X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectcommand.cpp;h=73de2a42ffb7fecfa6b5591f076bf7f893271b53;hb=49d2b7459c5027557564b21e9487dadafbbbdc96;hp=952131436cdb111a142970f3310b4283a1be7123;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git diff --git a/collectcommand.cpp b/collectcommand.cpp index 9521314..73de2a4 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); @@ -81,6 +81,50 @@ string CollectCommand::getHelpString(){ } } //********************************************************************************************************************** +string CollectCommand::getOutputFileNameTag(string type, string inputName=""){ + try { + string outputFileName = ""; + map >::iterator it; + + //is this a type this command creates + it = outputTypes.find(type); + if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); } + else { + if (type == "sobs") { outputFileName = "sobs"; } + else if (type == "chao") { outputFileName = "chao"; } + else if (type == "nseqs") { outputFileName = "nseqs"; } + else if (type == "coverage") { outputFileName = "coverage"; } + else if (type == "ace") { outputFileName = "ace"; } + else if (type == "jack") { outputFileName = "jack"; } + else if (type == "shannon") { outputFileName = "shannon"; } + else if (type == "shannoneven") { outputFileName = "shannoneven"; } + else if (type == "npshannon") { outputFileName = "npshannon"; } + else if (type == "heip") { outputFileName = "heip"; } + else if (type == "smithwilson") { outputFileName = "smithwilson"; } + else if (type == "simpson") { outputFileName = "simpson"; } + else if (type == "simpsoneven") { outputFileName = "simpsoneven"; } + else if (type == "invsimpson") { outputFileName = "invsimpson"; } + else if (type == "bootstrap") { outputFileName = "bootstrap"; } + else if (type == "geometric") { outputFileName = "geometric"; } + else if (type == "qstat") { outputFileName = "qstat"; } + else if (type == "logseries") { outputFileName = "logseries"; } + else if (type == "bergerparker") { outputFileName = "bergerparker"; } + else if (type == "bstick") { outputFileName = "bstick"; } + else if (type == "goodscoverage") { outputFileName = "goodscoverage"; } + else if (type == "efron") { outputFileName = "efron"; } + else if (type == "boneh") { outputFileName = "boneh"; } + else if (type == "solow") { outputFileName = "solow"; } + else if (type == "shen") { outputFileName = "shen"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; } + } + return outputFileName; + } + catch(exception& e) { + m->errorOut(e, "CollectCommand", "getOutputFileNameTag"); + exit(1); + } +} +//********************************************************************************************************************** CollectCommand::CollectCommand(){ try { abort = true; calledHelp = true; @@ -94,7 +138,7 @@ 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; @@ -151,7 +195,7 @@ 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; @@ -211,22 +255,22 @@ 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 @@ -272,16 +316,21 @@ 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); } } @@ -302,7 +351,7 @@ 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])); @@ -317,80 +366,80 @@ int CollectCommand::execute(){ for (int i=0; icontrol_pressed) { for(int i=0;imothurRemove(outputNames[i]); } outputTypes.clear(); delete input; delete order; - m->Groups.clear(); + m->clearGroups(); return 0; } @@ -420,10 +469,10 @@ int CollectCommand::execute(){ if (m->control_pressed) { for(int i=0;imothurRemove(outputNames[i]); } outputTypes.clear(); delete input; delete order; - m->Groups.clear(); + m->clearGroups(); return 0; } @@ -469,9 +518,9 @@ int CollectCommand::execute(){ if (m->control_pressed) { for(int i=0;imothurRemove(outputNames[i]); } outputTypes.clear(); delete input; - m->Groups.clear(); + m->clearGroups(); return 0; } @@ -501,10 +550,10 @@ int CollectCommand::execute(){ if (m->control_pressed) { for(int i=0;imothurRemove(outputNames[i]); } outputTypes.clear(); delete input; delete order; - m->Groups.clear(); + m->clearGroups(); return 0; } delete order; @@ -515,7 +564,7 @@ int CollectCommand::execute(){ 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(); @@ -546,7 +595,7 @@ 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")); }