-/***********************************************************************/
-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 readseqsArray[] = {"fasta","phylip","clustal","nexus","line"};
- commandParameters["read.seqs"] = addParameters(readseqsArray, sizeof(readseqsArray)/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[] = {"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));