initialVennSingle();
initialVennShared();
initialTreeGroups();
+ initialBoot();
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function ValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
if ((treegroup.find(calculator)) != (treegroup.end())) {
return true;
}else {
- cout << calculator << " is not a valid estimator for the tree.groups command in shared mode and will be disregarded. Valid estimators are ";
+ cout << calculator << " is not a valid estimator for the tree.shared command in shared mode and will be disregarded. Valid estimators are ";
for (it = treegroup.begin(); it != treegroup.end(); it++) {
cout << it->first << ", ";
}
cout << endl;
return false; }
-
+ }else if (parameter == "boot") {
+ //is it valid
+ if ((boot.find(calculator)) != (boot.end())) {
+ return true;
+ }else {
+ cout << calculator << " is not a valid estimator for the bootstrap.shared command in shared mode and will be disregarded. Valid estimators are ";
+ for (it = boot.begin(); it != boot.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
//not a valid parameter
}else { return false; }
single["simpson"] = "simpson";
single["bergerparker"] = "bergerparker";
single["bootstrap"] = "bootstrap";
- single["geom"] = "geom";
- single["logsd"] = "logsd";
+ single["geometric"] = "geometric";
+ single["logseries"] = "logseries";
single["qstat"] = "qstat";
single["bstick"] = "bstick";
single["nseqs"] = "nseqs";
+ single["coverage"] = "coverage";
+
single["default"] = "default";
}
catch(exception& e) {
shared["sharedchao"] = "sharedchao";
shared["sharedace"] = "sharedace";
shared["jabund"] = "jabund";
- shared["sorensonabund"] = "sorensonabund";
+ shared["sorabund"] = "sorabund";
shared["jclass"] = "jclass";
shared["sorclass"] = "sorclass";
shared["jest"] = "jest";
shared["thetayc"] = "thetayc";
shared["thetan"] = "thetan";
shared["kstest"] = "kstest";
- shared["bdiversity"] = "bdiversity";
+ shared["whittaker"] = "whittaker";
shared["sharednseqs"] = "sharednseqs";
shared["ochiai"] = "ochiai";
shared["anderberg"] = "anderberg";
rarefaction["simpson"] = "simpson";
rarefaction["bootstrap"] = "bootstrap";
rarefaction["nseqs"] = "nseqs";
+ rarefaction["coverage"] = "coverage";
rarefaction["default"] = "default";
}
catch(exception& e) {
summary["npshannon"] = "npshannon";
summary["simpson"] = "simpson";
summary["bergerparker"] = "bergerparker";
- summary["geom"] = "geom";
+ summary["geometric"] = "geometric";
summary["bootstrap"] = "bootstrap";
- summary["logsd"] = "logsd";
+ summary["logseries"] = "logseries";
summary["qstat"] = "qstat";
summary["bstick"] = "bstick";
summary["nseqs"] = "nseqs";
+ summary["coverage"] = "coverage";
summary["default"] = "default";
}
catch(exception& e) {
sharedsummary["sharedchao"] = "sharedchao";
sharedsummary["sharedace"] = "sharedace";
sharedsummary["jabund"] = "jabund";
- sharedsummary["sorensonabund"] = "sorensonabund";
+ sharedsummary["sorabund"] = "sorabund";
sharedsummary["jclass"] = "jclass";
sharedsummary["sorclass"] = "sorclass";
sharedsummary["jest"] = "jest";
sharedsummary["thetayc"] = "thetayc";
sharedsummary["thetan"] = "thetan";
sharedsummary["kstest"] = "kstest";
- sharedsummary["bdiversity"] = "bdiversity";
+ sharedsummary["whittaker"] = "whittaker";
sharedsummary["sharednseqs"] = "sharednseqs";
sharedsummary["ochiai"] = "ochiai";
sharedsummary["anderberg"] = "anderberg";
void ValidCalculators::initialTreeGroups() {
try {
treegroup["jabund"] = "jabund";
- treegroup["sorensonabund"] = "sorensonabund";
+ treegroup["sorabund"] = "sorabund";
treegroup["jclass"] = "jclass";
treegroup["sorclass"] = "sorclass";
treegroup["jest"] = "jest";
treegroup["thetayc"] = "thetayc";
treegroup["thetan"] = "thetan";
treegroup["morisitahorn"] = "morisitahorn";
+ treegroup["braycurtis"] = "braycurtis";
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialTreeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
}
-
-
/********************************************************************/
+void ValidCalculators::initialBoot() {
+ try {
+ boot["jabund"] = "jabund";
+ boot["sorabund"] = "sorabund";
+ boot["jclass"] = "jclass";
+ boot["sorclass"] = "orclass";
+ boot["jest"] = "jest";
+ boot["sorest"] = "sorest";
+ boot["thetayc"] = "thetayc";
+ boot["thetan"] = "thetan";
+ boot["morisitahorn"] = "morisitahorn";
+ boot["braycurtis"] = "braycurtis";
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialBoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ValidCalculator class function initialBoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/********************************************************************/
+void ValidCalculators::printCalc(string parameter, ostream& out) {
+ try{
+ out << "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++) {
+ out << it->first << ", ";
+ }
+ //are you looking for a calculator for a shared parameter
+ }else if (parameter == "shared") {
+ for (it = shared.begin(); it != shared.end(); it++) {
+ out << it->first << ", ";
+ }
+ //are you looking for a calculator for a rarefaction parameter
+ }else if (parameter == "rarefaction") {
+ for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
+ out << it->first << ", ";
+ }
+ //are you looking for a calculator for a summary parameter
+ }else if (parameter == "summary") {
+ for (it = summary.begin(); it != summary.end(); it++) {
+ out << it->first << ", ";
+ }
+ //are you looking for a calculator for a sharedsummary parameter
+ }else if (parameter == "sharedsummary") {
+ for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
+ out << it->first << ", ";
+ }
+ }else if (parameter == "sharedrarefaction") {
+ for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
+ out << it->first << ", ";
+ }
+ }else if (parameter == "vennsingle") {
+ for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
+ out << it->first << ", ";
+ }
+ }else if (parameter == "vennshared") {
+ for (it = vennshared.begin(); it != vennshared.end(); it++) {
+ out << it->first << ", ";
+ }
+ }else if (parameter == "treegroup") {
+ for (it = treegroup.begin(); it != treegroup.end(); it++) {
+ out << it->first << ", ";
+ }
+ }else if (parameter == "boot") {
+ for (it = boot.begin(); it != boot.end(); it++) {
+ out << it->first << ", ";
+ }
+ }
+ out << endl;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function printCalc. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ValidCalculator class function printCalc. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
-
+}
+/********************************************************************/
projects / mothur.git / blobdiff