made sorting optional but sort by default, in case the user wants to see the heatmap...

[mothur.git] / validparameter.cpp

diff --git a/validparameter.cpp b/validparameter.cpp
index 50610f0bbc43d0903e60d6def31fe46b0401ad65..51fefd837203aea8c3774d1581e9e579cf66fd55 100644 (file)
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -13,38 +13,9 @@
 
 ValidParameters::ValidParameters() {
        try {
-               parameters["phylip"]            = "phylip";
-               parameters["column"]                = "column";
-               parameters["list"]                      = "list"; 
-               parameters["rabund"]            = "rabund"; 
-               parameters["sabund"]            = "sabund"; 
-               parameters["name"]                      = "name"; 
-               parameters["group"]                     = "group"; 
-               parameters["order"]             = "order"; 
-               parameters["fasta"]                         = "fasta"; 
-               parameters["tree"]                      = "tree";
-               parameters["fileroot"]                  = "fileroot";
-               parameters["cutoff"]                    = "cutoff"; 
-               parameters["method"]                    = "method";
-               parameters["format"]                    = "format"; 
-               parameters["precision"]                 = "precision"; 
-               parameters["label"]                             = "label"; 
-               parameters["line"]                              = "line";
-               parameters["iters"]                             = "iters"; 
-               parameters["jumble"]                    = "jumble"; 
-               parameters["freq"]                              = "freq"; 
-               parameters["abund"]             = "abund";
-               parameters["random"]                    = "random";
-               parameters["groups"]                    = "groups";
-               parameters["calc"]                              = "calc";
-               parameters["sharedrarefaction"] = "sharedrarefaction";
-               parameters["sharedsummary"]     = "sharedsummary";
-               parameters["shared"]            = "shared";
-               parameters["single"]            = "single";
-               parameters["rarefaction"]       = "rarefaction";
-               
                initCommandParameters();                
                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";
@@ -252,22 +223,25 @@ void ValidParameters::initCommandParameters() {
        try {   
                //{"parameter1","parameter2",...,"last parameter"};
                
-               string readdistArray[] = {"phylip","name","cutoff","precision"};
+               string readdistArray[] = {"phylip","column", "name","cutoff","precision"};
                commandParameters["read.dist"] = addParameters(readdistArray, sizeof(readdistArray)/sizeof(string));
 
-               string readotuArray[] =  {"list","order","group","shared", "sabund"};
+               string readotuArray[] =  {"list","order","shared", "line", "label","group","shared", "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","single","precision","abund"};
+               string collectsingleArray[] =  {"freq","line","label","calc","precision","abund"};
                commandParameters["collect.single"] = addParameters(collectsingleArray, sizeof(collectsingleArray)/sizeof(string));
 
-               string collectsharedArray[] =  {"jumble","freq","line","label","shared","groups"};
+               string collectsharedArray[] =  {"jumble","freq","line","label","calc","groups"};
                commandParameters["collect.shared"] = addParameters(collectsharedArray, sizeof(collectsharedArray)/sizeof(string));
 
                string getgroupArray[] =  {};
@@ -279,18 +253,33 @@ void ValidParameters::initCommandParameters() {
                string getlineArray[] =  {};
                commandParameters["get.line"] = addParameters(getlineArray, sizeof(getlineArray)/sizeof(string));
 
-               string rarefactionsingleArray[] =  {"iters","freq","line","label","rarefaction","abund"};
+               string rarefactionsingleArray[] =  {"iters","freq","line","label","calc","abund"};
                commandParameters["rarefaction.single"] = addParameters(rarefactionsingleArray, sizeof(rarefactionsingleArray)/sizeof(string));
 
-               string rarefactionsharedArray[] =  {"iters","jumble","line","label","sharedrarefaction"};
+               string rarefactionsharedArray[] =  {"iters","jumble","line","label","calc"};
                commandParameters["rarefaction.shared"] = addParameters(rarefactionsharedArray, sizeof(rarefactionsharedArray)/sizeof(string));
-
-               string summarysingleArray[] =  {"line","label","summary","abund"};
+               
+               string libshuffArray[] =  {"iters","groups","step","form","cutoff"};
+               commandParameters["libshuff"] = addParameters(libshuffArray, sizeof(libshuffArray)/sizeof(string));
+               
+               string summarysingleArray[] =  {"line","label","calc","abund"};
                commandParameters["summary.single"] = addParameters(summarysingleArray, sizeof(summarysingleArray)/sizeof(string));
 
-               string summarysharedArray[] =  {"jumble","line","label","sharedsummary"};
+               string summarysharedArray[] =  {"jumble","line","label","calc"};
                commandParameters["summary.shared"] = addParameters(summarysharedArray, sizeof(summarysharedArray)/sizeof(string));
 
+               string parsimonyArray[] =  {"random","group","iters"};
+               commandParameters["parsimony"] = addParameters(parsimonyArray, sizeof(parsimonyArray)/sizeof(string));
+
+               string unifracWeightedArray[] =  {"group","iters"};
+               commandParameters["unifrac.weighted"] = addParameters(unifracWeightedArray, sizeof(unifracWeightedArray)/sizeof(string));
+
+               string unifracUnweightedArray[] =  {"group","iters"};
+               commandParameters["unifrac.unweighted"] = addParameters(unifracUnweightedArray, sizeof(unifracUnweightedArray)/sizeof(string));
+
+               string heatmapArray[] =  {"group","line","label","sorted"};
+               commandParameters["heatmap"] = addParameters(heatmapArray, sizeof(heatmapArray)/sizeof(string));
+
                string quitArray[] = {};
                commandParameters["quit"] = addParameters(quitArray, sizeof(quitArray)/sizeof(string));
 
@@ -369,5 +358,4 @@ vector<string> ValidParameters::addParameters(string parameters[], int size) {
        }
 }
 
-/***********************************************************************/