X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validparameter.cpp;h=5278d51fa3ef2da9429f12c89f4e12d4923d67fe;hb=f18d75f9c996cb619a5051a7664620c0c5ae05fb;hp=dc4ec6276a5b23d38358096373c802830c8e3756;hpb=d5c8caf2d08b7ac6de30e33b1d19cfd246d08f03;p=mothur.git diff --git a/validparameter.cpp b/validparameter.cpp index dc4ec62..5278d51 100644 --- a/validparameter.cpp +++ b/validparameter.cpp @@ -13,31 +13,8 @@ ValidParameters::ValidParameters() { try { - - parameters["phylipfile"] = "phylipfile"; - parameters["columnfile"] = "columnfile"; - parameters["listfile"] = "listfile"; - parameters["rabundfile"] = "rabundfile"; - parameters["sabundfile"] = "sabundfile"; - parameters["namefile"] = "namefile"; - parameters["groupfile"] = "groupfile"; - parameters["orderfile"] = "orderfile"; - 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"; + initCommandParameters(); + initParameterRanges(); } catch(exception& e) { @@ -54,18 +31,186 @@ ValidParameters::ValidParameters() { 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." << endl; + 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; + } + } + 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 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) + { + 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"; @@ -77,4 +222,152 @@ bool ValidParameters::isValidParameter(string parameter) { } } -/***********************************************************************/ \ No newline at end of file +/***********************************************************************/ + +/***********************************************************************/ +void ValidParameters::initCommandParameters() { + try { + //{"parameter1","parameter2",...,"last parameter"}; + + string readdistArray[] = {"phylip","column", "name","cutoff","precision"}; + commandParameters["read.dist"] = addParameters(readdistArray, sizeof(readdistArray)/sizeof(string)); + + string readotuArray[] = {"list","order","shared", "line", "label","group","shared", "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","precision","abund"}; + commandParameters["collect.single"] = addParameters(collectsingleArray, sizeof(collectsingleArray)/sizeof(string)); + + string collectsharedArray[] = {"jumble","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"}; + 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"}; + commandParameters["summary.single"] = addParameters(summarysingleArray, sizeof(summarysingleArray)/sizeof(string)); + + string summarysharedArray[] = {"jumble","line","label","calc"}; + commandParameters["summary.shared"] = addParameters(summarysharedArray, sizeof(summarysharedArray)/sizeof(string)); + + string parsimonyArray[] = {"random","group","iters"}; + commandParameters["parsimony"] = addParameters(parsimonyArray, sizeof(parsimonyArray)/sizeof(string)); + + string unifracWeightedArray[] = {"group","iters"}; + commandParameters["unifrac.weighted"] = addParameters(unifracWeightedArray, sizeof(unifracWeightedArray)/sizeof(string)); + + string unifracUnweightedArray[] = {"group","iters"}; + commandParameters["unifrac.unweighted"] = addParameters(unifracUnweightedArray, sizeof(unifracUnweightedArray)/sizeof(string)); + + string heatmapArray[] = {"group","line","label","sorted"}; + commandParameters["heatmap"] = addParameters(heatmapArray, sizeof(heatmapArray)/sizeof(string)); + + string vennArray[] = {"groups","line","label","calc"}; + commandParameters["venn"] = addParameters(vennArray, sizeof(vennArray)/sizeof(string)); + + string binseqsArray[] = {"fasta","line","label","name"}; + commandParameters["bin.seqs"] = addParameters(binseqsArray, sizeof(binseqsArray)/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::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); + } +} + +/***********************************************************************/ + +/***********************************************************************/ +vector ValidParameters::addParameters(string parameters[], int size) { + try { + vector 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); + } +} + +