本文整理汇总了C++中ParameterList::getValue方法的典型用法代码示例。如果您正苦于以下问题:C++ ParameterList::getValue方法的具体用法?C++ ParameterList::getValue怎么用?C++ ParameterList::getValue使用的例子?那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类ParameterList
的用法示例。
在下文中一共展示了ParameterList::getValue方法的8个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的C++代码示例。
示例1: getProjPath
//-----------------------------------------------------------------------------
string getProjPath(const ParameterList & pl, const string & addPath)
{
string projDir = pl.getValue("PROJECT_DIR", "");
bool relDir = pl.getValueBool("RELATIVE_DIR", true);
return getPath(projDir, addPath, relDir);
}
示例2: getScoreValue
bool MSMSFragmentation::getScoreValue ( const ParameterList& params, const string& name, ScoreType& value )
{
double dvalue;
bool flag = params.getValue ( name, dvalue );
if ( flag ) {
dvalue *= SCORE_TYPE_MULTIPLIER;
value = static_cast <ScoreType> ( dvalue );
}
return flag;
}
示例3: processOptions
int SpecCheckInterface::processOptions(int argc, char **argv)
{
//--------------------------------------------------------------------------------------------
// Initialize directories used
//--------------------------------------------------------------------------------------------
//--------------------------------------------------------------------------------------------
// Parse the command line parameters
//--------------------------------------------------------------------------------------------
vector<CommandLineParser::Option> listOptions;
// c++ instruction cmd line option parameter name takes value?
listOptions.push_back(CommandLineParser::Option("-help", "help", false));
listOptions.push_back(CommandLineParser::Option("-version", "VERSION", false));
listOptions.push_back(CommandLineParser::Option("-input-list", "INPUT_LIST", true));
listOptions.push_back(CommandLineParser::Option("-inputspectra", "INPUT_SPECS_MS", true));
// parameter file
listOptions.push_back(CommandLineParser::Option("-p", "PARAMETER_FILE", true));
////////////////////////////////////////////////////////////////////////////////
// Execute the command line parser
CommandLineParser clp(argc, argv, 0, listOptions);
////////////////////////////////////////////////////////////////////////////////
// Checking for errors
string parser_error;
if (!clp.validate(parser_error)) {
ERROR_MSG(parser_error);
return -1;
}
////////////////////////////////////////////////////////////////////////////////
// The parameters' values
ParameterList commandLineParams;
clp.getOptionsAsParameterList(commandLineParams);
////////////////////////////////////////////////////////////////////////////////
// Parameter file
////////////////////////////////////////////////////////////////////////////////
if (commandLineParams.exists("PARAMETER_FILE")) {
string parameterFilename = commandLineParams.getValue("PARAMETER_FILE");
ParameterList ip;
ip.readFromFile(parameterFilename);
// Combine the command line parameters to the file ones
// Command line parameters take precedence (hence the overwrite flag not set)
commandLineParams.addList(ip, false);
}
////////////////////////////////////////////////////////////////////////////////
// "help" prints help and exits
if (commandLineParams.exists("VERSION"))
return version(cout);
////////////////////////////////////////////////////////////////////////////////
// the same for "version"
if (commandLineParams.exists("help"))
return help(cout);
////////////////////////////////////////////////////////////////////////////////
// File load section
// input spectra file to load
if (commandLineParams.exists("INPUT_LIST")) {
inputFilesNames = commandLineParams.getValue("INPUT_LIST").c_str();
// load input files names
if(!loadStringVector(inputFilesNames, inputFiles)) {
cerr << "Unable to load file: " << inputFilesNames << endl;
exit(0);
}
}
if (commandLineParams.exists("INPUT_SPECS_MS")) {
string aux = commandLineParams.getValue("INPUT_SPECS_MS").c_str();
splitText(aux.c_str(), inputFiles, ";|");
}
// Keep record of loaded files
int filesLoaded = 0;
cout << "Loading " << inputFiles.size() << " files." << endl;
for(int i = 0 ; i < inputFiles.size() ; i++) {
SpecSet spec;
if(loadSpecset(inputFiles[i], spec)) {
inputData.push_back(spec);
filesLoaded++;
//.........这里部分代码省略.........
示例4: batchSubmission
void batchSubmission ( ostream& os, ParameterList& paramList )
{
init_html ( os, "Batch Submission" );
if ( paramList.empty () ) {
ErrorHandler::genError ()->error ( "No parameters passed to Prospector program.\n" );
}
string user = paramList.getStringValue ( "user" );
os << "<p>Creating Prospector files.</p>" << endl;
string searchKey = genRandomString ( 16 ); // Selects a unique string for the search
string searchName = paramList.getStringValue ( "search_name" ); // Program (eg batchtag)
string uploadFpath = paramList.getStringValue ( "upload_data_filepath" ); // This is the full path name of the uploaded file as named by PP
string resultsName = paramList.getStringValue ( "output_filename" );
bool searchKeyProblem;
try {
checkConstantAndVariableModCompatibility ( ¶mList );
}
catch ( runtime_error e ) { // Catch database login problems
genUnlink ( uploadFpath );
ErrorHandler::genError ()->error ( e );
}
try {
searchKeyProblem = MySQLPPSDDBase::instance ().checkSearchKey ( searchKey );// Checks it is unique
}
catch ( runtime_error e ) { // Catch database login problems
genUnlink ( uploadFpath );
ErrorHandler::genError ()->error ( e );
}
if ( searchKeyProblem ) {
genUnlink ( uploadFpath );
ErrorHandler::genError ()->error ( "Search key not unique.\n" );// The search key has to be unique to carry on.
}
if ( resultsName.empty () ) {
genUnlink ( uploadFpath );
ErrorHandler::genError ()->error ( "No results name has been chosen.\n" );
}
string password;
bool passwordFlag = paramList.getValue ( "password", password );
UserInfo* userInfo = MySQLPPSDDBase::instance ().getUserInfo ( user );
if ( !userInfo || ( passwordFlag && userInfo->getPassword () != password ) ) { // Get the user information
genUnlink ( uploadFpath );
ErrorHandler::genError ()->error ( "Unknown user and/or password.\n" );
}
if ( user == "root" ) { // Get the user information
genUnlink ( uploadFpath );
ErrorHandler::genError ()->error ( "Root user can't do searches.\n" );
}
if ( userInfo->getIsGuest () ) {
genUnlink ( uploadFpath );
ErrorHandler::genError ()->error ( "Guest users can't do searches.\n" );
}
if ( !InfoParams::instance ().getBoolValue ( "btag_daemon_remote" ) ) {
try {
startDaemonIfNecessary ();
}
catch ( runtime_error e ) {
genUnlink ( uploadFpath );
ErrorHandler::genError ()->error ( e );
}
}
string userID = userInfo->getUserID ();
Repository* reposit = new UserRepository ( searchName, userInfo->getDirectoryName () ); // Where to put files given a user. Also creates the directories.
string projectName;
if ( uploadFpath.empty () ) { // The project already exists
projectName = paramList.getStringValue ( "project_name" ); // From a form with a project name option.
}
else {
string uploadFname = paramList.getStringValue ( "upload_data_filename" ); // This is the original file name.
string instrument = paramList.getStringValue ( "instrument_name" );
uploadFname = genFilenameFromPath ( uploadFname ); // IE gives the full path whereas Mozilla give the filename (what we want)
projectName = getProjectName ( uploadFname ); // The project is named after the uploaded file. This has to be unique.
if ( projectName.length () > 58 ) {
genUnlink ( uploadFpath );
ErrorHandler::genError ()->error ( "The project name " + projectName + " is too long.\n" );
}
if ( MySQLPPSDDBase::instance ().checkProject ( userID, projectName ) ) {
genUnlink ( uploadFpath );
ErrorHandler::genError ()->error ( "Project already exists.\n" );
}
paramList.setValue ( "data_source", "List of Files" );
paramList.setValue ( "project_name", projectName );
paramList.removeName ( "upload_data_filename" );
paramList.removeName ( "upload_data_filepath" );
string uploadName = genPreprocessFile ( uploadFpath );
if ( uploadName == uploadFpath || isCompressedUpload ( uploadName ) ) { // If the file hasn't been preprocessed or it has just been uncompressed it must be a single file
string shortName = genShortFilenameFromPath ( uploadName );
string newDir = genDirectoryFromPath ( uploadName ) + SLASH + shortName;
if ( newDir == uploadName ) {
newDir += "_1";
}
genCreateDirectory ( newDir );
string newUploadName;
if ( isCompressedUpload ( uploadName ) )
newUploadName = newDir + SLASH + genShortFilenameFromPath ( uploadFname );
else
newUploadName = newDir + SLASH + uploadFname;
genRename ( uploadName, newUploadName );
uploadName = newDir;
}
PPProject ppp ( userInfo->getMaxMSMSSpectra (), userInfo->getAllowRaw (), projectName, uploadName, searchKey, reposit, MSMSDataSetInfo::setChargeRange ( ¶mList ) );
if ( ppp.initialised () ) {
//.........这里部分代码省略.........
示例5: main
// -------------------------------------------------------------------------
int main(int argc, char ** argv)
{
Logger::setDefaultLogger(Logger::getLogger(0));
if (argc < 3)
{
cerr << "Usage: main_execmodule moduleName parametersFileName [options]" << endl;
return -1;
}
// Parse the command line parameters
vector<CommandLineParser::Option> listOptions;
listOptions.push_back(CommandLineParser::Option("t", "NUM_THREADS", true));
listOptions.push_back(CommandLineParser::Option("lf", "LOG_FILE_NAME", true));
listOptions.push_back(CommandLineParser::Option("ll", "LOG_LEVEL", true));
// Command line parameters for ExecSpectraExtraction for CCMS Workflows
listOptions.push_back(CommandLineParser::Option("ccms_output_library", "OUTPUT_MGF", true));
listOptions.push_back(CommandLineParser::Option("ccms_input_library", "EXISTING_LIBRARY_MGF", true));
listOptions.push_back(CommandLineParser::Option("ccms_input_spectradir", "SPECTRA_DIR", true));
listOptions.push_back(CommandLineParser::Option("ccms_results_dir", "RESULTS_DIR", true));
listOptions.push_back(CommandLineParser::Option("ccms_newresults_dir", "NEWLIBRARYRESULTS_DIR", true));
listOptions.push_back(CommandLineParser::Option("ccms_input_spectradatafile", "INPUTSPECTRA_DATAFILE", true));
listOptions.push_back(CommandLineParser::Option("ccms", "CCMS", true));
CommandLineParser clp(argc, argv, 2, listOptions);
string parser_error;
if (!clp.validate(parser_error))
{
ERROR_MSG(parser_error);
return -2;
}
ParameterList commandLineParams;
clp.getOptionsAsParameterList(commandLineParams);
// Load the parameter file
ParameterList ip;
std::string paramsFileName = argv[2];
std::string::size_type idx = paramsFileName.rfind(".");
if( idx != std::string::npos &&
paramsFileName.substr(idx + 1) == "xml"){
if (!ip.readFromProteosafeXMLFile(argv[2]))
{
ERROR_MSG("Can not read parameter file [" << argv[2] << "].");
return -3;
}
}
else{
if (!ip.readFromFile(argv[2]))
{
ERROR_MSG("Can not read parameter file [" << argv[2] << "].");
return -3;
}
}
// Combine the command line parameters to the file ones
// Command line parameters take precedence (hence the overwrite flag set)
ip.addList(commandLineParams, true);
int logLevel = ip.getValueInt("LOG_LEVEL", 0);
if (ip.exists("LOG_FILE_NAME"))
{
string logFileName = ip.getValue("LOG_FILE_NAME");
Logger::setDefaultLogger(Logger::getLogger(logFileName, logLevel));
}
else
{
Logger::setDefaultLogger(Logger::getLogger(logLevel));
}
DEBUG_TRACE;
// Fill the factory with all known module types
ExecModuleFactoryLP::RegisterAllModules();
DEBUG_TRACE;
// Get the exemplar from the factory
ExecBase * moduleExemplar = ExecModuleFactoryLP::getModule(argv[1]);
if (moduleExemplar == 0)
{
ERROR_MSG("Module name [" << argv[1] << "] not found in factory.");
ExecModuleFactoryLP::cleanup();
return -4;
}
DEBUG_TRACE;
// Clone the exemplar and create a real module with the desired parameters
ExecBase * moduleReal = moduleExemplar->clone(ip);
string jobDoneFile(moduleReal->getName());
jobDoneFile += "_";
string numNode = moduleReal->m_params.getValue("NUM_SPLIT");
jobDoneFile += numNode;
jobDoneFile += "_results.param";
DEBUG_VAR(jobDoneFile);
// Validate all the parameters before invoking
//.........这里部分代码省略.........
示例6: main
// -------------------------------------------------------------------------
int main(int argc, char ** argv)
{
int logLevel = 5;
Logger::setDefaultLogger(Logger::getLogger(logLevel));
string initialStageString("");
string finalStageString("");
string statusFileName("status.txt");
bool resumeFlag = false;
bool gridExecutionFlag = false;
bool runGenoMSFlag = false;
bool runMergedFlag = false;
bool showHelp = false;
for (size_t i = 0; i < argc; i++)
{
string arg(argv[i]);
if (arg.compare("--help") == 0)
{
showHelp = true;
}
}
if (argc < 2 || showHelp)
{
if (showHelp)
{
cout << "Usage: main_flr [PARAM FILE] [OPTION]..." << endl << endl;
cout << "Optional arguments are listed below " << endl;
cout << " -i <intialstage> begin processing at specified stage:"
<< endl;
cout << " begin,pairspectra,lpsolver,flr" << endl;
cout
<< " -f <finalstage> end processing after completing specified stage:"
<< endl;
cout << " lpsolver,flr" << endl;
cout << " -g execution is on a grid" << endl;
cout << " -lf <filename> name of log file for output" << endl;
cout << " -ll <loglevel> log level for debug/warn/error output:"
<< endl;
cout << " 9 for errors only" << endl;
cout << " 5 for warnings and errors" << endl;
cout << " 0 for all debug output" << endl;
cout << " -s execute a single step then exit" << endl;
}
else
{
cerr << "main_specnets: insufficient arguments" << endl;
cerr << "Try \'main_specnets --help\' for more information." << endl
<< endl;
}
cout << PROGRAM_NAME << endl;
cout << "main_specnets 3.0." << XSTR(SPS_VERSION) << endl;
cout << endl;
cout << COPYRIGHT1 << endl;
cout << COPYRIGHT2 << endl;
cout << endl;
return -1;
}
// Parse the command line parameters
vector<CommandLineParser::Option> listOptions;
listOptions.push_back(CommandLineParser::Option("i", "INITIAL_STAGE", 1));
listOptions.push_back(CommandLineParser::Option("f", "FINAL_STAGE", 1));
listOptions.push_back(CommandLineParser::Option("g", "GRID_EXECUTION", 0));
listOptions.push_back(CommandLineParser::Option("lf", "LOG_FILE_NAME", 1));
listOptions.push_back(CommandLineParser::Option("ll", "LOG_LEVEL", 1));
listOptions.push_back(CommandLineParser::Option("s", "SINGLE_STEP", 0));
CommandLineParser clp(argc, argv, 1, listOptions);
string parser_error;
if (!clp.validate(parser_error))
{
ERROR_MSG(parser_error);
return -2;
}
ParameterList commandLineParams;
clp.getOptionsAsParameterList(commandLineParams);
ParameterList ip;
ip.readFromFile(argv[1]);
ip.writeToFile("debug_sps.params");
// Combine the command line parameters to the file ones
// Command line parameters take precedence (hence the overwrite flag set)
ip.addList(commandLineParams, true);
ip.writeToFile("debug_wcommand.params");
logLevel = ip.getValueInt("LOG_LEVEL", 5);
if (ip.exists("LOG_FILE_NAME"))
{
string logFileName = ip.getValue("LOG_FILE_NAME");
Logger::setDefaultLogger(Logger::getLogger(logFileName, logLevel));
}
//.........这里部分代码省略.........
示例7: performFlr
// -------------------------------------------------------------------------
bool performFlr(ParameterList & ip, bool gridExecutionFlag)
{
DEBUG_TRACE;
ExecFlr moduleFlr(ip);
DEBUG_TRACE;
string errorString;
bool isValid = moduleFlr.validateParams(errorString);
DEBUG_VAR(isValid);
if (!isValid)
{
ERROR_MSG(errorString);
return false;
}
isValid = moduleFlr.loadInputData();
DEBUG_VAR(isValid);
if (!isValid)
{
ERROR_MSG(errorString);
return false;
}
bool returnStatus;
if (!ip.exists("GRID_NUMNODES") || ip.getValueInt("GRID_NUMNODES") <= 0)
{
returnStatus = moduleFlr.invoke();
}
else
{
DEBUG_TRACE;
int numNodes = ip.getValueInt("GRID_NUMNODES");
string gridType = ip.getValue("GRID_TYPE");
if (gridType == "pbs")
{
ParallelPbsExecution exec(&moduleFlr,
gridExecutionFlag,
!gridExecutionFlag,
false);
returnStatus = exec.invoke(numNodes);
}
else if (gridType == "sge")
{
ParallelSgeExecution exec(&moduleFlr,
gridExecutionFlag,
!gridExecutionFlag,
false);
returnStatus = exec.invoke(numNodes);
}
}
// Test for return status
DEBUG_VAR( returnStatus);
if (!returnStatus)
{
ERROR_MSG("invoking moduleFlr exited in error.");
return false;
}
DEBUG_TRACE;
moduleFlr.saveOutputData();
return true;
}
示例8: fromFile
MSMSFragmentation::MSMSFragmentation ( const string& fragName ) :
fragName ( fragName ),
ammoniaLoss ( "RKNQ" ),
waterLoss ( "STED" ),
posChargeBearing( "RHK" ),
dIonExclude ( "FHPWY" ),
vIonExclude ( "GP" ),
wIonExclude ( "FHWY" ),
unmatchedScore ( DEFAULT_MISS_SCORE ),
immoniumScore ( DEFAULT_HIT_SCORE ),
relatedIonScore ( DEFAULT_HIT_SCORE ),
mScore ( DEFAULT_HIT_SCORE ),
aScore ( DEFAULT_HIT_SCORE ),
aLossScore ( DEFAULT_HIT_SCORE ),
aPhosLossScore ( DEFAULT_HIT_SCORE ),
bScore ( DEFAULT_HIT_SCORE ),
bPlusH2OScore ( DEFAULT_HIT_SCORE ),
bLossScore ( DEFAULT_HIT_SCORE ),
bPhosLossScore ( DEFAULT_HIT_SCORE ),
cLadderScore ( DEFAULT_HIT_SCORE ),
cPlus2DaScore ( DEFAULT_HIT_SCORE ),
cPlus1DaScore ( DEFAULT_HIT_SCORE ),
cScore ( DEFAULT_HIT_SCORE ),
cMinus1DaScore ( DEFAULT_HIT_SCORE ),
dScore ( DEFAULT_HIT_SCORE ),
vScore ( DEFAULT_HIT_SCORE ),
wScore ( DEFAULT_HIT_SCORE ),
xScore ( DEFAULT_HIT_SCORE ),
nLadderScore ( DEFAULT_HIT_SCORE ),
yScore ( DEFAULT_HIT_SCORE ),
yLossScore ( DEFAULT_HIT_SCORE ),
yPhosLossScore ( DEFAULT_HIT_SCORE ),
bigYScore ( DEFAULT_HIT_SCORE ),
zScore ( DEFAULT_HIT_SCORE ),
zPlus1DaScore ( DEFAULT_HIT_SCORE ),
zPlus2DaScore ( DEFAULT_HIT_SCORE ),
zPlus3DaScore ( DEFAULT_HIT_SCORE ),
bp2Score ( DEFAULT_HIT_SCORE ),
bp2LossScore ( DEFAULT_HIT_SCORE ),
bp2PhosLossScore ( DEFAULT_HIT_SCORE ),
yp2Score ( DEFAULT_HIT_SCORE ),
yp2LossScore ( DEFAULT_HIT_SCORE ),
yp2PhosLossScore ( DEFAULT_HIT_SCORE ),
internalAScore ( DEFAULT_HIT_SCORE ),
internalBScore ( DEFAULT_HIT_SCORE ),
internalLossScore ( DEFAULT_HIT_SCORE ),
MH3PO4Score ( DEFAULT_HIT_SCORE ),
MSOCH4Score ( DEFAULT_HIT_SCORE ),
scoring ( false ),
maximumInternalIonMass ( 700.0 ),
chargeReducedFragmentation ( false )
{
if ( !fragName.empty () ) {
GenIFStream fromFile ( MsparamsDir::instance ().getParamPath ( "fragmentation.txt" ) );
string line;
bool flag = false;
while ( getline ( fromFile, line ) ) {
if ( line == fragName ) {
ParameterList params ( fromFile );
params.getValue ( "nh3_loss", ammoniaLoss );
params.getValue ( "h2o_loss", waterLoss );
params.getValue ( "pos_charge", posChargeBearing );
params.getValue ( "d_ion_exclude", dIonExclude );
params.getValue ( "v_ion_exclude", vIonExclude );
params.getValue ( "w_ion_exclude", wIonExclude );
params.getValue ( "it", ionTypes );
params.getValue ( "max_internal_ion_mass", maximumInternalIonMass );
params.getValue ( "charge_reduced_fragmentation", chargeReducedFragmentation );
scoring = getScoreValue ( params, "unmatched_score", unmatchedScore );
scoring = getScoreValue ( params, "immonium_score", immoniumScore );
scoring = getScoreValue ( params, "related_ion_score", relatedIonScore );
scoring = getScoreValue ( params, "m_score", mScore );
scoring = getScoreValue ( params, "a_score", aScore );
scoring = getScoreValue ( params, "a_loss_score", aLossScore );
scoring = getScoreValue ( params, "a_phos_loss_score", aPhosLossScore );
scoring = getScoreValue ( params, "b_score", bScore );
scoring = getScoreValue ( params, "b_plus_h2o_score", bPlusH2OScore );
scoring = getScoreValue ( params, "b_loss_score", bLossScore );
scoring = getScoreValue ( params, "b_phos_loss_score", bPhosLossScore );
scoring = getScoreValue ( params, "c_ladder_score", cLadderScore );
scoring = getScoreValue ( params, "c_plus_2_score", cPlus2DaScore );
scoring = getScoreValue ( params, "c_plus_1_score", cPlus1DaScore );
scoring = getScoreValue ( params, "c_score", cScore );
scoring = getScoreValue ( params, "c_minus_1_score", cMinus1DaScore );
scoring = getScoreValue ( params, "d_score", dScore );
scoring = getScoreValue ( params, "v_score", vScore );
scoring = getScoreValue ( params, "w_score", wScore );
//.........这里部分代码省略.........