ValidParameters::ValidParameters() {
try {
- initialReaddist();
- initialReadotu();
- initialReadtree();
- initialCluster();
- initialDeconvolute();
- initialParsimony();
- initialCollectsingle();
- initialCollectshared();
- initialRarefactsingle();
- initialRarefactshared();
- initialSummarysingle();
- initialSummaryshared();
- initialUnifracweighted();
- initialUnifracunweighted();
- initialLibshuff();
+ parameters["phylip"] = "phylip";
+ parameters["column"] = "column";
+ parameters["list"] = "list";
+ parameters["rabund"] = "rabund";
+ parameters["sabund"] = "sabund";
+ 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["sharedrarefaction"] = "sharedrarefaction";
+ parameters["sharedsummary"] = "sharedsummary";
+ parameters["shared"] = "shared";
+ parameters["single"] = "single";
+ parameters["rarefaction"] = "rarefaction";
+
+ initCommandParameters();
+ initParameterRanges();
}
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, string command) {
+bool ValidParameters::isValidParameter(string parameter, string command, string value) {
try {
+ bool valid = false;
+ vector<string> cParams = commandParameters[command];
+ int numParams = cParams.size();
+ for(int i = 0; i < numParams; i++)
+ {
+ if(cParams.at(i).compare(parameter) == 0)
+ {
+ valid = true;
+ i = numParams;
+ }
+ }
+ if(!valid)
+ {
+ cout << "'" << parameter << "' is not a valid parameter for the " << command << " command.\n";
+ return false;
+ }
+
+ if(parameterRanges.count(parameter) != 1)
+ return true;
- 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 " + command + " 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 " + command + " 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 " + command + " 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 " + command + " 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 " + command + " command. Valid parameters are ";
- 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 " + command + " 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 " + command + " 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 " + command + " 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 " + command + " 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 " + command + " 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 " + command + " 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 " + command + " 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 " + command + " 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 " + command + " 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())) {
+ int pVal;
+ double piSentinel = 3.14159;
+ vector<string> range = parameterRanges[parameter];
+
+ valid = convertTest(value, pVal);
+
+ if(!valid)
+ return false;
+
+
+
+ /********************************************************************************************************
+ Special Cases
+ *********************************************************************************************************/
+
+ if(parameter.compare("precision") == 0)
+ {
+ double logNum = log10((double)pVal);
+ double diff = (double)((int)logNum - logNum);
+ if(diff != 0)
+ {
+ cout << "The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n";
+ return false;
+ }
+ }
+
+ /************************************************************************************************************/
+
+
+
+ double a,b,c,d,e;
+
+ if(range.at(1).compare("NA") == 0)
+ a = piSentinel;
+ else
+ a = atoi(range.at(1).c_str());
+
+ if(range.at(3).compare("NA") == 0)
+ b = piSentinel;
+ else
+ b = atoi(range.at(3).c_str());
+
+ if(range.at(4).compare("between") == 0)
+ c = 0;
+ else if(range.at(4).compare("only") == 0)
+ c = 1;
+ else
+ {
+ cout << "The range can only be 'between' or 'only' the bounding numbers.\n";
+ return false;
+ }
+
+ if(range.at(0).compare(">") == 0)
+ d = 0;
+ else if(range.at(0).compare(">=") == 0 || range[3].compare("=>") == 0)
+ d = 1;
+ else
+ {
+ cout << "The parameter value can only be '>', '>=', or '=>' the lower bounding number.\n";
+ return false;
+ }
+
+ if(range.at(2).compare("<") == 0)
+ e = 0;
+ else if(range.at(2).compare("<=") == 0 || range[4].compare("=<") == 0)
+ e = 1;
+ else
+ {
+ cout << "The parameter value can only be '<', '<=', or '=<' the upper bounding number.\n";
+ return false;
+ }
+
+ bool a0 = pVal > a;
+ bool a1 = pVal >= a;
+ bool b0 = pVal < b;
+ bool b1 = pVal <= b;
+
+ if(c != 1)
+ {
+ if(a == piSentinel && b == piSentinel)
return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = libshuff.begin(); it != libshuff.end(); it++) {
- cout << it->first << ", ";
- }
- cout << endl;
- return false; }
- }else if (command == "heatmap") {
- //is it valid
- if ((heatmap.find(parameter)) != (heatmap.end())) {
+ if(a != piSentinel && b == piSentinel)
+ {
+ if(d == 0)
+ valid = a0;
+ else
+ valid = a1;
+ }
+ else if(a == piSentinel && b != piSentinel)
+ {
+ if(e == 0)
+ valid = b0;
+ else
+ valid = b1;
+ }
+ else
+ {
+ if(d == 0 && e == 0)
+ valid = (a0 && b0);
+ else if(d == 0 && e == 1)
+ valid = (a0 && b1);
+ else if(d == 1 && e == 0)
+ valid = (a1 && b0);
+ else
+ valid = (a1 && b1);
+ }
+ }
+ else
+ {
+ if(a == piSentinel && b == piSentinel)
return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = heatmap.begin(); it != heatmap.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 " + command + " command. There are no vaild parameters." << endl;
- }else if (command == "quit") { cout << parameter << " is not a valid parameter for the " + command + " command. There are no vaild parameters." << endl;
- }else if (command == "get.group") { cout << parameter << " is not a valid parameter for the " + command + " command. There are no vaild parameters." << endl;
- }else if (command == "get.label") { cout << parameter << " is not a valid parameter for the " + command + " command. There are no vaild parameters." << endl;
- }else if (command == "get.line") { cout << parameter << " is not a valid parameter for the " + command + " command. There are no vaild parameters." << endl; }
+ if(a != piSentinel && b == piSentinel)
+ valid = (pVal == a);
+ else if(a == piSentinel && b != piSentinel)
+ valid = (pVal == b);
+ else
+ valid = (pVal == a || pVal == b);
+ }
- return false;
+ if(valid)
+ return true;
+ else
+ {
+ cout << "The '" << parameter << "' parameter needs to be ";
+ if(c == 1)
+ cout << "either '" << a << "' or '" << b << "'.\n";
+ else
+ {
+ if(a != piSentinel)
+ {
+ cout << ">";
+ if(d != 0)
+ cout << "=";
+ cout << " '" << a << "'";
+ }
+ if(b == piSentinel)
+ cout << ".\n";
+ else if(a != piSentinel)
+ cout << " and ";
+ if(b != piSentinel)
+ {
+ cout << "<";
+ if(e != 0)
+ cout << "=";
+ cout << " '" << b << ".\n";
+ }
+ }
+ return false;
+ }
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
}
/***********************************************************************/
-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::initCommandParameters() {
+ try {
+ //{"parameter1","parameter2",...,"last parameter"};
+
+ string readdistArray[] = {"phylip","name","cutoff","precision"};
+ commandParameters["read.dist"] = addParameters(readdistArray, sizeof(readdistArray)/sizeof(string));
+
+ string readotuArray[] = {"list","order","group","shared", "sabund"};
+ commandParameters["read.otu"] = addParameters(readotuArray, sizeof(readotuArray)/sizeof(string));
+
+ string clusterArray[] = {"cutoff","precision","method"};
+ commandParameters["cluster"] = addParameters(clusterArray, sizeof(clusterArray)/sizeof(string));
+
+ string deconvoluteArray[] = {"fasta"};
+ commandParameters["deconvolute"] = addParameters(deconvoluteArray, sizeof(deconvoluteArray)/sizeof(string));
+
+ string collectsingleArray[] = {"freq","line","label","single","precision","abund"};
+ commandParameters["collect.single"] = addParameters(collectsingleArray, sizeof(collectsingleArray)/sizeof(string));
+
+ string collectsharedArray[] = {"jumble","freq","line","label","shared","groups"};
+ commandParameters["collect.shared"] = addParameters(collectsharedArray, sizeof(collectsharedArray)/sizeof(string));
+
+ string getgroupArray[] = {};
+ commandParameters["get.group"] = addParameters(getgroupArray, sizeof(getgroupArray)/sizeof(string));
+
+ string getlabelArray[] = {};
+ commandParameters["get.label"] = addParameters(getlabelArray, sizeof(getlabelArray)/sizeof(string));
+
+ string getlineArray[] = {};
+ commandParameters["get.line"] = addParameters(getlineArray, sizeof(getlineArray)/sizeof(string));
+ string rarefactionsingleArray[] = {"iters","freq","line","label","rarefaction","abund"};
+ commandParameters["rarefaction.single"] = addParameters(rarefactionsingleArray, sizeof(rarefactionsingleArray)/sizeof(string));
+
+ string rarefactionsharedArray[] = {"iters","jumble","line","label","sharedrarefaction"};
+ commandParameters["rarefaction.shared"] = addParameters(rarefactionsharedArray, sizeof(rarefactionsharedArray)/sizeof(string));
+
+ string summarysingleArray[] = {"line","label","summary","abund"};
+ commandParameters["summary.single"] = addParameters(summarysingleArray, sizeof(summarysingleArray)/sizeof(string));
+
+ string summarysharedArray[] = {"jumble","line","label","sharedsummary"};
+ commandParameters["summary.shared"] = addParameters(summarysharedArray, sizeof(summarysharedArray)/sizeof(string));
+
+ string quitArray[] = {};
+ commandParameters["quit"] = addParameters(quitArray, sizeof(quitArray)/sizeof(string));
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ValidParameters class function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
}
+
/***********************************************************************/
-void ValidParameters::initialUnifracweighted() {
- unifracweighted["iters"] = "iters";
- unifracweighted["groups"] = "groups";
-}
+
/***********************************************************************/
-void ValidParameters::initialUnifracunweighted() {
- unifracunweighted["iters"] = "iters";
- unifracunweighted["groups"] = "groups";
+void ValidParameters::initParameterRanges() {
+ try {
+ int rangeSize = 5;
+
+ /**************************************************************************************************************
+ {">=" or "=>" or ">" if the value should be greater than or equal to or just greater than the lower bound,
+ A number representing the lower bound ("NA" if there is no lower bound),
+ "<=" or "=<" or "<" if the value shoud be less than or equal to or just less than the upper bound,
+ A number representing the upper bound ("NA" if there is no lower bound),
+ "between" if between lower and upper bounds or "only" if exactly one of the bounds};
+
+ # = parameter
+ # (>, >=) lower bound, # (<, <=) upperbound, # should be (between, only) lower and upper bounds.
+ ***********************************************************************************************************/
+
+ string precisionArray[] = {">=","10", "<","NA", "between"};
+ parameterRanges["precision"] = addParameters(precisionArray, rangeSize);
+
+ string itersArray[] = {">=","10", "<","NA", "between"};
+ parameterRanges["iters"] = addParameters(itersArray, rangeSize);
+
+ string jumbleArray[] = {">","0", "<","1", "only"};
+ parameterRanges["jumble"] = addParameters(jumbleArray, rangeSize);
+
+ string freqArray[] = {">","1", "<","NA", "between"};
+ parameterRanges["freq"] = addParameters(freqArray, rangeSize);
+
+ string lineArray[] = {">=","1", "<","NA", "between"};
+ parameterRanges["line"] = addParameters(lineArray, rangeSize);
+
+ string abundArray[] = {">=","5", "<","NA", "between"};
+ parameterRanges["abund"] = addParameters(abundArray, rangeSize);
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ValidParameters class function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
}
+
/***********************************************************************/
-void ValidParameters::initialLibshuff() {
- libshuff["cutoff"] = "cutoff";
- libshuff["iters"] = "iters";
- libshuff["groups"] = "groups";
- libshuff["step"] = "step";
- libshuff["form"] = "form";
-}
+
/***********************************************************************/
-void ValidParameters::initialHeatmap() {
- heatmap["label"] = "label";
- heatmap["line"] = "line";
+vector<string> ValidParameters::addParameters(string parameters[], int size) {
+ try {
+ vector<string> pVector (parameters, parameters+size);
+ return pVector;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ValidParameters class function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
}
/***********************************************************************/
+
projects / mothur.git / blobdiff