ValidCommands::ValidCommands() {
try {
- commands["read.phylip"] = "read.phylip";
- commands["read.column"] = "read.column";
+ commands["read.dist"] = "read.dist";
+ commands["read.otu"] = "read.otu";
commands["read.list"] = "read.list";
- commands["read.rabund"] = "read.rabund";
- commands["read.sabund"] = "read.sabund";
- commands["read.shared"] = "read.shared";
commands["cluster"] = "cluster";
commands["help"] = "help";
commands["quit"] = "quit";
commands["collect.single"] = "collect.single";
- commands["shared"] = "shared";
commands["collect.shared"] = "collect.shared";
commands["rarefaction.single"] = "rarefaction.single";
commands["rarefaction.shared"] = "rarefaction.shared";
commands["summary.single"] = "summary.single";
commands["summary.shared"] = "summary.shared";
- commands["parselist"] = "parselist";
-
+
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the ValidCommands class Function ValidCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
if ((commands.find(command)) != (commands.end())) {
return true;
}else{
- cout << command << " is not a valid command in Mothur. Valid commands are read.phylip(), read.column(), read.list(), read.rabund(), read.sabund(), read.shared(), cluster(), collect.single(), collect.shared(), parselist(), shared(), rarefaction.single(), rarefaction.shared(), summary.single(), summary.shared(), quit(), help()." << endl;
+ cout << command << " is not a valid command in Mothur. Valid commands are read.dist(), read.list(), cluster(), collect.single(), collect.shared(), rarefaction.single(), rarefaction.shared(), summary.single(), summary.shared(), quit(), help()." << endl;
return false;
}