engine.cpp

   1 /*
   2  *  engine.cpp
   3  *
   4  *
   5  *  Created by Pat Schloss on 8/15/08.
   6  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
   7  *
   8  *  There's a TON of duplicated code between InteractEngine and BatchEngine
   9  *  I couldn't figure out how to transition between ifstream (batch) and cin (interact)
  10  *  Fix later, don't have time now.
  11  *
  12  */
  13
  14
  15 #include "engine.hpp"
  16
  17 /***********************************************************************/
  18
  19 InteractEngine::InteractEngine(string path){
  20
  21         globaldata = GlobalData::getInstance();
  22         globaldata->argv = path;
  23
  24         system("clear");
  25 //      char buffer = ' ';
  26 //      ifstream header("introtext.txt");
  27 //      while(!header.eof()){
  28 //              cout << buffer;
  29 //              buffer = header.get();
  30 //      }
  31 }
  32
  33 /***********************************************************************/
  34
  35 InteractEngine::~InteractEngine(){
  36         }
  37
  38 /***********************************************************************/
  39 //This function allows the user to input commands one line at a time until they quit.
  40 //If the command is garbage it does nothing.
  41 bool InteractEngine::getInput(){
  42         try {
  43                 string input = "";
  44                 string commandName = "";
  45                 string options = "";
  46                 int quitCommandCalled = 0;
  47                 //bool errorFree;
  48                 //ErrorCheck* errorCheckor = new ErrorCheck();
  49
  50                 cout << "mothur v.1.3.0" << endl;
  51                 cout << "Last updated: 5/29/2009" << endl << endl;
  52                 cout << "by" << endl;
  53                 cout << "Patrick D. Schloss" << endl << endl;
  54                 cout << "Department of Microbiology" << endl;
  55                 cout << "The University of Massachusetts" << endl;
  56                 cout << "pschloss@micro.umass.edu" << endl;
  57                 cout << "http://schloss.micro.umass.edu/mothur" << endl << endl << endl;
  58                 cout << "Distributed under the GNU General Public License" << endl << endl;
  59                 cout << "Type 'help()' for information on the commands that are available" << endl << endl;
  60                 cout << "Type 'quit()' to exit program" << endl;
  61
  62                 while(quitCommandCalled != 1){
  63
  64                         cout << endl << "mothur > ";
  65                         getline(cin, input);
  66                         if (cin.eof()) { input = "quit()"; }
  67
  68                         //allow user to omit the () on the quit command
  69                         if (input == "quit") { input = "quit()"; }
  70
  71                         //errorFree = errorCheckor->checkInput(input);
  72                         //if (errorFree == true) {
  73                         CommandOptionParser parser(input);
  74                         commandName = parser.getCommandString();
  75                         options = parser.getOptionString();
  76
  77                         if (commandName != "") {
  78
  79                                 //executes valid command
  80                                 CommandFactory cFactory;
  81                                 Command* command = cFactory.getCommand(commandName, options);
  82                                 quitCommandCalled = command->execute();
  83
  84                         }else {
  85                                 cout << "Your input contains errors. Please try again." << endl;
  86                         }
  87                 }
  88                 return 1;
  89         }
  90         catch(exception& e) {
  91                 cout << "Standard Error: " << e.what() << " has occurred in the InteractEngine class Function getInput. 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 InteractEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  96                 exit(1);
  97         }
  98
  99 }
 100
 101 /***********************************************************************/
 102 //This function opens the batchfile to be used by BatchEngine::getInput.
 103 BatchEngine::BatchEngine(string path, string batchFileName){
 104         try {
 105                 globaldata = GlobalData::getInstance();
 106                 openedBatch = openInputFile(batchFileName, inputBatchFile);
 107                 globaldata->argv = path;
 108
 109                 system("clear");
 110
 111         //      char buffer = ' ';
 112         //      ifstream header("introtext.txt");
 113         //      while(!header.eof()){
 114         //              cout << buffer;
 115         //              buffer = header.get();
 116         //      }
 117         }
 118         catch(exception& e) {
 119                 cout << "Standard Error: " << e.what() << " has occurred in the BatchEngine class Function BatchEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 120                 exit(1);
 121         }
 122         catch(...) {
 123                 cout << "An unknown error has occurred in the BatchEngine class function BatchEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 124                 exit(1);
 125         }
 126 }
 127
 128 /***********************************************************************/
 129
 130 BatchEngine::~BatchEngine(){
 131         }
 132
 133 /***********************************************************************/
 134 //This Function allows the user to run a batchfile containing several commands on Dotur
 135 bool BatchEngine::getInput(){
 136         try {
 137                 //check if this is a valid batchfile
 138                 if (openedBatch == 1) {  cout << "unable to open batchfile" << endl;  return 1; }
 139
 140                 string input = "";
 141                 string commandName = "";
 142                 string options = "";
 143
 144                 //CommandFactory cFactory;
 145                 int quitCommandCalled = 0;
 146
 147                 while(quitCommandCalled == 0){
 148
 149                         if (inputBatchFile.eof()) { input = "quit()"; }
 150                         else { getline(inputBatchFile, input); }
 151
 152                         if (input[0] != '#') {
 153
 154                                 cout << endl << "mothur > " << input << endl;
 155
 156                                 //allow user to omit the () on the quit command
 157                                 if (input == "quit") { input = "quit()"; }
 158
 159                                 CommandOptionParser parser(input);
 160                                 commandName = parser.getCommandString();
 161                                 options = parser.getOptionString();
 162
 163                                 if (commandName != "") {
 164
 165                                         //executes valid command
 166                                         CommandFactory cFactory;
 167                                         Command* command = cFactory.getCommand(commandName, options);
 168                                         quitCommandCalled = command->execute();
 169                                 }else {         cout << "Invalid." << endl;             }
 170
 171                         }
 172                 }
 173                 return 1;
 174         }
 175         catch(exception& e) {
 176                 cout << "Standard Error: " << e.what() << " has occurred in the BatchEngine class Function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 177                 exit(1);
 178         }
 179         catch(...) {
 180                 cout << "An unknown error has occurred in the BatchEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 181                 exit(1);
 182         }
 183 }
 184
 185
 186 /***********************************************************************/
 187