CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","outputType",false,true); parameters.push_back(pshared);
CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
- CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson-jsd", "jsd", "", "", "","",false,false,true); parameters.push_back(pcalc);
+ CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson-jsd-rjsd", "rjsd", "", "", "","",false,false,true); parameters.push_back(pcalc);
CommandParameter psubsample("subsample", "String", "", "", "", "", "","",false,false); parameters.push_back(psubsample);
CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
CommandParameter pminpartitions("minpartitions", "Number", "", "5", "", "", "","",false,false,true); parameters.push_back(pminpartitions);
else { m->mothurOut("[ERROR]: " + method + " is not a valid method. Valid algorithms are dmm, kmeans and pam."); m->mothurOutEndLine(); abort = true; }
calc = validParameter.validFile(parameters, "calc", false);
- if (calc == "not found") { calc = "jsd"; }
+ if (calc == "not found") { calc = "rjsd"; }
else {
- if (calc == "default") { calc = "jsd"; }
+ if (calc == "default") { calc = "rjsd"; }
}
m->splitAtDash(calc, Estimators);
if (m->inUsersGroups("citation", Estimators)) {
matrixCalculator = new MemPearson();
}else if (Estimators[i] == "jsd") {
matrixCalculator = new JSD();
+ }else if (Estimators[i] == "rjsd") {
+ matrixCalculator = new RJSD();
}else {
m->mothurOut("[ERROR]: " + Estimators[i] + " is not a valid calculator, please correct.\n"); m->control_pressed = true; return results;
}