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
  16 #include "utilities.hpp"
  17 #include "globaldata.hpp"
  18 #include "commandoptionparser.hpp"
  19 #include "command.hpp"
  20 #include "commandfactory.hpp"
  21 #include "errorchecking.h"
  22 #include "engine.hpp"
  23
  24 /***********************************************************************/
  25
  26 InteractEngine::InteractEngine(){
  27
  28         globaldata = GlobalData::getInstance();
  29
  30         system("clear");
  31 //      char buffer = ' ';
  32 //      ifstream header("introtext.txt");
  33 //      while(!header.eof()){
  34 //              cout << buffer;
  35 //              buffer = header.get();
  36 //      }
  37 }
  38
  39 /***********************************************************************/
  40
  41 InteractEngine::~InteractEngine(){
  42         }
  43
  44 /***********************************************************************/
  45 //This function allows the user to input commands one line at a time until they quit.
  46 //If the command is garbage it does nothing.
  47 bool InteractEngine::getInput(){
  48         try {
  49                 string input = "";
  50                 string commandName = "";
  51                 int quitCommandCalled = 0;
  52                 bool errorFree;
  53                 ErrorCheck* errorCheckor = new ErrorCheck();
  54
  55                 cout << "mothur v1.0" << endl;
  56                 cout << "Last updated: 1/29/2009" << endl << endl;
  57                 cout << "by" << endl;
  58                 cout << "Patrick D. Schloss" << endl << endl;
  59                 cout << "Department of Microbiology" << endl;
  60                 cout << "The University of Massachusetts" << endl;
  61                 cout << "pschloss@micro.umass.edu" << endl;
  62                 cout << "http://schloss.micro.umass.edu/mothur" << endl << endl << endl;
  63                 cout << "Distributed under the GNU General Public License" << endl << endl;
  64                 cout << "Type 'help()' for information on the commands that are available" << endl << endl;
  65                 cout << "Type 'quit()' to exit program" << endl;
  66
  67                 while(quitCommandCalled != 1){
  68
  69                         cout << endl << "mothur > ";
  70                         getline(cin, input);
  71                         if (cin.eof()) { input = "quit()"; }
  72
  73                         errorFree = errorCheckor->checkInput(input);
  74                         if (errorFree == true) {
  75                                 CommandOptionParser parser(input);
  76                                 commandName = parser.getCommandString();
  77
  78                                 //executes valid command
  79                                 CommandFactory cFactory;
  80                                 Command* command = cFactory.getCommand(commandName);
  81                                 quitCommandCalled = command->execute();
  82
  83                         }else {
  84                                         cout << "Your input contains errors. Please try again." << endl;
  85                         }
  86                 }
  87                 return 1;
  88         }
  89         catch(exception& e) {
  90                 cout << "Standard Error: " << e.what() << " has occurred in the InteractEngine class Function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  91                 exit(1);
  92         }
  93         catch(...) {
  94                 cout << "An unknown error has occurred in the InteractEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  95                 exit(1);
  96         }
  97
  98 }
  99
 100 /***********************************************************************/
 101 //This function opens the batchfile to be used by BatchEngine::getInput.
 102 BatchEngine::BatchEngine(string batchFileName){
 103         try {
 104                 globaldata = GlobalData::getInstance();
 105                 openedBatch = openInputFile(batchFileName, inputBatchFile);
 106
 107                 system("clear");
 108
 109         //      char buffer = ' ';
 110         //      ifstream header("introtext.txt");
 111         //      while(!header.eof()){
 112         //              cout << buffer;
 113         //              buffer = header.get();
 114         //      }
 115         }
 116         catch(exception& e) {
 117                 cout << "Standard Error: " << e.what() << " has occurred in the BatchEngine class Function BatchEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 118                 exit(1);
 119         }
 120         catch(...) {
 121                 cout << "An unknown error has occurred in the BatchEngine class function BatchEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 122                 exit(1);
 123         }
 124 }
 125
 126 /***********************************************************************/
 127
 128 BatchEngine::~BatchEngine(){
 129         }
 130
 131 /***********************************************************************/
 132 //This Function allows the user to run a batchfile containing several commands on Dotur
 133 bool BatchEngine::getInput(){
 134         try {
 135                 string input = "";
 136                 string commandName = "";
 137                 bool errorFree;
 138                 ErrorCheck* errorCheckor = new ErrorCheck();
 139
 140                 CommandFactory cFactory;
 141                 int quitCommandCalled = 0;
 142
 143                 while(quitCommandCalled == 0){
 144
 145                         getline(inputBatchFile, input);
 146                         if (inputBatchFile.eof()) { input = "quit()"; }
 147
 148                         cout << endl << "mothur > " << input << endl;
 149                         errorFree = errorCheckor->checkInput(input);
 150                         if (errorFree == true) {
 151                                 CommandOptionParser parser(input);
 152                                 commandName = parser.getCommandString();
 153                                 ifstream filehandle;
 154
 155                                 if (openedBatch == 0) { //able to open batchfile
 156                                         //executes valid command
 157                                         CommandFactory cFactory;
 158                                         Command* command = cFactory.getCommand(commandName);
 159                                         quitCommandCalled = command->execute();
 160                                 }
 161                                 else {
 162                                         cout << "Invalid." << endl;
 163                                 }
 164                         }
 165                         else {
 166                                 cout << "Unable to open batchfile." << endl;
 167                         }
 168                 }
 169                 return 1;
 170         }
 171         catch(exception& e) {
 172                 cout << "Standard Error: " << e.what() << " has occurred in the BatchEngine class Function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 173                 exit(1);
 174         }
 175         catch(...) {
 176                 cout << "An unknown error has occurred in the BatchEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 177                 exit(1);
 178         }
 179 }
 180
 181
 182 /***********************************************************************/
 183