ValidParameters::ValidParameters() {
try {
-
- 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";
+ initCommandParameters();
+ initParameterRanges();
}
catch(exception& e) {
ValidParameters::~ValidParameters() {}
/***********************************************************************/
-bool ValidParameters::isValidParameter(string parameter) {
+bool ValidParameters::isValidParameter(string parameter, string command, string value) {
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 << ", ";
+ 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;
}
- cout << endl;
-
+ }
+ if(!valid) {
+ cout << "'" << parameter << "' is not a valid parameter for the " << command << " command.\n";
+ cout << "The valid paramters for the " << command << " command are: ";
+ for(int i = 0; i < numParams-1; i++)
+ cout << cParams.at(i) << ", ";
+ cout << "and " << cParams.at(numParams-1) << ".\n";
return false;
}
+ if(parameterRanges.count(parameter) != 1)
+ return true;
+
+ int pVal;
+ double piSentinel = 3.14159;
+ vector<string> range = parameterRanges[parameter];
+
+ vector<string> values;
+ splitAtDash(value, values);
+
+ for(int i = 0; i < values.size(); i++) {
+ value = values.at(i);
+ 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) {
+ 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)
+ valid = (pVal == a);
+ else if(a == piSentinel && b != piSentinel)
+ valid = (pVal == b);
+ else
+ valid = (pVal == a || pVal == b);
+ }
+
+
+ if(!valid) {
+ 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;
+ }
+ }
+ return true;
+ }
+ 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::initCommandParameters() {
+ try {
+ //{"parameter1","parameter2",...,"last parameter"};
+
+ string readdistArray[] = {"phylip","column", "name","cutoff","precision", "group"};
+ commandParameters["read.dist"] = addParameters(readdistArray, sizeof(readdistArray)/sizeof(string));
+
+ string readotuArray[] = {"list","order","shared", "line", "label","group","sabund", "rabund"};
+ commandParameters["read.otu"] = addParameters(readotuArray, sizeof(readotuArray)/sizeof(string));
+
+ string readtreeArray[] = {"tree","group"};
+ commandParameters["read.tree"] = addParameters(readtreeArray, sizeof(readtreeArray)/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","calc","abund","size"};
+ commandParameters["collect.single"] = addParameters(collectsingleArray, sizeof(collectsingleArray)/sizeof(string));
+
+ string collectsharedArray[] = {"freq","line","label","calc","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","calc","abund"};
+ commandParameters["rarefaction.single"] = addParameters(rarefactionsingleArray, sizeof(rarefactionsingleArray)/sizeof(string));
+
+ string rarefactionsharedArray[] = {"iters","jumble","line","label","calc","groups"};
+ commandParameters["rarefaction.shared"] = addParameters(rarefactionsharedArray, sizeof(rarefactionsharedArray)/sizeof(string));
+
+ string libshuffArray[] = {"iters","groups","step","form","cutoff"};
+ commandParameters["libshuff"] = addParameters(libshuffArray, sizeof(libshuffArray)/sizeof(string));
+
+ string summarysingleArray[] = {"line","label","calc","abund","size"};
+ commandParameters["summary.single"] = addParameters(summarysingleArray, sizeof(summarysingleArray)/sizeof(string));
+
+ string summarysharedArray[] = {"line","label","calc","groups"};
+ commandParameters["summary.shared"] = addParameters(summarysharedArray, sizeof(summarysharedArray)/sizeof(string));
+
+ string parsimonyArray[] = {"random","groups","iters"};
+ commandParameters["parsimony"] = addParameters(parsimonyArray, sizeof(parsimonyArray)/sizeof(string));
+
+ string unifracWeightedArray[] = {"groups","iters"};
+ commandParameters["unifrac.weighted"] = addParameters(unifracWeightedArray, sizeof(unifracWeightedArray)/sizeof(string));
+
+ string unifracUnweightedArray[] = {"groups","iters"};
+ commandParameters["unifrac.unweighted"] = addParameters(unifracUnweightedArray, sizeof(unifracUnweightedArray)/sizeof(string));
+
+ string heatmapArray[] = {"groups","line","label","sorted","scale"};
+ commandParameters["heatmap"] = addParameters(heatmapArray, sizeof(heatmapArray)/sizeof(string));
+
+ string filterseqsArray[] = {"fasta","phylip","clustal","nexus", "trump", "soft", "filter"};
+ commandParameters["filter.seqs"] = addParameters(filterseqsArray, sizeof(filterseqsArray)/sizeof(string));
+
+ string vennArray[] = {"groups","line","label","calc"};
+ commandParameters["venn"] = addParameters(vennArray, sizeof(vennArray)/sizeof(string));
+
+ string binseqsArray[] = {"fasta","line","label","name", "group"};
+ commandParameters["bin.seqs"] = addParameters(binseqsArray, sizeof(binseqsArray)/sizeof(string));
+
+ string distsharedArray[] = {"line","label","calc","groups"};
+ commandParameters["dist.shared"] = addParameters(distsharedArray, sizeof(distsharedArray)/sizeof(string));
+
+ string getOTURepArray[] = {"fasta","list","line","label","name", "group"};
+ commandParameters["get.oturep"] = addParameters(getOTURepArray, sizeof(getOTURepArray)/sizeof(string));
+
+ string treeGroupsArray[] = {"line","label","calc","groups"};
+ commandParameters["tree.shared"] = addParameters(treeGroupsArray, sizeof(treeGroupsArray)/sizeof(string));
+
+ string bootstrapArray[] = {"line","label","calc","groups","iters"};
+ commandParameters["bootstrap.shared"] = addParameters(bootstrapArray, sizeof(bootstrapArray)/sizeof(string));
+
+ string concensusArray[] = {};
+ commandParameters["concensus"] = addParameters(concensusArray, sizeof(concensusArray)/sizeof(string));
+
+ string distanceArray[] = {"fasta","phylip","clustal","nexus", "calc", "ends", "cutoff", "processors"};
+ commandParameters["dist.seqs"] = addParameters(distanceArray, sizeof(distanceArray)/sizeof(string));
+
+ string AlignArray[] = {"fasta", "candidate", "search", "ksize", "align", "match", "mismatch", "gapopen", "gapextend"};
+ commandParameters["align.seqs"] = addParameters(AlignArray, sizeof(AlignArray)/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";
}
/***********************************************************************/
+
+/***********************************************************************/
+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);
+
+ string softArray[] = {">=","0", "<=","100", "between"};
+ parameterRanges["soft"] = addParameters(softArray, rangeSize);
+
+ string sizeArray[] = {">=","1", "<","NA", "between"};
+ parameterRanges["size"] = addParameters(sizeArray, 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);
+ }
+}
+
+/***********************************************************************/
+
+/***********************************************************************/
+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