+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","size"};
+ 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));
+
+ string libshuffArray[] = {"iters","groups","step","form","cutoff"};
+ commandParameters["libshuff"] = addParameters(libshuffArray, sizeof(libshuffArray)/sizeof(string));
+
+ string summarysingleArray[] = {"line","label","calc","abund","size"};
+ commandParameters["summary.single"] = addParameters(summarysingleArray, sizeof(summarysingleArray)/sizeof(string));
+
+ string summarysharedArray[] = {"line","label","calc","groups"};
+ commandParameters["summary.shared"] = addParameters(summarysharedArray, sizeof(summarysharedArray)/sizeof(string));
+
+ string parsimonyArray[] = {"random","groups","iters"};
+ commandParameters["parsimony"] = addParameters(parsimonyArray, sizeof(parsimonyArray)/sizeof(string));
+
+ string unifracWeightedArray[] = {"groups","iters"};
+ commandParameters["unifrac.weighted"] = addParameters(unifracWeightedArray, sizeof(unifracWeightedArray)/sizeof(string));
+
+ 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 filterseqsArray[] = {"fasta","phylip","clustal","nexus", "trump", "soft", "hard", "vertical"};
+ 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", "group"};
+ 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 getOTURepArray[] = {"fasta","list","line","label","name", "group"};
+ commandParameters["get.oturep"] = addParameters(getOTURepArray, sizeof(getOTURepArray)/sizeof(string));
+
+ string treeGroupsArray[] = {"line","label","calc","groups", "phylip", "column", "name"};
+ 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", "countends", "cutoff", "processors"};
+ commandParameters["dist.seqs"] = addParameters(distanceArray, sizeof(distanceArray)/sizeof(string));
+
+ string AlignArray[] = {"fasta", "candidate", "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));
+
+ }
+ 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";
+ exit(1);
+ }