*/
#include "validcalculator.h"
+#include "ace.h"
+#include "sobs.h"
+#include "nseqs.h"
+#include "chao1.h"
+#include "bootstrap.h"
+#include "simpson.h"
+#include "simpsoneven.h"
+#include "invsimpson.h"
+#include "npshannon.h"
+#include "shannon.h"
+#include "smithwilson.h"
+#include "heip.h"
+#include "shannoneven.h"
+#include "jackknife.h"
+#include "geom.h"
+#include "qstat.h"
+#include "logsd.h"
+#include "bergerparker.h"
+#include "bstick.h"
+#include "goodscoverage.h"
+#include "efron.h"
+#include "boneh.h"
+#include "solow.h"
+#include "shen.h"
+#include "coverage.h"
+#include "sharedsobscollectsummary.h"
+#include "sharedchao1.h"
+#include "sharedace.h"
+#include "sharedjabund.h"
+#include "sharedsorabund.h"
+#include "sharedjclass.h"
+#include "sharedsorclass.h"
+#include "sharedjest.h"
+#include "sharedsorest.h"
+#include "sharedthetayc.h"
+#include "sharedthetan.h"
+#include "sharedkstest.h"
+#include "whittaker.h"
+#include "sharednseqs.h"
+#include "sharedochiai.h"
+#include "sharedanderbergs.h"
+#include "sharedkulczynski.h"
+#include "sharedkulczynskicody.h"
+#include "sharedlennon.h"
+#include "sharedmorisitahorn.h"
+#include "sharedbraycurtis.h"
+#include "sharedjackknife.h"
+#include "whittaker.h"
+#include "odum.h"
+#include "canberra.h"
+#include "structeuclidean.h"
+#include "structchord.h"
+#include "hellinger.h"
+#include "manhattan.h"
+#include "structpearson.h"
+#include "soergel.h"
+#include "spearman.h"
+#include "structkulczynski.h"
+#include "structchi2.h"
+#include "speciesprofile.h"
+#include "hamming.h"
+#include "gower.h"
+#include "memchi2.h"
+#include "memchord.h"
+#include "memeuclidean.h"
+#include "mempearson.h"
+#include "sharedsobs.h"
+#include "sharednseqs.h"
+
/********************************************************************/
ValidCalculators::ValidCalculators() {
try {
- m = MothurOut::getInstance();
+ m = MothurOut::getInstance();
+
+ initialSingle();
+ initialShared();
+ initialRarefaction();
+ initialSharedRarefact();
+ initialSummary();
+ initialSharedSummary();
+ initialVennSingle();
+ initialVennShared();
+ initialTreeGroups();
+ initialBoot();
+ initialDistance();
+ initialMatrix();
+ initialHeat();
+
+ for(it = single.begin(); it != single.end(); it++) { allCalcs.insert(it->first); }
+ for(it = shared.begin(); it != shared.end(); it++) { allCalcs.insert(it->first); }
+ for(it = rarefaction.begin(); it != rarefaction.end(); it++) { allCalcs.insert(it->first); }
+ for(it = summary.begin(); it != summary.end(); it++) { allCalcs.insert(it->first); }
+ for(it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) { allCalcs.insert(it->first); }
+ for(it = sharedsummary.begin(); it != sharedsummary.end(); it++) { allCalcs.insert(it->first); }
+ for(it = vennsingle.begin(); it != vennsingle.end(); it++) { allCalcs.insert(it->first); }
+ for(it = vennshared.begin(); it != vennshared.end(); it++) { allCalcs.insert(it->first); }
+ for(it = treegroup.begin(); it != treegroup.end(); it++) { allCalcs.insert(it->first); }
+ for(it = matrix.begin(); it != matrix.end(); it++) { allCalcs.insert(it->first); }
+ for(it = heat.begin(); it != heat.end(); it++) { allCalcs.insert(it->first); }
+ for(it = boot.begin(); it != boot.end(); it++) { allCalcs.insert(it->first); }
+ for(it = distance.begin(); it != distance.end(); it++) { allCalcs.insert(it->first); }
- initialSingle();
- initialShared();
- initialRarefaction();
- initialSharedRarefact();
- initialSummary();
- initialSharedSummary();
- initialVennSingle();
- initialVennShared();
- initialTreeGroups();
- initialBoot();
- initialDistance();
- initialMatrix();
- initialHeat();
}
catch(exception& e) {
m->errorOut(e, "ValidCalculator", "ValidCalculator");
exit(1);
}
}
-
/********************************************************************/
-
ValidCalculators::~ValidCalculators() {}
-
+/********************************************************************/
+void ValidCalculators::printCitations(vector<string> Estimators) {
+ try {
+
+ for (int i = 0; i < Estimators.size(); i++) {
+ //is this citation, do nothing
+ if ((Estimators[i] == "citation") || (Estimators[i] == "default") || (Estimators[i] == "eachgap") || (Estimators[i] == "nogaps") || (Estimators[i] == "onegap")) {}
+ //is this a valid calculator
+ else if (allCalcs.count(Estimators[i]) != 0) {
+ if (Estimators[i] == "sobs") { Calculator* temp = new Sobs(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "chao") { Calculator* temp = new Chao1(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "nseqs") { Calculator* temp = new NSeqs(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "coverage") { Calculator* temp = new Coverage(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "ace") { Calculator* temp = new Ace(10); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+
+ }else if (Estimators[i] == "jack") { Calculator* temp = new Jackknife(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "shannon") { Calculator* temp = new Shannon(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "shannoneven") { Calculator* temp = new ShannonEven(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "npshannon") { Calculator* temp = new NPShannon(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "heip") { Calculator* temp = new Heip(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+
+ }else if (Estimators[i] == "smithwilson") { Calculator* temp = new SmithWilson(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "simpson") { Calculator* temp = new Simpson(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "simpsoneven") { Calculator* temp = new SimpsonEven(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "invsimpson") { Calculator* temp = new InvSimpson(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "bootstrap") { Calculator* temp = new Bootstrap(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+
+ }else if (Estimators[i] == "geometric") { Calculator* temp = new Geom(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "qstat") { Calculator* temp = new QStat(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "logseries") { Calculator* temp = new LogSD(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "bergerparker") { Calculator* temp = new BergerParker(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "bstick") { Calculator* temp = new BStick(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+
+ }else if (Estimators[i] == "goodscoverage") { Calculator* temp = new GoodsCoverage(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "efron") { Calculator* temp = new Efron(10); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "boneh") { Calculator* temp = new Boneh(10); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "solow") { Calculator* temp = new Solow(10); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "shen") { Calculator* temp = new Shen(10, 10); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+
+ }else if (Estimators[i] == "sharedchao") { Calculator* temp = new SharedChao1(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "sharedsobs") { Calculator* temp = new SharedSobsCS(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "sharedace") { Calculator* temp = new SharedAce(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "jabund") { Calculator* temp = new JAbund(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "sorabund") { Calculator* temp = new SorAbund(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+
+ }else if (Estimators[i] == "jclass") { Calculator* temp = new Jclass(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "sorclass") { Calculator* temp = new SorClass(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "jest") { Calculator* temp = new Jest(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "sorest") { Calculator* temp = new SorEst(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "thetayc") { Calculator* temp = new ThetaYC(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+
+ }else if (Estimators[i] == "thetan") { Calculator* temp = new ThetaN(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "kstest") { Calculator* temp = new KSTest(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "whittaker") { Calculator* temp = new Whittaker(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "sharednseqs") { Calculator* temp = new SharedNSeqs(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "ochiai") { Calculator* temp = new Ochiai(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+
+ }else if (Estimators[i] == "anderberg") { Calculator* temp = new Anderberg(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "kulczynski") { Calculator* temp = new Kulczynski(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "kulczynskicody") { Calculator* temp = new KulczynskiCody(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "lennon") { Calculator* temp = new Lennon(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "morisitahorn") { Calculator* temp = new MorHorn(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+
+ }else if (Estimators[i] == "braycurtis") { Calculator* temp = new BrayCurtis(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "odum") { Calculator* temp = new Odum(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "canberra") { Calculator* temp = new Canberra(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "structeuclidean") { Calculator* temp = new StructEuclidean(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "structchord") { Calculator* temp = new StructChord(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+
+ }else if (Estimators[i] == "hellinger") { Calculator* temp = new Hellinger(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "manhattan") { Calculator* temp = new Manhattan(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "structpearson") { Calculator* temp = new StructPearson(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "soergel") { Calculator* temp = new Soergel(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "spearman") { Calculator* temp = new Spearman(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+
+ }else if (Estimators[i] == "structkulczynski") { Calculator* temp = new StructKulczynski(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "speciesprofile") { Calculator* temp = new SpeciesProfile(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "hamming") { Calculator* temp = new Hamming(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "structchi2") { Calculator* temp = new StructChi2(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "gower") { Calculator* temp = new Gower(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+
+ }else if (Estimators[i] == "memchi2") { Calculator* temp = new MemChi2(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "memchord") { Calculator* temp = new MemChord(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "memeuclidean") { Calculator* temp = new MemEuclidean(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "mempearson") { Calculator* temp = new MemPearson(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "sharedobserved") { Calculator* temp = new SharedSobs(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else if (Estimators[i] == "kulczynski") { Calculator* temp = new Kulczynski(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+ }else { m->mothurOut("[ERROR]: Missing else if for " + Estimators[i] + " in printCitations."); m->mothurOutEndLine(); }
+ }else { m->mothurOut(Estimators[i] + " is not a valid calculator, no citation will be given."); m->mothurOutEndLine(); }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ValidCalculator", "printCitations");
+ exit(1);
+ }
+}
/********************************************************************/
bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
/********************************************************************/
void ValidCalculators::initialTreeGroups() {
try {
+ treegroup["sharedsobs"] = "sharedsobs";
+ treegroup["sharedchao"] = "sharedchao";
+ treegroup["sharedace"] = "sharedace";
treegroup["jabund"] = "jabund";
treegroup["sorabund"] = "sorabund";
treegroup["jclass"] = "jclass";
treegroup["sorest"] = "sorest";
treegroup["thetayc"] = "thetayc";
treegroup["thetan"] = "thetan";
+ treegroup["kstest"] = "kstest";
+ treegroup["whittaker"] = "whittaker";
+ treegroup["sharednseqs"] = "sharednseqs";
+ treegroup["ochiai"] = "ochiai";
+ treegroup["anderberg"] = "anderberg";
+ treegroup["kulczynski"] = "kulczynski";
+ treegroup["kulczynskicody"] = "kulczynskicody";
+ treegroup["lennon"] = "lennon";
treegroup["morisitahorn"] = "morisitahorn";
treegroup["braycurtis"] = "braycurtis";
+ treegroup["odum"] = "odum";
+ treegroup["canberra"] = "canberra";
+ treegroup["structeuclidean"] = "structeuclidean";
+ treegroup["structchord"] = "structchord";
+ treegroup["hellinger"] = "hellinger";
+ treegroup["manhattan"] = "manhattan";
+ treegroup["structpearson"] = "structpearson";
+ treegroup["structkulczynski"] = "structkulczynski";
+ treegroup["structchi2"] = "structchi2";
+ treegroup["soergel"] = "soergel";
+ treegroup["spearman"] = "spearman";
+ treegroup["speciesprofile"] = "speciesprofile";
+ treegroup["hamming"] = "hamming";
+ treegroup["gower"] = "gower";
+ treegroup["memchi2"] = "memchi2";
+ treegroup["memchord"] = "memchord";
+ treegroup["memeuclidean"] = "memeuclidean";
+ treegroup["mempearson"] = "mempearson";
+
}
catch(exception& e) {
m->errorOut(e, "ValidCalculator", "initialTreeGroups");
/********************************************************************/
void ValidCalculators::initialMatrix() {
try {
- matrix["jabund"] = "jabund";
+ matrix["sharedsobs"] = "sharedsobs";
+ matrix["sharedchao"] = "sharedchao";
+ matrix["sharedace"] = "sharedace";
+ matrix["jabund"] = "jabund";
matrix["sorabund"] = "sorabund";
- matrix["jclass"] = "jclass";
+ matrix["jclass"] = "jclass";
matrix["sorclass"] = "sorclass";
matrix["jest"] = "jest";
- matrix["sorest"] = "sorest";
+ matrix["sorest"] = "sorest";
matrix["thetayc"] = "thetayc";
- matrix["thetan"] = "thetan";
+ matrix["thetan"] = "thetan";
+ matrix["kstest"] = "kstest";
+ matrix["whittaker"] = "whittaker";
+ matrix["sharednseqs"] = "sharednseqs";
+ matrix["ochiai"] = "ochiai";
+ matrix["anderberg"] = "anderberg";
+ matrix["kulczynski"] = "kulczynski";
+ matrix["kulczynskicody"] = "kulczynskicody";
+ matrix["lennon"] = "lennon";
matrix["morisitahorn"] = "morisitahorn";
- matrix["braycurtis"] = "braycurtis";
+ matrix["braycurtis"] = "braycurtis";
+ matrix["odum"] = "odum";
+ matrix["canberra"] = "canberra";
+ matrix["structeuclidean"] = "structeuclidean";
+ matrix["structchord"] = "structchord";
+ matrix["hellinger"] = "hellinger";
+ matrix["manhattan"] = "manhattan";
+ matrix["structpearson"] = "structpearson";
+ matrix["structkulczynski"] = "structkulczynski";
+ matrix["structchi2"] = "structchi2";
+ matrix["soergel"] = "soergel";
+ matrix["spearman"] = "spearman";
+ matrix["speciesprofile"] = "speciesprofile";
+ matrix["hamming"] = "hamming";
+ matrix["gower"] = "gower";
+ matrix["memchi2"] = "memchi2";
+ matrix["memchord"] = "memchord";
+ matrix["memeuclidean"] = "memeuclidean";
+ matrix["mempearson"] = "mempearson";
+
}
catch(exception& e) {
m->errorOut(e, "ValidCalculator", "initialMatrix");
}
}
/********************************************************************/
+string ValidCalculators::printCalc(string parameter) {
+ try{
+ string output = "The available estimators for calc are ";
+ //are you looking for a calculator for a single parameter
+ if (parameter == "single") {
+ for (it = single.begin(); it != single.end(); it++) {
+ output += it->first + ", ";
+ }
+ //are you looking for a calculator for a shared parameter
+ }else if (parameter == "shared") {
+ for (it = shared.begin(); it != shared.end(); it++) {
+ output += it->first + ", ";
+ }
+ //are you looking for a calculator for a rarefaction parameter
+ }else if (parameter == "rarefaction") {
+ for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
+ output += it->first + ", ";
+ }
+ //are you looking for a calculator for a summary parameter
+ }else if (parameter == "summary") {
+ for (it = summary.begin(); it != summary.end(); it++) {
+ output += it->first + ", ";
+ }
+ //are you looking for a calculator for a sharedsummary parameter
+ }else if (parameter == "sharedsummary") {
+ for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
+ output += it->first + ", ";
+ }
+ }else if (parameter == "sharedrarefaction") {
+ for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
+ output += it->first + ", ";
+ }
+ }else if (parameter == "vennsingle") {
+ for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
+ output += it->first + ", ";
+ }
+ }else if (parameter == "vennshared") {
+ for (it = vennshared.begin(); it != vennshared.end(); it++) {
+ output += it->first + ", ";
+ }
+ }else if (parameter == "treegroup") {
+ for (it = treegroup.begin(); it != treegroup.end(); it++) {
+ output += it->first + ", ";
+ }
+ }else if (parameter == "matrix") {
+ for (it = matrix.begin(); it != matrix.end(); it++) {
+ output += it->first + ", ";
+ }
+ }else if (parameter == "heat") {
+ for (it = heat.begin(); it != heat.end(); it++) {
+ output += it->first + ", ";
+ }
+ }else if (parameter == "boot") {
+ for (it = boot.begin(); it != boot.end(); it++) {
+ output += it->first + ", ";
+ }
+ }else if (parameter == "distance") {
+ for (it = distance.begin(); it != distance.end(); it++) {
+ output += it->first + ", ";
+ }
+ }
+
+ //rip off comma
+ output = output.substr(0, output.length()-1);
+ output += "\n";
+
+ return output;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ValidCalculator", "printCalc");
+ exit(1);
+ }
+}
+/********************************************************************/
+
projects / mothur.git / blobdiff