X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectcommand.cpp;h=7ad41367f795abe7aeeda1052a8211daf72aeaf4;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=adaff9b1bc7b17d979b30106de2ee88c0d03631d;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git diff --git a/collectcommand.cpp b/collectcommand.cpp index adaff9b..7ad4136 100644 --- a/collectcommand.cpp +++ b/collectcommand.cpp @@ -44,7 +44,7 @@ vector CollectCommand::setParameters(){ 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 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); 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); @@ -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 += "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) { @@ -93,7 +94,7 @@ 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 +124,8 @@ 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 +151,7 @@ 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 +211,22 @@ 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 +272,21 @@ 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); } } @@ -300,7 +307,7 @@ 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])); @@ -310,10 +317,10 @@ int CollectCommand::execute(){ 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"); @@ -339,8 +346,8 @@ int CollectCommand::execute(){ cDisplays.push_back(new CollectDisplay(new ShannonEven(), new OneColumnFile(fileNameRoot+"shannoneven"))); outputNames.push_back(fileNameRoot+"shannoneven"); outputTypes["shannoneven"].push_back(fileNameRoot+"shannoneven"); }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(fileNameRoot+"npshannon"))); + outputNames.push_back(fileNameRoot+"npshannon"); outputTypes["npshannon"].push_back(fileNameRoot+"npshannon"); }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"); @@ -406,11 +413,10 @@ 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 +425,10 @@ 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 +474,9 @@ 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 +506,10 @@ 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 +518,9 @@ 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 +551,7 @@ 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")); }