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 using namespace std;
  14
  15 #include "engine.hpp"
  16
  17 /***********************************************************************/
  18
  19 InteractEngine::InteractEngine(){
  20
  21         globaldata = GlobalData::getInstance();
  22
  23         system("clear");
  24 //      char buffer = ' ';
  25 //      ifstream header("introtext.txt");
  26 //      while(!header.eof()){
  27 //              cout << buffer;
  28 //              buffer = header.get();
  29 //      }
  30 }
  31
  32 /***********************************************************************/
  33
  34 InteractEngine::~InteractEngine(){
  35         }
  36
  37 /***********************************************************************/
  38 //This function allows the user to input commands one line at a time until they quit.
  39 //If the command is garbage it does nothing.
  40 bool InteractEngine::getInput(){
  41         try {
  42                 string input = "";
  43                 string commandName = "";
  44                 int quitCommandCalled = 0;
  45                 bool errorFree;
  46                 ErrorCheck* errorCheckor = new ErrorCheck();
  47
  48                 cout << "mothur v1.0" << endl;
  49                 cout << "Last updated: 1/29/2009" << endl << endl;
  50                 cout << "by" << endl;
  51                 cout << "Patrick D. Schloss" << endl << endl;
  52                 cout << "Department of Microbiology" << endl;
  53                 cout << "The University of Massachusetts" << endl;
  54                 cout << "pschloss@micro.umass.edu" << endl;
  55                 cout << "http://schloss.micro.umass.edu/mothur" << endl << endl << endl;
  56                 cout << "Distributed under the GNU General Public License" << endl << endl;
  57                 cout << "Type 'help()' for information on the commands that are available" << endl << endl;
  58                 cout << "Type 'quit()' to exit program" << endl;
  59
  60                 while(quitCommandCalled != 1){
  61
  62                         cout << endl << "mothur > ";
  63                         getline(cin, input);
  64                         if (cin.eof()) { input = "quit()"; }
  65
  66                         errorFree = errorCheckor->checkInput(input);
  67                         if (errorFree == true) {
  68                                 CommandOptionParser parser(input);
  69                                 commandName = parser.getCommandString();
  70
  71                                 //executes valid command
  72                                 CommandFactory cFactory;
  73                                 Command* command = cFactory.getCommand(commandName);
  74                                 quitCommandCalled = command->execute();
  75
  76                         }else {
  77                                         cout << "Your input contains errors. Please try again." << endl;
  78                         }
  79                 }
  80                 return 1;
  81         }
  82         catch(exception& e) {
  83                 cout << "Standard Error: " << e.what() << " has occurred in the InteractEngine class Function getInput. 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 InteractEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  88                 exit(1);
  89         }
  90
  91 }
  92
  93 /***********************************************************************/
  94 //This function opens the batchfile to be used by BatchEngine::getInput.
  95 BatchEngine::BatchEngine(string batchFileName){
  96         try {
  97                 globaldata = GlobalData::getInstance();
  98                 openedBatch = openInputFile(batchFileName, inputBatchFile);
  99
 100                 system("clear");
 101
 102         //      char buffer = ' ';
 103         //      ifstream header("introtext.txt");
 104         //      while(!header.eof()){
 105         //              cout << buffer;
 106         //              buffer = header.get();
 107         //      }
 108         }
 109         catch(exception& e) {
 110                 cout << "Standard Error: " << e.what() << " has occurred in the BatchEngine class Function BatchEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 111                 exit(1);
 112         }
 113         catch(...) {
 114                 cout << "An unknown error has occurred in the BatchEngine class function BatchEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 115                 exit(1);
 116         }
 117 }
 118
 119 /***********************************************************************/
 120
 121 BatchEngine::~BatchEngine(){
 122         }
 123
 124 /***********************************************************************/
 125 //This Function allows the user to run a batchfile containing several commands on Dotur
 126 bool BatchEngine::getInput(){
 127         try {
 128                 string input = "";
 129                 string commandName = "";
 130                 bool errorFree;
 131                 ErrorCheck* errorCheckor = new ErrorCheck();
 132
 133                 CommandFactory cFactory;
 134                 int quitCommandCalled = 0;
 135
 136                 while(quitCommandCalled == 0){
 137
 138                         getline(inputBatchFile, input);
 139                         if (inputBatchFile.eof()) { input = "quit()"; }
 140
 141                         cout << endl << "mothur > " << input << endl;
 142                         errorFree = errorCheckor->checkInput(input);
 143                         if (errorFree == true) {
 144                                 CommandOptionParser parser(input);
 145                                 commandName = parser.getCommandString();
 146                                 ifstream filehandle;
 147
 148                                 if (openedBatch == 0) { //able to open batchfile
 149                                         //executes valid command
 150                                         CommandFactory cFactory;
 151                                         Command* command = cFactory.getCommand(commandName);
 152                                         quitCommandCalled = command->execute();
 153                                 }
 154                                 else {
 155                                         cout << "Invalid." << endl;
 156                                 }
 157                         }
 158                         else {
 159                                 cout << "Unable to open batchfile." << endl;
 160                         }
 161                 }
 162                 return 1;
 163         }
 164         catch(exception& e) {
 165                 cout << "Standard Error: " << e.what() << " has occurred in the BatchEngine class Function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 166                 exit(1);
 167         }
 168         catch(...) {
 169                 cout << "An unknown error has occurred in the BatchEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 170                 exit(1);
 171         }
 172 }
 173
 174
 175 /***********************************************************************/
 176