commandFactory = CommandFactory::getInstance();
+ m->mothurOut("Mothur's directories:"); m->mothurOutEndLine();
+
//redirect output
if ((output == "clear") || (output == "")) { output = ""; commandFactory->setOutputDirectory(output); }
else if (output == "default") {
string exepath = m->argv;
output = exepath.substr(0, (exepath.find_last_of('m')));
- m->mothurOut("Changing output directory to " + output); m->mothurOutEndLine();
+ m->mothurOut("outputDir=" + output); m->mothurOutEndLine();
commandFactory->setOutputDirectory(output);
}else {
//add / to name if needed
}else{
out.close();
remove(outTemp.c_str());
- m->mothurOut("Changing output directory to " + output); m->mothurOutEndLine();
+ m->mothurOut("outputDir=" + output); m->mothurOutEndLine();
commandFactory->setOutputDirectory(output);
}
}
string exepath = m->argv;
input = exepath.substr(0, (exepath.find_last_of('m')));
- m->mothurOut("Changing input directory to " + input); m->mothurOutEndLine();
+ m->mothurOut("inputDir=" + input); m->mothurOutEndLine();
commandFactory->setInputDirectory(input);
}else {
//add / to name if needed
}else{
in.close();
remove(inTemp.c_str());
- m->mothurOut("Changing input directory to " + input); m->mothurOutEndLine();
+ m->mothurOut("inputDir=" + input); m->mothurOutEndLine();
commandFactory->setInputDirectory(input);
}
}
if (tempdefault == "clear") {
#ifdef MOTHUR_FILES
string temp = MOTHUR_FILES;
- m->mothurOut("Resetting default directory to " + temp); m->mothurOutEndLine();
+ m->mothurOut("tempDefault=" + temp); m->mothurOutEndLine();
m->setDefaultPath(temp);
#else
string temp = "";
string exepath = m->argv;
tempdefault = exepath.substr(0, (exepath.find_last_of('m')));
- m->mothurOut("Changing default directory to " + tempdefault); m->mothurOutEndLine();
+ m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine();
m->setDefaultPath(tempdefault);
}else {
//add / to name if needed
if (lastChar != "\\") { tempdefault += "\\"; }
#endif
- m->mothurOut("Changing default directory to " + tempdefault); m->mothurOutEndLine();
+ m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine();
m->setDefaultPath(tempdefault);
}