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
 107                 openedBatch = openInputFile(batchFileName, inputBatchFile);
 108                 globaldata->argv = path;
 109
 110                 system("clear");
 111
 112         //      char buffer = ' ';
 113         //      ifstream header("introtext.txt");
 114         //      while(!header.eof()){
 115         //              cout << buffer;
 116         //              buffer = header.get();
 117         //      }
 118         }
 119         catch(exception& e) {
 120                 cout << "Standard Error: " << e.what() << " has occurred in the BatchEngine class Function BatchEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 121                 exit(1);
 122         }
 123         catch(...) {
 124                 cout << "An unknown error has occurred in the BatchEngine class function BatchEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 125                 exit(1);
 126         }
 127 }
 128
 129 /***********************************************************************/
 130
 131 BatchEngine::~BatchEngine(){
 132         }
 133
 134 /***********************************************************************/
 135 //This Function allows the user to run a batchfile containing several commands on Dotur
 136 bool BatchEngine::getInput(){
 137         try {
 138                 //check if this is a valid batchfile
 139                 if (openedBatch == 1) {  cout << "unable to open batchfile" << endl;  return 1; }
 140
 141                 string input = "";
 142                 string commandName = "";
 143                 string options = "";
 144                 //int count = 1;
 145
 146                 //CommandFactory cFactory;
 147                 int quitCommandCalled = 0;
 148
 149                 while(quitCommandCalled == 0){
 150
 151                         if (inputBatchFile.eof()) { input = "quit()"; }
 152                         else { getline(inputBatchFile, input); }
 153
 154                         //cout << "command number" << count << endl; count++;
 155
 156                         if (input[0] != '#') {
 157
 158                                 cout << endl << "mothur > " << input << endl;
 159
 160                                 //allow user to omit the () on the quit command
 161                                 if (input == "quit") { input = "quit()"; }
 162
 163                                 CommandOptionParser parser(input);
 164                                 commandName = parser.getCommandString();
 165                                 options = parser.getOptionString();
 166
 167                                 if (commandName != "") {
 168
 169                                         //executes valid command
 170                                         CommandFactory cFactory;
 171                                         Command* command = cFactory.getCommand(commandName, options);
 172                                         quitCommandCalled = command->execute();
 173                                 }else {         cout << "Invalid." << endl;             }
 174
 175                         }
 176                         gobble(inputBatchFile);
 177                 }
 178                 return 1;
 179         }
 180         catch(exception& e) {
 181                 cout << "Standard Error: " << e.what() << " has occurred in the BatchEngine class Function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 182                 exit(1);
 183         }
 184         catch(...) {
 185                 cout << "An unknown error has occurred in the BatchEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 186                 exit(1);
 187         }
 188 }
 189
 190
 191 /***********************************************************************/
 192 /***********************************************************************/
 193 //This function opens the batchfile to be used by BatchEngine::getInput.
 194 ScriptEngine::ScriptEngine(string path, string commandString){
 195         try {
 196                 globaldata = GlobalData::getInstance();
 197
 198                 //remove quotes
 199                 listOfCommands = commandString.substr(1, (commandString.length()-1));
 200
 201                 globaldata->argv = path;
 202
 203                 system("clear");
 204
 205         }
 206         catch(exception& e) {
 207                 cout << "Standard Error: " << e.what() << " has occurred in the ScriptEngine class Function ScriptEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 208                 exit(1);
 209         }
 210         catch(...) {
 211                 cout << "An unknown error has occurred in the ScriptEngine class function ScriptEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 212                 exit(1);
 213         }
 214 }
 215
 216 /***********************************************************************/
 217
 218 ScriptEngine::~ScriptEngine(){
 219         }
 220
 221 /***********************************************************************/
 222 //This Function allows the user to run a batchfile containing several commands on Dotur
 223 bool ScriptEngine::getInput(){
 224         try {
 225
 226                 string input = "";
 227                 string commandName = "";
 228                 string options = "";
 229                 //int count = 1;
 230
 231                 //CommandFactory cFactory;
 232                 int quitCommandCalled = 0;
 233
 234                 while(quitCommandCalled == 0){
 235
 236                         input = getNextCommand(listOfCommands);
 237
 238                         if (input == "") { input = "quit()"; }
 239                         //cout << "command number" << count << endl; count++;
 240
 241                         cout << endl << "mothur > " << input << endl;
 242
 243                         //allow user to omit the () on the quit command
 244                         if (input == "quit") { input = "quit()"; }
 245
 246                         CommandOptionParser parser(input);
 247                         commandName = parser.getCommandString();
 248                         options = parser.getOptionString();
 249
 250                         if (commandName != "") {
 251
 252                                 //executes valid command
 253                                 CommandFactory cFactory;
 254                                 Command* command = cFactory.getCommand(commandName, options);
 255                                 quitCommandCalled = command->execute();
 256                         }else {         cout << "Invalid." << endl;             }
 257
 258                 }
 259
 260                 return 1;
 261         }
 262         catch(exception& e) {
 263                 cout << "Standard Error: " << e.what() << " has occurred in the ScriptEngine class Function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 264                 exit(1);
 265         }
 266         catch(...) {
 267                 cout << "An unknown error has occurred in the ScriptEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 268                 exit(1);
 269         }
 270 }
 271 /***********************************************************************/
 272 string ScriptEngine::getNextCommand(string& commandString) {
 273         try {
 274                 string nextcommand = "";
 275
 276                 nextcommand = commandString.substr(0,commandString.find_first_of(';'));
 277
 278
 279                 if ((commandString.find_first_of(';')+1) <= commandString.length()) {
 280                         commandString = commandString.substr(commandString.find_first_of(';')+1, commandString.length());
 281                 }else { commandString = ""; } //you have reached the last command.
 282
 283                 //get rid of any extra spaces in between commands
 284                 //string space = " ";
 285
 286                 //while(commandString.at(0) == ' ')
 287                         //commandString = commandString.substr(1, commandString.length());
 288
 289                 return nextcommand;
 290         }
 291         catch(exception& e) {
 292                 cout << "Standard Error: " << e.what() << " has occurred in the ScriptEngine class Function getNextCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 293                 exit(1);
 294         }
 295         catch(...) {
 296                 cout << "An unknown error has occurred in the ScriptEngine class function getNextCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 297                 exit(1);
 298         }
 299 }
 300 /***********************************************************************/