X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validparameter.cpp;h=d693bcb721184c251896c917328f9d9d07b3fc18;hb=e189982e0a9b7352ad57cc38ccee675f128be22e;hp=a82962f1e0096e406e7cc21d03dba08a3039ea3a;hpb=16bea3130e36addc54e2116dfbcd02d706ebee45;p=mothur.git diff --git a/validparameter.cpp b/validparameter.cpp index a82962f..d693bcb 100644 --- a/validparameter.cpp +++ b/validparameter.cpp @@ -13,46 +13,13 @@ 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["single"] = "single"; - parameters["rarefaction"] = "rarefaction"; - parameters["sharedrarefaction"] = "sharedrarefaction"; - parameters["shared"] = "shared"; - parameters["summary"] = "summary"; - parameters["sharedsummary"] = "sharedsummary"; - parameters["random"] = "random"; - parameters["groups"] = "groups"; - parameters["calc"] = "calc"; - + m = MothurOut::getInstance(); + 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"; + m->errorOut(e, "ValidParameters", "ValidParameters"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the ValidParameters class function ValidParameters. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } /***********************************************************************/ @@ -60,31 +27,273 @@ ValidParameters::ValidParameters() { ValidParameters::~ValidParameters() {} /***********************************************************************/ -bool ValidParameters::isValidParameter(string parameter) { +bool ValidParameters::isValidParameter(string parameter, vector cParams, 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 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) { + m->mothurOut(parameter + " is not a valid parameter."); m->mothurOutEndLine(); + m->mothurOut("The valid parameters are: "); + for(int i = 0; i < numParams-1; i++) + m->mothurOut(cParams.at(i) + ", "); + m->mothurOut("and " + cParams.at(numParams-1) + ".\n"); return false; } + if(parameterRanges.count(parameter) != 1) + return true; + + int pVal; + double piSentinel = 3.14159; + vector range = parameterRanges[parameter]; + + vector 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) { + m->mothurOut("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 { + m->mothurOut("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 { + m->mothurOut("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 { + m->mothurOut("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) { + m->mothurOut("The '" + parameter + "' parameter needs to be "); + if(c == 1) + m->mothurOut("either '" + toString(a) + "' or '" + toString(b) + "'.\n"); + else { + if(a != piSentinel) { + m->mothurOut(">"); + if(d != 0) + m->mothurOut("="); + m->mothurOut(" '" + toString(a) + "'"); + } + if(b == piSentinel) + m->mothurOut( "'.\n"); + else if(a != piSentinel) + m->mothurOut(" and "); + if(b != piSentinel) { + m->mothurOut("<"); + if(e != 0) + m->mothurOut("="); + m->mothurOut(" '" + toString(b) + "'.\n"); + } + } + return false; + } + } + return true; + } + catch(exception& e) { + m->errorOut(e, "ValidParameters", "isValidParameters"); + exit(1); + } +} +/*******************************************************/ + +/******************************************************/ + +string ValidParameters::validFile(map container, string parameter, bool isFile) { + try { + int ableToOpen; + ifstream in; + map::iterator it; + + it = container.find(parameter); + if(it != container.end()){ //no parameter given + + if(isFile == true) { + + #ifdef USE_MPI + int pid; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are + + if (pid == 0) { + #endif + + ableToOpen = openInputFile(it->second, in); + in.close(); + + #ifdef USE_MPI + MPI_Bcast(&ableToOpen, 1, MPI_INT, 0, MPI_COMM_WORLD); //send ableToOPen + }else { + MPI_Bcast(&ableToOpen, 1, MPI_INT, 0, MPI_COMM_WORLD); //get ableToOPen + } + #endif + + if (ableToOpen == 1) { return "not open"; } + } + }else { return "not found"; } + + return it->second; + } 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"; + m->errorOut(e, "ValidParameters", "validFile"); 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"; +} + +/***********************************************************************/ + +/***********************************************************************/ +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 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) { + m->errorOut(e, "ValidParameters", "initParameterRanges"); exit(1); } } /***********************************************************************/ + +/***********************************************************************/ +vector ValidParameters::addParameters(string parameters[], int size) { + try { + vector pVector (parameters, parameters+size); + return pVector; + } + catch(exception& e) { + m->errorOut(e, "ValidParameters", "addParameters"); + exit(1); + } +} +