X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getsabundcommand.cpp;h=3637d2903112154c6af122e1bac68a2a0ab65f1a;hb=432ddfdccc4ca0ed83c62747956a472af29e9183;hp=3dd58c117945a299154ebd09cc60b0688ea9f714;hpb=72ebb6fa35b45b149812d47c2b1cb8acaca64659;p=mothur.git diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp index 3dd58c1..3637d29 100644 --- a/getsabundcommand.cpp +++ b/getsabundcommand.cpp @@ -10,8 +10,55 @@ #include "getsabundcommand.h" //********************************************************************************************************************** - -GetSAbundCommand::GetSAbundCommand(string option){ +vector GetSAbundCommand::getValidParameters(){ + try { + string Array[] = {"label","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "GetSAbundCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +GetSAbundCommand::GetSAbundCommand(){ + try { + abort = true; + //initialize outputTypes + vector tempOutNames; + outputTypes["sabund"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "GetSAbundCommand", "GetSAbundCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector GetSAbundCommand::getRequiredParameters(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "GetSAbundCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector GetSAbundCommand::getRequiredFiles(){ + try { + string Array[] = {"list","rabund"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "GetSAbundCommand", "getRequiredFiles"); + exit(1); + } +} +//********************************************************************************************************************** +GetSAbundCommand::GetSAbundCommand(string option) { try { globaldata = GlobalData::getInstance(); abort = false; @@ -23,7 +70,7 @@ GetSAbundCommand::GetSAbundCommand(string option){ else { //valid paramters for this command - string Array[] = {"label"}; + string Array[] = {"label","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); @@ -36,15 +83,25 @@ GetSAbundCommand::GetSAbundCommand(string option){ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } + //initialize outputTypes + vector tempOutNames; + outputTypes["sabund"] = tempOutNames; + + //if the user changes the output directory command factory will send this info to us in the output parameter + string outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ + outputDir = ""; + outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it + } + //make sure the user has already run the read.otu command - if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "")) { mothurOut("You must read a list or rabund before you can use the get.sabund command."); mothurOutEndLine(); abort = true; } + if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "")) { m->mothurOut("You must read a list or rabund before you can use the get.sabund command."); m->mothurOutEndLine(); abort = true; } //check for optional parameter and set defaults // ...at some point should added some additional type checking... label = validParameter.validFile(parameters, "label", false); if (label == "not found") { label = ""; } else { - if(label != "all") { splitAtDash(label, labels); allLines = 0; } + if(label != "all") { m->splitAtDash(label, labels); allLines = 0; } else { allLines = 1; } } @@ -55,14 +112,14 @@ GetSAbundCommand::GetSAbundCommand(string option){ } if (abort == false) { - filename = getRootName(globaldata->inputFileName) + "sabund"; - openOutputFile(filename, out); + filename = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "sabund"; + m->openOutputFile(filename, out); } } } catch(exception& e) { - errorOut(e, "GetSAbundCommand", "GetSAbundCommand"); + m->errorOut(e, "GetSAbundCommand", "GetSAbundCommand"); exit(1); } } @@ -70,17 +127,17 @@ GetSAbundCommand::GetSAbundCommand(string option){ void GetSAbundCommand::help(){ try { - mothurOut("The get.sabund command can only be executed after a successful read.otu of a listfile or rabundfile.\n"); - mothurOut("The get.sabund command parameters is label. No parameters are required.\n"); - mothurOut("The label parameter allows you to select what distance levels you would like included in your .sabund file, and are separated by dashes.\n"); - mothurOut("The get.sabund command should be in the following format: get.sabund(label=yourLabels).\n"); - mothurOut("Example get.sabund().\n"); - mothurOut("The default value for label is all labels in your inputfile.\n"); - mothurOut("The get.sabund command outputs a .sabund file containing the labels you selected.\n"); - mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n"); + m->mothurOut("The get.sabund command can only be executed after a successful read.otu of a listfile or rabundfile.\n"); + m->mothurOut("The get.sabund command parameters is label. No parameters are required.\n"); + m->mothurOut("The label parameter allows you to select what distance levels you would like included in your .sabund file, and are separated by dashes.\n"); + m->mothurOut("The get.sabund command should be in the following format: get.sabund(label=yourLabels).\n"); + m->mothurOut("Example get.sabund().\n"); + m->mothurOut("The default value for label is all labels in your inputfile.\n"); + m->mothurOut("The get.sabund command outputs a .sabund file containing the labels you selected.\n"); + m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n"); } catch(exception& e) { - errorOut(e, "GetSAbundCommand", "help"); + m->errorOut(e, "GetSAbundCommand", "help"); exit(1); } } @@ -109,30 +166,37 @@ int GetSAbundCommand::execute(){ set processedLabels; set userLabels = labels; + if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; } + + while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { if(allLines == 1 || labels.count(order->getLabel()) == 1){ - mothurOut(order->getLabel()); mothurOutEndLine(); + m->mothurOut(order->getLabel()); m->mothurOutEndLine(); sabund = new SAbundVector(); *sabund = (order->getSAbundVector()); sabund->print(out); delete sabund; + + if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; } processedLabels.insert(order->getLabel()); userLabels.erase(order->getLabel()); } - if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { string saveLabel = order->getLabel(); delete order; order = (input->getOrderVector(lastLabel)); - mothurOut(order->getLabel()); mothurOutEndLine(); + m->mothurOut(order->getLabel()); m->mothurOutEndLine(); sabund = new SAbundVector(); *sabund = (order->getSAbundVector()); sabund->print(out); delete sabund; + + if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; } processedLabels.insert(order->getLabel()); userLabels.erase(order->getLabel()); @@ -152,12 +216,12 @@ int GetSAbundCommand::execute(){ set::iterator it; bool needToRun = false; for (it = userLabels.begin(); it != userLabels.end(); it++) { - mothurOut("Your file does not include the label " + *it); + m->mothurOut("Your file does not include the label " + *it); if (processedLabels.count(lastLabel) != 1) { - mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine(); + m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); needToRun = true; }else { - mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine(); + m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine(); } } @@ -166,21 +230,30 @@ int GetSAbundCommand::execute(){ if (order != NULL) { delete order; } order = (input->getOrderVector(lastLabel)); - mothurOut(order->getLabel()); mothurOutEndLine(); + m->mothurOut(order->getLabel()); m->mothurOutEndLine(); sabund = new SAbundVector(); *sabund = (order->getSAbundVector()); sabund->print(out); delete sabund; + + if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; } + delete order; } globaldata->gorder = NULL; out.close(); + + m->mothurOutEndLine(); + m->mothurOut("Output File Name: "); m->mothurOutEndLine(); + m->mothurOut(filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["sabund"].push_back(filename); + m->mothurOutEndLine(); + return 0; } catch(exception& e) { - errorOut(e, "GetSAbundCommand", "execute"); + m->errorOut(e, "GetSAbundCommand", "execute"); exit(1); } }