey(

"genome"

120 "Source build or genome number"

124

arg_desc->AddOptionalKey(

"mapfile"

126 "Mapper configuration file"

129

arg_desc->AddDefaultKey(

"mapdb"

131 "Mapper database in the form \"host:database\""

146

vector< string > SourceIds;

149

vector<string>::iterator it;

150 for

( it = SourceIds.begin(); it != SourceIds.end(); ++it ) {

151 string

strSource = *it;

156

cout << strSource <<

" : "

<< strTarget << endl;

168 string

strGenome =

GetArgs

()[

"genome"

].AsString();

169 string

strMapFile =

GetArgs

()[

"mapfile"

].AsString();

170 string

strMapDb =

GetArgs

()[

"mapdb"

].AsString();

171 bool

bReverse =

GetArgs

()[

"reverse"

];

173 if

( strGenome.empty() && strMapFile.empty() && strMapDb.empty() ) {

174 return new CIdMapper

( strGenome, bReverse );

176 if

( !strMapFile.empty() ) {

180 if

( !strMapDb.empty() ) {

192

vector< string >& Ids )

196 for

(

unsigned int

u = 1; u <= args.

GetNExtra

(); ++u ) {

197

Ids.push_back( args[ u ].AsString() );

204 const string

& strSource )

232 int main

(

int

argc,

const char

** argv)

User-defined methods of the data storage class.

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

void Init()

Initialize the application.

void GetSourceIds(std::vector< std::string > &)

string GetTargetString(CSeq_id_Handle)

CSeq_id_Handle GetSourceHandle(const std::string &)

int Run()

Run the application.

IdMapper implementation using hardcoded values.

IdMapper implementation using an external configuration file.

IdMapper implementation using an external database.

IdMapper base class implementation.

virtual CSeq_id_Handle Map(const CSeq_id_Handle &)

Map a single given CSeq_id_Handle to another.

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

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.

const CNcbiArguments & GetArguments(void) const

Get the application's cached unprocessed command-line arguments.

size_t GetNExtra(void) const

Get the number of unnamed positional (a.k.a. extra) args.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eDS_ToStderr

To standard error stream.

static CSeq_id_Handle GetGiHandle(TGi gi)

Faster way to create a handle for a gi.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

string AsString(void) const

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

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.

@ fConvErr_NoThrow

Do not throw an exception on error.

const CharType(& source)[N]

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

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