X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readotucommand.cpp;h=f39e8df2c382f02451848ca41ec6edb23e07aa49;hb=ee8403d4eb5760187d62b42a9cf4272de8fc0ec4;hp=c7e83e4db2e5a3048fcf9144db13c8044eada09c;hpb=fd282e6b4be2560f5b1bd154a9e8d24b798eefaf;p=mothur.git diff --git a/readotucommand.cpp b/readotucommand.cpp index c7e83e4..f39e8df 100644 --- a/readotucommand.cpp +++ b/readotucommand.cpp @@ -9,56 +9,269 @@ #include "readotucommand.h" + //********************************************************************************************************************** -ReadOtuCommand::ReadOtuCommand(){ +ReadOtuCommand::ReadOtuCommand(){ try { - globaldata = GlobalData::getInstance(); - filename = globaldata->inputFileName; - read = new ReadPhilFile(filename); - if (globaldata->getFormat() == "shared") { - //read in group map info. - groupMap = new GroupMap(globaldata->getGroupFile()); - } + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["rabund"] = tempOutNames; + outputTypes["shared"] = tempOutNames; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ReadOtuCommand class Function ReadOtuCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ReadOtuCommand class function ReadOtuCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ReadOtuCommand", "ReadOtuCommand"); exit(1); } } - //********************************************************************************************************************** +ReadOtuCommand::ReadOtuCommand(string option) { + try { + abort = false; calledHelp = false; + allLines = 1; + + //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[] = {"list","order","shared","relabund","label","group","sabund", "rabund","groups","ordergroup","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + + OptionParser parser(option); + map parameters = parser.getParameters(); + + ValidParameters validParameter; + map::iterator it; + + //check to make sure all parameters are valid for command + for (it = parameters.begin(); it != parameters.end(); it++) { + if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } + } + + //initialize outputTypes + vector tempOutNames; + outputTypes["rabund"] = tempOutNames; + outputTypes["shared"] = tempOutNames; + + globaldata->newRead(); + + //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("order"); + //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["order"] = inputDir + it->second; } + } + + it = parameters.find("shared"); + //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["shared"] = inputDir + it->second; } + } + + it = parameters.find("group"); + //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["group"] = 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; } + } + + it = parameters.find("rabund"); + //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["rabund"] = inputDir + it->second; } + } + + it = parameters.find("ordergroup"); + //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["ordergroup"] = inputDir + it->second; } + } + + it = parameters.find("relabund"); + //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["relabund"] = inputDir + it->second; } + } + } -ReadOtuCommand::~ReadOtuCommand(){ - delete read; -} + + //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 = ""; } -//********************************************************************************************************************** + //check for required parameters + listfile = validParameter.validFile(parameters, "list", true); + if (listfile == "not open") { abort = true; } + else if (listfile == "not found") { listfile = ""; } + else { globaldata->setListFile(listfile); globaldata->setFormat("list"); } + + sabundfile = validParameter.validFile(parameters, "sabund", true); + if (sabundfile == "not open") { abort = true; } + else if (sabundfile == "not found") { sabundfile = ""; } + else { globaldata->setSabundFile(sabundfile); globaldata->setFormat("sabund"); } + + rabundfile = validParameter.validFile(parameters, "rabund", true); + if (rabundfile == "not open") { abort = true; } + else if (rabundfile == "not found") { rabundfile = ""; } + else { globaldata->setRabundFile(rabundfile); globaldata->setFormat("rabund");} + + ordergroupfile = validParameter.validFile(parameters, "ordergroup", true); + if (ordergroupfile == "not open") { abort = true; } + else if (ordergroupfile == "not found") { ordergroupfile = ""; } + else { globaldata->setOrderGroupFile(ordergroupfile); } + + sharedfile = validParameter.validFile(parameters, "shared", true); + if (sharedfile == "not open") { abort = true; } + else if (sharedfile == "not found") { sharedfile = ""; } + else { globaldata->setSharedFile(sharedfile); globaldata->setFormat("sharedfile"); } + + relAbundfile = validParameter.validFile(parameters, "relabund", true); + if (relAbundfile == "not open") { abort = true; } + else if (relAbundfile == "not found") { relAbundfile = ""; } + else { globaldata->setRelAbundFile(relAbundfile); globaldata->setFormat("relabund"); } + + + groupfile = validParameter.validFile(parameters, "group", true); + if (groupfile == "not open") { abort = true; } + else if (groupfile == "not found") { groupfile = ""; } + else { + globaldata->setGroupFile(groupfile); + groupMap = new GroupMap(groupfile); + + int error = groupMap->readMap(); + if (error == 1) { abort = true; } + + globaldata->gGroupmap = groupMap; + } + + groups = validParameter.validFile(parameters, "groups", false); + if (groups == "not found") { groups = ""; } + else { + m->splitAtDash(groups, Groups); + globaldata->Groups = Groups; + } + + //you are doing a list and group shared + if ((listfile != "") && (groupfile != "")) { globaldata->setFormat("shared"); } + + //you have not given a file + if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "") && (relAbundfile == "")) { + m->mothurOut("You must enter either a listfile, rabundfile, sabundfile, relabund or a sharedfile with the read.otu 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") { m->splitAtDash(label, labels); allLines = 0; } + else { allLines = 1; } + globaldata->labels = labels; + } + + globaldata->allLines = allLines; + + orderfile = validParameter.validFile(parameters, "order", true); + if (orderfile == "not open") { abort = true; } + else if (orderfile == "not found") { orderfile = ""; } + else { globaldata->setOrderFile(orderfile); } + + + if (abort == false) { + //gets whichever one of the above is set + filename = globaldata->inputFileName; + } + */ + } + + } + catch(exception& e) { + m->errorOut(e, "ReadOtuCommand", "ReadOtuCommand"); + exit(1); + } +} +///********************************************************************************************************************** int ReadOtuCommand::execute(){ try { - read->read(&*globaldata); + + if (abort == true) { if (calledHelp) { return 0; } return 2; } + m->mothurOut(getHelpString()); m->mothurOutEndLine(); + + /* if (globaldata->getFormat() == "shared") { - groupMap->readMap(); - globaldata->gGroupmap = groupMap; - - shared = new SharedCommand(); - shared->execute(); - parselist = new ParseListCommand(); - parselist->execute(); + + shared = new SharedCommand(outputDir); + int okay = shared->execute(); + + //problem with shared + if (okay == 1) { + globaldata->setListFile(""); + globaldata->setGroupFile(""); + globaldata->setSharedFile(""); + }else { //shared command outputs the filenames + //m->mothurOutEndLine(); + //m->mothurOut("Output File Name: "); m->mothurOutEndLine(); + //m->mothurOut(globaldata->getSharedFile()); m->mothurOutEndLine(); + //m->mothurOutEndLine(); + } + + outputTypes = shared->getOutputFiles(); + + //set rabund file as new current rabundfile + string current = ""; + itTypes = outputTypes.find("rabund"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); } + } + + itTypes = outputTypes.find("shared"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); } + } + + delete shared; } + */ + return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ReadOtuCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ReadOtuCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ReadOtuCommand", "execute"); exit(1); } } -//********************************************************************************************************************** \ No newline at end of file +//**********************************************************************************************************************