#include "solow.h"
#include "shen.h"
#include "coverage.h"
+#include "shannonrange.h"
//**********************************************************************************************************************
vector<string> 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-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);
- 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-shannonrange", "", "", "","",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 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<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
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 parameters are list, sabund, rabund, shared, label, freq, calc, alpha 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 += "The alpha parameter is used to set the alpha value for the shannonrange calculator.\n";
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";
}
}
//**********************************************************************************************************************
-string CollectCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string CollectCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //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);
- }
+ 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 == "shannonrange"){ pattern = "[filename],shannonrange"; }
+ 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(){
outputTypes["jack"] = tempOutNames;
outputTypes["shannon"] = tempOutNames;
outputTypes["shannoneven"] = tempOutNames;
+ outputTypes["shannonrange"] = tempOutNames;
outputTypes["npshannon"] = tempOutNames;
outputTypes["heip"] = tempOutNames;
outputTypes["smithwilson"] = tempOutNames;
outputTypes["smithwilson"] = tempOutNames;
outputTypes["simpson"] = tempOutNames;
outputTypes["simpsoneven"] = tempOutNames;
+ outputTypes["shannonrange"] = tempOutNames;
outputTypes["invsimpson"] = tempOutNames;
outputTypes["bootstrap"] = tempOutNames;
outputTypes["geometric"] = tempOutNames;
string temp;
temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
- m->mothurConvert(temp, freq);
+ m->mothurConvert(temp, freq);
+
+ 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, "abund", false); if (temp == "not found") { temp = "10"; }
m->mothurConvert(temp, abund);
if (outputDir == "") { outputDir += m->hasPath(inputFileNames[p]); }
string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
+ map<string, string> variables;
+ variables["[filename]"] = fileNameRoot;
//globaldata->inputFileName = inputFileNames[p];
if (inputFileNames.size() > 1) {
for (int i=0; i<Estimators.size(); i++) {
if (validCalculator.isValidCalculator("single", Estimators[i]) == true) {
if (Estimators[i] == "sobs") {
- cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("sobs"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("sobs")); outputTypes["sobs"].push_back(fileNameRoot+getOutputFileNameTag("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+getOutputFileNameTag("chao"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("chao")); outputTypes["chao"].push_back(fileNameRoot+getOutputFileNameTag("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+getOutputFileNameTag("nseqs"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("nseqs")); outputTypes["nseqs"].push_back(fileNameRoot+getOutputFileNameTag("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+getOutputFileNameTag("coverage"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("coverage")); outputTypes["coverage"].push_back(fileNameRoot+getOutputFileNameTag("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+getOutputFileNameTag("ace"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("ace")); outputTypes["ace"].push_back(fileNameRoot+getOutputFileNameTag("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+getOutputFileNameTag("jack"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("jack")); outputTypes["jack"].push_back(fileNameRoot+getOutputFileNameTag("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+getOutputFileNameTag("shannon"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("shannon")); outputTypes["shannon"].push_back(fileNameRoot+getOutputFileNameTag("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+getOutputFileNameTag("shannoneven"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("shannoneven")); outputTypes["shannoneven"].push_back(fileNameRoot+getOutputFileNameTag("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] == "shannonrange") {
+ cDisplays.push_back(new CollectDisplay(new RangeShannon(alpha), new ThreeColumnFile(getOutputFileName("shannonrange", variables))));
+ outputNames.push_back(getOutputFileName("shannonrange", variables)); outputTypes["shannoneven"].push_back(getOutputFileName("shannonrange", variables));
}else if (Estimators[i] == "npshannon") {
- cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("npshannon"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("npshannon")); outputTypes["npshannon"].push_back(fileNameRoot+getOutputFileNameTag("npshannon"));
+ 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+getOutputFileNameTag("heip"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("heip")); outputTypes["heip"].push_back(fileNameRoot+getOutputFileNameTag("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+getOutputFileNameTag("smithwilson"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("smithwilson")); outputTypes["smithwilson"].push_back(fileNameRoot+getOutputFileNameTag("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+getOutputFileNameTag("simpson"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("simpson")); outputTypes["simpson"].push_back(fileNameRoot+getOutputFileNameTag("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+getOutputFileNameTag("simpsoneven"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("simpsoneven")); outputTypes["simpsoneven"].push_back(fileNameRoot+getOutputFileNameTag("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+getOutputFileNameTag("invsimpson"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("invsimpson")); outputTypes["invsimpson"].push_back(fileNameRoot+getOutputFileNameTag("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+getOutputFileNameTag("bootstrap"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("bootstrap")); outputTypes["bootstrap"].push_back(fileNameRoot+getOutputFileNameTag("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+getOutputFileNameTag("geometric"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("geometric")); outputTypes["geometric"].push_back(fileNameRoot+getOutputFileNameTag("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+getOutputFileNameTag("qstat"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("qstat")); outputTypes["qstat"].push_back(fileNameRoot+getOutputFileNameTag("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+getOutputFileNameTag("logseries"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("logseries")); outputTypes["logseries"].push_back(fileNameRoot+getOutputFileNameTag("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+getOutputFileNameTag("bergerparker"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("bergerparker")); outputTypes["bergerparker"].push_back(fileNameRoot+getOutputFileNameTag("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+getOutputFileNameTag("bstick"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("bstick")); outputTypes["bstick"].push_back(fileNameRoot+getOutputFileNameTag("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+getOutputFileNameTag("goodscoverage"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("goodscoverage")); outputTypes["goodscoverage"].push_back(fileNameRoot+getOutputFileNameTag("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+getOutputFileNameTag("efron"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("efron")); outputTypes["efron"].push_back(fileNameRoot+getOutputFileNameTag("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+getOutputFileNameTag("boneh"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("boneh")); outputTypes["boneh"].push_back(fileNameRoot+getOutputFileNameTag("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+getOutputFileNameTag("solow"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("solow")); outputTypes["solow"].push_back(fileNameRoot+getOutputFileNameTag("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+getOutputFileNameTag("shen"))));
- outputNames.push_back(fileNameRoot+getOutputFileNameTag("shen")); outputTypes["shen"].push_back(fileNameRoot+getOutputFileNameTag("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));
}
}
}
projects / mothur.git / blobdiff