//**********************************************************************************************************************
vector<string> GetCurrentCommand::setParameters(){
try {
- CommandParameter pclear("clear", "String", "", "", "", "", "",false,false); parameters.push_back(pclear);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pclear("clear", "String", "", "", "", "", "","",false,false); parameters.push_back(pclear);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
+
+ cFactory = CommandFactory::getInstance();
+
//user wants to clear a type
if (types.size() != 0) {
for (int i = 0; i < types.size(); i++) {
m->setTaxonomyFile("");
}else if (types[i] == "flow") {
m->setFlowFile("");
+ }else if (types[i] == "biom") {
+ m->setBiomFile("");
+ }else if (types[i] == "count") {
+ m->setCountTableFile("");
+ }else if (types[i] == "summary") {
+ m->setSummaryFile("");
}else if (types[i] == "processors") {
m->setProcessors("1");
}else if (types[i] == "all") {
m->mothurOutEndLine(); m->mothurOut("Current files saved by mothur:"); m->mothurOutEndLine();
m->printCurrentFiles();
}
+
+ string inputDir = cFactory->getInputDir();
+ if (inputDir != "") {
+ m->mothurOutEndLine(); m->mothurOut("Current input directory saved by mothur: " + inputDir); m->mothurOutEndLine();
+ }
+
+ string outputDir = cFactory->getOutputDir();
+ if (outputDir != "") {
+ m->mothurOutEndLine(); m->mothurOut("Current output directory saved by mothur: " + outputDir); m->mothurOutEndLine();
+ }
+ string defaultPath = m->getDefaultPath();
+ if (defaultPath != "") {
+ m->mothurOutEndLine(); m->mothurOut("Current default directory saved by mothur: " + defaultPath); m->mothurOutEndLine();
+ }
+
+
+ string temp = "./";
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+#else
+ temp = ".\\";
+#endif
+ temp = m->getFullPathName(temp);
+ m->mothurOutEndLine(); m->mothurOut("Current working directory: " + temp); m->mothurOutEndLine();
- return 0;
+ return 0;
}
catch(exception& e) {