X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getlistcountcommand.cpp;h=b7c4f1790b152371a6e302f3d56ae79fc60badf1;hb=006601d68abe8d0061f77e8d28323b160750e343;hp=eb9c980075a069b1e0f08f6f01fc64e4f1a6b358;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git diff --git a/getlistcountcommand.cpp b/getlistcountcommand.cpp index eb9c980..b7c4f17 100644 --- a/getlistcountcommand.cpp +++ b/getlistcountcommand.cpp @@ -49,6 +49,26 @@ string GetListCountCommand::getHelpString(){ } } //********************************************************************************************************************** +string GetListCountCommand::getOutputFileNameTag(string type, string inputName=""){ + try { + string outputFileName = ""; + map >::iterator it; + + //is this a type this command creates + it = outputTypes.find(type); + if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); } + else { + if (type == "otu") { outputFileName = "otu"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; } + } + return outputFileName; + } + catch(exception& e) { + m->errorOut(e, "GetListCountCommand", "getOutputFileNameTag"); + exit(1); + } +} +//********************************************************************************************************************** GetListCountCommand::GetListCountCommand(){ try { abort = true; calledHelp = true; @@ -69,6 +89,7 @@ GetListCountCommand::GetListCountCommand(string option) { //allow user to run help if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { vector myArray = setParameters(); @@ -113,6 +134,7 @@ GetListCountCommand::GetListCountCommand(string option) { else { m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; } } else if (listfile == "not open") { abort = true; } + else { m->setListFile(listfile); } //check for optional parameter and set defaults @@ -147,7 +169,7 @@ int GetListCountCommand::execute(){ set processedLabels; set userLabels = labels; - if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { @@ -155,7 +177,7 @@ int GetListCountCommand::execute(){ process(list); - if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } processedLabels.insert(list->getLabel()); userLabels.erase(list->getLabel()); @@ -169,7 +191,7 @@ int GetListCountCommand::execute(){ process(list); - if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } processedLabels.insert(list->getLabel()); @@ -206,7 +228,7 @@ int GetListCountCommand::execute(){ process(list); - if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } delete list; } @@ -232,7 +254,7 @@ void GetListCountCommand::process(ListVector* list) { try { string binnames; if (outputDir == "") { outputDir += m->hasPath(listfile); } - string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + ".otu"; + string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + "." +getOutputFileNameTag("otu"); m->openOutputFile(outputFileName, out); outputNames.push_back(outputFileName); outputTypes["otu"].push_back(outputFileName);