X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getrabundcommand.cpp;h=d5f5a8b8b8450deef538f564d59885b57647c430;hb=b0997605981902442138b9309e9c43d95c3ba10a;hp=3b03f3694967d6d480ba0dc00153454c7e8b074f;hpb=348de0f8b17d84ede77081dcf67bd6ef43496677;p=mothur.git diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp index 3b03f36..d5f5a8b 100644 --- a/getrabundcommand.cpp +++ b/getrabundcommand.cpp @@ -10,95 +10,137 @@ #include "getrabundcommand.h" //********************************************************************************************************************** -vector GetRAbundCommand::getValidParameters(){ +vector GetRAbundCommand::setParameters(){ try { - string Array[] = {"label","sorted","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","rabund",false,false, true); parameters.push_back(plist); + CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","rabund",false,false, true); parameters.push_back(psabund); + CommandParameter psorted("sorted", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(psorted); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir); + + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } return myArray; } catch(exception& e) { - m->errorOut(e, "GetRAbundCommand", "getValidParameters"); + m->errorOut(e, "GetRAbundCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -GetRAbundCommand::GetRAbundCommand(){ +string GetRAbundCommand::getHelpString(){ try { - abort = true; calledHelp = true; - vector tempOutNames; - outputTypes["rabund"] = tempOutNames; + string helpString = ""; + helpString += "The get.rabund command parameters are list, sabund, label and sorted. list or sabund parameters are required, unless you have valid current files.\n"; + helpString += "The label parameter allows you to select what distance levels you would like included in your .rabund file, and are separated by dashes.\n"; + helpString += "The sorted parameters allows you to print the rabund results sorted by abundance or not. The default is sorted.\n"; + helpString += "The get.rabund command should be in the following format: get.rabund(label=yourLabels, sorted=yourSorted).\n"; + helpString += "Example get.rabund(sorted=F).\n"; + helpString += "The default value for label is all labels in your inputfile.\n"; + helpString += "The get.rabund command outputs a .rabund file containing the lines you selected.\n"; + helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n"; + return helpString; } catch(exception& e) { - m->errorOut(e, "GetRAbundCommand", "GetRAbundCommand"); + m->errorOut(e, "GetRAbundCommand", "getHelpString"); exit(1); } } //********************************************************************************************************************** -vector GetRAbundCommand::getRequiredParameters(){ - try { - vector myArray; - return myArray; - } - catch(exception& e) { - m->errorOut(e, "GetRAbundCommand", "getRequiredParameters"); - exit(1); - } +string GetRAbundCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "rabund") { pattern = "[filename],rabund"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "GetRAbundCommand", "getOutputPattern"); + exit(1); + } } + //********************************************************************************************************************** -vector GetRAbundCommand::getRequiredFiles(){ +GetRAbundCommand::GetRAbundCommand(){ try { - string Array[] = {"list"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - - return myArray; + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["rabund"] = tempOutNames; } catch(exception& e) { - m->errorOut(e, "GetRAbundCommand", "getRequiredFiles"); + m->errorOut(e, "GetRAbundCommand", "GetRAbundCommand"); exit(1); } } //********************************************************************************************************************** GetRAbundCommand::GetRAbundCommand(string option) { try { - globaldata = GlobalData::getInstance(); abort = false; calledHelp = false; allLines = 1; - labels.clear(); //allow user to run help if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { - //valid paramters for this command - string Array[] = {"label","sorted","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); + map::iterator it; ValidParameters validParameter; //check to make sure all parameters are valid for command - for (map::iterator it = parameters.begin(); it != parameters.end(); it++) { + for (it = parameters.begin(); it != parameters.end(); it++) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } - //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 - } - //initialize outputTypes vector tempOutNames; outputTypes["rabund"] = tempOutNames; - //make sure the user has already run the read.otu command - if (globaldata->getListFile() == "") { m->mothurOut("You must read a listfile before you can use the get.rabund command."); m->mothurOutEndLine(); abort = true; } + //if the user changes the input directory command factory will send this info to us in the output parameter + string inputDir = validParameter.validFile(parameters, "inputdir", false); + if (inputDir == "not found"){ inputDir = ""; } + else { + string path; + it = parameters.find("list"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["list"] = inputDir + it->second; } + } + + it = parameters.find("sabund"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["sabund"] = inputDir + it->second; } + } + } + + + //check for required parameters + listfile = validParameter.validFile(parameters, "list", true); + if (listfile == "not open") { listfile = ""; abort = true; } + else if (listfile == "not found") { listfile = ""; } + else { format = "list"; inputfile = listfile; m->setListFile(listfile); } + + sabundfile = validParameter.validFile(parameters, "sabund", true); + if (sabundfile == "not open") { sabundfile = ""; abort = true; } + else if (sabundfile == "not found") { sabundfile = ""; } + else { format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); } + //check for optional parameter and set defaults // ...at some point should added some additional type checking... - string temp; temp = validParameter.validFile(parameters, "sorted", false); if (temp == "not found") { temp = "T"; } sorted = m->isTrue(temp); @@ -110,17 +152,28 @@ GetRAbundCommand::GetRAbundCommand(string option) { else { allLines = 1; } } - //if the user has not specified any labels use the ones from read.otu - if(label == "") { - allLines = globaldata->allLines; - labels = globaldata->labels; - } - - if (abort == false) { - filename = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "rabund"; - m->openOutputFile(filename, out); + if ((listfile == "") && (sabundfile == "")) { + //is there are current file available for any of these? + //give priority to shared, then list, then rabund, then sabund + //if there is a current shared file, use it + listfile = m->getListFile(); + if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); } + else { + sabundfile = m->getSabundFile(); + if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); } + else { + m->mothurOut("No valid current files. You must provide a list or sabund file."); m->mothurOutEndLine(); + abort = true; + } + } } + + + //if the user changes the output directory command factory will send this info to us in the output parameter + outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(inputfile); } + } + } catch(exception& e) { @@ -130,96 +183,64 @@ GetRAbundCommand::GetRAbundCommand(string option) { } //********************************************************************************************************************** -void GetRAbundCommand::help(){ - try { - m->mothurOut("The get.rabund command can only be executed after a successful read.otu of a listfile.\n"); - m->mothurOut("The get.rabund command parameters are label and sorted. No parameters are required.\n"); - m->mothurOut("The label parameter allows you to select what distance levels you would like included in your .rabund file, and are separated by dashes.\n"); - m->mothurOut("The sorted parameters allows you to print the rabund results sorted by abundance or not. The default is sorted.\n"); - m->mothurOut("The get.rabund command should be in the following format: get.rabund(label=yourLabels, sorted=yourSorted).\n"); - m->mothurOut("Example get.rabund(sorted=F).\n"); - m->mothurOut("The default value for label is all labels in your inputfile.\n"); - m->mothurOut("The get.rabund command outputs a .rabund file containing the lines you selected.\n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n\n"); - } - catch(exception& e) { - m->errorOut(e, "GetRAbundCommand", "help"); - exit(1); - } -} - -//********************************************************************************************************************** - -GetRAbundCommand::~GetRAbundCommand(){} - -//********************************************************************************************************************** - int GetRAbundCommand::execute(){ try { if (abort == true) { if (calledHelp) { return 0; } return 2; } - //read first line - read = new ReadOTUFile(globaldata->inputFileName); - read->read(&*globaldata); - - input = globaldata->ginput; - list = globaldata->gListVector; - string lastLabel = list->getLabel(); + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile)); + filename = getOutputFileName("rabund", variables); + m->openOutputFile(filename, out); + + input = new InputData(inputfile, format); + rabund = input->getRAbundVector(); + string lastLabel = rabund->getLabel(); //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. set processedLabels; set userLabels = labels; - if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete list; globaldata->gListVector = NULL; return 0; } + if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete rabund; delete input; return 0; } - while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { + while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { - if(allLines == 1 || labels.count(list->getLabel()) == 1){ - m->mothurOut(list->getLabel()); m->mothurOutEndLine(); - rabund = new RAbundVector(); - *rabund = (list->getRAbundVector()); + if(allLines == 1 || labels.count(rabund->getLabel()) == 1){ + m->mothurOut(rabund->getLabel()); m->mothurOutEndLine(); - if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete list; delete rabund; globaldata->gListVector = NULL; return 0; } - + if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete input; delete rabund; return 0; } if(sorted) { rabund->print(out); } else { rabund->nonSortedPrint(out); } - - delete rabund; - processedLabels.insert(list->getLabel()); - userLabels.erase(list->getLabel()); + processedLabels.insert(rabund->getLabel()); + userLabels.erase(rabund->getLabel()); } - if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { - string saveLabel = list->getLabel(); + if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = rabund->getLabel(); - delete list; - list = input->getListVector(lastLabel); + delete rabund; + rabund = input->getRAbundVector(lastLabel); - m->mothurOut(list->getLabel()); m->mothurOutEndLine(); - rabund = new RAbundVector(); - *rabund = (list->getRAbundVector()); + m->mothurOut(rabund->getLabel()); m->mothurOutEndLine(); - if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete list; delete rabund; globaldata->gListVector = NULL; return 0; } + if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete input; delete rabund; return 0; } if(sorted) { rabund->print(out); } else { rabund->nonSortedPrint(out); } - delete rabund; - - processedLabels.insert(list->getLabel()); - userLabels.erase(list->getLabel()); + processedLabels.insert(rabund->getLabel()); + userLabels.erase(rabund->getLabel()); //restore real lastlabel to save below - list->setLabel(saveLabel); + rabund->setLabel(saveLabel); } - lastLabel = list->getLabel(); + lastLabel = rabund->getLabel(); - delete list; - list = input->getListVector(); + delete rabund; + rabund = input->getRAbundVector(); } //output error messages about any remaining user labels @@ -237,31 +258,26 @@ int GetRAbundCommand::execute(){ //run last label if you need to if (needToRun == true) { - if (list != NULL) { delete list; } - list = input->getListVector(lastLabel); - - m->mothurOut(list->getLabel()); m->mothurOutEndLine(); - rabund = new RAbundVector(); - *rabund = (list->getRAbundVector()); + if (rabund != NULL) { delete rabund; } + rabund = input->getRAbundVector(lastLabel); - if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete list; delete rabund; globaldata->gListVector = NULL; return 0; } + m->mothurOut(rabund->getLabel()); m->mothurOutEndLine(); + + if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete input; delete rabund; return 0; } if(sorted) { rabund->print(out); } else { rabund->nonSortedPrint(out); } delete rabund; - delete list; } m->mothurOutEndLine(); - m->mothurOut("Output File Name: "); m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); m->mothurOut(filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["rabund"].push_back(filename); m->mothurOutEndLine(); out.close(); - - globaldata->gListVector = NULL; - + //set rabund file as new current rabundfile string current = ""; itTypes = outputTypes.find("rabund");