X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=98d730c31c2d03e3222057f8cef3da571aca0877;hb=2009a1a1f47e7467094d844e7c07ab8ddf7bb447;hp=54197174e1fa3da14861614734b1dc58314a466a;hpb=7b80945ef716dd72d00563a5a4d692394f7f84c3;p=mothur.git diff --git a/engine.cpp b/engine.cpp index 5419717..98d730c 100644 --- a/engine.cpp +++ b/engine.cpp @@ -34,7 +34,7 @@ string Engine::findMothursPath(){ //delimiting path char char delim; - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) delim = ':'; #else delim = ';'; @@ -44,8 +44,13 @@ string Engine::findMothursPath(){ vector dirs; mout->splitAtChar(envPath, dirs, delim); + if (mout->debug) { mout->mothurOut("[DEBUG]: dir's in path: \n"); } + //get path related to mothur for (int i = 0; i < dirs.size(); i++) { + + if (mout->debug) { mout->mothurOut("[DEBUG]: " + dirs[i] + "\n"); } + //to lower so we can find it string tempLower = ""; for (int j = 0; j < dirs[i].length(); j++) { tempLower += tolower(dirs[i][j]); } @@ -53,10 +58,12 @@ string Engine::findMothursPath(){ //is this mothurs path? if (tempLower.find("mothur") != -1) { mothurPath = dirs[i]; break; } } - + + if (mout->debug) { mout->mothurOut("[DEBUG]: mothurPath = " + mothurPath + "\n"); } + if (mothurPath != "") { //add mothur so it looks like what argv would look like - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) mothurPath += "/mothur"; #else mothurPath += "\\mothur"; @@ -71,7 +78,7 @@ string Engine::findMothursPath(){ //is this mothurs path? ifstream in; string tempIn = dirs[i]; - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) tempIn += "/mothur"; #else tempIn += "\\mothur"; @@ -79,7 +86,7 @@ string Engine::findMothursPath(){ mout->openInputFile(tempIn, in, ""); //if this file exists - if (in) { in.close(); mothurPath = tempIn; break; } + if (in) { in.close(); mothurPath = tempIn; break; if (mout->debug) { mout->mothurOut("[DEBUG]: found it, mothurPath = " + mothurPath + "\n"); } } } } @@ -95,14 +102,13 @@ string Engine::findMothursPath(){ InteractEngine::InteractEngine(string path){ - globaldata = GlobalData::getInstance(); string temppath = path.substr(0, (path.find_last_of("othur")-5)); //this will happen if you set the path variable to contain mothur's exe location if (temppath == "") { path = findMothursPath(); } - globaldata->argv = path; + mout->argv = path; } /***********************************************************************/ @@ -180,8 +186,19 @@ bool InteractEngine::getInput(){ //cout << pid << " is in execute " << commandName << endl; #endif //executes valid command + mout->runParse = true; + mout->clearGroups(); + mout->clearAllGroups(); + mout->Treenames.clear(); + mout->saveNextLabel = ""; + mout->printedHeaders = false; + mout->commandInputsConvertError = false; + mout->currentBinLabels.clear(); + mout->binLabelsInFile.clear(); + Command* command = cFactory->getCommand(commandName, options); - quitCommandCalled = command->execute(); + if (mout->commandInputsConvertError) { quitCommandCalled = 2; } + else { quitCommandCalled = command->execute(); } //if we aborted command if (quitCommandCalled == 2) { mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); } @@ -208,14 +225,14 @@ bool InteractEngine::getInput(){ string Engine::getCommand() { try { - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) #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 - strcpy(nextCommand, "quit"); + nextCommand = strdup("quit"); mout->mothurOut(nextCommand); } @@ -250,7 +267,6 @@ string Engine::getCommand() { //This function opens the batchfile to be used by BatchEngine::getInput. BatchEngine::BatchEngine(string path, string batchFileName){ try { - globaldata = GlobalData::getInstance(); openedBatch = mout->openInputFile(batchFileName, inputBatchFile); @@ -259,7 +275,7 @@ BatchEngine::BatchEngine(string path, string batchFileName){ //this will happen if you set the path variable to contain mothur's exe location if (temppath == "") { path = findMothursPath(); } - globaldata->argv = path; + mout->argv = path; } catch(exception& e) { @@ -355,8 +371,20 @@ bool BatchEngine::getInput(){ if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) { #endif //executes valid command + mout->runParse = true; + mout->clearGroups(); + mout->clearAllGroups(); + mout->Treenames.clear(); + mout->saveNextLabel = ""; + mout->printedHeaders = false; + mout->commandInputsConvertError = false; + mout->currentBinLabels.clear(); + mout->binLabelsInFile.clear(); + + Command* command = cFactory->getCommand(commandName, options); - quitCommandCalled = command->execute(); + if (mout->commandInputsConvertError) { quitCommandCalled = 2; } + else { quitCommandCalled = command->execute(); } //if we aborted command if (quitCommandCalled == 2) { mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); } @@ -387,7 +415,7 @@ bool BatchEngine::getInput(){ /***********************************************************************/ string BatchEngine::getNextCommand(ifstream& inputBatchFile) { try { - + string nextcommand = ""; if (inputBatchFile.eof()) { nextcommand = "quit()"; } @@ -406,7 +434,6 @@ string BatchEngine::getNextCommand(ifstream& inputBatchFile) { //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)); @@ -416,7 +443,7 @@ ScriptEngine::ScriptEngine(string path, string commandString){ //this will happen if you set the path variable to contain mothur's exe location if (temppath == "") { path = findMothursPath(); } - globaldata->argv = path; + mout->argv = path; } catch(exception& e) { @@ -458,9 +485,13 @@ bool ScriptEngine::getInput(){ if (input == "") { input = "quit()"; } - mout->mothurOutEndLine(); - mout->mothurOut("mothur > " + input); - mout->mothurOutEndLine(); + if (mout->gui) { + if ((input.find("quit") != string::npos) || (input.find("set.logfile") != string::npos)) {} + else if ((input.find("get.current") != string::npos) && (!mout->hasCurrentFiles())) {} + else { mout->mothurOutEndLine(); mout->mothurOut("mothur > " + input); mout->mothurOutEndLine(); } + }else{ + mout->mothurOutEndLine(); mout->mothurOut("mothur > " + input); mout->mothurOutEndLine(); + } #ifdef USE_MPI //send commandName @@ -508,8 +539,19 @@ bool ScriptEngine::getInput(){ //cout << pid << " is in execute" << endl; #endif //executes valid command + mout->runParse = true; + mout->clearGroups(); + mout->clearAllGroups(); + mout->Treenames.clear(); + mout->saveNextLabel = ""; + mout->printedHeaders = false; + mout->commandInputsConvertError = false; + mout->currentBinLabels.clear(); + mout->binLabelsInFile.clear(); + Command* command = cFactory->getCommand(commandName, options); - quitCommandCalled = command->execute(); + if (mout->commandInputsConvertError) { quitCommandCalled = 2; } + else { quitCommandCalled = command->execute(); } //if we aborted command if (quitCommandCalled == 2) { mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }