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 <string>
  16 #include <iostream>
  17 #include <iomanip>
  18 #include <fstream>
  19 #include <vector>
  20 #include <set>
  21 #include <exception>
  22
  23 #include "utilities.hpp"
  24 #include "globaldata.hpp"
  25 #include "commandoptionparser.hpp"
  26 #include "command.hpp"
  27 #include "commandfactory.hpp"
  28 #include "errorchecking.h"
  29 #include "engine.hpp"
  30
  31 /***********************************************************************/
  32
  33 InteractEngine::InteractEngine(){
  34
  35         globaldata = GlobalData::getInstance();
  36
  37         system("clear");
  38 //      char buffer = ' ';
  39 //      ifstream header("introtext.txt");
  40 //      while(!header.eof()){
  41 //              cout << buffer;
  42 //              buffer = header.get();
  43 //      }
  44 }
  45
  46 /***********************************************************************/
  47
  48 InteractEngine::~InteractEngine(){
  49         }
  50
  51 /***********************************************************************/
  52 //This function allows the user to input commands one line at a time until they quit.
  53 //If the command is garbage it does nothing.
  54 bool InteractEngine::getInput(){
  55         try {
  56                 string input = "";
  57                 string commandName = "";
  58                 int quitCommandCalled = 0;
  59                 bool errorFree;
  60                 ErrorCheck* errorCheckor = new ErrorCheck();
  61
  62                 cout << "mothur v1.0" << endl;
  63                 cout << "Last updated: 1/29/2009" << endl << endl;
  64                 cout << "by" << endl;
  65                 cout << "Patrick D. Schloss" << endl << endl;
  66                 cout << "Department of Microbiology" << endl;
  67                 cout << "The University of Massachusetts" << endl;
  68                 cout << "pschloss@micro.umass.edu" << endl;
  69                 cout << "http://schloss.micro.umass.edu/mothur" << endl << endl << endl;
  70                 cout << "Distributed under the GNU General Public License" << endl << endl;
  71                 cout << "Type 'help()' for information on the commands that are available" << endl << endl;
  72                 cout << "Type 'quit()' to exit program" << endl;
  73
  74                 while(quitCommandCalled != 1){
  75
  76                         cout << endl << "mothur > ";
  77                         getline(cin, input);
  78                         errorFree = errorCheckor->checkInput(input);
  79                         if (errorFree == true) {
  80                                 CommandOptionParser parser(input);
  81                                 commandName = parser.getCommandString();
  82
  83                                 //executes valid command
  84                                 CommandFactory cFactory;
  85                                 Command* command = cFactory.getCommand(commandName);
  86                                 quitCommandCalled = command->execute();
  87
  88                         }else {
  89                                         cout << "Your input contains errors. Please try again." << endl;
  90                         }
  91                 }
  92                 return 1;
  93         }
  94         catch(exception& e) {
  95                 cout << "Standard Error: " << e.what() << " has occurred in the InteractEngine class Function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  96                 exit(1);
  97         }
  98         catch(...) {
  99                 cout << "An unknown error has occurred in the InteractEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 100                 exit(1);
 101         }
 102
 103 }
 104
 105 /***********************************************************************/
 106 //This function opens the batchfile to be used by BatchEngine::getInput.
 107 BatchEngine::BatchEngine(string batchFileName){
 108         try {
 109                 globaldata = GlobalData::getInstance();
 110                 openedBatch = openInputFile(batchFileName, inputBatchFile);
 111
 112                 system("clear");
 113
 114         //      char buffer = ' ';
 115         //      ifstream header("introtext.txt");
 116         //      while(!header.eof()){
 117         //              cout << buffer;
 118         //              buffer = header.get();
 119         //      }
 120         }
 121         catch(exception& e) {
 122                 cout << "Standard Error: " << e.what() << " has occurred in the BatchEngine class Function BatchEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 123                 exit(1);
 124         }
 125         catch(...) {
 126                 cout << "An unknown error has occurred in the BatchEngine class function BatchEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 127                 exit(1);
 128         }
 129 }
 130
 131 /***********************************************************************/
 132
 133 BatchEngine::~BatchEngine(){
 134         }
 135
 136 /***********************************************************************/
 137 //This Function allows the user to run a batchfile containing several commands on Dotur
 138 bool BatchEngine::getInput(){
 139         try {
 140                 string input = "";
 141                 string commandName = "";
 142                 bool errorFree;
 143                 ErrorCheck* errorCheckor = new ErrorCheck();
 144
 145                 CommandFactory cFactory;
 146                 int quitCommandCalled = 0;
 147
 148                 while(quitCommandCalled == 0){
 149
 150                         getline(inputBatchFile, input);
 151                         cout << endl << "dotur > " << input << endl;
 152                         errorFree = errorCheckor->checkInput(input);
 153                         if (errorFree == true) {
 154                                 CommandOptionParser parser(input);
 155                                 commandName = parser.getCommandString();
 156                                 ifstream filehandle;
 157
 158                                 if (openedBatch == 0) { //able to open batchfile
 159                                         //executes valid command
 160                                         CommandFactory cFactory;
 161                                         Command* command = cFactory.getCommand(commandName);
 162                                         quitCommandCalled = command->execute();
 163                                 }
 164                                 else {
 165                                         cout << "Invalid." << endl;
 166                                 }
 167                         }
 168                         else {
 169                                 cout << "Unable to open batchfile." << endl;
 170                         }
 171                 }
 172                 return 1;
 173         }
 174         catch(exception& e) {
 175                 cout << "Standard Error: " << e.what() << " has occurred in the BatchEngine class Function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 176                 exit(1);
 177         }
 178         catch(...) {
 179                 cout << "An unknown error has occurred in the BatchEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 180                 exit(1);
 181         }
 182 }
 183
 184
 185 /***********************************************************************/
 186