X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validparameter.cpp;h=0c32a3e1c7b00e9fa90c8a5e4ca7fb759238c9e2;hb=5d176c0f8049654ec3ae5a869c9ee3cecb991dc6;hp=3fbf307b69918626e097e2e61a11cfcf54244bb4;hpb=51cf89e90eef8b300c2786eb1560dd89e6e83445;p=mothur.git diff --git a/validparameter.cpp b/validparameter.cpp index 3fbf307..0c32a3e 100644 --- a/validparameter.cpp +++ b/validparameter.cpp @@ -13,18 +13,13 @@ ValidParameters::ValidParameters() { try { - initCommandParameters(); + 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); - } } /***********************************************************************/ @@ -32,26 +27,23 @@ ValidParameters::ValidParameters() { ValidParameters::~ValidParameters() {} /***********************************************************************/ -bool ValidParameters::isValidParameter(string parameter, string command, string value) { +bool ValidParameters::isValidParameter(string parameter, vector cParams, string value) { try { bool valid = false; - vector cParams = commandParameters[command]; + //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) - { - cout << "'" << parameter << "' is not a valid parameter for the " << command << " command.\n"; - cout << "The valid paramters for the " << command << " command are: "; + 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++) - cout << cParams.at(i) << ", "; - cout << "and " << cParams.at(numParams-1) << ".\n"; + m->mothurOut(cParams.at(i) + ", "); + m->mothurOut("and " + cParams.at(numParams-1) + ".\n"); return false; } @@ -65,8 +57,7 @@ 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); @@ -79,13 +70,11 @@ 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) - { - cout << "The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n"; + 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; } } @@ -110,9 +99,8 @@ bool ValidParameters::isValidParameter(string parameter, string command, string 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"; + else { + m->mothurOut("The range can only be 'between' or 'only' the bounding numbers.\n"); return false; } @@ -120,9 +108,8 @@ bool ValidParameters::isValidParameter(string parameter, string command, string 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"; + else { + m->mothurOut("The parameter value can only be '>', '>=', or '=>' the lower bounding number.\n"); return false; } @@ -130,9 +117,8 @@ bool ValidParameters::isValidParameter(string parameter, string command, string 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"; + else { + m->mothurOut("The parameter value can only be '<', '<=', or '=<' the upper bounding number.\n"); return false; } @@ -141,24 +127,20 @@ 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) @@ -169,8 +151,7 @@ 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) @@ -180,30 +161,26 @@ bool ValidParameters::isValidParameter(string parameter, string command, string } - if(!valid) - { - cout << "The '" << parameter << "' parameter needs to be "; + if(!valid) { + m->mothurOut("The '" + parameter + "' parameter needs to be "); if(c == 1) - cout << "either '" << a << "' or '" << b << "'.\n"; - else - { - if(a != piSentinel) - { - cout << ">"; + m->mothurOut("either '" + toString(a) + "' or '" + toString(b) + "'.\n"); + else { + if(a != piSentinel) { + m->mothurOut(">"); if(d != 0) - cout << "="; - cout << " '" << a << "'"; + m->mothurOut("="); + m->mothurOut(" '" + toString(a) + "'"); } if(b == piSentinel) - cout << ".\n"; + m->mothurOut( "'.\n"); else if(a != piSentinel) - cout << " and "; - if(b != piSentinel) - { - cout << "<"; + m->mothurOut(" and "); + if(b != piSentinel) { + m->mothurOut("<"); if(e != 0) - cout << "="; - cout << " '" << b << ".\n"; + m->mothurOut("="); + m->mothurOut(" '" + toString(b) + "'.\n"); } } return false; @@ -212,105 +189,37 @@ bool ValidParameters::isValidParameter(string parameter, string command, string 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"; + m->errorOut(e, "ValidParameters", "isValidParameters"); 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"}; - 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","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 ValidParameters::validFile(map container, string parameter, bool isFile) { + try { + int ableToOpen; + ifstream in; + map::iterator it; - string summarysingleArray[] = {"line","label","calc","abund"}; - commandParameters["summary.single"] = addParameters(summarysingleArray, sizeof(summarysingleArray)/sizeof(string)); - - string summarysharedArray[] = {"jumble","line","label","calc","groups"}; - commandParameters["summary.shared"] = addParameters(summarysharedArray, sizeof(summarysharedArray)/sizeof(string)); + it = container.find(parameter); + if(it != container.end()){ //no parameter given - string parsimonyArray[] = {"random","groups","iters"}; - commandParameters["parsimony"] = addParameters(parsimonyArray, sizeof(parsimonyArray)/sizeof(string)); + if(isFile == true) { - string unifracWeightedArray[] = {"groups","iters"}; - commandParameters["unifrac.weighted"] = addParameters(unifracWeightedArray, sizeof(unifracWeightedArray)/sizeof(string)); + ableToOpen = openInputFile(it->second, in); - 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 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)); + if (ableToOpen == 1) { return "not open"; } + in.close(); + } + }else { return "not found"; } - string quitArray[] = {}; - commandParameters["quit"] = addParameters(quitArray, sizeof(quitArray)/sizeof(string)); - + 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"; - 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"; + m->errorOut(e, "ValidParameters", "validFile"); exit(1); } } @@ -339,10 +248,7 @@ void ValidParameters::initParameterRanges() { 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"}; + string freqArray[] = {">=","1", "<","NA", "between"}; parameterRanges["freq"] = addParameters(freqArray, rangeSize); //string lineArray[] = {">=","1", "<","NA", "between"}; @@ -350,13 +256,15 @@ void ValidParameters::initParameterRanges() { 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"; + m->errorOut(e, "ValidParameters", "initParameterRanges"); exit(1); } } @@ -370,11 +278,7 @@ vector ValidParameters::addParameters(string parameters[], int 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"; + m->errorOut(e, "ValidParameters", "addParameters"); exit(1); } }