added help for heatmap.sim

[mothur.git] / validparameter.cpp

diff --git a/validparameter.cpp b/validparameter.cpp
index 05cdb1a1ff6829863770a05b31a2bd6e72cabc65..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));
@@ -285,6 +288,9 @@ void ValidParameters::initCommandParameters() {
                string reverseseqsArray[] =  {"fasta"};
                commandParameters["reverse.seqs"] = addParameters(reverseseqsArray, sizeof(reverseseqsArray)/sizeof(string));
 
+               string trimseqsArray[] =  {"fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength"};
+               commandParameters["trim.seqs"] = addParameters(trimseqsArray, sizeof(trimseqsArray)/sizeof(string));
+
                string vennArray[] =  {"groups","line","label","calc"};
                commandParameters["venn"] = addParameters(vennArray, sizeof(vennArray)/sizeof(string));
                
@@ -306,7 +312,7 @@ void ValidParameters::initCommandParameters() {
                string concensusArray[] =  {};
                commandParameters["concensus"] = addParameters(concensusArray, sizeof(concensusArray)/sizeof(string));
                
-               string distanceArray[] =  {"fasta", "calc", "countends", "cutoff", "processors"};
+               string distanceArray[] =  {"fasta", "phylip", "calc", "countends", "cutoff", "processors"};
                commandParameters["dist.seqs"] = addParameters(distanceArray, sizeof(distanceArray)/sizeof(string));
                
                string AlignArray[] =  {"fasta", "candidate", "search", "ksize", "align", "match", "mismatch", "gapopen", "gapextend"};