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 v.1.3.0" << endl;
  50                 cout << "Last updated: 4/25/2009" << 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                         //allow user to omit the () on the quit command
  68                         if (input == "quit") { input = "quit()"; }
  69
  70                         errorFree = errorCheckor->checkInput(input);
  71                         if (errorFree == true) {
  72                                 CommandOptionParser parser(input);
  73                                 commandName = parser.getCommandString();
  74
  75                                 //executes valid command
  76                                 CommandFactory cFactory;
  77                                 Command* command = cFactory.getCommand(commandName);
  78                                 quitCommandCalled = command->execute();
  79
  80                         }else {
  81                                         cout << "Your input contains errors. Please try again." << endl;
  82                         }
  83                 }
  84                 return 1;
  85         }
  86         catch(exception& e) {
  87                 cout << "Standard Error: " << e.what() << " has occurred in the InteractEngine class Function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  88                 exit(1);
  89         }
  90         catch(...) {
  91                 cout << "An unknown error has occurred in the InteractEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  92                 exit(1);
  93         }
  94
  95 }
  96
  97 /***********************************************************************/
  98 //This function opens the batchfile to be used by BatchEngine::getInput.
  99 BatchEngine::BatchEngine(string path, string batchFileName){
 100         try {
 101                 globaldata = GlobalData::getInstance();
 102                 openedBatch = openInputFile(batchFileName, inputBatchFile);
 103                 globaldata->argv = path;
 104
 105                 system("clear");
 106
 107         //      char buffer = ' ';
 108         //      ifstream header("introtext.txt");
 109         //      while(!header.eof()){
 110         //              cout << buffer;
 111         //              buffer = header.get();
 112         //      }
 113         }
 114         catch(exception& e) {
 115                 cout << "Standard Error: " << e.what() << " has occurred in the BatchEngine class Function BatchEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 116                 exit(1);
 117         }
 118         catch(...) {
 119                 cout << "An unknown error has occurred in the BatchEngine class function BatchEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 120                 exit(1);
 121         }
 122 }
 123
 124 /***********************************************************************/
 125
 126 BatchEngine::~BatchEngine(){
 127         }
 128
 129 /***********************************************************************/
 130 //This Function allows the user to run a batchfile containing several commands on Dotur
 131 bool BatchEngine::getInput(){
 132         try {
 133                 //check if this is a valid batchfile
 134                 if (openedBatch == 1) {  cout << "unable to open batchfile" << endl;  return 1; }
 135
 136                 string input = "";
 137                 string commandName = "";
 138                 bool errorFree;
 139                 ErrorCheck* errorCheckor = new ErrorCheck();
 140
 141                 CommandFactory cFactory;
 142                 int quitCommandCalled = 0;
 143
 144                 while(quitCommandCalled == 0){
 145
 146                         getline(inputBatchFile, input);
 147                         if (input[0] != '#') {
 148                                 if (inputBatchFile.eof()) { input = "quit()"; }
 149
 150                                 cout << endl << "mothur > " << input << endl;
 151
 152                                 //allow user to omit the () on the quit command
 153                                 if (input == "quit") { input = "quit()"; }
 154
 155                                 errorFree = errorCheckor->checkInput(input);
 156                                 if (errorFree == true) {
 157                                         CommandOptionParser parser(input);
 158                                         commandName = parser.getCommandString();
 159                                         ifstream filehandle;
 160
 161                                         if (openedBatch == 0) { //able to open batchfile
 162                                                 //executes valid command
 163                                                 CommandFactory cFactory;
 164                                                 Command* command = cFactory.getCommand(commandName);
 165                                                 quitCommandCalled = command->execute();
 166                                         }
 167                                         else {
 168                                                 cout << "Invalid." << endl;
 169                                         }
 170                                 }
 171                                 else {
 172                                         cout << "Unable to open batchfile." << endl;
 173                                 }
 174                         }else { if (inputBatchFile.eof()) { input = "quit()"; } }
 175                 }
 176                 return 1;
 177         }
 178         catch(exception& e) {
 179                 cout << "Standard Error: " << e.what() << " has occurred in the BatchEngine class Function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 180                 exit(1);
 181         }
 182         catch(...) {
 183                 cout << "An unknown error has occurred in the BatchEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 184                 exit(1);
 185         }
 186 }
 187
 188
 189 /***********************************************************************/
 190