X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validparameter.cpp;h=e97df8b0fc8e0efc9f02f6c61987f59ea1c75b89;hb=d5d2761f88b41f1006d0b700e0ab51e2ce48b875;hp=11e7bf93cb91079ce0feb8ead87f41a953cfd136;hpb=5d3f35ac36e3f55d3d031016340ec99420fd1b24;p=mothur.git diff --git a/validparameter.cpp b/validparameter.cpp index 11e7bf9..e97df8b 100644 --- a/validparameter.cpp +++ b/validparameter.cpp @@ -31,23 +31,19 @@ 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++) @@ -66,8 +62,7 @@ bool ValidParameters::isValidParameter(string parameter, string command, string vector values; splitAtDash(value, values); - for(int i = 0; i < values.size(); i++) - { + for(int i = 0; i < values.size(); i++) { value = values.at(i); valid = convertTest(value, pVal); @@ -80,12 +75,10 @@ bool ValidParameters::isValidParameter(string parameter, string command, string Special Cases *********************************************************************************************************/ - if(parameter.compare("precision") == 0) - { + if(parameter.compare("precision") == 0) { double logNum = log10((double)pVal); double diff = (double)((int)logNum - logNum); - if(diff != 0) - { + 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; } @@ -111,8 +104,7 @@ bool ValidParameters::isValidParameter(string parameter, string command, string c = 0; else if(range.at(4).compare("only") == 0) c = 1; - else - { + else { cout << "The range can only be 'between' or 'only' the bounding numbers.\n"; return false; } @@ -121,8 +113,7 @@ bool ValidParameters::isValidParameter(string parameter, string command, string d = 0; else if(range.at(0).compare(">=") == 0 || range[3].compare("=>") == 0) d = 1; - else - { + else { cout << "The parameter value can only be '>', '>=', or '=>' the lower bounding number.\n"; return false; } @@ -131,8 +122,7 @@ bool ValidParameters::isValidParameter(string parameter, string command, string e = 0; else if(range.at(2).compare("<=") == 0 || range[4].compare("=<") == 0) e = 1; - else - { + else { cout << "The parameter value can only be '<', '<=', or '=<' the upper bounding number.\n"; return false; } @@ -142,24 +132,20 @@ bool ValidParameters::isValidParameter(string parameter, string command, string bool b0 = pVal < b; bool b1 = pVal <= b; - if(c != 1) - { - if(a != piSentinel && b == piSentinel) - { + if(c != 1) { + if(a != piSentinel && b == piSentinel) { if(d == 0) valid = a0; else valid = a1; } - else if(a == piSentinel && b != piSentinel) - { + else if(a == piSentinel && b != piSentinel) { if(e == 0) valid = b0; else valid = b1; } - else - { + else { if(d == 0 && e == 0) valid = (a0 && b0); else if(d == 0 && e == 1) @@ -170,8 +156,7 @@ bool ValidParameters::isValidParameter(string parameter, string command, string valid = (a1 && b1); } } - else - { + else { if(a != piSentinel && b == piSentinel) valid = (pVal == a); else if(a == piSentinel && b != piSentinel) @@ -181,30 +166,26 @@ bool ValidParameters::isValidParameter(string parameter, string command, string } - if(!valid) - { + if(!valid) { cout << "The '" << parameter << "' parameter needs to be "; if(c == 1) cout << "either '" << a << "' or '" << b << "'.\n"; - else - { - if(a != piSentinel) - { + else { + if(a != piSentinel) { cout << ">"; if(d != 0) cout << "="; cout << " '" << a << "'"; } if(b == piSentinel) - cout << ".\n"; + cout << "'.\n"; else if(a != piSentinel) cout << " and "; - if(b != piSentinel) - { + if(b != piSentinel) { cout << "<"; if(e != 0) cout << "="; - cout << " '" << b << ".\n"; + cout << " '" << b << "'.\n"; } } return false; @@ -229,10 +210,11 @@ 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"}; @@ -244,10 +226,10 @@ void ValidParameters::initCommandParameters() { string deconvoluteArray[] = {"fasta"}; commandParameters["deconvolute"] = addParameters(deconvoluteArray, sizeof(deconvoluteArray)/sizeof(string)); - string collectsingleArray[] = {"freq","line","label","calc","precision","abund"}; + string collectsingleArray[] = {"freq","line","label","calc","abund"}; 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[] = {}; @@ -262,7 +244,7 @@ void ValidParameters::initCommandParameters() { 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"}; @@ -271,21 +253,45 @@ void ValidParameters::initCommandParameters() { string summarysingleArray[] = {"line","label","calc","abund"}; 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","sorted"}; + 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"}; + commandParameters["bin.seqs"] = addParameters(binseqsArray, sizeof(binseqsArray)/sizeof(string)); + + string getOTURepArray[] = {"fasta","list","line","label","name"}; + 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["distance"] = addParameters(distanceArray, sizeof(distanceArray)/sizeof(string)); + string quitArray[] = {}; commandParameters["quit"] = addParameters(quitArray, sizeof(quitArray)/sizeof(string)); @@ -327,14 +333,17 @@ 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); } 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"; @@ -364,4 +373,3 @@ vector ValidParameters::addParameters(string parameters[], int size) { } } -