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