fixed multiple bugs for 1.4 release

[mothur.git] / validparameter.cpp

diff --git a/validparameter.cpp b/validparameter.cpp
index 6719e2c4eb706db4a99b6620eb861e3f41268971..4aad1c22c037515fcb5d6f166aae8af4842d8fd4 100644 (file)
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -267,7 +267,7 @@ void ValidParameters::initCommandParameters() {
                string heatmapArray[] =  {"groups","line","label","sorted","scale"};
                commandParameters["heatmap"] = addParameters(heatmapArray, sizeof(heatmapArray)/sizeof(string));
                
-               string filterseqsArray[] =  {"fasta","phylip","clustal","nexus", "trump", "soft", "filter"};
+               string filterseqsArray[] =  {"fasta","phylip","clustal","nexus", "trump", "soft", "hard", "vertical"};
                commandParameters["filter.seqs"] = addParameters(filterseqsArray, sizeof(filterseqsArray)/sizeof(string));
 
                string vennArray[] =  {"groups","line","label","calc"};
@@ -282,7 +282,7 @@ void ValidParameters::initCommandParameters() {
                string getOTURepArray[] =  {"fasta","list","line","label","name", "group"};
                commandParameters["get.oturep"] = addParameters(getOTURepArray, sizeof(getOTURepArray)/sizeof(string));
                
-               string treeGroupsArray[] =  {"line","label","calc","groups"};
+               string treeGroupsArray[] =  {"line","label","calc","groups", "phylip", "column", "name"};
                commandParameters["tree.shared"] = addParameters(treeGroupsArray, sizeof(treeGroupsArray)/sizeof(string));
                
                string bootstrapArray[] =  {"line","label","calc","groups","iters"};
@@ -291,10 +291,10 @@ void ValidParameters::initCommandParameters() {
                string concensusArray[] =  {};
                commandParameters["concensus"] = addParameters(concensusArray, sizeof(concensusArray)/sizeof(string));
                
-               string distanceArray[] =  {"fasta","phylip","clustal","nexus", "calc", "ends", "cutoff", "processors"};
+               string distanceArray[] =  {"fasta","phylip","clustal","nexus", "calc", "countends", "cutoff", "processors"};
                commandParameters["dist.seqs"] = addParameters(distanceArray, sizeof(distanceArray)/sizeof(string));
                
-               string AlignArray[] =  {"fasta","phylip","clustal","nexus", "template", "search", "ksize", "align", "match", "mismatch", "gapopen", "gapextend"};
+               string AlignArray[] =  {"fasta", "candidate", "search", "ksize", "align", "match", "mismatch", "gapopen", "gapextend"};
                commandParameters["align.seqs"] = addParameters(AlignArray, sizeof(AlignArray)/sizeof(string));
                
                string quitArray[] = {};