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