//{"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"};
string deconvoluteArray[] = {"fasta"};
commandParameters["deconvolute"] = addParameters(deconvoluteArray, sizeof(deconvoluteArray)/sizeof(string));
- string collectsingleArray[] = {"freq","line","label","calc","abund"};
+ string collectsingleArray[] = {"freq","line","label","calc","abund","size"};
commandParameters["collect.single"] = addParameters(collectsingleArray, sizeof(collectsingleArray)/sizeof(string));
string collectsharedArray[] = {"freq","line","label","calc","groups"};
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[] = {"line","label","calc","groups"};
string binseqsArray[] = {"fasta","line","label","name"};
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 getrepseqsArray[] = {"fasta","line","label","name", "group"};
+ commandParameters["get.repseqs"] = addParameters(getrepseqsArray, sizeof(getrepseqsArray)/sizeof(string));
+
string getOTURepArray[] = {"fasta","list","line","label","name"};
commandParameters["get.oturep"] = addParameters(getOTURepArray, sizeof(getOTURepArray)/sizeof(string));
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));
+ commandParameters["dist.seqs"] = addParameters(distanceArray, sizeof(distanceArray)/sizeof(string));
+
+ string AlignArray[] = {"fasta","phylip","clustal","nexus", "template", "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));
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";