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["unique.seqs"] = "unique.seqs";
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.bin"] = "heatmap.bin";
38 commands["heatmap.sim"] = "heatmap.sim";
39 commands["venn"] = "venn";
40 commands["get.group"] = "get.group";
41 commands["get.label"] = "get.label";
42 commands["get.line"] = "get.line";
43 commands["get.sabund"] = "get.sabund";
44 commands["get.rabund"] = "get.rabund";
45 commands["bootstrap.shared"] = "bootstrap.shared";
46 commands["concensus"] = "concensus";
47 commands["help"] = "help";
48 commands["filter.seqs"] = "filter.seqs";
49 commands["align.seqs"] = "align.seqs";
50 commands["summary.seqs"] = "summary.seqs";
51 commands["screen.seqs"] = "screen.seqs";
52 commands["reverse.seqs"] = "reverse.seqs";
53 commands["trim.seqs"] = "trim.seqs";
54 commands["quit"] = "quit";
59 cout << "Standard Error: " << e.what() << " has occurred in the ValidCommands class Function ValidCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
63 cout << "An unknown error has occurred in the ValidCommands class function ValidCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
68 /***********************************************************************/
70 ValidCommands::~ValidCommands() {}
72 /***********************************************************************/
73 bool ValidCommands::isValidCommand(string command) {
76 //is the command in the map
77 if ((commands.find(command)) != (commands.end())) {
80 cout << command << " is not a valid command in Mothur. Valid commands are ";
81 for (it = commands.begin(); it != commands.end(); it++) {
82 cout << it->first << ", ";
90 cout << "Standard Error: " << e.what() << " has occurred in the ValidCommands class Function isValidCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
94 cout << "An unknown error has occurred in the ValidCommands class function isValidCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
99 /***********************************************************************/
100 void ValidCommands::printCommands(ostream& out) {
102 out << "Valid commands are ";
103 for (it = commands.begin(); it != commands.end(); it++) {
104 out << it->first << ", ";
108 catch(exception& e) {
109 cout << "Standard Error: " << e.what() << " has occurred in the ValidCommands class Function printCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
113 cout << "An unknown error has occurred in the ValidCommands class function printCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";