X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectcommand.cpp;h=b892a91bee89e9b6d01ac7bda8e40833fd4db3b0;hb=1a968f34ae2d2680eaf189a197d1a21b8dfd6c03;hp=adaff9b1bc7b17d979b30106de2ee88c0d03631d;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git diff --git a/collectcommand.cpp b/collectcommand.cpp index adaff9b..b892a91 100644 --- a/collectcommand.cpp +++ b/collectcommand.cpp @@ -38,17 +38,17 @@ //********************************************************************************************************************** vector CollectCommand::setParameters(){ try { - CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist); - CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund); - CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund); - CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); 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-np_shannon-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); 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); + 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); } @@ -63,15 +63,16 @@ vector CollectCommand::setParameters(){ 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, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n"; - helpString += "Example collect(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-chao-ace-jack).\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 += 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\n"; + helpString += "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n"; return helpString; } catch(exception& e) { @@ -80,6 +81,45 @@ string CollectCommand::getHelpString(){ } } //********************************************************************************************************************** +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; @@ -93,7 +133,7 @@ CollectCommand::CollectCommand(){ outputTypes["jack"] = tempOutNames; outputTypes["shannon"] = tempOutNames; outputTypes["shannoneven"] = tempOutNames; - outputTypes["np_shannon"] = tempOutNames; + outputTypes["npshannon"] = tempOutNames; outputTypes["heip"] = tempOutNames; outputTypes["smithwilson"] = tempOutNames; outputTypes["simpson"] = tempOutNames; @@ -123,7 +163,8 @@ CollectCommand::CollectCommand(string option) { allLines = 1; //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 { vector myArray = setParameters(); @@ -149,7 +190,7 @@ CollectCommand::CollectCommand(string option) { outputTypes["jack"] = tempOutNames; outputTypes["shannon"] = tempOutNames; outputTypes["shannoneven"] = tempOutNames; - outputTypes["np_shannon"] = tempOutNames; + outputTypes["npshannon"] = tempOutNames; outputTypes["heip"] = tempOutNames; outputTypes["smithwilson"] = tempOutNames; outputTypes["simpson"] = tempOutNames; @@ -209,22 +250,22 @@ CollectCommand::CollectCommand(string option) { listfile = validParameter.validFile(parameters, "list", true); if (listfile == "not open") { listfile = ""; abort = true; } else if (listfile == "not found") { listfile = ""; } - else { format = "list"; inputfile = 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; } + 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; } + 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; } + 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 @@ -270,16 +311,21 @@ CollectCommand::CollectCommand(string option) { if (calc == "default") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; } } 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); } } @@ -300,95 +346,97 @@ int CollectCommand::execute(){ for (int p = 0; p < inputFileNames.size(); p++) { - if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } m->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 += 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"); outputTypes["sobs"].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"); outputTypes["chao"].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"); outputTypes["nseqs"].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"); outputTypes["coverage"].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"); outputTypes["ace"].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"); outputTypes["jack"].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"); outputTypes["shannon"].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(fileNameRoot+"shannoneven"))); - outputNames.push_back(fileNameRoot+"shannoneven"); outputTypes["shannoneven"].push_back(fileNameRoot+"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"); outputTypes["np_shannon"].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(fileNameRoot+"heip"))); - outputNames.push_back(fileNameRoot+"heip"); outputTypes["heip"].push_back(fileNameRoot+"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(fileNameRoot+"smithwilson"))); - outputNames.push_back(fileNameRoot+"smithwilson"); outputTypes["smithwilson"].push_back(fileNameRoot+"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"); outputTypes["simpson"].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(fileNameRoot+"simpsoneven"))); - outputNames.push_back(fileNameRoot+"simpsoneven"); outputTypes["simpsoneven"].push_back(fileNameRoot+"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(fileNameRoot+"invsimpson"))); - outputNames.push_back(fileNameRoot+"invsimpson"); outputTypes["invsimpson"].push_back(fileNameRoot+"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"); outputTypes["bootstrap"].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"); outputTypes["geometric"].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"); outputTypes["qstat"].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"); outputTypes["logseries"].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"); outputTypes["bergerparker"].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"); outputTypes["bstick"].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"); outputTypes["goodscoverage"].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"); outputTypes["efron"].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"); outputTypes["boneh"].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"); outputTypes["solow"].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"); outputTypes["shen"].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)); } } } @@ -406,11 +454,10 @@ int CollectCommand::execute(){ if (m->control_pressed) { for(int i=0;imothurRemove(outputNames[i]); } outputTypes.clear(); delete input; delete order; - delete validCalculator; - m->Groups.clear(); + m->clearGroups(); return 0; } @@ -419,11 +466,10 @@ int CollectCommand::execute(){ if (m->control_pressed) { for(int i=0;imothurRemove(outputNames[i]); } outputTypes.clear(); delete input; delete order; - delete validCalculator; - m->Groups.clear(); + m->clearGroups(); return 0; } @@ -469,10 +515,9 @@ int CollectCommand::execute(){ if (m->control_pressed) { for(int i=0;imothurRemove(outputNames[i]); } outputTypes.clear(); delete input; - delete validCalculator; - m->Groups.clear(); + m->clearGroups(); return 0; } @@ -502,11 +547,10 @@ int CollectCommand::execute(){ if (m->control_pressed) { for(int i=0;imothurRemove(outputNames[i]); } outputTypes.clear(); delete input; - delete order; - delete validCalculator; - m->Groups.clear(); + delete order; + m->clearGroups(); return 0; } delete order; @@ -515,10 +559,9 @@ int CollectCommand::execute(){ for(int i=0;icontrol_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(); @@ -549,7 +592,7 @@ vector CollectCommand::parseSharedFile(string 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")); }