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.seqs"]           = "read.seqs";
  21                 commands["bin.seqs"]                    = "bin.seqs";
  22                 commands["get.oturep"]                  = "get.oturep";
  23                 commands["cluster"]                             = "cluster";
  24                 commands["deconvolute"]                 = "deconvolute";
  25                 commands["dist.seqs"]                   = "dist.seqs";
  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["bootstrap.shared"]    = "bootstrap.shared";
  43                 commands["concensus"]                   = "concensus";
  44                 commands["help"]                                = "help";
  45                 commands["filter.seqs"]                 = "filter.seqs";
  46                 commands["align.seqs"]                  = "align.seqs";
  47                 commands["quit"]                                = "quit";
  48
  49
  50         }
  51         catch(exception& e) {
  52                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCommands class Function ValidCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  53                 exit(1);
  54         }
  55         catch(...) {
  56                 cout << "An unknown error has occurred in the ValidCommands class function ValidCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  57                 exit(1);
  58         }
  59 }
  60
  61 /***********************************************************************/
  62
  63 ValidCommands::~ValidCommands() {}
  64
  65 /***********************************************************************/
  66 bool ValidCommands::isValidCommand(string command) {
  67         try {
  68
  69                 //is the command in the map
  70                 if ((commands.find(command)) != (commands.end())) {
  71                         return true;
  72                 }else{
  73                         cout << command << " is not a valid command in Mothur.  Valid commands are ";
  74                         for (it = commands.begin(); it != commands.end(); it++) {
  75                                 cout << it->first << ", ";
  76                         }
  77                         cout << endl;
  78                         return false;
  79                 }
  80
  81         }
  82         catch(exception& e) {
  83                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCommands class Function isValidCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  84                 exit(1);
  85         }
  86         catch(...) {
  87                 cout << "An unknown error has occurred in the ValidCommands class function isValidCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  88                 exit(1);
  89         }
  90 }
  91
  92 /***********************************************************************/
  93 void ValidCommands::printCommands(ostream& out) {
  94         try {
  95                 out << "Valid commands are ";
  96                 for (it = commands.begin(); it != commands.end(); it++) {
  97                         out << it->first << ", ";
  98                 }
  99                 out << endl;
 100         }
 101         catch(exception& e) {
 102                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCommands class Function printCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 103                 exit(1);
 104         }
 105         catch(...) {
 106                 cout << "An unknown error has occurred in the ValidCommands class function printCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 107                 exit(1);
 108         }
 109 }
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