//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); }
rabundfile = validParameter.validFile(parameters, "rabund", true);
if (rabundfile == "not open") { rabundfile = ""; abort = true; }
else if (rabundfile == "not found") { rabundfile = ""; }
- else { format = "rabund"; inputfile = rabundfile; }
+ else { format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
sharedfile = validParameter.validFile(parameters, "shared", true);
if (sharedfile == "not open") { sharedfile = ""; abort = true; }
else if (sharedfile == "not found") { sharedfile = ""; }
- else { format = "sharedfile"; inputfile = sharedfile; }
+ else { format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
relabundfile = validParameter.validFile(parameters, "relabund", true);
if (relabundfile == "not open") { relabundfile = ""; abort = true; }
else if (relabundfile == "not found") { relabundfile = ""; }
- else { format = "relabund"; inputfile = relabundfile; }
+ else { format = "relabund"; inputfile = relabundfile; m->setRelAbundFile(relabundfile); }
if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "") && (relabundfile == "")) {