+
+ //if the user has not specified any labels use the ones from read.otu
+ if(label == "") {
+ allLines = globaldata->allLines;
+ labels = globaldata->labels;
+ }
+
+ calc = validParameter.validFile(parameters, "calc", false);
+ if (calc == "not found") { calc = "sharedobserved"; }
+ else {
+ if (calc == "default") { calc = "sharedobserved"; }
+ }
+ splitAtDash(calc, Estimators);
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ splitAtDash(groups, Groups);
+ }
+ globaldata->Groups = Groups;
+
+ string temp;
+ temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
+ convert(temp, nIters);
+
+ temp = validParameter.validFile(parameters, "jumble", false); if (temp == "not found") { temp = "T"; }
+ if (isTrue(temp)) { jumble = true; }
+ else { jumble = false; }
+ globaldata->jumble = jumble;
+
+ if (abort == false) {
+
+ string fileNameRoot = outputDir + getRootName(getSimpleName(globaldata->inputFileName));
+// format = globaldata->getFormat();
+
+
+ validCalculator = new ValidCalculators();
+
+ for (int i=0; i<Estimators.size(); i++) {
+ if (validCalculator->isValidCalculator("sharedrarefaction", Estimators[i]) == true) {
+ if (Estimators[i] == "sharedobserved") {
+ rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));
+ outputNames.push_back(fileNameRoot+"shared.rarefaction");
+ }else if (Estimators[i] == "sharednseqs") {
+ rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(fileNameRoot+"shared.r_nseqs", "")));
+ outputNames.push_back(fileNameRoot+"shared.r_nseqs");
+ }
+ }
+ }
+ }
+