ValidParameters::ValidParameters() {
try {
-
- parameters["phylip"] = "phylip";
- parameters["column"] = "column";
- parameters["list"] = "list";
- parameters["rabund"] = "rabund";
- parameters["sabund"] = "sabund";
- parameters["shared"] = "shared";
- parameters["name"] = "name";
- parameters["group"] = "group";
- parameters["order"] = "order";
- parameters["fasta"] = "fasta";
- parameters["tree"] = "tree";
- parameters["fileroot"] = "fileroot";
- parameters["cutoff"] = "cutoff";
- parameters["method"] = "method";
- parameters["format"] = "format";
- parameters["precision"] = "precision";
- parameters["label"] = "label";
- parameters["line"] = "line";
- parameters["iters"] = "iters";
- parameters["jumble"] = "jumble";
- parameters["freq"] = "freq";
- parameters["abund"] = "abund";
- parameters["random"] = "random";
- parameters["groups"] = "groups";
- parameters["calc"] = "calc";
- parameters["step"] = "step";
- parameters["form"] = "form";
-
+ initialReaddist();
+ initialReadotu();
+ initialReadtree();
+ initialCluster();
+ initialDeconvolute();
+ initialParsimony();
+ initialCollectsingle();
+ initialCollectshared();
+ initialRarefactsingle();
+ initialRarefactshared();
+ initialSummarysingle();
+ initialSummaryshared();
+ initialUnifracweighted();
+ initialUnifracunweighted();
+ initialLibshuff();
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function ValidParameters. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
ValidParameters::~ValidParameters() {}
/***********************************************************************/
-bool ValidParameters::isValidParameter(string parameter) {
+bool ValidParameters::isValidParameter(string parameter, string command) {
try {
- //is the parameter in the map
- if ((parameters.find(parameter)) != (parameters.end())) {
- return true;
- }else{
- cout << parameter << " is not a valid parameter in Mothur. Valid parameters are " << endl;
- for (it = parameters.begin(); it != parameters.end(); it++) {
- cout << it->first << ", ";
- }
- cout << endl;
-
- return false;
- }
+ if (command == "read.dist") {
+ //is it valid
+ if ((readdist.find(parameter)) != (readdist.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the read.dist command. Valid parameters are ";
+ for (it = readdist.begin(); it != readdist.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
+ }else if (command == "read.otu") {
+ //is it valid
+ if ((readotu.find(parameter)) != (readotu.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the read.otu command. Valid parameters are ";
+ for (it = readotu.begin(); it != readotu.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
+ //are you looking for a calculator for a rarefaction parameter
+ }else if (command == "read.tree") {
+ //is it valid
+ if ((readtree.find(parameter)) != (readtree.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the read.tree command. Valid parameters are ";
+ for (it = readtree.begin(); it != readtree.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
+ //are you looking for a calculator for a summary parameter
+ }else if (command == "cluster") {
+ //is it valid
+ if ((cluster.find(parameter)) != (cluster.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the cluster command. Valid parameters are ";
+ for (it = cluster.begin(); it != cluster.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; } //are you looking for a calculator for a sharedsummary parameter
+ }else if (command == "deconvolute") {
+ //is it valid
+ if ((deconvolute.find(parameter)) != (deconvolute.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the deconvolute command. Valid parameter is ";
+ for (it = deconvolute.begin(); it != deconvolute.end(); it++) {
+ cout << it->first;
+ }
+ cout << endl;
+ return false; }
+ }else if (command == "parsimony") {
+ //is it valid
+ if ((parsimony.find(parameter)) != (parsimony.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the parsimony command. Valid parameters are ";
+ for (it = parsimony.begin(); it != parsimony.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
+ }else if (command == "collect.single") {
+ //is it valid
+ if ((collectsingle.find(parameter)) != (collectsingle.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the collect.single command. Valid parameters are ";
+ for (it = collectsingle.begin(); it != collectsingle.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
+ }else if (command == "collect.shared") {
+ //is it valid
+ if ((collectshared.find(parameter)) != (collectshared.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the collect.shared command. Valid parameters are ";
+ for (it = collectshared.begin(); it != collectshared.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
+ }else if (command == "rarefaction.single") {
+ //is it valid
+ if ((rarefactsingle.find(parameter)) != (rarefactsingle.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the rarefaction.single command. Valid parameters are ";
+ for (it = rarefactsingle.begin(); it != rarefactsingle.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
+ }else if (command == "rarefaction.shared") {
+ //is it valid
+ if ((rarefactshared.find(parameter)) != (rarefactshared.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the rarefaction.shared command. Valid parameters are ";
+ for (it = rarefactshared.begin(); it != rarefactshared.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
+ }else if (command == "summary.single") {
+ //is it valid
+ if ((summarysingle.find(parameter)) != (summarysingle.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the summary.single command. Valid parameters are ";
+ for (it = summarysingle.begin(); it != summarysingle.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
+ }else if (command == "summary.shared") {
+ //is it valid
+ if ((summaryshared.find(parameter)) != (summaryshared.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the summary.shared command. Valid parameters are ";
+ for (it = summaryshared.begin(); it != summaryshared.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
+ }else if (command == "unifrac.weighted") {
+ //is it valid
+ if ((unifracweighted.find(parameter)) != (unifracweighted.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the unifrac.weighted command. Valid parameters are ";
+ for (it = unifracweighted.begin(); it != unifracweighted.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
+ }else if (command == "unifrac.unweighted") {
+ //is it valid
+ if ((unifracunweighted.find(parameter)) != (unifracunweighted.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the unifrac.unweighted command. Valid parameters are ";
+ for (it = unifracunweighted.begin(); it != unifracunweighted.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
+ }else if (command == "libshuff") {
+ //is it valid
+ if ((libshuff.find(parameter)) != (libshuff.end())) {
+ return true;
+ }else {
+ cout << parameter << " is not a valid parameter for the libshuff command. Valid parameters are ";
+ for (it = libshuff.begin(); it != libshuff.end(); it++) {
+ cout << it->first << ", ";
+ }
+ cout << endl;
+ return false; }
+ //not a valid paramter
+ }else if (command == "help") { cout << parameter << " is not a valid parameter for the help command. There are no vaild parameters.";
+ }else if (command == "quit") { cout << parameter << " is not a valid parameter for the quit command. There are no vaild parameters.";
+ }else if (command == "get.group") { cout << parameter << " is not a valid parameter for the get.group command. There are no vaild parameters.";
+ }else if (command == "get.label") { cout << parameter << " is not a valid parameter for the get.label command. There are no vaild parameters.";
+ }else if (command == "get.line") { cout << parameter << " is not a valid parameter for the get.line command. There are no vaild parameters."; }
+
+ return false;
}
catch(exception& e) {
}
/***********************************************************************/
+void ValidParameters::initialReaddist() {
+ readdist["phylip"] = "phylip";
+ readdist["column"] = "column";
+ readdist["name"] = "name";
+ readdist["group"] = "group";
+ readdist["cutoff"] = "cutoff";
+ readdist["precision"] = "precision";
+}
+/***********************************************************************/
+void ValidParameters::initialReadotu() {
+ readotu["list"] = "list";
+ readotu["rabund"] = "rabund";
+ readotu["sabund"] = "sabund";
+ readotu["shared"] = "shared";
+ readotu["group"] = "group";
+ readotu["order"] = "order";
+ readotu["label"] = "label";
+ readotu["line"] = "line";
+}
+/***********************************************************************/
+void ValidParameters::initialReadtree() {
+ readtree["group"] = "group";
+ readtree["tree"] = "tree";
+}
+/***********************************************************************/
+void ValidParameters::initialCluster() {
+ cluster["cutoff"] = "cutoff";
+ cluster["method"] = "method";
+ cluster["precision"] = "precision";
+}
+/***********************************************************************/
+void ValidParameters::initialDeconvolute() {
+ deconvolute["fasta"] = "fasta";
+}
+/***********************************************************************/
+void ValidParameters::initialParsimony() {
+ parsimony["iters"] = "iters";
+ parsimony["random"] = "random";
+ parsimony["groups"] = "groups";
+}
+/***********************************************************************/
+void ValidParameters::initialCollectsingle() {
+ collectsingle["label"] = "label";
+ collectsingle["line"] = "line";
+ collectsingle["freq"] = "freq";
+ collectsingle["calc"] = "calc";
+}
+/***********************************************************************/
+void ValidParameters::initialCollectshared() {
+ collectshared["label"] = "label";
+ collectshared["line"] = "line";
+ collectshared["freq"] = "freq";
+ collectshared["calc"] = "calc";
+ collectshared["jumble"] = "jumble";
+}
+/***********************************************************************/
+void ValidParameters::initialRarefactsingle() {
+ rarefactsingle["label"] = "label";
+ rarefactsingle["line"] = "line";
+ rarefactsingle["freq"] = "freq";
+ rarefactsingle["calc"] = "calc";
+ rarefactsingle["iters"] = "iters";
+}
+/***********************************************************************/
+void ValidParameters::initialRarefactshared() {
+ rarefactshared["label"] = "label";
+ rarefactshared["line"] = "line";
+ rarefactshared["jumble"] = "jumble";
+ rarefactshared["calc"] = "calc";
+ rarefactshared["iters"] = "iters";
+}
+/***********************************************************************/
+void ValidParameters::initialSummarysingle() {
+ summarysingle["label"] = "label";
+ summarysingle["line"] = "line";
+ summarysingle["calc"] = "calc";
+}
+/***********************************************************************/
+void ValidParameters::initialSummaryshared() {
+ summaryshared["label"] = "label";
+ summaryshared["line"] = "line";
+ summaryshared["calc"] = "calc";
+ summaryshared["jumble"] = "jumble";
+
+}
+/***********************************************************************/
+void ValidParameters::initialUnifracweighted() {
+ unifracweighted["iters"] = "iters";
+ unifracweighted["groups"] = "groups";
+}
+/***********************************************************************/
+void ValidParameters::initialUnifracunweighted() {
+ unifracunweighted["iters"] = "iters";
+ unifracunweighted["groups"] = "groups";
+}
+/***********************************************************************/
+void ValidParameters::initialLibshuff() {
+ libshuff["cutoff"] = "cutoff";
+ libshuff["iters"] = "iters";
+ libshuff["groups"] = "groups";
+ libshuff["step"] = "step";
+ libshuff["form"] = "form";
+}
+/***********************************************************************/
projects / mothur.git / blobdiff