X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validcalculator.cpp;h=bc8c4b8d7ab4b753cfa3f75a7c7da0b8ba740bc0;hb=61798fe609675abfedf511e542cc48c56a531199;hp=f6fe280a86474ea35e78a18245ac24a0ba5e5349;hpb=c196b6b4768ccb84955d773ff0f22e4994d1ba7b;p=mothur.git diff --git a/validcalculator.cpp b/validcalculator.cpp index f6fe280..bc8c4b8 100644 --- a/validcalculator.cpp +++ b/validcalculator.cpp @@ -12,6 +12,8 @@ /********************************************************************/ ValidCalculators::ValidCalculators() { try { + m = MothurOut::getInstance(); + initialSingle(); initialShared(); initialRarefaction(); @@ -22,15 +24,14 @@ ValidCalculators::ValidCalculators() { 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); - } } /********************************************************************/ @@ -47,11 +48,11 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) { 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") { @@ -59,11 +60,11 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) { 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") { @@ -71,11 +72,11 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) { 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") { @@ -83,11 +84,11 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) { 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") { @@ -95,79 +96,108 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) { 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 in shared mode 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 + ", "); + } + 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 + ", "); } - 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 in shared mode 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 + ", "); + } + 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 + ", "); } - 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); - } } /********************************************************************/ @@ -179,26 +209,31 @@ void ValidCalculators::initialSingle() { 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["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); - } } /********************************************************************/ @@ -208,7 +243,7 @@ void ValidCalculators::initialShared() { shared["sharedchao"] = "sharedchao"; shared["sharedace"] = "sharedace"; shared["jabund"] = "jabund"; - shared["sorabund"] = "sorabund"; + shared["sorabund"] = "sorabund"; shared["jclass"] = "jclass"; shared["sorclass"] = "sorclass"; shared["jest"] = "jest"; @@ -228,13 +263,9 @@ void ValidCalculators::initialShared() { 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); - } } /********************************************************************/ @@ -245,21 +276,22 @@ void ValidCalculators::initialRarefaction() { 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); - } } /********************************************************************/ @@ -271,8 +303,13 @@ void ValidCalculators::initialSummary() { 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"; @@ -282,16 +319,16 @@ void ValidCalculators::initialSummary() { 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); - } } /********************************************************************/ @@ -321,13 +358,9 @@ void ValidCalculators::initialSharedSummary() { 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); - } } @@ -340,13 +373,9 @@ void ValidCalculators::initialSharedRarefact() { 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); - } } @@ -360,13 +389,9 @@ void ValidCalculators::initialVennSingle() { 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); - } } /********************************************************************/ @@ -378,20 +403,16 @@ void ValidCalculators::initialVennShared() { 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); - } } /********************************************************************/ void ValidCalculators::initialTreeGroups() { try { treegroup["jabund"] = "jabund"; - treegroup["sorabund"] = "sorabund"; + treegroup["sorabund"] = "sorabund"; treegroup["jclass"] = "jclass"; treegroup["sorclass"] = "sorclass"; treegroup["jest"] = "jest"; @@ -399,22 +420,58 @@ void ValidCalculators::initialTreeGroups() { treegroup["thetayc"] = "thetayc"; treegroup["thetan"] = "thetan"; treegroup["morisitahorn"] = "morisitahorn"; - treegroup["braycurtis"] = "braycurtis"; + 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) { - 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", "initialHeat"); 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::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["sorabund"] = "sorabund"; boot["jclass"] = "jclass"; boot["sorclass"] = "orclass"; boot["jest"] = "jest"; @@ -425,13 +482,21 @@ void ValidCalculators::initialBoot() { 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"; +} +/********************************************************************/ +void ValidCalculators::initialDistance() { + try { + distance["nogaps"] = "nogaps"; + distance["eachgap"] = "eachgap"; + distance["onegap"] = "onegap"; + } + catch(exception& e) { + m->errorOut(e, "ValidCalculator", "initialDistance"); exit(1); - } + } } /********************************************************************/ @@ -479,22 +544,30 @@ 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) { - 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); - } - } /********************************************************************/