validcommands.cpp

   1 /*
   2  *  validcommands.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/5/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "validcommands.h"
  11
  12 /***********************************************************************/
  13
  14 ValidCommands::ValidCommands() {
  15         try {
  16
  17                 commands["read.dist"]                   = "read.dist";
  18                 commands["read.otu"]                    = "read.otu";
  19         //      commands["read.tree"]                   = "read.tree";
  20                 commands["cluster"]                             = "cluster";
  21                 commands["deconvolute"]                 = "deconvolute";
  22                 commands["help"]                                = "help";
  23                 commands["quit"]                                = "quit";
  24                 commands["collect.single"]              = "collect.single";
  25                 commands["collect.shared"]              = "collect.shared";
  26                 commands["rarefaction.single"]  = "rarefaction.single";
  27                 commands["rarefaction.shared"]  = "rarefaction.shared";
  28                 commands["summary.single"]              = "summary.single";
  29                 commands["summary.shared"]              = "summary.shared";
  30
  31         }
  32         catch(exception& e) {
  33                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCommands class Function ValidCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  34                 exit(1);
  35         }
  36         catch(...) {
  37                 cout << "An unknown error has occurred in the ValidCommands class function ValidCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  38                 exit(1);
  39         }
  40 }
  41
  42 /***********************************************************************/
  43
  44 ValidCommands::~ValidCommands() {}
  45
  46 /***********************************************************************/
  47 bool ValidCommands::isValidCommand(string command) {
  48         try {
  49
  50                 //is the command in the map
  51                 if ((commands.find(command)) != (commands.end())) {
  52                         return true;
  53                 }else{
  54                         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;
  55                         return false;
  56                 }
  57
  58         }
  59         catch(exception& e) {
  60                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCommands class Function isValidCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  61                 exit(1);
  62         }
  63         catch(...) {
  64                 cout << "An unknown error has occurred in the ValidCommands class function isValidCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  65                 exit(1);
  66         }
  67 }
  68
  69 /***********************************************************************/