for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
-
+
globaldata->newRead();
//if the user changes the input directory command factory will send this info to us in the output parameter
}
globaldata->allLines = allLines;
-
+
orderfile = validParameter.validFile(parameters, "order", true);
if (orderfile == "not open") { abort = true; }
else if (orderfile == "not found") { orderfile = ""; }
else { globaldata->setOrderFile(orderfile); }
-
+
if (abort == false) {
//gets whichever one of the above is set
filename = globaldata->inputFileName;
}
-
}
}
//**********************************************************************************************************************
-
-ReadOtuCommand::~ReadOtuCommand(){
- }
-
+ReadOtuCommand::~ReadOtuCommand(){}
//**********************************************************************************************************************
int ReadOtuCommand::execute(){
try {
if (abort == true) { return 0; }
-
+
if (globaldata->getFormat() == "shared") {
shared = new SharedCommand(outputDir);
globaldata->setListFile("");
globaldata->setGroupFile("");
globaldata->setSharedFile("");
- }else {
- m->mothurOutEndLine();
- m->mothurOut("Output File Name: "); m->mothurOutEndLine();
- m->mothurOut(globaldata->getSharedFile()); m->mothurOutEndLine();
- m->mothurOutEndLine();
+ }else { //shared command outputs the filenames
+ //m->mothurOutEndLine();
+ //m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ //m->mothurOut(globaldata->getSharedFile()); m->mothurOutEndLine();
+ //m->mothurOutEndLine();
}
delete shared;