//**********************************************************************************************************************
AmovaCommand::AmovaCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["amova"] = tempOutNames;
}
AmovaCommand::AmovaCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
void AmovaCommand::help(){
try {
+ m->mothurOut("Referenced: Anderson MJ (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46.\n");
m->mothurOut("The amova command can only be executed after a successful read.otu command of a list and group or shared file, or by providing a phylip formatted distance matrix.\n");
m->mothurOut("The amova command outputs a .amova file. \n");
m->mothurOut("The amova command parameters are phylip, iters, groups, label, design, sets and processors. The design parameter is required.\n");
int AmovaCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//read design file
designMap = new GroupMap(designfile);