path = path.substr(0, (path.find_last_of("othur")-5));
path = m->getFullPathName(path);
+ savedOutputDir = outputDir;
string catchAllCommandExe = "";
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
catchAllCommandExe += "mono " + path + "CatchAllcmdL.exe ";
remove(filename.c_str());
filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+ if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
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 .
+ if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
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 .
+ if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
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");
}
if (sharedfile == "") {
- string summaryfilename = outputDir + m->getRootName(m->getSimpleName(inputFileNames[0])) + "catchall.summary";
+ string summaryfilename = savedOutputDir + m->getRootName(m->getSimpleName(inputFileNames[0])) + "catchall.summary";
summaryfilename = m->getFullPathName(summaryfilename);
outputNames.push_back(summaryfilename); outputTypes["summary"].push_back(summaryfilename);
}else { //combine summaries
try {
ofstream out;
- string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "catchall.summary";
+ string combineFileName = savedOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + "catchall.summary";
//open combined file
m->openOutputFile(combineFileName, out);
GlobalData* globaldata;
- string outputDir, sharedfile, sabundfile, rabundfile, listfile, format, path;
+ string outputDir, sharedfile, sabundfile, rabundfile, listfile, format, path, savedOutputDir;
bool abort, allLines;
set<string> labels;
vector<string> outputNames;