//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; }
+ }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; }
//not a valid paramter
}else { return false; }
void ValidCalculators::initialSingle() {
try {
- single["sobs"] = "sobs";
+ single["sobs"] = "sobs";
single["chao"] = "chao";
single["ace"] = "ace";
single["jack"] = "jack";
single["simpson"] = "simpson";
single["bootstrap"] = "bootstrap";
single["default"] = "default";
+ single["nseqs"] = "nseqs";
}
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["sharedjabund"] = "sharedjabund";
+ shared["sharedsorensonabund"] = "sharedsorensonabund";
+ shared["sharedjclass"] = "sharedjclass";
+ shared["sharedsorclass"] = "sharedsorclass";
+ shared["sharedjest"] = "sharedjest";
+ shared["sharedsorest"] = "sharedsorest";
+ shared["sharedthetayc"] = "sharedthetayc";
+ shared["sharedthetan"] = "sharedthetan";
+ shared["sharednseqs"] = "sharednseqs";
+ shared["sharedochiai"] = "sharedochiai";
+ shared["sharedanderberg"] = "sharedanderberg";
shared["default"] = "default";
}
catch(exception& e) {
rarefaction["npshannon"] = "npshannon";
rarefaction["simpson"] = "simpson";
rarefaction["bootstrap"] = "bootstrap";
+ rarefaction["nseqs"] = "nseqs";
rarefaction["default"] = "default";
}
catch(exception& e) {
summary["npshannon"] = "npshannon";
summary["simpson"] = "simpson";
summary["bootstrap"] = "bootstrap";
+ summary["nseqs"] = "nseqs";
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["sharedjabund"] = "sharedjabund";
+ sharedsummary["sharedsorensonabund"] = "sharedsorensonabund";
+ sharedsummary["sharedjclass"] = "sharedjclass";
+ sharedsummary["sharedsorclass"] = "sharedsorclass";
+ sharedsummary["sharedjest"] = "sharedjest";
+ sharedsummary["sharedsorest"] = "sharedsorest";
+ sharedsummary["sharedthetayc"] = "sharedthetayc";
+ sharedsummary["sharedthetan"] = "sharedthetan";
+ sharedsummary["sharednseqs"] = "sharednseqs";
+ sharedsummary["sharedochiai"] = "sharedochiai";
+ sharedsummary["sharedanderberg"] = "sharedanderberg";
sharedsummary["default"] = "default";
}
catch(exception& e) {
void ValidCalculators::initialSharedRarefact() {
try {
sharedrarefaction["sharedobserved"] = "sharedobserved";
+ sharedrarefaction["sharednseqs"] = "sharednseqs";
sharedrarefaction["default"] = "default";
}
catch(exception& e) {
projects / mothur.git / blobdiff