//**********************************************************************************************************************
CatchAllCommand::CatchAllCommand(){
try {
//**********************************************************************************************************************
CatchAllCommand::CatchAllCommand(){
try {
string catchAllCommandExe = "";
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
catchAllCommandExe += "mono " + path + "CatchAllcmdL.exe ";
string catchAllCommandExe = "";
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
catchAllCommandExe += "mono " + path + "CatchAllcmdL.exe ";
vector<string> inputFileNames;
if (sharedfile != "") { inputFileNames = parseSharedFile(sharedfile); globaldata->setFormat("sabund"); }
else { inputFileNames.push_back(sabundfile); }
vector<string> inputFileNames;
if (sharedfile != "") { inputFileNames = parseSharedFile(sharedfile); globaldata->setFormat("sabund"); }
else { inputFileNames.push_back(sabundfile); }
system(catchAllCommand.c_str());
remove(filename.c_str());
filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
system(catchAllCommand.c_str());
remove(filename.c_str());
filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
remove(filename.c_str());
filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
remove(filename.c_str());
filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
remove(filename.c_str());
filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
remove(filename.c_str());
filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
summaryfilename = m->getFullPathName(summaryfilename);
outputNames.push_back(summaryfilename); outputTypes["summary"].push_back(summaryfilename);
}else { //combine summaries
summaryfilename = m->getFullPathName(summaryfilename);
outputNames.push_back(summaryfilename); outputTypes["summary"].push_back(summaryfilename);
}else { //combine summaries
}
string summaryfilename = combineSummmary(sumNames);
outputNames.push_back(summaryfilename); outputTypes["summary"].push_back(summaryfilename);
}
string summaryfilename = combineSummmary(sumNames);
outputNames.push_back(summaryfilename); outputTypes["summary"].push_back(summaryfilename);