/********************************************************************/
ValidCalculators::ValidCalculators() {
try {
+ m = MothurOut::getInstance();
+
initialSingle();
initialShared();
initialRarefaction();
initialSharedRarefact();
initialSummary();
initialSharedSummary();
+ initialVennSingle();
+ initialVennShared();
+ initialTreeGroups();
+ initialBoot();
+ initialDistance();
+ initialMatrix();
+ initialHeat();
}
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";
+ m->errorOut(e, "ValidCalculator", "ValidCalculator");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the ValidCalculator class function ValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/********************************************************************/
if ((single.find(calculator)) != (single.end())) {
return true;
}else {
- cout << calculator << " is not a valid estimator for the collect.single command and will be disregarded. Valid estimators are ";
+ m->mothurOut(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 << ", ";
+ m->mothurOut(it->first + ", ");
}
- cout << endl;
+ m->mothurOutEndLine();
return false; }
//are you looking for a calculator for a shared parameter
}else if (parameter == "shared") {
if ((shared.find(calculator)) != (shared.end())) {
return true;
}else {
- cout << calculator << " is not a valid estimator for the collect.shared command and will be disregarded. Valid estimators are ";
+ m->mothurOut(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 << ", ";
+ m->mothurOut(it->first + ", ");
}
- cout << endl;
+ m->mothurOutEndLine();
return false; }
//are you looking for a calculator for a rarefaction parameter
}else if (parameter == "rarefaction") {
if ((rarefaction.find(calculator)) != (rarefaction.end())) {
return true;
}else {
- cout << calculator << " is not a valid estimator for the rarefaction.single command and will be disregarded. Valid estimators are ";
+ m->mothurOut(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 << ", ";
+ m->mothurOut(it->first + ", ");
}
- cout << endl;
+ m->mothurOutEndLine();
return false; }
//are you looking for a calculator for a summary parameter
}else if (parameter == "summary") {
if ((summary.find(calculator)) != (summary.end())) {
return true;
}else {
- cout << calculator << " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ";
+ m->mothurOut(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 << ", ";
+ m->mothurOut(it->first + ", ");
}
- cout << endl;
+ m->mothurOutEndLine();
return false; }
//are you looking for a calculator for a sharedsummary parameter
}else if (parameter == "sharedsummary") {
if ((sharedsummary.find(calculator)) != (sharedsummary.end())) {
return true;
}else {
- cout << calculator << " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ";
+ m->mothurOut(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 << ", ";
+ m->mothurOut(it->first + ", ");
}
- cout << endl;
+ m->mothurOutEndLine();
return false; }
}else if (parameter == "sharedrarefaction") {
//is it valid
if ((sharedrarefaction.find(calculator)) != (sharedrarefaction.end())) {
return true;
}else {
- cout << calculator << " is not a valid estimator for the rarefaction.shared command and will be disregarded. Valid estimator is ";
+ m->mothurOut(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 << ", ";
+ m->mothurOut(it->first + ", ");
+ }
+ m->mothurOutEndLine();
+ return false; }
+ }else if (parameter == "vennsingle") {
+ //is it valid
+ if ((vennsingle.find(calculator)) != (vennsingle.end())) {
+ return true;
+ }else {
+ m->mothurOut(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++) {
+ m->mothurOut(it->first + ", ");
}
- cout << endl;
+ m->mothurOutEndLine();
return false; }
- //not a valid paramter
+ }else if (parameter == "vennshared") {
+ //is it valid
+ if ((vennshared.find(calculator)) != (vennshared.end())) {
+ return true;
+ }else {
+ m->mothurOut(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++) {
+ m->mothurOut(it->first + ", ");
+ }
+ m->mothurOutEndLine();
+ return false; }
+ }else if (parameter == "treegroup") {
+ //is it valid
+ if ((treegroup.find(calculator)) != (treegroup.end())) {
+ return true;
+ }else {
+ m->mothurOut(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++) {
+ m->mothurOut(it->first + ", ");
+ }
+ m->mothurOutEndLine();
+ return false; }
+ }else if (parameter == "matrix") {
+ //is it valid
+ if ((matrix.find(calculator)) != (matrix.end())) {
+ return true;
+ }else {
+ m->mothurOut(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++) {
+ m->mothurOut(it->first + ", ");
+ }
+ m->mothurOutEndLine();
+ return false; }
+ }else if (parameter == "heat") {
+ //is it valid
+ if ((heat.find(calculator)) != (heat.end())) {
+ return true;
+ }else {
+ m->mothurOut(calculator + " is not a valid estimator for the heatmap.sim command and will be disregarded. Valid estimators are ");
+ for (it = heat.begin(); it != heat.end(); it++) {
+ m->mothurOut(it->first + ", ");
+ }
+ m->mothurOutEndLine();
+ return false; }
+ }else if (parameter == "boot") {
+ //is it valid
+ if ((boot.find(calculator)) != (boot.end())) {
+ return true;
+ }else {
+ m->mothurOut(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++) {
+ m->mothurOut(it->first + ", ");
+ }
+ m->mothurOutEndLine();
+ return false; }
+ }else if (parameter == "distance") {
+ //is it valid
+ if ((distance.find(calculator)) != (distance.end())) {
+ return true;
+ }else {
+ m->mothurOut(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++) {
+ m->mothurOut(it->first + ", ");
+ }
+ m->mothurOutEndLine();
+ return false; }
+ //not a valid parameter
}else { return false; }
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function isValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ValidCalculator", "isValidCalculator");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the ValidCalculator class function isValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/********************************************************************/
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["nseqs"] = "nseqs";
+ single["sobs"] = "sobs";
+ single["chao"] = "chao";
+ single["ace"] = "ace";
+ single["jack"] = "jack";
+ single["shannon"] = "shannon";
+ single["npshannon"] = "npshannon";
+ single["shannoneven"] = "shannoneven";
+ single["smithwilson"] = "smithwilson";
+ single["heip"] = "heip";
+ single["simpson"] = "simpson";
+ single["simpsoneven"] = "simpsoneven";
+ single["invsimpson"] = "invsimpson";
+ 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";
+ m->errorOut(e, "ValidCalculator", "initialSingle");
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);
- }
}
/********************************************************************/
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["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["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) {
- cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ValidCalculator", "initialShared");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the ValidCalculator class function initialShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/********************************************************************/
rarefaction["ace"] = "ace";
rarefaction["jack"] = "jack";
rarefaction["shannon"] = "shannon";
+ rarefaction["smithwilson"] = "smithwilson";
+ rarefaction["heip"] = "heip";
rarefaction["npshannon"] = "npshannon";
+ rarefaction["shannoneven"] = "shannoneven";
rarefaction["simpson"] = "simpson";
+ rarefaction["invsimpson"] = "invsimpson";
+ rarefaction["simpsoneven"] = "simpsoneven";
rarefaction["bootstrap"] = "bootstrap";
rarefaction["nseqs"] = "nseqs";
+ rarefaction["coverage"] = "coverage";
rarefaction["default"] = "default";
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialRarefaction. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ValidCalculator", "initialRarefaction");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the ValidCalculator class function initialRarefaction. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/********************************************************************/
summary["ace"] = "ace";
summary["jack"] = "jack";
summary["shannon"] = "shannon";
+ summary["heip"] = "heip";
+ summary["shannoneven"] = "shannoneven";
+ summary["smithwilson"] = "smithwilson";
+ summary["invsimpson"] = "invsimpson";
summary["npshannon"] = "npshannon";
summary["simpson"] = "simpson";
+ summary["simpsoneven"] = "simpsoneven";
+ 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) {
- cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ValidCalculator", "initialSummary");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the ValidCalculator class function initialSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/********************************************************************/
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["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["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) {
- cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSharedSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ValidCalculator", "initialSharedSummary");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the ValidCalculator class function initialSharedSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
sharedrarefaction["default"] = "default";
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSharedRarefact. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ValidCalculator", "initialSharedRarefact");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the ValidCalculator class function initialSharedRarefact. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+
+
+/********************************************************************/
+void ValidCalculators::initialVennSingle() {
+ try {
+ vennsingle["sobs"] = "sobs";
+ vennsingle["chao"] = "chao";
+ vennsingle["ace"] = "ace";
+ vennsingle["jack"] = "jack";
+ vennsingle["default"] = "default";
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ValidCalculator", "initialVennSingle");
exit(1);
- }
+ }
}
/********************************************************************/
+void ValidCalculators::initialVennShared() {
+ try {
+ vennshared["sharedsobs"] = "sharedsobs";
+ vennshared["sharedchao"] = "sharedchao";
+ vennshared["sharedace"] = "sharedace";
+ vennshared["default"] = "default";
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ValidCalculator", "initialVennShared");
+ 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) {
+ m->errorOut(e, "ValidCalculator", "initialTreeGroups");
+ exit(1);
+ }
+}
+/********************************************************************/
+void ValidCalculators::initialHeat() {
+ try {
+ heat["jabund"] = "jabund";
+ heat["sorabund"] = "sorabund";
+ heat["jclass"] = "jclass";
+ heat["sorclass"] = "sorclass";
+ heat["jest"] = "jest";
+ heat["sorest"] = "sorest";
+ heat["thetayc"] = "thetayc";
+ heat["thetan"] = "thetan";
+ heat["morisitahorn"] = "morisitahorn";
+ heat["braycurtis"] = "braycurtis";
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ValidCalculator", "initialHeat");
+ 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) {
+ m->errorOut(e, "ValidCalculator", "initialMatrix");
+ 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) {
+ m->errorOut(e, "ValidCalculator", "initialBoot");
+ exit(1);
+ }
+}
+/********************************************************************/
+void ValidCalculators::initialDistance() {
+ try {
+ distance["nogaps"] = "nogaps";
+ distance["eachgap"] = "eachgap";
+ distance["onegap"] = "onegap";
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ValidCalculator", "initialDistance");
+ 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 == "matrix") {
+ for (it = matrix.begin(); it != matrix.end(); it++) {
+ out << it->first << ", ";
+ }
+ }else if (parameter == "heat") {
+ for (it = heat.begin(); it != heat.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) {
+ m->errorOut(e, "ValidCalculator", "printCalc");
+ exit(1);
+ }
+}
+/********************************************************************/
projects / mothur.git / blobdiff