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(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                 int quitCommandCalled = 0;
  46                 bool errorFree;
  47                 ErrorCheck* errorCheckor = new ErrorCheck();
  48
  49                 cout << "mothur v1.2.0" << endl;
  50                 cout << "Last updated: 4/14/2009" << endl << endl;
  51                 cout << "by" << endl;
  52                 cout << "Patrick D. Schloss" << endl << endl;
  53                 cout << "Department of Microbiology" << endl;
  54                 cout << "The University of Massachusetts" << endl;
  55                 cout << "pschloss@micro.umass.edu" << endl;
  56                 cout << "http://schloss.micro.umass.edu/mothur" << endl << endl << endl;
  57                 cout << "Distributed under the GNU General Public License" << endl << endl;
  58                 cout << "Type 'help()' for information on the commands that are available" << endl << endl;
  59                 cout << "Type 'quit()' to exit program" << endl;
  60
  61                 while(quitCommandCalled != 1){
  62
  63                         cout << endl << "mothur > ";
  64                         getline(cin, input);
  65                         if (cin.eof()) { input = "quit()"; }
  66
  67                         errorFree = errorCheckor->checkInput(input);
  68                         if (errorFree == true) {
  69                                 CommandOptionParser parser(input);
  70                                 commandName = parser.getCommandString();
  71
  72                                 //executes valid command
  73                                 CommandFactory cFactory;
  74                                 Command* command = cFactory.getCommand(commandName);
  75                                 quitCommandCalled = command->execute();
  76
  77                         }else {
  78                                         cout << "Your input contains errors. Please try again." << endl;
  79                         }
  80                 }
  81                 return 1;
  82         }
  83         catch(exception& e) {
  84                 cout << "Standard Error: " << e.what() << " has occurred in the InteractEngine class Function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  85                 exit(1);
  86         }
  87         catch(...) {
  88                 cout << "An unknown error has occurred in the InteractEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  89                 exit(1);
  90         }
  91
  92 }
  93
  94 /***********************************************************************/
  95 //This function opens the batchfile to be used by BatchEngine::getInput.
  96 BatchEngine::BatchEngine(string path, string batchFileName){
  97         try {
  98                 globaldata = GlobalData::getInstance();
  99                 openedBatch = openInputFile(batchFileName, inputBatchFile);
 100                 globaldata->argv = path;
 101
 102                 system("clear");
 103
 104         //      char buffer = ' ';
 105         //      ifstream header("introtext.txt");
 106         //      while(!header.eof()){
 107         //              cout << buffer;
 108         //              buffer = header.get();
 109         //      }
 110         }
 111         catch(exception& e) {
 112                 cout << "Standard Error: " << e.what() << " has occurred in the BatchEngine class Function BatchEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 113                 exit(1);
 114         }
 115         catch(...) {
 116                 cout << "An unknown error has occurred in the BatchEngine class function BatchEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 117                 exit(1);
 118         }
 119 }
 120
 121 /***********************************************************************/
 122
 123 BatchEngine::~BatchEngine(){
 124         }
 125
 126 /***********************************************************************/
 127 //This Function allows the user to run a batchfile containing several commands on Dotur
 128 bool BatchEngine::getInput(){
 129         try {
 130                 //check if this is a valid batchfile
 131                 if (openedBatch == 1) {  cout << "unable to open batchfile" << endl;  return 1; }
 132
 133                 string input = "";
 134                 string commandName = "";
 135                 bool errorFree;
 136                 ErrorCheck* errorCheckor = new ErrorCheck();
 137
 138                 CommandFactory cFactory;
 139                 int quitCommandCalled = 0;
 140
 141                 while(quitCommandCalled == 0){
 142
 143                         getline(inputBatchFile, input);
 144                         if (input[0] != '#') {
 145                                 if (inputBatchFile.eof()) { input = "quit()"; }
 146
 147                                 cout << endl << "mothur > " << input << endl;
 148                                 errorFree = errorCheckor->checkInput(input);
 149                                 if (errorFree == true) {
 150                                         CommandOptionParser parser(input);
 151                                         commandName = parser.getCommandString();
 152                                         ifstream filehandle;
 153
 154                                         if (openedBatch == 0) { //able to open batchfile
 155                                                 //executes valid command
 156                                                 CommandFactory cFactory;
 157                                                 Command* command = cFactory.getCommand(commandName);
 158                                                 quitCommandCalled = command->execute();
 159                                         }
 160                                         else {
 161                                                 cout << "Invalid." << endl;
 162                                         }
 163                                 }
 164                                 else {
 165                                         cout << "Unable to open batchfile." << endl;
 166                                 }
 167                         }else { if (inputBatchFile.eof()) { input = "quit()"; } }
 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