initialSharedRarefact();
initialSummary();
initialSharedSummary();
+ initialVennSingle();
+ initialVennShared();
+ initialTreeGroups();
+ initialBoot();
+ initialDistance();
}
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";
//is it valid
if ((single.find(calculator)) != (single.end())) {
return true;
- }else { cout << calculator << " is not a valid single estimator. Valid single estimators are collect-chao-ace-jack-bootstrap-shannon-npshannon-simpson." << endl; return false; }
+ }else {
+ cout << calculator << " is not a valid estimator for the collect.single command and will be disregarded. Valid estimators are ";
+ for (it = single.begin(); it != single.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
//are you looking for a calculator for a shared parameter
}else if (parameter == "shared") {
//is it valid
if ((shared.find(calculator)) != (shared.end())) {
return true;
- }else { cout << calculator << " is not a valid shared estimator. Valid shared estimators are sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN." << endl; return false; }
+ }else {
+ cout << calculator << " is not a valid estimator for the collect.shared command and will be disregarded. Valid estimators are ";
+ for (it = shared.begin(); it != shared.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
//are you looking for a calculator for a rarefaction parameter
}else if (parameter == "rarefaction") {
//is it valid
if ((rarefaction.find(calculator)) != (rarefaction.end())) {
return true;
- }else { cout << calculator << " is not a valid rarefaction estimator. Valid rarefaction estimators are rarefaction-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson." << endl; return false; }
+ }else {
+ cout << calculator << " is not a valid estimator for the rarefaction.single command and will be disregarded. Valid estimators are ";
+ for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
//are you looking for a calculator for a summary parameter
}else if (parameter == "summary") {
//is it valid
if ((summary.find(calculator)) != (summary.end())) {
return true;
- }else { cout << calculator << " is not a valid summary estimator. Valid summary estimators are collect-chao-ace-jack-bootstrap-shannon-npshannon-simpson." << endl; return false; }
+ }else {
+ cout << calculator << " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ";
+ for (it = summary.begin(); it != summary.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
//are you looking for a calculator for a sharedsummary parameter
}else if (parameter == "sharedsummary") {
//is it valid
if ((sharedsummary.find(calculator)) != (sharedsummary.end())) {
return true;
- }else { cout << calculator << " is not a valid sharedsummary estimator. Valid sharedsummary estimators are: sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN." << endl; return false; }
-
+ }else {
+ cout << calculator << " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ";
+ for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
}else if (parameter == "sharedrarefaction") {
//is it valid
if ((sharedrarefaction.find(calculator)) != (sharedrarefaction.end())) {
return true;
- }else { cout << calculator << " is not a valid sharedrarefaction estimator. Valid sharedrarefaction estimator is sharedobserved." << endl; return false; }
- //not a valid paramter
+ }else {
+ cout << calculator << " is not a valid estimator for the rarefaction.shared command and will be disregarded. Valid estimator is ";
+ for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
+ }else if (parameter == "vennsingle") {
+ //is it valid
+ if ((vennsingle.find(calculator)) != (vennsingle.end())) {
+ return true;
+ }else {
+ cout << calculator << " is not a valid estimator for the venn command in single mode and will be disregarded. Valid estimators are ";
+ for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
+ }else if (parameter == "vennshared") {
+ //is it valid
+ if ((vennshared.find(calculator)) != (vennshared.end())) {
+ return true;
+ }else {
+ cout << calculator << " is not a valid estimator for the venn command in shared mode and will be disregarded. Valid estimators are ";
+ for (it = vennshared.begin(); it != vennshared.end(); it++) {
+ cout << it->first << ", ";
+ }
+ 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 == "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; }
}
/********************************************************************/
void ValidCalculators::initialSingle() {
try {
-
- single["sobs"] = "sobs";
- single["chao"] = "chao";
- single["ace"] = "ace";
- single["jack"] = "jack";
- single["shannon"] = "shannon";
- single["npshannon"] = "npshannon";
- single["simpson"] = "simpson";
- single["bootstrap"] = "bootstrap";
- single["default"] = "default";
+ single["sobs"] = "sobs";
+ single["chao"] = "chao";
+ single["ace"] = "ace";
+ single["jack"] = "jack";
+ single["shannon"] = "shannon";
+ single["npshannon"] = "npshannon";
+ single["simpson"] = "simpson";
+ single["bergerparker"] = "bergerparker";
+ single["bootstrap"] = "bootstrap";
+ single["geometric"] = "geometric";
+ single["logseries"] = "logseries";
+ single["qstat"] = "qstat";
+ single["bstick"] = "bstick";
+ 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) {
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::initialShared() {
try {
- 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["sharedsobs"] = "sharedsobs";
+ shared["sharedchao"] = "sharedchao";
+ shared["sharedace"] = "sharedace";
+ 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["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["npshannon"] = "npshannon";
rarefaction["simpson"] = "simpson";
rarefaction["bootstrap"] = "bootstrap";
+ rarefaction["nseqs"] = "nseqs";
+ rarefaction["coverage"] = "coverage";
rarefaction["default"] = "default";
}
catch(exception& e) {
summary["shannon"] = "shannon";
summary["npshannon"] = "npshannon";
summary["simpson"] = "simpson";
+ summary["bergerparker"] = "bergerparker";
+ summary["geometric"] = "geometric";
summary["bootstrap"] = "bootstrap";
+ 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) {
/********************************************************************/
void ValidCalculators::initialSharedSummary() {
try {
- 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["sharedsobs"] = "sharedsobs";
+ sharedsummary["sharedchao"] = "sharedchao";
+ sharedsummary["sharedace"] = "sharedace";
+ 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["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) {
void ValidCalculators::initialSharedRarefact() {
try {
sharedrarefaction["sharedobserved"] = "sharedobserved";
+ sharedrarefaction["sharednseqs"] = "sharednseqs";
sharedrarefaction["default"] = "default";
}
catch(exception& e) {
}
}
+
/********************************************************************/
+void ValidCalculators::initialVennSingle() {
+ try {
+ vennsingle["sobs"] = "sobs";
+ vennsingle["chao"] = "chao";
+ vennsingle["ace"] = "ace";
+ vennsingle["jack"] = "jack";
+ 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";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ValidCalculator class function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/********************************************************************/
+void ValidCalculators::initialVennShared() {
+ try {
+ vennshared["sharedsobs"] = "sharedsobs";
+ vennshared["sharedchao"] = "sharedchao";
+ vennshared["sharedace"] = "sharedace";
+ vennshared["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";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ValidCalculator class function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/********************************************************************/
+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::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