added bootstrap.shared command and fixed some bugs with heatmap

[mothur.git] / validparameter.cpp

diff --git a/validparameter.cpp b/validparameter.cpp
index f4780a710a40a0c9ea5d621f6f354c2503f6196a..3fbf307b69918626e097e2e61a11cfcf54244bb4 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 {   
@@ -229,7 +228,8 @@ void ValidParameters::initCommandParameters() {
        try {   
                //{"parameter1","parameter2",...,"last parameter"};
                
-               string readdistArray[] = {"phylip","column","name","cutoff","precision","group"};
+               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"};
@@ -283,7 +283,7 @@ void ValidParameters::initCommandParameters() {
                string unifracUnweightedArray[] =  {"groups","iters"};
                commandParameters["unifrac.unweighted"] = addParameters(unifracUnweightedArray, sizeof(unifracUnweightedArray)/sizeof(string));
 
-               string heatmapArray[] =  {"groups","line","label","sorted"};
+               string heatmapArray[] =  {"groups","line","label","sorted","scale"};
                commandParameters["heatmap"] = addParameters(heatmapArray, sizeof(heatmapArray)/sizeof(string));
 
                string vennArray[] =  {"groups","line","label","calc"};
@@ -295,6 +295,12 @@ void ValidParameters::initCommandParameters() {
                string getOTURepArray[] =  {"fasta","list","line","label","name"};
                commandParameters["get.oturep"] = addParameters(getOTURepArray, sizeof(getOTURepArray)/sizeof(string));
                
+               string treeGroupsArray[] =  {"line","label","calc","groups"};
+               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 quitArray[] = {};
                commandParameters["quit"] = addParameters(quitArray, sizeof(quitArray)/sizeof(string));
 
@@ -373,4 +379,3 @@ vector<string> ValidParameters::addParameters(string parameters[], int size) {
        }
 }
 
-