5 * Created by Sarah Westcott on 1/5/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "validcommands.h"
12 /***********************************************************************/
14 ValidCommands::ValidCommands() {
17 commands["read.dist"] = "read.dist";
18 commands["read.otu"] = "read.otu";
19 commands["read.tree"] = "read.tree";
20 commands["bin.seqs"] = "bin.seqs";
21 commands["get.oturep"] = "get.oturep";
22 commands["cluster"] = "cluster";
23 commands["deconvolute"] = "deconvolute";
24 commands["dist.seqs"] = "dist.seqs";
25 commands["dist.shared"] = "dist.shared";
26 commands["collect.single"] = "collect.single";
27 commands["collect.shared"] = "collect.shared";
28 commands["rarefaction.single"] = "rarefaction.single";
29 commands["rarefaction.shared"] = "rarefaction.shared";
30 commands["summary.single"] = "summary.single";
31 commands["summary.shared"] = "summary.shared";
32 commands["parsimony"] = "parsimony";
33 commands["unifrac.weighted"] = "unifrac.weighted";
34 commands["unifrac.unweighted"] = "unifrac.unweighted";
35 commands["libshuff"] = "libshuff";
36 commands["tree.shared"] = "tree.shared";
37 commands["heatmap"] = "heatmap";
38 commands["venn"] = "venn";
39 commands["get.group"] = "get.group";
40 commands["get.label"] = "get.label";
41 commands["get.line"] = "get.line";
42 commands["get.sabund"] = "get.sabund";
43 commands["get.rabund"] = "get.rabund";
44 commands["bootstrap.shared"] = "bootstrap.shared";
45 commands["concensus"] = "concensus";
46 commands["help"] = "help";
47 commands["filter.seqs"] = "filter.seqs";
48 commands["align.seqs"] = "align.seqs";
49 commands["summary.seqs"] = "summary.seqs";
50 commands["quit"] = "quit";
55 cout << "Standard Error: " << e.what() << " has occurred in the ValidCommands class Function ValidCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
59 cout << "An unknown error has occurred in the ValidCommands class function ValidCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
64 /***********************************************************************/
66 ValidCommands::~ValidCommands() {}
68 /***********************************************************************/
69 bool ValidCommands::isValidCommand(string command) {
72 //is the command in the map
73 if ((commands.find(command)) != (commands.end())) {
76 cout << command << " is not a valid command in Mothur. Valid commands are ";
77 for (it = commands.begin(); it != commands.end(); it++) {
78 cout << it->first << ", ";
86 cout << "Standard Error: " << e.what() << " has occurred in the ValidCommands class Function isValidCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
90 cout << "An unknown error has occurred in the ValidCommands class function isValidCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
95 /***********************************************************************/
96 void ValidCommands::printCommands(ostream& out) {
98 out << "Valid commands are ";
99 for (it = commands.begin(); it != commands.end(); it++) {
100 out << it->first << ", ";
104 catch(exception& e) {
105 cout << "Standard Error: " << e.what() << " has occurred in the ValidCommands class Function printCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
109 cout << "An unknown error has occurred in the ValidCommands class function printCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";