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["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"]                             = "heatmap";
  38                 commands["venn"]                                = "venn";
  39                 commands["get.group"]           = "get.group";
  40                 commands["get.label"]           = "get.label";
  41                 commands["get.line"]            = "get.line";
  42                 commands["get.sabund"]          = "get.sabund";
  43                 commands["get.rabund"]          = "get.rabund";
  44                 commands["bootstrap.shared"]    = "bootstrap.shared";
  45                 commands["concensus"]                   = "concensus";
  46                 commands["help"]                                = "help";
  47                 commands["filter.seqs"]                 = "filter.seqs";
  48                 commands["align.seqs"]                  = "align.seqs";
  49                 commands["summary.seqs"]                = "summary.seqs";
  50                 commands["screen.seqs"]                 = "screen.seqs";
  51                 commands["reverse.seqs"]                = "reverse.seqs";
  52                 commands["quit"]                                = "quit";
  53
  54
  55         }
  56         catch(exception& e) {
  57                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCommands class Function ValidCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  58                 exit(1);
  59         }
  60         catch(...) {
  61                 cout << "An unknown error has occurred in the ValidCommands class function ValidCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  62                 exit(1);
  63         }
  64 }
  65
  66 /***********************************************************************/
  67
  68 ValidCommands::~ValidCommands() {}
  69
  70 /***********************************************************************/
  71 bool ValidCommands::isValidCommand(string command) {
  72         try {
  73
  74                 //is the command in the map
  75                 if ((commands.find(command)) != (commands.end())) {
  76                         return true;
  77                 }else{
  78                         cout << command << " is not a valid command in Mothur.  Valid commands are ";
  79                         for (it = commands.begin(); it != commands.end(); it++) {
  80                                 cout << it->first << ", ";
  81                         }
  82                         cout << endl;
  83                         return false;
  84                 }
  85
  86         }
  87         catch(exception& e) {
  88                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCommands class Function isValidCommand. 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 isValidCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  93                 exit(1);
  94         }
  95 }
  96
  97 /***********************************************************************/
  98 void ValidCommands::printCommands(ostream& out) {
  99         try {
 100                 out << "Valid commands are ";
 101                 for (it = commands.begin(); it != commands.end(); it++) {
 102                         out << it->first << ", ";
 103                 }
 104                 out << endl;
 105         }
 106         catch(exception& e) {
 107                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCommands class Function printCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 108                 exit(1);
 109         }
 110         catch(...) {
 111                 cout << "An unknown error has occurred in the ValidCommands class function printCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 112                 exit(1);
 113         }
 114 }
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