X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactcommand.cpp;h=1775944ad1b53c6e9677fe5c2b1280a9171432da;hb=fefd5ee1517abd3bc38b469cb2dffc85a1571c7e;hp=75a87efa3a2f95259488b0abf15887fb39ee1955;hpb=deba0af0ccdcb6005ed5b2b82649b137c63fbdf7;p=mothur.git diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp index 75a87ef..1775944 100644 --- a/rarefactcommand.cpp +++ b/rarefactcommand.cpp @@ -23,6 +23,7 @@ #include "shannon.h" #include "jackknife.h" #include "coverage.h" +#include "shannonrange.h" //********************************************************************************************************************** @@ -35,8 +36,9 @@ vector RareFactCommand::setParameters(){ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); CommandParameter pfreq("freq", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pfreq); CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters); - CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap", "sobs", "", "", "","",true,false,true); parameters.push_back(pcalc); + CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-shannonrange", "sobs", "", "", "","",true,false,true); parameters.push_back(pcalc); CommandParameter pabund("abund", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pabund); + CommandParameter palpha("alpha", "Multiple", "0-1-2", "1", "", "", "","",false,false,true); parameters.push_back(palpha); CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors); CommandParameter pgroupmode("groupmode", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pgroupmode); CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); @@ -63,6 +65,7 @@ string RareFactCommand::getHelpString(){ helpString += "rarefaction.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n"; helpString += "Example rarefaction.single(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson).\n"; helpString += "The default values for iters is 1000, freq is 100, and calc is rarefaction which calculates the rarefaction curve for the observed richness.\n"; + helpString += "The alpha parameter is used to set the alpha value for the shannonrange calculator.\n"; validCalculator.printCalc("rarefaction"); helpString += "If you are running rarefaction.single with a shared file and would like your results collated in one file, set groupmode=t. (Default=true).\n"; helpString += "The label parameter is used to analyze specific labels in your input.\n"; @@ -86,6 +89,7 @@ string RareFactCommand::getOutputPattern(string type) { else if (type == "r_shannoneven") { pattern = "[filename],r_shannoneven"; } else if (type == "r_smithwilson") { pattern = "[filename],r_smithwilson"; } else if (type == "r_npshannon") { pattern = "[filename],r_npshannon"; } + else if (type == "r_shannonrange"){ pattern = "[filename],r_shannonrange"; } else if (type == "r_simpson") { pattern = "[filename],r_simpson"; } else if (type == "r_simpsoneven") { pattern = "[filename],r_simpsoneven"; } else if (type == "r_invsimpson") { pattern = "[filename],r_invsimpson"; } @@ -114,6 +118,7 @@ RareFactCommand::RareFactCommand(){ outputTypes["r_jack"] = tempOutNames; outputTypes["r_shannon"] = tempOutNames; outputTypes["r_shannoneven"] = tempOutNames; + outputTypes["r_shannonrange"] = tempOutNames; outputTypes["r_heip"] = tempOutNames; outputTypes["r_smithwilson"] = tempOutNames; outputTypes["r_npshannon"] = tempOutNames; @@ -161,6 +166,7 @@ RareFactCommand::RareFactCommand(string option) { outputTypes["r_jack"] = tempOutNames; outputTypes["r_shannon"] = tempOutNames; outputTypes["r_shannoneven"] = tempOutNames; + outputTypes["r_shannonrange"] = tempOutNames; outputTypes["r_heip"] = tempOutNames; outputTypes["r_smithwilson"] = tempOutNames; outputTypes["r_npshannon"] = tempOutNames; @@ -291,6 +297,11 @@ RareFactCommand::RareFactCommand(string option) { temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } m->setProcessors(temp); m->mothurConvert(temp, processors); + + temp = validParameter.validFile(parameters, "alpha", false); if (temp == "not found") { temp = "1"; } + m->mothurConvert(temp, alpha); + + if ((alpha != 0) && (alpha != 1) && (alpha != 2)) { m->mothurOut("[ERROR]: Not a valid alpha value. Valid values are 0, 1 and 2."); m->mothurOutEndLine(); abort=true; } temp = validParameter.validFile(parameters, "groupmode", false); if (temp == "not found") { temp = "T"; } groupMode = m->isTrue(temp); @@ -356,7 +367,10 @@ int RareFactCommand::execute(){ }else if (Estimators[i] == "heip") { rDisplays.push_back(new RareDisplay(new Heip(), new ThreeColumnFile(getOutputFileName("r_heip",variables)))); outputNames.push_back(getOutputFileName("r_heip",variables)); outputTypes["r_heip"].push_back(getOutputFileName("r_heip",variables)); - }else if (Estimators[i] == "smithwilson") { + }else if (Estimators[i] == "r_shannonrange") { + rDisplays.push_back(new RareDisplay(new RangeShannon(alpha), new ThreeColumnFile(getOutputFileName("r_shannonrange", variables)))); + outputNames.push_back(getOutputFileName("r_shannonrange", variables)); outputTypes["r_shannoneven"].push_back(getOutputFileName("r_shannonrange", variables)); + }else if (Estimators[i] == "smithwilson") { rDisplays.push_back(new RareDisplay(new SmithWilson(), new ThreeColumnFile(getOutputFileName("r_smithwilson",variables)))); outputNames.push_back(getOutputFileName("r_smithwilson",variables)); outputTypes["r_smithwilson"].push_back(getOutputFileName("r_smithwilson",variables)); }else if (Estimators[i] == "npshannon") { @@ -556,6 +570,7 @@ vector RareFactCommand::createGroupFile(vector& outputNames, map typesFiles[extension] = temp; } if (!(m->inUsersGroups(file2Group[i], groupNames))) { groupNames.push_back(file2Group[i]); } + } //for each type create a combo file @@ -634,9 +649,8 @@ vector RareFactCommand::createGroupFile(vector& outputNames, map for (int k = 1; k < fileLabels[combineFileName].size(); k++) { //each chunk //grab data for each group - for (map > > >::iterator itFileNameGroup = files.begin(); itFileNameGroup != files.end(); itFileNameGroup++) { - - string group = itFileNameGroup->first; + for (int n = 0; n < groupNames.size(); n++) { + string group = groupNames[n]; map > >::iterator itLine = files[group].find(*itNumSampled); if (itLine != files[group].end()) {