helpString += "Example get.rabund(sorted=F).\n";
helpString += "The default value for label is all labels in your inputfile.\n";
helpString += "The get.rabund command outputs a .rabund file containing the lines you selected.\n";
- helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n\n";
+ helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n";
return helpString;
}
catch(exception& e) {
//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();
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") { listfile = ""; abort = true; }
else if (listfile == "not found") { listfile = ""; }
- else { format = "list"; inputfile = listfile; }
+ else { format = "list"; inputfile = listfile; m->setListFile(listfile); }
sabundfile = validParameter.validFile(parameters, "sabund", true);
if (sabundfile == "not open") { sabundfile = ""; abort = true; }
else if (sabundfile == "not found") { sabundfile = ""; }
- else { format = "sabund"; inputfile = sabundfile; }
+ else { format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
//check for optional parameter and set defaults
if(sorted) { rabund->print(out); }
else { rabund->nonSortedPrint(out); }
-
- delete rabund;
processedLabels.insert(rabund->getLabel());
userLabels.erase(rabund->getLabel());
if(sorted) { rabund->print(out); }
else { rabund->nonSortedPrint(out); }
- delete rabund;
-
processedLabels.insert(rabund->getLabel());
userLabels.erase(rabund->getLabel());