*** empty log message ***

[mothur.git] / validparameter.cpp

diff --git a/validparameter.cpp b/validparameter.cpp
index 084068df81f6f2e9c4263e9a58f9549443bf69aa..98dbde868627018c08221875a65c10426a9f0947 100644 (file)
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -31,7 +31,6 @@ ValidParameters::ValidParameters() {
 
 ValidParameters::~ValidParameters() {}
 
-
 /***********************************************************************/
 bool ValidParameters::isValidParameter(string parameter, string command, string value) {
        try {   
@@ -229,10 +228,11 @@ void ValidParameters::initCommandParameters() {
        try {   
                //{"parameter1","parameter2",...,"last parameter"};
                
-               string readdistArray[] = {"phylip","column", "name","cutoff","precision"};
+               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","shared", "sabund", "rabund"};
+               string readotuArray[] =  {"list","order","shared", "line", "label","group","sabund", "rabund"};
                commandParameters["read.otu"] = addParameters(readotuArray, sizeof(readotuArray)/sizeof(string));
                
                string readtreeArray[] = {"tree","group"};
@@ -244,7 +244,7 @@ void ValidParameters::initCommandParameters() {
                string deconvoluteArray[] =  {"fasta"};
                commandParameters["deconvolute"] = addParameters(deconvoluteArray, sizeof(deconvoluteArray)/sizeof(string));
                
-               string collectsingleArray[] =  {"freq","line","label","calc","precision","abund"};
+               string collectsingleArray[] =  {"freq","line","label","calc","abund"};
                commandParameters["collect.single"] = addParameters(collectsingleArray, sizeof(collectsingleArray)/sizeof(string));
 
                string collectsharedArray[] =  {"jumble","freq","line","label","calc","groups"};
@@ -262,7 +262,7 @@ void ValidParameters::initCommandParameters() {
                string rarefactionsingleArray[] =  {"iters","freq","line","label","calc","abund"};
                commandParameters["rarefaction.single"] = addParameters(rarefactionsingleArray, sizeof(rarefactionsingleArray)/sizeof(string));
 
-               string rarefactionsharedArray[] =  {"iters","jumble","line","label","calc"};
+               string rarefactionsharedArray[] =  {"iters","jumble","line","label","calc","groups"};
                commandParameters["rarefaction.shared"] = addParameters(rarefactionsharedArray, sizeof(rarefactionsharedArray)/sizeof(string));
                
                string libshuffArray[] =  {"iters","groups","step","form","cutoff"};
@@ -271,24 +271,33 @@ void ValidParameters::initCommandParameters() {
                string summarysingleArray[] =  {"line","label","calc","abund"};
                commandParameters["summary.single"] = addParameters(summarysingleArray, sizeof(summarysingleArray)/sizeof(string));
 
-               string summarysharedArray[] =  {"jumble","line","label","calc"};
+               string summarysharedArray[] =  {"jumble","line","label","calc","groups"};
                commandParameters["summary.shared"] = addParameters(summarysharedArray, sizeof(summarysharedArray)/sizeof(string));
 
-               string parsimonyArray[] =  {"random","group","iters"};
+               string parsimonyArray[] =  {"random","groups","iters"};
                commandParameters["parsimony"] = addParameters(parsimonyArray, sizeof(parsimonyArray)/sizeof(string));
 
-               string unifracWeightedArray[] =  {"group","iters"};
+               string unifracWeightedArray[] =  {"groups","iters"};
                commandParameters["unifrac.weighted"] = addParameters(unifracWeightedArray, sizeof(unifracWeightedArray)/sizeof(string));
 
-               string unifracUnweightedArray[] =  {"group","iters"};
+               string unifracUnweightedArray[] =  {"groups","iters"};
                commandParameters["unifrac.unweighted"] = addParameters(unifracUnweightedArray, sizeof(unifracUnweightedArray)/sizeof(string));
 
-               string heatmapArray[] =  {"group","line","label","sorted"};
+               string heatmapArray[] =  {"groups","line","label","sorted","scaler"};
                commandParameters["heatmap"] = addParameters(heatmapArray, sizeof(heatmapArray)/sizeof(string));
 
-               string vennArray[] =  {"groups","line","label"};
+               string vennArray[] =  {"groups","line","label","calc"};
                commandParameters["venn"] = addParameters(vennArray, sizeof(vennArray)/sizeof(string));
                
+               string binseqsArray[] =  {"fasta","line","label","name"};
+               commandParameters["bin.seqs"] = addParameters(binseqsArray, sizeof(binseqsArray)/sizeof(string));
+               
+               string getOTURepArray[] =  {"fasta","list","line","label","name"};
+               commandParameters["get.oturep"] = addParameters(getOTURepArray, sizeof(getOTURepArray)/sizeof(string));
+               
+               string treeGroupsArray[] =  {"line","label","calc","groups"};
+               commandParameters["tree.groups"] = addParameters(treeGroupsArray, sizeof(treeGroupsArray)/sizeof(string));
+               
                string quitArray[] = {};
                commandParameters["quit"] = addParameters(quitArray, sizeof(quitArray)/sizeof(string));
 
@@ -333,8 +342,8 @@ void ValidParameters::initParameterRanges() {
                string freqArray[] = {">","1", "<","NA", "between"};
                parameterRanges["freq"] = addParameters(freqArray, rangeSize);
 
-               string lineArray[] = {">=","1", "<","NA", "between"};
-               parameterRanges["line"] = addParameters(lineArray, rangeSize);
+               //string lineArray[] = {">=","1", "<","NA", "between"};
+               //parameterRanges["line"] = addParameters(lineArray, rangeSize);
 
                string abundArray[] = {">=","5", "<","NA", "between"};
                parameterRanges["abund"] = addParameters(abundArray, rangeSize);