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.1.4.1" << endl;
  51                 cout << "Last updated: 6/23/2009" << 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
 179                 inputBatchFile.close();
 180                 return 1;
 181         }
 182         catch(exception& e) {
 183                 cout << "Standard Error: " << e.what() << " has occurred in the BatchEngine class Function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 184                 exit(1);
 185         }
 186         catch(...) {
 187                 cout << "An unknown error has occurred in the BatchEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 188                 exit(1);
 189         }
 190 }
 191
 192
 193 /***********************************************************************/
 194 /***********************************************************************/
 195 //This function opens the batchfile to be used by BatchEngine::getInput.
 196 ScriptEngine::ScriptEngine(string path, string commandString){
 197         try {
 198                 globaldata = GlobalData::getInstance();
 199
 200                 //remove quotes
 201                 listOfCommands = commandString.substr(1, (commandString.length()-1));
 202
 203                 globaldata->argv = path;
 204
 205                 system("clear");
 206
 207         }
 208         catch(exception& e) {
 209                 cout << "Standard Error: " << e.what() << " has occurred in the ScriptEngine class Function ScriptEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 210                 exit(1);
 211         }
 212         catch(...) {
 213                 cout << "An unknown error has occurred in the ScriptEngine class function ScriptEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 214                 exit(1);
 215         }
 216 }
 217
 218 /***********************************************************************/
 219
 220 ScriptEngine::~ScriptEngine(){
 221         }
 222
 223 /***********************************************************************/
 224 //This Function allows the user to run a batchfile containing several commands on Dotur
 225 bool ScriptEngine::getInput(){
 226         try {
 227
 228                 string input = "";
 229                 string commandName = "";
 230                 string options = "";
 231                 //int count = 1;
 232
 233                 //CommandFactory cFactory;
 234                 int quitCommandCalled = 0;
 235
 236                 while(quitCommandCalled == 0){
 237
 238                         input = getNextCommand(listOfCommands);
 239
 240                         if (input == "") { input = "quit()"; }
 241                         //cout << "command number" << count << endl; count++;
 242
 243                         cout << endl << "mothur > " << input << endl;
 244
 245                         //allow user to omit the () on the quit command
 246                         if (input == "quit") { input = "quit()"; }
 247
 248                         CommandOptionParser parser(input);
 249                         commandName = parser.getCommandString();
 250                         options = parser.getOptionString();
 251
 252                         if (commandName != "") {
 253
 254                                 //executes valid command
 255                                 CommandFactory cFactory;
 256                                 Command* command = cFactory.getCommand(commandName, options);
 257                                 quitCommandCalled = command->execute();
 258                         }else {         cout << "Invalid." << endl;             }
 259
 260                 }
 261
 262                 return 1;
 263         }
 264         catch(exception& e) {
 265                 cout << "Standard Error: " << e.what() << " has occurred in the ScriptEngine class Function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 266                 exit(1);
 267         }
 268         catch(...) {
 269                 cout << "An unknown error has occurred in the ScriptEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 270                 exit(1);
 271         }
 272 }
 273 /***********************************************************************/
 274 string ScriptEngine::getNextCommand(string& commandString) {
 275         try {
 276                 string nextcommand = "";
 277
 278                 nextcommand = commandString.substr(0,commandString.find_first_of(';'));
 279
 280
 281                 if ((commandString.find_first_of(';')+1) <= commandString.length()) {
 282                         commandString = commandString.substr(commandString.find_first_of(';')+1, commandString.length());
 283                 }else { commandString = ""; } //you have reached the last command.
 284
 285                 //get rid of spaces in between commands if any
 286                 if (commandString.length() > 0) {
 287                         while (commandString[0] == ' ') {
 288                                 commandString = commandString.substr(1,commandString.length());
 289                                 if (commandString.length() == 0) {  break;  }
 290                         }
 291                 }
 292
 293                 return nextcommand;
 294         }
 295         catch(exception& e) {
 296                 cout << "Standard Error: " << e.what() << " has occurred in the ScriptEngine class Function getNextCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 297                 exit(1);
 298         }
 299         catch(...) {
 300                 cout << "An unknown error has occurred in the ScriptEngine class function getNextCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 301                 exit(1);
 302         }
 303 }
 304 /***********************************************************************/