added help for heatmap.sim

[mothur.git] / validparameter.cpp

diff --git a/validparameter.cpp b/validparameter.cpp
index 4845425883cfbb57b05eac1aa2156efd1841090f..d6fde63045c51d56449b14701dde04974503fb82 100644 (file)
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -271,7 +271,10 @@ void ValidParameters::initCommandParameters() {
                commandParameters["unifrac.unweighted"] = addParameters(unifracUnweightedArray, sizeof(unifracUnweightedArray)/sizeof(string));
 
                string heatmapArray[] =  {"groups","line","label","sorted","scale"};
-               commandParameters["heatmap"] = addParameters(heatmapArray, sizeof(heatmapArray)/sizeof(string));
+               commandParameters["heatmap.bin"] = addParameters(heatmapArray, sizeof(heatmapArray)/sizeof(string));
+               
+               string heatmapSimArray[] =  {"groups","line","label"};
+               commandParameters["heatmap.sim"] = addParameters(heatmapSimArray, sizeof(heatmapSimArray)/sizeof(string));
                
                string filterseqsArray[] =  {"fasta", "trump", "soft", "hard", "vertical"};
                commandParameters["filter.seqs"] = addParameters(filterseqsArray, sizeof(filterseqsArray)/sizeof(string));
@@ -285,7 +288,7 @@ void ValidParameters::initCommandParameters() {
                string reverseseqsArray[] =  {"fasta"};
                commandParameters["reverse.seqs"] = addParameters(reverseseqsArray, sizeof(reverseseqsArray)/sizeof(string));
 
-               string trimseqsArray[] =  {"fasta", "flip", "oligos"};
+               string trimseqsArray[] =  {"fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength"};
                commandParameters["trim.seqs"] = addParameters(trimseqsArray, sizeof(trimseqsArray)/sizeof(string));
 
                string vennArray[] =  {"groups","line","label","calc"};