ValidParameters::~ValidParameters() {}
-
/***********************************************************************/
bool ValidParameters::isValidParameter(string parameter, string command, string value) {
try {
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"};
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 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"};
string summarysingleArray[] = {"line","label","calc","abund"};
commandParameters["summary.single"] = addParameters(summarysingleArray, sizeof(summarysingleArray)/sizeof(string));
- string summarysharedArray[] = {"jumble","line","label","calc"};
+ string summarysharedArray[] = {"jumble","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 vennArray[] = {"groups","line","label"};
+ 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 quitArray[] = {};
commandParameters["quit"] = addParameters(quitArray, sizeof(quitArray)/sizeof(string));
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);
}
}
-