X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=0a0f5a0ce7f0f4f0a120509e2c3d5c0e51471ecb;hb=03193ff423c9526ff6525040cab60ff715d8cc48;hp=e251f0031d5ffa2bc9685702ef76ae0489af8449;hpb=16bea3130e36addc54e2116dfbcd02d706ebee45;p=mothur.git diff --git a/engine.cpp b/engine.cpp index e251f00..0a0f5a0 100644 --- a/engine.cpp +++ b/engine.cpp @@ -10,37 +10,18 @@ * Fix later, don't have time now. * */ -using namespace std; - -#include -#include -#include -#include -#include -#include -#include - -#include "utilities.hpp" -#include "globaldata.hpp" -#include "commandoptionparser.hpp" -#include "command.hpp" -#include "commandfactory.hpp" -#include "errorchecking.h" + + #include "engine.hpp" /***********************************************************************/ -InteractEngine::InteractEngine(){ +InteractEngine::InteractEngine(string path){ globaldata = GlobalData::getInstance(); - - system("clear"); -// char buffer = ' '; -// ifstream header("introtext.txt"); -// while(!header.eof()){ -// cout << buffer; -// buffer = header.get(); -// } + globaldata->argv = path; + + } /***********************************************************************/ @@ -55,77 +36,59 @@ bool InteractEngine::getInput(){ try { string input = ""; string commandName = ""; + string options = ""; int quitCommandCalled = 0; - bool errorFree; - ErrorCheck* errorCheckor = new ErrorCheck(); - cout << "mothur v1.0" << endl; - cout << "Last updated: 1/29/2009" << endl << endl; - cout << "by" << endl; - cout << "Patrick D. Schloss" << endl << endl; - cout << "Department of Microbiology" << endl; - cout << "The University of Massachusetts" << endl; - cout << "pschloss@micro.umass.edu" << endl; - cout << "http://schloss.micro.umass.edu/mothur" << endl << endl << endl; - cout << "Distributed under the GNU General Public License" << endl << endl; - cout << "Type 'help()' for information on the commands that are available" << endl << endl; - cout << "Type 'quit()' to exit program" << endl; - + while(quitCommandCalled != 1){ - - cout << endl << "mothur > "; + + mothurOutEndLine(); + mothurOut("mothur > "); getline(cin, input); if (cin.eof()) { input = "quit()"; } - errorFree = errorCheckor->checkInput(input); - if (errorFree == true) { - CommandOptionParser parser(input); - commandName = parser.getCommandString(); + mothurOutJustToLog(input); + mothurOutEndLine(); + + //allow user to omit the () on the quit command + if (input == "quit") { input = "quit()"; } + + CommandOptionParser parser(input); + commandName = parser.getCommandString(); + options = parser.getOptionString(); + + if (commandName != "") { //executes valid command CommandFactory cFactory; - Command* command = cFactory.getCommand(commandName); + Command* command = cFactory.getCommand(commandName, options); quitCommandCalled = command->execute(); - + }else { - cout << "Your input contains errors. Please try again." << endl; + mothurOut("Your input contains errors. Please try again."); + mothurOutEndLine(); } } return 1; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the InteractEngine class Function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the InteractEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "InteractEngine", "getInput"); exit(1); } - } /***********************************************************************/ //This function opens the batchfile to be used by BatchEngine::getInput. -BatchEngine::BatchEngine(string batchFileName){ +BatchEngine::BatchEngine(string path, string batchFileName){ try { globaldata = GlobalData::getInstance(); - openedBatch = openInputFile(batchFileName, inputBatchFile); - - system("clear"); - // char buffer = ' '; - // ifstream header("introtext.txt"); - // while(!header.eof()){ - // cout << buffer; - // buffer = header.get(); - // } + openedBatch = openInputFile(batchFileName, inputBatchFile); + globaldata->argv = path; + } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the BatchEngine class Function BatchEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the BatchEngine class function BatchEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "BatchEngine", "BatchEngine"); exit(1); } } @@ -139,52 +102,175 @@ BatchEngine::~BatchEngine(){ //This Function allows the user to run a batchfile containing several commands on Dotur bool BatchEngine::getInput(){ try { + //check if this is a valid batchfile + if (openedBatch == 1) { + mothurOut("unable to open batchfile"); + mothurOutEndLine(); + return 1; + } + string input = ""; string commandName = ""; - bool errorFree; - ErrorCheck* errorCheckor = new ErrorCheck(); - - CommandFactory cFactory; + string options = ""; + + //CommandFactory cFactory; int quitCommandCalled = 0; while(quitCommandCalled == 0){ - - getline(inputBatchFile, input); + if (inputBatchFile.eof()) { input = "quit()"; } + else { input = getline(inputBatchFile); } - cout << endl << "mothur > " << input << endl; - errorFree = errorCheckor->checkInput(input); - if (errorFree == true) { + if (input[0] != '#') { + + mothurOutEndLine(); + mothurOut("mothur > " + input); + mothurOutEndLine(); + + + //allow user to omit the () on the quit command + if (input == "quit") { input = "quit()"; } + CommandOptionParser parser(input); commandName = parser.getCommandString(); - ifstream filehandle; - - if (openedBatch == 0) { //able to open batchfile + options = parser.getOptionString(); + + if (commandName != "") { + //executes valid command CommandFactory cFactory; - Command* command = cFactory.getCommand(commandName); + Command* command = cFactory.getCommand(commandName, options); quitCommandCalled = command->execute(); + }else { + mothurOut("Invalid."); + mothurOutEndLine(); } - else { - cout << "Invalid." << endl; - } - } - else { - cout << "Unable to open batchfile." << endl; + } + gobble(inputBatchFile); } + + inputBatchFile.close(); return 1; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the BatchEngine class Function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "BatchEngine", "getInput"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the BatchEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} + + +/***********************************************************************/ +/***********************************************************************/ +//This function opens the batchfile to be used by BatchEngine::getInput. +ScriptEngine::ScriptEngine(string path, string commandString){ + try { + globaldata = GlobalData::getInstance(); + + //remove quotes + listOfCommands = commandString.substr(1, (commandString.length()-1)); + + globaldata->argv = path; + + + + } + catch(exception& e) { + errorOut(e, "ScriptEngine", "ScriptEngine"); exit(1); } } +/***********************************************************************/ + +ScriptEngine::~ScriptEngine(){ + } /***********************************************************************/ +//This Function allows the user to run a batchfile containing several commands on mothur +bool ScriptEngine::getInput(){ + try { + + string input = ""; + string commandName = ""; + string options = ""; + + + //CommandFactory cFactory; + int quitCommandCalled = 0; + + while(quitCommandCalled == 0){ + + input = getNextCommand(listOfCommands); + + if (input == "") { input = "quit()"; } + + + mothurOutEndLine(); + mothurOut("mothur > " + input); + mothurOutEndLine(); + + + //allow user to omit the () on the quit command + if (input == "quit") { input = "quit()"; } + CommandOptionParser parser(input); + commandName = parser.getCommandString(); + options = parser.getOptionString(); + + if (commandName != "") { + + //executes valid command + CommandFactory cFactory; + Command* command = cFactory.getCommand(commandName, options); + quitCommandCalled = command->execute(); + }else { + mothurOut("Invalid."); + mothurOutEndLine(); + } + + } + + return 1; + } + catch(exception& e) { + errorOut(e, "ScriptEngine", "getInput"); + exit(1); + } +} +/***********************************************************************/ +string ScriptEngine::getNextCommand(string& commandString) { + try { + string nextcommand = ""; + int count = 0; + + //go through string until you reach ; or end + while (count < commandString.length()) { + + if (commandString[count] == ';') { break; } + else { nextcommand += commandString[count]; } + + count++; + } + + //if you are not at the end + if (count != commandString.length()) { commandString = commandString.substr(count+1, commandString.length()); } + else { commandString = ""; } + + + //get rid of spaces in between commands if any + if (commandString.length() > 0) { + while (commandString[0] == ' ') { + commandString = commandString.substr(1,commandString.length()); + if (commandString.length() == 0) { break; } + } + } + + return nextcommand; + } + catch(exception& e) { + errorOut(e, "ScriptEngine", "getNextCommand"); + exit(1); + } +} +/***********************************************************************/