/********************************************************************/
ValidCalculators::ValidCalculators() {
try {
+ m = MothurOut::getInstance();
+
initialSingle();
initialShared();
initialRarefaction();
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 + ", ");
}
- cout << endl;
+ m->mothurOutEndLine();
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 ";
+ 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++) {
- cout << it->first << ", ";
+ m->mothurOut(it->first + ", ");
}
- cout << endl;
+ m->mothurOutEndLine();
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 ";
+ 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++) {
- cout << it->first << ", ";
+ m->mothurOut(it->first + ", ");
}
- cout << endl;
+ m->mothurOutEndLine();
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 ";
+ 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++) {
- cout << it->first << ", ";
+ m->mothurOut(it->first + ", ");
}
- cout << endl;
+ m->mothurOutEndLine();
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 ";
+ 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++) {
- cout << it->first << ", ";
+ m->mothurOut(it->first + ", ");
}
- cout << endl;
+ 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 {
- cout << calculator << " is not a valid estimator for the bootstrap.shared command and will be disregarded. Valid estimators are ";
+ 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++) {
- cout << it->first << ", ";
+ m->mothurOut(it->first + ", ");
}
- cout << endl;
+ m->mothurOutEndLine();
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 ";
+ 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++) {
- cout << it->first << ", ";
+ m->mothurOut(it->first + ", ");
}
- cout << endl;
+ 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);
- }
}
/********************************************************************/
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["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["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["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["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";
- exit(1);
- }
}
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";
+ m->errorOut(e, "ValidCalculator", "initialVennSingle");
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);
- }
}
/********************************************************************/
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";
+ m->errorOut(e, "ValidCalculator", "initialVennShared");
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);
- }
}
/********************************************************************/
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";
+ m->errorOut(e, "ValidCalculator", "initialTreeGroups");
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";
+}
+/********************************************************************/
+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["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";
+ m->errorOut(e, "ValidCalculator", "initialMatrix");
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);
- }
}
/********************************************************************/
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";
+ m->errorOut(e, "ValidCalculator", "initialBoot");
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() {
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";
+ m->errorOut(e, "ValidCalculator", "initialDistance");
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);
- }
}
/********************************************************************/
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 << ", ";
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";
+ m->errorOut(e, "ValidCalculator", "printCalc");
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);
- }
-
}
/********************************************************************/