line and label no longer persist between commands. Added phylip formated output...

[mothur.git] / validparameter.cpp

diff --git a/validparameter.cpp b/validparameter.cpp
index cd3b05474e18fe4eb49c3173408f5b9f0b2daba7..c8144d0cb32fbcd38138986316f607e9f42346df 100644 (file)
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -223,7 +223,7 @@ void ValidParameters::initCommandParameters() {
                commandParameters["cluster"] = addParameters(clusterArray, sizeof(clusterArray)/sizeof(string));
                
                string deconvoluteArray[] =  {"fasta"};
-               commandParameters["deconvolute"] = addParameters(deconvoluteArray, sizeof(deconvoluteArray)/sizeof(string));
+               commandParameters["unique.seqs"] = addParameters(deconvoluteArray, sizeof(deconvoluteArray)/sizeof(string));
                
                string collectsingleArray[] =  {"freq","line","label","calc","abund","size"};
                commandParameters["collect.single"] = addParameters(collectsingleArray, sizeof(collectsingleArray)/sizeof(string));
@@ -273,10 +273,10 @@ 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", "hard", "vertical"};
+               string filterseqsArray[] =  {"fasta", "trump", "soft", "hard", "vertical"};
                commandParameters["filter.seqs"] = addParameters(filterseqsArray, sizeof(filterseqsArray)/sizeof(string));
 
-               string summaryseqsArray[] =  {"fasta","phylip","clustal","nexus"};
+               string summaryseqsArray[] =  {"fasta"};
                commandParameters["summary.seqs"] = addParameters(summaryseqsArray, sizeof(summaryseqsArray)/sizeof(string));
 
                string screenseqsArray[] =  {"fasta", "start", "end", "maxambig", "maxhomop", "minlength", "maxlength", "name", "group"};
@@ -303,7 +303,7 @@ void ValidParameters::initCommandParameters() {
                string concensusArray[] =  {};
                commandParameters["concensus"] = addParameters(concensusArray, sizeof(concensusArray)/sizeof(string));
                
-               string distanceArray[] =  {"fasta","phylip","clustal","nexus", "calc", "countends", "cutoff", "processors"};
+               string distanceArray[] =  {"fasta", "calc", "countends", "cutoff", "processors"};
                commandParameters["dist.seqs"] = addParameters(distanceArray, sizeof(distanceArray)/sizeof(string));
                
                string AlignArray[] =  {"fasta", "candidate", "search", "ksize", "align", "match", "mismatch", "gapopen", "gapextend"};