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["get.group"]           = "get.group";
  28                 commands["get.label"]           = "get.label";
  29                 commands["get.line"]            = "get.line";
  30                 commands["rarefaction.single"]  = "rarefaction.single";
  31                 commands["rarefaction.shared"]  = "rarefaction.shared";
  32                 commands["summary.single"]              = "summary.single";
  33                 commands["summary.shared"]              = "summary.shared";
  34                 commands["unifrac.weighted"]    = "unifrac.weighted";
  35                 commands["unifrac.unweighted"]  = "unifrac.unweighted";
  36                 commands["libshuff"]                    = "libshuff";
  37
  38
  39         }
  40         catch(exception& e) {
  41                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCommands class Function ValidCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  42                 exit(1);
  43         }
  44         catch(...) {
  45                 cout << "An unknown error has occurred in the ValidCommands class function ValidCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  46                 exit(1);
  47         }
  48 }
  49
  50 /***********************************************************************/
  51
  52 ValidCommands::~ValidCommands() {}
  53
  54 /***********************************************************************/
  55 bool ValidCommands::isValidCommand(string command) {
  56         try {
  57
  58                 //is the command in the map
  59                 if ((commands.find(command)) != (commands.end())) {
  60                         return true;
  61                 }else{
  62                         cout << command << " is not a valid command in Mothur.  Valid commands are ";
  63                         for (it = commands.begin(); it != commands.end(); it++) {
  64                                 cout << it->first << ", ";
  65                         }
  66                         cout << endl;
  67                         return false;
  68                 }
  69
  70         }
  71         catch(exception& e) {
  72                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCommands class Function isValidCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  73                 exit(1);
  74         }
  75         catch(...) {
  76                 cout << "An unknown error has occurred in the ValidCommands class function isValidCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  77                 exit(1);
  78         }
  79 }
  80
  81 /***********************************************************************/
  82 void ValidCommands::printCommands(ostream& out) {
  83         try {
  84                 out << "Valid commands are ";
  85                 for (it = commands.begin(); it != commands.end(); it++) {
  86                         out << it->first << ", ";
  87                 }
  88                 out << endl;
  89         }
  90         catch(exception& e) {
  91                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCommands class Function printCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  92                 exit(1);
  93         }
  94         catch(...) {
  95                 cout << "An unknown error has occurred in the ValidCommands class function printCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  96                 exit(1);
  97         }
  98 }
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