X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=collectcommand.cpp;h=b892a91bee89e9b6d01ac7bda8e40833fd4db3b0;hp=cf8ba10e8e43054304c42892cbfb9c2014a8da1f;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3 diff --git a/collectcommand.cpp b/collectcommand.cpp index cf8ba10..b892a91 100644 --- a/collectcommand.cpp +++ b/collectcommand.cpp @@ -14,8 +14,13 @@ #include "chao1.h" #include "bootstrap.h" #include "simpson.h" +#include "simpsoneven.h" +#include "invsimpson.h" #include "npshannon.h" #include "shannon.h" +#include "smithwilson.h" +#include "heip.h" +#include "shannoneven.h" #include "jackknife.h" #include "geom.h" #include "qstat.h" @@ -30,70 +35,297 @@ #include "coverage.h" +//********************************************************************************************************************** +vector CollectCommand::setParameters(){ + try { + CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(plist); + CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(prabund); + CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(psabund); + CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(pshared); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); + CommandParameter pfreq("freq", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pfreq); + CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "","",true,false,true); parameters.push_back(pcalc); + CommandParameter pabund("abund", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pabund); + CommandParameter psize("size", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psize); + 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, "CollectCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string CollectCommand::getHelpString(){ + try { + string helpString = ""; + ValidCalculators validCalculator; + helpString += "The collect.single command parameters are list, sabund, rabund, shared, label, freq, calc and abund. list, sabund, rabund or shared is required unless you have a valid current file. \n"; + helpString += "The collect.single command should be in the following format: \n"; + helpString += "The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n"; + helpString += "collect.single(label=yourLabel, freq=yourFreq, calc=yourEstimators).\n"; + helpString += "Example collect(label=unique-.01-.03, freq=10, calc=sobs-chao-ace-jack).\n"; + helpString += "The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson.\n"; + helpString += validCalculator.printCalc("single"); + helpString += "The label parameter is used to analyze specific labels in your input.\n"; + helpString += "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "CollectCommand", "getHelpString"); + exit(1); + } +} +//********************************************************************************************************************** +string CollectCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "sobs") { pattern = "[filename],sobs"; } + else if (type == "chao") { pattern = "[filename],chao"; } + else if (type == "nseqs") { pattern = "[filename],nseqs"; } + else if (type == "coverage") { pattern = "[filename],coverage"; } + else if (type == "ace") { pattern = "[filename],ace"; } + else if (type == "jack") { pattern = "[filename],jack"; } + else if (type == "shannon") { pattern = "[filename],shannon"; } + else if (type == "shannoneven") { pattern = "[filename],shannoneven"; } + else if (type == "npshannon") { pattern = "[filename],npshannon"; } + else if (type == "heip") { pattern = "[filename],heip"; } + else if (type == "smithwilson") { pattern = "[filename],smithwilson"; } + else if (type == "simpson") { pattern = "[filename],simpson"; } + else if (type == "simpsoneven") { pattern = "[filename],simpsoneven"; } + else if (type == "invsimpson") { pattern = "[filename],invsimpson"; } + else if (type == "bootstrap") { pattern = "[filename],bootstrap"; } + else if (type == "geometric") { pattern = "[filename],geometric"; } + else if (type == "qstat") { pattern = "[filename],qstat"; } + else if (type == "logseries") { pattern = "[filename],logseries"; } + else if (type == "bergerparker") { pattern = "[filename],bergerparker"; } + else if (type == "bstick") { pattern = "[filename],bstick"; } + else if (type == "goodscoverage") { pattern = "[filename],goodscoverage"; } + else if (type == "efron") { pattern = "[filename],efron"; } + else if (type == "boneh") { pattern = "[filename],boneh"; } + else if (type == "solow") { pattern = "[filename],solow"; } + else if (type == "shen") { pattern = "[filename],shen"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "CollectCommand", "getOutputPattern"); + exit(1); + } +} +//********************************************************************************************************************** +CollectCommand::CollectCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["sobs"] = tempOutNames; + outputTypes["chao"] = tempOutNames; + outputTypes["nseqs"] = tempOutNames; + outputTypes["coverage"] = tempOutNames; + outputTypes["ace"] = tempOutNames; + outputTypes["jack"] = tempOutNames; + outputTypes["shannon"] = tempOutNames; + outputTypes["shannoneven"] = tempOutNames; + outputTypes["npshannon"] = tempOutNames; + outputTypes["heip"] = tempOutNames; + outputTypes["smithwilson"] = tempOutNames; + outputTypes["simpson"] = tempOutNames; + outputTypes["simpsoneven"] = tempOutNames; + outputTypes["invsimpson"] = tempOutNames; + outputTypes["bootstrap"] = tempOutNames; + outputTypes["geometric"] = tempOutNames; + outputTypes["qstat"] = tempOutNames; + outputTypes["logseries"] = tempOutNames; + outputTypes["bergerparker"] = tempOutNames; + outputTypes["bstick"] = tempOutNames; + outputTypes["goodscoverage"] = tempOutNames; + outputTypes["efron"] = tempOutNames; + outputTypes["boneh"] = tempOutNames; + outputTypes["solow"] = tempOutNames; + outputTypes["shen"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "CollectCommand", "CollectCommand"); + exit(1); + } +} //********************************************************************************************************************** CollectCommand::CollectCommand(string option) { try { - globaldata = GlobalData::getInstance(); - abort = false; + abort = false; calledHelp = false; allLines = 1; - labels.clear(); - Estimators.clear(); //allow user to run help - if(option == "help") { validCalculator = new ValidCalculators(); help(); delete validCalculator; abort = true; } + if(option == "help") { help(); calledHelp = true; abort = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { - //valid paramters for this command - string Array[] = {"freq","label","calc","abund","size","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; } } + + //initialize outputTypes + vector tempOutNames; + outputTypes["sobs"] = tempOutNames; + outputTypes["chao"] = tempOutNames; + outputTypes["nseqs"] = tempOutNames; + outputTypes["coverage"] = tempOutNames; + outputTypes["ace"] = tempOutNames; + outputTypes["jack"] = tempOutNames; + outputTypes["shannon"] = tempOutNames; + outputTypes["shannoneven"] = tempOutNames; + outputTypes["npshannon"] = tempOutNames; + outputTypes["heip"] = tempOutNames; + outputTypes["smithwilson"] = tempOutNames; + outputTypes["simpson"] = tempOutNames; + outputTypes["simpsoneven"] = tempOutNames; + outputTypes["invsimpson"] = tempOutNames; + outputTypes["bootstrap"] = tempOutNames; + outputTypes["geometric"] = tempOutNames; + outputTypes["qstat"] = tempOutNames; + outputTypes["logseries"] = tempOutNames; + outputTypes["bergerparker"] = tempOutNames; + outputTypes["bstick"] = tempOutNames; + outputTypes["goodscoverage"] = tempOutNames; + outputTypes["efron"] = tempOutNames; + outputTypes["boneh"] = tempOutNames; + outputTypes["solow"] = tempOutNames; + outputTypes["shen"] = tempOutNames; + + //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("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("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("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("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; } + } + } + + //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); } + + rabundfile = validParameter.validFile(parameters, "rabund", true); + if (rabundfile == "not open") { rabundfile = ""; abort = true; } + else if (rabundfile == "not found") { rabundfile = ""; } + else { format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); } + + sharedfile = validParameter.validFile(parameters, "shared", true); + if (sharedfile == "not open") { sharedfile = ""; abort = true; } + else if (sharedfile == "not found") { sharedfile = ""; } + else { format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); } + //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 = ""; } - //make sure the user has already run the read.otu command - if ((globaldata->getSharedFile() == "") && (globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { m->mothurOut("You must read a list, sabund, rabund or shared file before you can use the collect.single command."); m->mothurOutEndLine(); abort = true; } + if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (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 + sharedfile = m->getSharedFile(); + if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); } + else { + listfile = m->getListFile(); + if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); } + else { + rabundfile = m->getRabundFile(); + if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund 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, sabund, rabund or shared file before you can use the collect.single 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; } } - //if the user has not specified any labels use the ones from read.otu - if (label == "") { - allLines = globaldata->allLines; - labels = globaldata->labels; - } - + //NOTE: if you add new calc options, don't forget to add them to the parameter initialize in setParameters or the gui won't be able to use them calc = validParameter.validFile(parameters, "calc", false); if (calc == "not found") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; } else { if (calc == "default") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; } } - splitAtDash(calc, Estimators); + m->splitAtDash(calc, Estimators); + if (m->inUsersGroups("citation", Estimators)) { + ValidCalculators validCalc; validCalc.printCitations(Estimators); + //remove citation from list of calcs + for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } } + } string temp; temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; } - convert(temp, freq); + m->mothurConvert(temp, freq); temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; } - convert(temp, abund); + m->mothurConvert(temp, abund); temp = validParameter.validFile(parameters, "size", false); if (temp == "not found") { temp = "0"; } - convert(temp, size); + m->mothurConvert(temp, size); } } @@ -104,117 +336,107 @@ CollectCommand::CollectCommand(string option) { } //********************************************************************************************************************** -void CollectCommand::help(){ - try { - m->mothurOut("The collect.single command can only be executed after a successful read.otu command. WITH ONE EXECEPTION. \n"); - m->mothurOut("The collect.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster.\n"); - m->mothurOut("The collect.single command parameters are label, freq, calc and abund. No parameters are required. \n"); - m->mothurOut("The collect.single command should be in the following format: \n"); - m->mothurOut("collect.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n"); - m->mothurOut("Example collect(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-chao-ace-jack).\n"); - m->mothurOut("The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson.\n"); - validCalculator->printCalc("single", cout); - m->mothurOut("The label parameter is used to analyze specific labels in your input.\n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n"); - } - catch(exception& e) { - m->errorOut(e, "CollectCommand", "help"); - exit(1); - } -} - -//********************************************************************************************************************** - -CollectCommand::~CollectCommand(){} - -//********************************************************************************************************************** - int CollectCommand::execute(){ try { - if (abort == true) { return 0; } - - vector outputNames; - - if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName); } - else { inputFileNames = parseSharedFile(globaldata->getSharedFile()); globaldata->setFormat("rabund"); } + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + if ((format != "sharedfile")) { inputFileNames.push_back(inputfile); } + else { inputFileNames = parseSharedFile(sharedfile); format = "rabund"; } for (int p = 0; p < inputFileNames.size(); p++) { - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0; } + if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0; } - if (outputDir == "") { outputDir += hasPath(inputFileNames[p]); } - string fileNameRoot = outputDir + getRootName(getSimpleName(inputFileNames[p])); - globaldata->inputFileName = inputFileNames[p]; + if (outputDir == "") { outputDir += m->hasPath(inputFileNames[p]); } + string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])); + map variables; + variables["[filename]"] = fileNameRoot; + //globaldata->inputFileName = inputFileNames[p]; if (inputFileNames.size() > 1) { m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine(); } - validCalculator = new ValidCalculators(); + ValidCalculators validCalculator; for (int i=0; iisValidCalculator("single", Estimators[i]) == true) { + if (validCalculator.isValidCalculator("single", Estimators[i]) == true) { if (Estimators[i] == "sobs") { - cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs"))); - outputNames.push_back(fileNameRoot+"sobs"); + cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(getOutputFileName("sobs", variables)))); + outputNames.push_back(getOutputFileName("sobs", variables)); outputTypes["sobs"].push_back(getOutputFileName("sobs", variables)); }else if (Estimators[i] == "chao") { - cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao"))); - outputNames.push_back(fileNameRoot+"chao"); + cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(getOutputFileName("chao", variables)))); + outputNames.push_back(getOutputFileName("chao", variables)); outputTypes["chao"].push_back(getOutputFileName("chao", variables)); }else if (Estimators[i] == "nseqs") { - cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+"nseqs"))); - outputNames.push_back(fileNameRoot+"nseqs"); + cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(getOutputFileName("nseqs", variables)))); + outputNames.push_back(getOutputFileName("nseqs", variables)); outputTypes["nseqs"].push_back(getOutputFileName("nseqs", variables)); }else if (Estimators[i] == "coverage") { - cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+"coverage"))); - outputNames.push_back(fileNameRoot+"coverage"); + cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(getOutputFileName("coverage", variables)))); + outputNames.push_back(getOutputFileName("coverage", variables)); outputTypes["coverage"].push_back(getOutputFileName("coverage", variables)); }else if (Estimators[i] == "ace") { - cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace"))); - outputNames.push_back(fileNameRoot+"ace"); + cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(getOutputFileName("ace", variables)))); + outputNames.push_back(getOutputFileName("ace", variables)); outputTypes["ace"].push_back(getOutputFileName("ace", variables)); }else if (Estimators[i] == "jack") { - cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack"))); - outputNames.push_back(fileNameRoot+"jack"); + cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(getOutputFileName("jack", variables)))); + outputNames.push_back(getOutputFileName("jack", variables)); outputTypes["jack"].push_back(getOutputFileName("jack", variables)); }else if (Estimators[i] == "shannon") { - cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon"))); - outputNames.push_back(fileNameRoot+"shannon"); + cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(getOutputFileName("shannon", variables)))); + outputNames.push_back(getOutputFileName("shannon", variables)); outputTypes["shannon"].push_back(getOutputFileName("shannon", variables)); + }else if (Estimators[i] == "shannoneven") { + cDisplays.push_back(new CollectDisplay(new ShannonEven(), new OneColumnFile(getOutputFileName("shannoneven", variables)))); + outputNames.push_back(getOutputFileName("shannoneven", variables)); outputTypes["shannoneven"].push_back(getOutputFileName("shannoneven", variables)); }else if (Estimators[i] == "npshannon") { - cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon"))); - outputNames.push_back(fileNameRoot+"np_shannon"); + cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(getOutputFileName("npshannon", variables)))); + outputNames.push_back(getOutputFileName("npshannon", variables)); outputTypes["npshannon"].push_back(getOutputFileName("npshannon", variables)); + }else if (Estimators[i] == "heip") { + cDisplays.push_back(new CollectDisplay(new Heip(), new OneColumnFile(getOutputFileName("heip", variables)))); + outputNames.push_back(getOutputFileName("heip", variables)); outputTypes["heip"].push_back(getOutputFileName("heip", variables)); + }else if (Estimators[i] == "smithwilson") { + cDisplays.push_back(new CollectDisplay(new SmithWilson(), new OneColumnFile(getOutputFileName("smithwilson", variables)))); + outputNames.push_back(getOutputFileName("smithwilson", variables)); outputTypes["smithwilson"].push_back(getOutputFileName("smithwilson", variables)); }else if (Estimators[i] == "simpson") { - cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson"))); - outputNames.push_back(fileNameRoot+"simpson"); + cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(getOutputFileName("simpson", variables)))); + outputNames.push_back(getOutputFileName("simpson", variables)); outputTypes["simpson"].push_back(getOutputFileName("simpson", variables)); + }else if (Estimators[i] == "simpsoneven") { + cDisplays.push_back(new CollectDisplay(new SimpsonEven(), new OneColumnFile(getOutputFileName("simpsoneven", variables)))); + outputNames.push_back(getOutputFileName("simpsoneven", variables)); outputTypes["simpsoneven"].push_back(getOutputFileName("simpsoneven", variables)); + }else if (Estimators[i] == "invsimpson") { + cDisplays.push_back(new CollectDisplay(new InvSimpson(), new ThreeColumnFile(getOutputFileName("invsimpson", variables)))); + outputNames.push_back(getOutputFileName("invsimpson", variables)); outputTypes["invsimpson"].push_back(getOutputFileName("invsimpson", variables)); }else if (Estimators[i] == "bootstrap") { - cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap"))); - outputNames.push_back(fileNameRoot+"bootstrap"); + cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(getOutputFileName("bootstrap", variables)))); + outputNames.push_back(getOutputFileName("bootstrap", variables)); outputTypes["bootstrap"].push_back(getOutputFileName("bootstrap", variables)); }else if (Estimators[i] == "geometric") { - cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geometric"))); - outputNames.push_back(fileNameRoot+"geometric"); + cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(getOutputFileName("geometric", variables)))); + outputNames.push_back(getOutputFileName("geometric", variables)); outputTypes["geometric"].push_back(getOutputFileName("geometric", variables)); }else if (Estimators[i] == "qstat") { - cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat"))); - outputNames.push_back(fileNameRoot+"qstat"); + cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(getOutputFileName("qstat", variables)))); + outputNames.push_back(getOutputFileName("qstat", variables)); outputTypes["qstat"].push_back(getOutputFileName("qstat", variables)); }else if (Estimators[i] == "logseries") { - cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logseries"))); - outputNames.push_back(fileNameRoot+"logseries"); + cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(getOutputFileName("logseries", variables)))); + outputNames.push_back(getOutputFileName("logseries", variables)); outputTypes["logseries"].push_back(getOutputFileName("logseries", variables)); }else if (Estimators[i] == "bergerparker") { - cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker"))); - outputNames.push_back(fileNameRoot+"bergerparker"); + cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(getOutputFileName("bergerparker", variables)))); + outputNames.push_back(getOutputFileName("bergerparker", variables)); outputTypes["bergerparker"].push_back(getOutputFileName("bergerparker", variables)); }else if (Estimators[i] == "bstick") { - cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(fileNameRoot+"bstick"))); - outputNames.push_back(fileNameRoot+"bstick"); + cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(getOutputFileName("bstick", variables)))); + outputNames.push_back(getOutputFileName("bstick", variables)); outputTypes["bstick"].push_back(getOutputFileName("bstick", variables)); }else if (Estimators[i] == "goodscoverage") { - cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(fileNameRoot+"goodscoverage"))); - outputNames.push_back(fileNameRoot+"goodscoverage"); + cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(getOutputFileName("goodscoverage", variables)))); + outputNames.push_back(getOutputFileName("goodscoverage", variables)); outputTypes["goodscoverage"].push_back(getOutputFileName("goodscoverage", variables)); }else if (Estimators[i] == "efron") { - cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(fileNameRoot+"efron"))); - outputNames.push_back(fileNameRoot+"efron"); + cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(getOutputFileName("efron", variables)))); + outputNames.push_back(getOutputFileName("efron", variables)); outputTypes["efron"].push_back(getOutputFileName("efron", variables)); }else if (Estimators[i] == "boneh") { - cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(fileNameRoot+"boneh"))); - outputNames.push_back(fileNameRoot+"boneh"); + cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(getOutputFileName("boneh", variables)))); + outputNames.push_back(getOutputFileName("boneh", variables)); outputTypes["boneh"].push_back(getOutputFileName("boneh", variables)); }else if (Estimators[i] == "solow") { - cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(fileNameRoot+"solow"))); - outputNames.push_back(fileNameRoot+"solow"); + cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(getOutputFileName("solow", variables)))); + outputNames.push_back(getOutputFileName("solow", variables)); outputTypes["solow"].push_back(getOutputFileName("solow", variables)); }else if (Estimators[i] == "shen") { - cDisplays.push_back(new CollectDisplay(new Shen(size, abund), new OneColumnFile(fileNameRoot+"shen"))); - outputNames.push_back(fileNameRoot+"shen"); + cDisplays.push_back(new CollectDisplay(new Shen(size, abund), new OneColumnFile(getOutputFileName("shen", variables)))); + outputNames.push_back(getOutputFileName("shen", variables)); outputTypes["shen"].push_back(getOutputFileName("shen", variables)); } } } @@ -222,12 +444,9 @@ int CollectCommand::execute(){ //if the users entered no valid calculators don't execute command if (cDisplays.size() == 0) { return 0; } - read = new ReadOTUFile(inputFileNames[p]); - read->read(&*globaldata); - - order = globaldata->gorder; + input = new InputData(inputFileNames[p], format); + order = input->getOrderVector(); string lastLabel = order->getLabel(); - input = globaldata->ginput; //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. set processedLabels; @@ -235,12 +454,10 @@ int CollectCommand::execute(){ if (m->control_pressed) { for(int i=0;iginput = NULL; - delete read; - delete order; globaldata->gorder = NULL; - delete validCalculator; - globaldata->Groups.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); + delete input; + delete order; + m->clearGroups(); return 0; } @@ -249,12 +466,10 @@ int CollectCommand::execute(){ if (m->control_pressed) { for(int i=0;iginput = NULL; - delete read; - delete order; globaldata->gorder = NULL; - delete validCalculator; - globaldata->Groups.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); + delete input; + delete order; + m->clearGroups(); return 0; } @@ -272,7 +487,7 @@ int CollectCommand::execute(){ } //you have a label the user want that is smaller than this label and the last label has not already been processed - 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; @@ -300,11 +515,9 @@ int CollectCommand::execute(){ if (m->control_pressed) { for(int i=0;iginput = NULL; - delete read; - delete validCalculator; - globaldata->Groups.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); + delete input; + m->clearGroups(); return 0; } @@ -334,12 +547,10 @@ int CollectCommand::execute(){ if (m->control_pressed) { for(int i=0;iginput = NULL; - delete read; - delete order; globaldata->gorder = NULL; - delete validCalculator; - globaldata->Groups.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); + delete input; + delete order; + m->clearGroups(); return 0; } delete order; @@ -347,14 +558,11 @@ int CollectCommand::execute(){ for(int i=0;iginput = NULL; - delete read; - globaldata->gorder = NULL; - delete validCalculator; + delete input; } - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } - + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } @@ -376,20 +584,15 @@ vector CollectCommand::parseSharedFile(string filename) { map filehandles; map::iterator it3; - - - //read first line - read = new ReadOTUFile(filename); - read->read(&*globaldata); - - input = globaldata->ginput; + + input = new InputData(filename, "sharedfile"); vector lookup = input->getSharedRAbundVectors(); - string sharedFileRoot = getRootName(filename); + string sharedFileRoot = m->getRootName(filename); //clears file before we start to write to it below for (int i=0; igetGroup() + ".rabund").c_str()); + m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".rabund")); filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund")); } @@ -404,7 +607,7 @@ vector CollectCommand::parseSharedFile(string filename) { for (int i = 0; i < lookup.size(); i++) { RAbundVector rav = lookup[i]->getRAbundVector(); - openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()])); + m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()])); rav.print(*(filehandles[lookup[i]->getGroup()])); (*(filehandles[lookup[i]->getGroup()])).close(); } @@ -417,9 +620,8 @@ vector CollectCommand::parseSharedFile(string filename) { for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; } - delete read; + delete input; - globaldata->ginput = NULL; return filenames; }