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 v2.0 (Martha)" << endl;
  63                 cout << "Last updated: 1/07/2009" << endl << endl;
  64                 cout << "(Distance-based OTU and Richness)" << endl << endl;
  65                 cout << "by" << endl;
  66                 cout << "Patrick D. Schloss" << endl << endl;
  67                 cout << "Department of Microbiology" << endl;
  68                 cout << "The University of Massachusetts" << endl;
  69                 cout << "pschloss@micro.umass.edu" << endl;
  70                 cout << "http://schloss.micro.umass.edu" << endl << endl << endl;
  71                 cout << "Distributed under the GNU General Public License" << endl << endl;
  72                 cout << "Type 'help()' for information on the commands that are available" << endl << endl;
  73                 cout << "Type 'quit()' to exit program" << endl;
  74
  75                 while(quitCommandCalled != 1){
  76
  77                         cout << endl << "mothur > ";
  78                         getline(cin, input);
  79                         errorFree = errorCheckor->checkInput(input);
  80                         if (errorFree == true) {
  81                                 CommandOptionParser parser(input);
  82                                 commandName = parser.getCommandString();
  83
  84                                 //executes valid command
  85                                 CommandFactory cFactory;
  86                                 Command* command = cFactory.getCommand(commandName);
  87                                 quitCommandCalled = command->execute();
  88
  89                         }else {
  90                                         cout << "Your input contains errors. Please try again." << endl;
  91                         }
  92                 }
  93                 return 1;
  94         }
  95         catch(exception& e) {
  96                 cout << "Standard Error: " << e.what() << " has occurred in the InteractEngine class Function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  97                 exit(1);
  98         }
  99         catch(...) {
 100                 cout << "An unknown error has occurred in the InteractEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 101                 exit(1);
 102         }
 103
 104 }
 105
 106 /***********************************************************************/
 107 //This function opens the batchfile to be used by BatchEngine::getInput.
 108 BatchEngine::BatchEngine(string batchFileName){
 109         try {
 110                 globaldata = GlobalData::getInstance();
 111                 openedBatch = openInputFile(batchFileName, inputBatchFile);
 112
 113                 system("clear");
 114
 115         //      char buffer = ' ';
 116         //      ifstream header("introtext.txt");
 117         //      while(!header.eof()){
 118         //              cout << buffer;
 119         //              buffer = header.get();
 120         //      }
 121         }
 122         catch(exception& e) {
 123                 cout << "Standard Error: " << e.what() << " has occurred in the BatchEngine class Function BatchEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 124                 exit(1);
 125         }
 126         catch(...) {
 127                 cout << "An unknown error has occurred in the BatchEngine class function BatchEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 128                 exit(1);
 129         }
 130 }
 131
 132 /***********************************************************************/
 133
 134 BatchEngine::~BatchEngine(){
 135         }
 136
 137 /***********************************************************************/
 138 //This Function allows the user to run a batchfile containing several commands on Dotur
 139 bool BatchEngine::getInput(){
 140         try {
 141                 string input = "";
 142                 string commandName = "";
 143                 bool errorFree;
 144                 ErrorCheck* errorCheckor = new ErrorCheck();
 145
 146                 CommandFactory cFactory;
 147                 int quitCommandCalled = 0;
 148
 149                 while(quitCommandCalled == 0){
 150
 151                         getline(inputBatchFile, input);
 152                         cout << endl << "dotur > " << input << endl;
 153                         errorFree = errorCheckor->checkInput(input);
 154                         if (errorFree == true) {
 155                                 CommandOptionParser parser(input);
 156                                 commandName = parser.getCommandString();
 157                                 ifstream filehandle;
 158
 159                                 if (openedBatch == 0) { //able to open batchfile
 160                                         //executes valid command
 161                                         CommandFactory cFactory;
 162                                         Command* command = cFactory.getCommand(commandName);
 163                                         quitCommandCalled = command->execute();
 164                                 }
 165                                 else {
 166                                         cout << "Invalid." << endl;
 167                                 }
 168                         }
 169                         else {
 170                                 cout << "Unable to open batchfile." << endl;
 171                         }
 172                 }
 173                 return 1;
 174         }
 175         catch(exception& e) {
 176                 cout << "Standard Error: " << e.what() << " has occurred in the BatchEngine class Function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 177                 exit(1);
 178         }
 179         catch(...) {
 180                 cout << "An unknown error has occurred in the BatchEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 181                 exit(1);
 182         }
 183 }
 184
 185
 186 /***********************************************************************/
 187