X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validparameter.cpp;h=d6fde63045c51d56449b14701dde04974503fb82;hb=f15f7092c97277337d4fdd9ef674015c15a13220;hp=bd1698468116f39ec112e075e8001c47a7ef3199;hpb=64eee3a595ae53817f52807d7393b22e74e31f56;p=mothur.git

diff --git a/validparameter.cpp b/validparameter.cpp
index bd16984..d6fde63 100644
--- 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", "forward", "reverse", "barcode"};
+		string trimseqsArray[] =  {"fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength"};
 		commandParameters["trim.seqs"] = addParameters(trimseqsArray, sizeof(trimseqsArray)/sizeof(string));
 
 		string vennArray[] =  {"groups","line","label","calc"};
@@ -309,7 +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"};