added distance command and filterseqs

[mothur.git] / validparameter.cpp

diff --git a/validparameter.cpp b/validparameter.cpp
index 3e6a9799353a78e4e87a7cd72ebc4d78a7199aa5..e97df8b0fc8e0efc9f02f6c61987f59ea1c75b89 100644 (file)
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -220,9 +220,6 @@ void ValidParameters::initCommandParameters() {
                string readtreeArray[] = {"tree","group"};
                commandParameters["read.tree"] = addParameters(readtreeArray, sizeof(readtreeArray)/sizeof(string));
                
-               string readseqsArray[] = {"fasta","phylip","clustal","nexus","line"};
-               commandParameters["read.seqs"] = addParameters(readseqsArray, sizeof(readseqsArray)/sizeof(string));
-               
                string clusterArray[] =  {"cutoff","precision","method"};
                commandParameters["cluster"] = addParameters(clusterArray, sizeof(clusterArray)/sizeof(string));
                
@@ -271,7 +268,7 @@ void ValidParameters::initCommandParameters() {
                string heatmapArray[] =  {"groups","line","label","sorted","scale"};
                commandParameters["heatmap"] = addParameters(heatmapArray, sizeof(heatmapArray)/sizeof(string));
                
-               string filterseqsArray[] =  {"trump", "soft", "filter"};
+               string filterseqsArray[] =  {"fasta","phylip","clustal","nexus", "trump", "soft", "filter"};
                commandParameters["filter.seqs"] = addParameters(filterseqsArray, sizeof(filterseqsArray)/sizeof(string));
 
                string vennArray[] =  {"groups","line","label","calc"};
@@ -292,7 +289,7 @@ void ValidParameters::initCommandParameters() {
                string concensusArray[] =  {};
                commandParameters["concensus"] = addParameters(concensusArray, sizeof(concensusArray)/sizeof(string));
                
-               string distanceArray[] =  {"calc", "ends", "cutoff", "processors"};
+               string distanceArray[] =  {"fasta","phylip","clustal","nexus", "calc", "ends", "cutoff", "processors"};
                commandParameters["distance"] = addParameters(distanceArray, sizeof(distanceArray)/sizeof(string));
                
                string quitArray[] = {};