-/*
- * validcommands.cpp
- * Dotur
- *
- * Created by Sarah Westcott on 1/5/09.
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "validcommands.h"
-
-/***********************************************************************/
-
-ValidCommands::ValidCommands() {
- try {
-
- 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["unique.seqs"] = "unique.seqs";
- commands["dist.seqs"] = "dist.seqs";
- commands["dist.shared"] = "dist.shared";
- 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.bin"] = "heatmap.bin";
- commands["heatmap.sim"] = "heatmap.sim";
- commands["venn"] = "venn";
- commands["get.group"] = "get.group";
- commands["get.label"] = "get.label";
- commands["get.line"] = "get.line";
- commands["get.sabund"] = "get.sabund";
- commands["get.rabund"] = "get.rabund";
- commands["bootstrap.shared"] = "bootstrap.shared";
- commands["concensus"] = "concensus";
- commands["help"] = "help";
- commands["filter.seqs"] = "filter.seqs";
- commands["align.seqs"] = "align.seqs";
- commands["summary.seqs"] = "summary.seqs";
- commands["screen.seqs"] = "screen.seqs";
- commands["reverse.seqs"] = "reverse.seqs";
- commands["trim.seqs"] = "trim.seqs";
- commands["quit"] = "quit";
-
-
- }
- 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";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ValidCommands class function ValidCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-ValidCommands::~ValidCommands() {}
-
-/***********************************************************************/
-bool ValidCommands::isValidCommand(string command) {
- try {
-
- //is the command in the map
- if ((commands.find(command)) != (commands.end())) {
- return true;
- }else{
- 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;
- }
-
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ValidCommands class Function isValidCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ValidCommands class function isValidCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-
-/***********************************************************************/
-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);
- }
-}
-
-
-
-