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["parsimony"]                   = "parsimony";
  23                 commands["help"]                                = "help";
  24                 commands["quit"]                                = "quit";
  25                 commands["collect.single"]              = "collect.single";
  26                 commands["collect.shared"]              = "collect.shared";
  27                 commands["rarefaction.single"]  = "rarefaction.single";
  28                 commands["rarefaction.shared"]  = "rarefaction.shared";
  29                 commands["summary.single"]              = "summary.single";
  30                 commands["summary.shared"]              = "summary.shared";
  31                 commands["unifrac.weighted"]    = "unifrac.weighted";
  32                 commands["unifrac.unweighted"]  = "unifrac.unweighted";
  33
  34
  35         }
  36         catch(exception& e) {
  37                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCommands class Function ValidCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  38                 exit(1);
  39         }
  40         catch(...) {
  41                 cout << "An unknown error has occurred in the ValidCommands class function ValidCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  42                 exit(1);
  43         }
  44 }
  45
  46 /***********************************************************************/
  47
  48 ValidCommands::~ValidCommands() {}
  49
  50 /***********************************************************************/
  51 bool ValidCommands::isValidCommand(string command) {
  52         try {
  53
  54                 //is the command in the map
  55                 if ((commands.find(command)) != (commands.end())) {
  56                         return true;
  57                 }else{
  58                         cout << command << " is not a valid command in Mothur.  Valid commands are read.dist(), read.otu(), read.tree(), cluster(), deconvolute(), collect.single(), collect.shared(), rarefaction.single(), rarefaction.shared(), summary.single(), summary.shared(), parsimony(), unifrac.weighted(), unifrac.unweighted(), quit(), help()." << endl;
  59                         return false;
  60                 }
  61
  62         }
  63         catch(exception& e) {
  64                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCommands class Function isValidCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  65                 exit(1);
  66         }
  67         catch(...) {
  68                 cout << "An unknown error has occurred in the ValidCommands class function isValidCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  69                 exit(1);
  70         }
  71 }
  72
  73 /***********************************************************************/