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";
if ((treegroup.find(calculator)) != (treegroup.end())) {
return true;
}else {
- cout << calculator << " is not a valid estimator for the tree.shared command in shared mode and will be disregarded. Valid estimators are ";
+ 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 == "heat") {
+ //is it valid
+ if ((heat.find(calculator)) != (heat.end())) {
+ return true;
+ }else {
+ cout << 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++) {
+ 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 in shared mode and will be disregarded. Valid estimators are ";
+ 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["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) {
shared["sharedchao"] = "sharedchao";
shared["sharedace"] = "sharedace";
shared["jabund"] = "jabund";
- shared["sorabund"] = "sorabund";
+ shared["sorabund"] = "sorabund";
shared["jclass"] = "jclass";
shared["sorclass"] = "sorclass";
shared["jest"] = "jest";
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::initialTreeGroups() {
try {
treegroup["jabund"] = "jabund";
- treegroup["sorabund"] = "sorabund";
+ treegroup["sorabund"] = "sorabund";
treegroup["jclass"] = "jclass";
treegroup["sorclass"] = "sorclass";
treegroup["jest"] = "jest";
treegroup["thetayc"] = "thetayc";
treegroup["thetan"] = "thetan";
treegroup["morisitahorn"] = "morisitahorn";
- treegroup["braycurtis"] = "braycurtis";
+ 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);
}
}
+/********************************************************************/
+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) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialHeat. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ValidCalculator class function initialHeat. 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["sorabund"] = "sorabund";
boot["jclass"] = "jclass";
boot["sorclass"] = "orclass";
boot["jest"] = "jest";
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) {
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) {
projects / mothur.git / blobdiff