added alignment code

[mothur.git] / validparameter.cpp

diff --git a/validparameter.cpp b/validparameter.cpp
index 8af4a8154e74fab87e3985222a0e0e8ac93a0bfd..e79a2db2663a48ceee335dba6c1a77973dd09bb6 100644 (file)
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -211,7 +211,6 @@ void ValidParameters::initCommandParameters() {
                //{"parameter1","parameter2",...,"last parameter"};
                
                string readdistArray[] = {"phylip","column", "name","cutoff","precision", "group"};
-
                commandParameters["read.dist"] = addParameters(readdistArray, sizeof(readdistArray)/sizeof(string));
 
                string readotuArray[] =  {"list","order","shared", "line", "label","group","sabund", "rabund"};
@@ -292,6 +291,9 @@ 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"};
+               commandParameters["align.seqs"] = addParameters(AlignArray, sizeof(AlignArray)/sizeof(string));
+               
                string quitArray[] = {};
                commandParameters["quit"] = addParameters(quitArray, sizeof(quitArray)/sizeof(string));