commands["read.dist"] = "read.dist";
commands["read.otu"] = "read.otu";
commands["read.tree"] = "read.tree";
+ commands["bin.seqs"] = "bin.seqs";
+ commands["get.oturep"] = "get.oturep";
commands["cluster"] = "cluster";
commands["deconvolute"] = "deconvolute";
- commands["parsimony"] = "parsimony";
- commands["help"] = "help";
- commands["quit"] = "quit";
commands["collect.single"] = "collect.single";
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["parsimony"] = "parsimony";
commands["unifrac.weighted"] = "unifrac.weighted";
commands["unifrac.unweighted"] = "unifrac.unweighted";
+ commands["libshuff"] = "libshuff";
+ commands["tree.shared"] = "tree.shared";
+ commands["heatmap"] = "heatmap";
+ commands["venn"] = "venn";
+ commands["get.group"] = "get.group";
+ commands["get.label"] = "get.label";
+ commands["get.line"] = "get.line";
+ commands["bootstrap.shared"] = "bootstrap.shared";
+ commands["help"] = "help";
+ commands["quit"] = "quit";
}
if ((commands.find(command)) != (commands.end())) {
return true;
}else{
- cout << command << " is not a valid command in Mothur. Valid commands are read.dist(), read.otu(), cluster(), collect.single(), collect.shared(), rarefaction.single(), rarefaction.shared(), summary.single(), summary.shared(), quit(), help()." << endl;
+ cout << command << " is not a valid command in Mothur. Valid commands are ";
+ for (it = commands.begin(); it != commands.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
return false;
}
}
/***********************************************************************/
+void ValidCommands::printCommands(ostream& out) {
+ try {
+ out << "Valid commands are ";
+ for (it = commands.begin(); it != commands.end(); it++) {
+ out << it->first << ", ";
+ }
+ out << endl;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ValidCommands class Function printCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ValidCommands class function printCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+
+
+