initialSharedSummary();
initialVennSingle();
initialVennShared();
+ initialTreeGroups();
+ initialBoot();
+ initialDistance();
+ initialMatrix();
}
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";
}
cout << endl;
return false; }
+ }else if (parameter == "treegroup") {
+ //is it valid
+ if ((treegroup.find(calculator)) != (treegroup.end())) {
+ return true;
+ }else {
+ cout << calculator << " is not a valid estimator for the tree.shared command 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 == "matrix") {
+ //is it valid
+ if ((matrix.find(calculator)) != (matrix.end())) {
+ return true;
+ }else {
+ cout << calculator << " is not a valid estimator for the matrix.output command and will be disregarded. Valid estimators are ";
+ for (it = matrix.begin(); it != matrix.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 and will be disregarded. Valid estimators are ";
+ for (it = boot.begin(); it != boot.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
+ }else if (parameter == "distance") {
+ //is it valid
+ if ((distance.find(calculator)) != (distance.end())) {
+ return true;
+ }else {
+ cout << calculator << " is not a valid estimator for the distance command and will be disregarded. Valid calculators are ";
+ for (it = distance.begin(); it != distance.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["goodscoverage"] = "goodscoverage";
+ single["nseqs"] = "nseqs";
+ single["coverage"] = "coverage";
+ single["efron"] = "efron";
+ single["boneh"] = "boneh";
+ single["solow"] = "solow";
+ single["shen"] = "shen";
single["default"] = "default";
}
catch(exception& e) {
shared["sharedsobs"] = "sharedsobs";
shared["sharedchao"] = "sharedchao";
shared["sharedace"] = "sharedace";
- shared["sharedjabund"] = "sharedjabund";
- shared["sharedsorensonabund"] = "sharedsorensonabund";
- shared["sharedjclass"] = "sharedjclass";
- shared["sharedsorclass"] = "sharedsorclass";
- shared["sharedjest"] = "sharedjest";
- shared["sharedsorest"] = "sharedsorest";
- shared["sharedthetayc"] = "sharedthetayc";
- shared["sharedthetan"] = "sharedthetan";
- shared["sharedkstest"] = "sharedkstest";
- shared["sharedbdiversity"] = "sharedbdiversity";
+ shared["jabund"] = "jabund";
+ shared["sorabund"] = "sorabund";
+ shared["jclass"] = "jclass";
+ shared["sorclass"] = "sorclass";
+ shared["jest"] = "jest";
+ shared["sorest"] = "sorest";
+ shared["thetayc"] = "thetayc";
+ shared["thetan"] = "thetan";
+ shared["kstest"] = "kstest";
+ shared["whittaker"] = "whittaker";
shared["sharednseqs"] = "sharednseqs";
- shared["sharedochiai"] = "sharedochiai";
- shared["sharedanderberg"] = "sharedanderberg";
- shared["sharedkulczynski"] = "sharedkulczynski";
- shared["sharedkulczynskicody"] = "sharedkulczynskicody";
- shared["sharedlennon"] = "sharedlennon";
- shared["sharedmorisitahorn"] = "sharedmorisitahorn";
- shared["sharedbraycurtis"] = "sharedbraycurtis";
+ shared["ochiai"] = "ochiai";
+ shared["anderberg"] = "anderberg";
+ shared["kulczynski"] = "kulczynski";
+ shared["kulczynskicody"] = "kulczynskicody";
+ shared["lennon"] = "lennon";
+ shared["morisitahorn"] = "morisitahorn";
+ shared["braycurtis"] = "braycurtis";
shared["default"] = "default";
}
catch(exception& e) {
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["goodscoverage"]= "goodscoverage";
+ summary["coverage"] = "coverage";
+ summary["efron"] = "efron";
+ summary["boneh"] = "boneh";
+ summary["solow"] = "solow";
+ summary["shen"] = "shen";
summary["default"] = "default";
}
catch(exception& e) {
sharedsummary["sharedsobs"] = "sharedsobs";
sharedsummary["sharedchao"] = "sharedchao";
sharedsummary["sharedace"] = "sharedace";
- sharedsummary["sharedjabund"] = "sharedjabund";
- sharedsummary["sharedsorensonabund"] = "sharedsorensonabund";
- sharedsummary["sharedjclass"] = "sharedjclass";
- sharedsummary["sharedsorclass"] = "sharedsorclass";
- sharedsummary["sharedjest"] = "sharedjest";
- sharedsummary["sharedsorest"] = "sharedsorest";
- sharedsummary["sharedthetayc"] = "sharedthetayc";
- sharedsummary["sharedthetan"] = "sharedthetan";
- sharedsummary["sharedkstest"] = "sharedkstest";
- sharedsummary["sharedbdiversity"] = "sharedbdiversity";
+ sharedsummary["jabund"] = "jabund";
+ sharedsummary["sorabund"] = "sorabund";
+ sharedsummary["jclass"] = "jclass";
+ sharedsummary["sorclass"] = "sorclass";
+ sharedsummary["jest"] = "jest";
+ sharedsummary["sorest"] = "sorest";
+ sharedsummary["thetayc"] = "thetayc";
+ sharedsummary["thetan"] = "thetan";
+ sharedsummary["kstest"] = "kstest";
+ sharedsummary["whittaker"] = "whittaker";
sharedsummary["sharednseqs"] = "sharednseqs";
- sharedsummary["sharedochiai"] = "sharedochiai";
- sharedsummary["sharedanderberg"] = "sharedanderberg";
- sharedsummary["sharedkulczynski"] = "sharedkulczynski";
- sharedsummary["sharedkulczynskicody"] = "sharedkulczynskicody";
- sharedsummary["sharedlennon"] = "sharedlennon";
- sharedsummary["sharedmorisitahorn"] = "sharedmorisitahorn";
- sharedsummary["sharedbraycurtis"] = "sharedbraycurtis";
+ sharedsummary["ochiai"] = "ochiai";
+ sharedsummary["anderberg"] = "anderberg";
+ sharedsummary["kulczynski"] = "kulczynski";
+ sharedsummary["kulczynskicody"] = "kulczynskicody";
+ sharedsummary["lennon"] = "lennon";
+ sharedsummary["morisitahorn"] = "morisitahorn";
+ sharedsummary["braycurtis"] = "braycurtis";
sharedsummary["default"] = "default";
}
catch(exception& e) {
try {
vennsingle["sobs"] = "sobs";
vennsingle["chao"] = "chao";
- vennsingle["ace"] = "ace";
+ vennsingle["ace"] = "ace";
vennsingle["jack"] = "jack";
- vennsingle["default"] = "default";
+ vennsingle["default"] = "default";
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
}
/********************************************************************/
+void ValidCalculators::initialTreeGroups() {
+ try {
+ treegroup["jabund"] = "jabund";
+ treegroup["sorabund"] = "sorabund";
+ treegroup["jclass"] = "jclass";
+ treegroup["sorclass"] = "sorclass";
+ treegroup["jest"] = "jest";
+ treegroup["sorest"] = "sorest";
+ 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);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ValidCalculator class function initialTreeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/********************************************************************/
+void ValidCalculators::initialMatrix() {
+ try {
+ matrix["jabund"] = "jabund";
+ matrix["sorabund"] = "sorabund";
+ matrix["jclass"] = "jclass";
+ matrix["sorclass"] = "sorclass";
+ matrix["jest"] = "jest";
+ matrix["sorest"] = "sorest";
+ matrix["thetayc"] = "thetayc";
+ matrix["thetan"] = "thetan";
+ matrix["morisitahorn"] = "morisitahorn";
+ matrix["braycurtis"] = "braycurtis";
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ValidCalculator class function initialMatrix. 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::initialDistance() {
+ try {
+ distance["nogaps"] = "nogaps";
+ distance["eachgap"] = "eachgap";
+ distance["onegap"] = "onegap";
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialDistance. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ValidCalculator class function initialDistance. 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 << ", ";
+ }
+ }else if (parameter == "distance") {
+ for (it = distance.begin(); it != distance.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