X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=engine.cpp;h=18e1a595c06343a521d9bcd6458b95db4d863db7;hb=2397df97b12cd5d21ea10dc4248c18a5803ddd41;hp=a2d525011ad2823d1c72e07e24a6c4974d98644c;hpb=02909d6cae9963ba00dc746969a370fa8ca934fc;p=mothur.git diff --git a/engine.cpp b/engine.cpp index a2d5250..18e1a59 100644 --- a/engine.cpp +++ b/engine.cpp @@ -14,26 +14,28 @@ #include "engine.hpp" +/***********************************************************************/ +Engine::Engine(){ + try { + cFactory = CommandFactory::getInstance(); + } + catch(exception& e) { + errorOut(e, "Engine", "Engine"); + exit(1); + } +} + /***********************************************************************/ InteractEngine::InteractEngine(string path){ globaldata = GlobalData::getInstance(); globaldata->argv = path; - - system("clear"); -// char buffer = ' '; -// ifstream header("introtext.txt"); -// while(!header.eof()){ -// cout << buffer; -// buffer = header.get(); -// } } /***********************************************************************/ -InteractEngine::~InteractEngine(){ - } +InteractEngine::~InteractEngine(){} /***********************************************************************/ //This function allows the user to input commands one line at a time until they quit. @@ -44,60 +46,78 @@ bool InteractEngine::getInput(){ string commandName = ""; string options = ""; int quitCommandCalled = 0; - //bool errorFree; - //ErrorCheck* errorCheckor = new ErrorCheck(); - cout << "mothur v.1.4.0" << endl; - cout << "Last updated: 6/21/2009" << 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 > "; - getline(cin, input); - if (cin.eof()) { input = "quit()"; } + mothurOutEndLine(); + + input = getCommand(); //allow user to omit the () on the quit command if (input == "quit") { input = "quit()"; } - //errorFree = errorCheckor->checkInput(input); - //if (errorFree == true) { CommandOptionParser parser(input); commandName = parser.getCommandString(); + options = parser.getOptionString(); if (commandName != "") { //executes valid command - CommandFactory cFactory; - Command* command = cFactory.getCommand(commandName, options); + 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"; + errorOut(e, "InteractEngine", "getInput"); 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"; +} +/***********************************************************************/ +string Engine::getCommand() { + try { + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #ifdef USE_READLINE + char* nextCommand = NULL; + nextCommand = readline("mothur > "); + + if(nextCommand != NULL) { add_history(nextCommand); } + else{ //^D causes null string and we want it to quit mothur + nextCommand = "quit"; + cout << nextCommand << endl; + } + + mothurOutJustToLog("mothur > " + toString(nextCommand)); + return nextCommand; + #else + string nextCommand = ""; + mothurOut("mothur > "); + getline(cin, nextCommand); + mothurOutJustToLog("mothur > " + toString(nextCommand)); + return nextCommand; + #endif + #else + string nextCommand = ""; + mothurOut("mothur > "); + getline(cin, nextCommand); + mothurOutJustToLog("mothur > " + toString(nextCommand)); + return nextCommand; + #endif + + mothurOutEndLine(); + + } + catch(exception& e) { + errorOut(e, "Engine", "getCommand"); exit(1); } - } - /***********************************************************************/ //This function opens the batchfile to be used by BatchEngine::getInput. BatchEngine::BatchEngine(string path, string batchFileName){ @@ -106,42 +126,32 @@ BatchEngine::BatchEngine(string path, string batchFileName){ openedBatch = openInputFile(batchFileName, inputBatchFile); globaldata->argv = path; - - system("clear"); - - // char buffer = ' '; - // ifstream header("introtext.txt"); - // while(!header.eof()){ - // cout << buffer; - // buffer = header.get(); - // } + } 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); } } /***********************************************************************/ -BatchEngine::~BatchEngine(){ - } +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) { cout << "unable to open batchfile" << endl; return 1; } + if (openedBatch == 1) { + mothurOut("unable to open batchfile"); + mothurOutEndLine(); + return 1; + } string input = ""; string commandName = ""; string options = ""; - //int count = 1; //CommandFactory cFactory; int quitCommandCalled = 0; @@ -149,13 +159,14 @@ bool BatchEngine::getInput(){ while(quitCommandCalled == 0){ if (inputBatchFile.eof()) { input = "quit()"; } - else { getline(inputBatchFile, input); } - - //cout << "command number" << count << endl; count++; + else { input = getline(inputBatchFile); } if (input[0] != '#') { - - cout << endl << "mothur > " << input << endl; + + mothurOutEndLine(); + mothurOut("mothur > " + input); + mothurOutEndLine(); + //allow user to omit the () on the quit command if (input == "quit") { input = "quit()"; } @@ -167,10 +178,12 @@ bool BatchEngine::getInput(){ if (commandName != "") { //executes valid command - CommandFactory cFactory; - Command* command = cFactory.getCommand(commandName, options); + Command* command = cFactory->getCommand(commandName, options); quitCommandCalled = command->execute(); - }else { cout << "Invalid." << endl; } + }else { + mothurOut("Invalid."); + mothurOutEndLine(); + } } gobble(inputBatchFile); @@ -180,11 +193,7 @@ bool BatchEngine::getInput(){ 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"; - 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"; + errorOut(e, "BatchEngine", "getInput"); exit(1); } } @@ -201,34 +210,27 @@ ScriptEngine::ScriptEngine(string path, string commandString){ listOfCommands = commandString.substr(1, (commandString.length()-1)); globaldata->argv = path; - - system("clear"); - + } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ScriptEngine class Function ScriptEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ScriptEngine class function ScriptEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "ScriptEngine", "ScriptEngine"); exit(1); } } /***********************************************************************/ -ScriptEngine::~ScriptEngine(){ - } +ScriptEngine::~ScriptEngine(){ } /***********************************************************************/ -//This Function allows the user to run a batchfile containing several commands on Dotur +//This Function allows the user to run a batchfile containing several commands on mothur bool ScriptEngine::getInput(){ try { string input = ""; string commandName = ""; string options = ""; - //int count = 1; + //CommandFactory cFactory; int quitCommandCalled = 0; @@ -238,9 +240,12 @@ bool ScriptEngine::getInput(){ input = getNextCommand(listOfCommands); if (input == "") { input = "quit()"; } - //cout << "command number" << count << endl; count++; - cout << endl << "mothur > " << input << endl; + + mothurOutEndLine(); + mothurOut("mothur > " + input); + mothurOutEndLine(); + //allow user to omit the () on the quit command if (input == "quit") { input = "quit()"; } @@ -252,21 +257,19 @@ bool ScriptEngine::getInput(){ if (commandName != "") { //executes valid command - CommandFactory cFactory; - Command* command = cFactory.getCommand(commandName, options); + Command* command = cFactory->getCommand(commandName, options); quitCommandCalled = command->execute(); - }else { cout << "Invalid." << endl; } + }else { + mothurOut("Invalid."); + mothurOutEndLine(); + } } return 1; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ScriptEngine class Function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ScriptEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "ScriptEngine", "getInput"); exit(1); } } @@ -274,13 +277,21 @@ bool ScriptEngine::getInput(){ string ScriptEngine::getNextCommand(string& commandString) { try { string nextcommand = ""; + int count = 0; - nextcommand = commandString.substr(0,commandString.find_first_of(';')); - + //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 = ""; } - if ((commandString.find_first_of(';')+1) <= commandString.length()) { - commandString = commandString.substr(commandString.find_first_of(';')+1, commandString.length()); - }else { commandString = ""; } //you have reached the last command. //get rid of spaces in between commands if any if (commandString.length() > 0) { @@ -293,12 +304,8 @@ string ScriptEngine::getNextCommand(string& commandString) { return nextcommand; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ScriptEngine class Function getNextCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ScriptEngine class function getNextCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "ScriptEngine", "getNextCommand"); exit(1); } } -/***********************************************************************/ \ No newline at end of file +/***********************************************************************/