X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectcommand.cpp;h=7ad41367f795abe7aeeda1052a8211daf72aeaf4;hb=ee8403d4eb5760187d62b42a9cf4272de8fc0ec4;hp=952131436cdb111a142970f3310b4283a1be7123;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git diff --git a/collectcommand.cpp b/collectcommand.cpp index 9521314..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); @@ -94,7 +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; @@ -151,7 +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; @@ -211,22 +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 @@ -272,16 +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); } } @@ -302,7 +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])); @@ -341,8 +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"); @@ -408,10 +413,10 @@ 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; } @@ -420,10 +425,10 @@ 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 +474,9 @@ 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 +506,10 @@ 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 +520,7 @@ 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 +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")); }