X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validparameter.cpp;h=bd1698468116f39ec112e075e8001c47a7ef3199;hb=64eee3a595ae53817f52807d7393b22e74e31f56;hp=6af6c15e313975ade4d17d6bd91141defbf205fc;hpb=2657127a3e1f3b5463f2b3a3b49bc19843f5c9d2;p=mothur.git diff --git a/validparameter.cpp b/validparameter.cpp index 6af6c15..bd16984 100644 --- a/validparameter.cpp +++ b/validparameter.cpp @@ -31,24 +31,24 @@ ValidParameters::ValidParameters() { ValidParameters::~ValidParameters() {} - /***********************************************************************/ bool ValidParameters::isValidParameter(string parameter, string command, string value) { try { 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) - { + for(int i = 0; i < numParams; i++) { + if(cParams.at(i).compare(parameter) == 0) { valid = true; i = numParams; } } - if(!valid) - { + 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; } @@ -58,153 +58,140 @@ bool ValidParameters::isValidParameter(string parameter, string command, string int pVal; double piSentinel = 3.14159; vector range = parameterRanges[parameter]; - - valid = convertTest(value, pVal); - - if(!valid) - return false; - + vector values; + splitAtDash(value, values); - /******************************************************************************************************** - Special Cases - *********************************************************************************************************/ + for(int i = 0; i < values.size(); i++) { + value = values.at(i); + valid = convertTest(value, pVal); - 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"; + 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; - if(a != piSentinel && b == piSentinel) - { - if(d == 0) - valid = a0; - else - valid = a1; + /************************************************************************************************************/ + + + + 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; } - else if(a == piSentinel && b != piSentinel) - { - if(e == 0) - valid = b0; - else - valid = b1; + + 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; } - 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); + + 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; } - } - else - { - if(a == piSentinel && b == piSentinel) - return true; - 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) - 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 << "'"; + + 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; } - if(b == piSentinel) - cout << ".\n"; - else if(a != piSentinel) - cout << " and "; - if(b != piSentinel) - { - cout << "<"; - if(e != 0) - cout << "="; - cout << " '" << b << ".\n"; + 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); } } - return false; + 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"; @@ -223,10 +210,10 @@ void ValidParameters::initCommandParameters() { try { //{"parameter1","parameter2",...,"last parameter"}; - string readdistArray[] = {"phylip","column", "name","cutoff","precision"}; + 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","shared", "sabund", "rabund"}; + string readotuArray[] = {"list","order","shared", "line", "label","group","sabund", "rabund"}; commandParameters["read.otu"] = addParameters(readotuArray, sizeof(readotuArray)/sizeof(string)); string readtreeArray[] = {"tree","group"}; @@ -236,12 +223,12 @@ void ValidParameters::initCommandParameters() { commandParameters["cluster"] = addParameters(clusterArray, sizeof(clusterArray)/sizeof(string)); string deconvoluteArray[] = {"fasta"}; - commandParameters["deconvolute"] = addParameters(deconvoluteArray, sizeof(deconvoluteArray)/sizeof(string)); + commandParameters["unique.seqs"] = addParameters(deconvoluteArray, sizeof(deconvoluteArray)/sizeof(string)); - string collectsingleArray[] = {"freq","line","label","calc","precision","abund"}; + string collectsingleArray[] = {"freq","line","label","calc","abund","size"}; commandParameters["collect.single"] = addParameters(collectsingleArray, sizeof(collectsingleArray)/sizeof(string)); - string collectsharedArray[] = {"jumble","freq","line","label","calc","groups"}; + string collectsharedArray[] = {"freq","line","label","calc","groups"}; commandParameters["collect.shared"] = addParameters(collectsharedArray, sizeof(collectsharedArray)/sizeof(string)); string getgroupArray[] = {}; @@ -252,34 +239,82 @@ void ValidParameters::initCommandParameters() { string getlineArray[] = {}; commandParameters["get.line"] = addParameters(getlineArray, sizeof(getlineArray)/sizeof(string)); + + string getsabundArray[] = {"line", "label"}; + commandParameters["get.sabund"] = addParameters(getsabundArray, sizeof(getsabundArray)/sizeof(string)); + + string getrabundArray[] = {"line", "label"}; + commandParameters["get.rabund"] = addParameters(getrabundArray, sizeof(getrabundArray)/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"}; + 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"}; + string summarysingleArray[] = {"line","label","calc","abund","size"}; commandParameters["summary.single"] = addParameters(summarysingleArray, sizeof(summarysingleArray)/sizeof(string)); - string summarysharedArray[] = {"jumble","line","label","calc"}; + string summarysharedArray[] = {"line","label","calc","groups"}; commandParameters["summary.shared"] = addParameters(summarysharedArray, sizeof(summarysharedArray)/sizeof(string)); - string parsimonyArray[] = {"random","group","iters"}; + string parsimonyArray[] = {"random","groups","iters"}; commandParameters["parsimony"] = addParameters(parsimonyArray, sizeof(parsimonyArray)/sizeof(string)); - string unifracWeightedArray[] = {"group","iters"}; + string unifracWeightedArray[] = {"groups","iters"}; commandParameters["unifrac.weighted"] = addParameters(unifracWeightedArray, sizeof(unifracWeightedArray)/sizeof(string)); - string unifracUnweightedArray[] = {"group","iters"}; + string unifracUnweightedArray[] = {"groups","iters"}; commandParameters["unifrac.unweighted"] = addParameters(unifracUnweightedArray, sizeof(unifracUnweightedArray)/sizeof(string)); - string heatmapArray[] = {"group","line","label"}; + string heatmapArray[] = {"groups","line","label","sorted","scale"}; commandParameters["heatmap"] = addParameters(heatmapArray, sizeof(heatmapArray)/sizeof(string)); + + string filterseqsArray[] = {"fasta", "trump", "soft", "hard", "vertical"}; + commandParameters["filter.seqs"] = addParameters(filterseqsArray, sizeof(filterseqsArray)/sizeof(string)); + + string summaryseqsArray[] = {"fasta"}; + commandParameters["summary.seqs"] = addParameters(summaryseqsArray, sizeof(summaryseqsArray)/sizeof(string)); + + string screenseqsArray[] = {"fasta", "start", "end", "maxambig", "maxhomop", "minlength", "maxlength", "name", "group"}; + commandParameters["screen.seqs"] = addParameters(screenseqsArray, sizeof(screenseqsArray)/sizeof(string)); + string reverseseqsArray[] = {"fasta"}; + commandParameters["reverse.seqs"] = addParameters(reverseseqsArray, sizeof(reverseseqsArray)/sizeof(string)); + + string trimseqsArray[] = {"fasta", "flip", "oligos", "forward", "reverse", "barcode"}; + commandParameters["trim.seqs"] = addParameters(trimseqsArray, sizeof(trimseqsArray)/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", "phylip", "column", "name"}; + 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", "calc", "countends", "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)); @@ -321,14 +356,20 @@ void ValidParameters::initParameterRanges() { string jumbleArray[] = {">","0", "<","1", "only"}; parameterRanges["jumble"] = addParameters(jumbleArray, rangeSize); - string freqArray[] = {">","1", "<","NA", "between"}; + string freqArray[] = {">=","1", "<","NA", "between"}; parameterRanges["freq"] = addParameters(freqArray, rangeSize); - string lineArray[] = {">=","1", "<","NA", "between"}; - parameterRanges["line"] = addParameters(lineArray, 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"; @@ -358,4 +399,3 @@ vector ValidParameters::addParameters(string parameters[], int size) { } } -