added sort to heatmap to put shared otus at the top and updated some error checking

[mothur.git] / validparameter.cpp

diff --git a/validparameter.cpp b/validparameter.cpp
index 9c8ce2e89136a671d775cb6b41484b3bc6cc869a..6af6c15e313975ade4d17d6bd91141defbf205fc 100644 (file)
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -223,22 +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[] =  {};
@@ -250,21 +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 libshuffArray[] =  {"iters","groups","step","form","cutoff"};
                commandParameters["libshuff"] = addParameters(libshuffArray, sizeof(libshuffArray)/sizeof(string));
                
-               string summarysingleArray[] =  {"line","label","summary","abund"};
+               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"};
+               commandParameters["heatmap"] = addParameters(heatmapArray, sizeof(heatmapArray)/sizeof(string));
+
                string quitArray[] = {};
                commandParameters["quit"] = addParameters(quitArray, sizeof(quitArray)/sizeof(string));