added help for alignment code and thomas' calcs to project

[mothur.git] / validparameter.cpp

diff --git a/validparameter.cpp b/validparameter.cpp
index 1a1555df410d25f18b11176ffe2fb5aa0f1af6d6..3e4d16bb77fe04911bc9c50553a431aae99b4849 100644 (file)
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -291,7 +291,7 @@ void ValidParameters::initCommandParameters() {
                string distanceArray[] =  {"fasta","phylip","clustal","nexus", "calc", "ends", "cutoff", "processors"};
                commandParameters["dist.seqs"] = addParameters(distanceArray, sizeof(distanceArray)/sizeof(string));
                
-               string AlignArray[] =  {"fasta","phylip","clustal","nexus", "template", "ksize", "align", "match", "mismatch", "gapopen", "gapextend"};
+               string AlignArray[] =  {"fasta","phylip","clustal","nexus", "template", "search", "ksize", "align", "match", "mismatch", "gapopen", "gapextend"};
                commandParameters["align.seqs"] = addParameters(AlignArray, sizeof(AlignArray)/sizeof(string));
                
                string quitArray[] = {};