X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.h;fp=aligncommand.h;h=5432d00564b2151fabaf09e9d16258dff0d298ae;hb=49d2b7459c5027557564b21e9487dadafbbbdc96;hp=d4b7e78ce01ba2b9e6507a2b5a502bae9dbb8b68;hpb=ee8403d4eb5760187d62b42a9cf4272de8fc0ec4;p=mothur.git

diff --git a/aligncommand.h b/aligncommand.h
index d4b7e78..5432d00 100644
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -34,6 +34,7 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "align.seqs";			}
 	string getCommandCategory()		{ return "Sequence Processing"; }
+	string getOutputFileNameTag(string, string);
 	string getHelpString();	
 	string getCitation() { return "DeSantis TZ, Jr., Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R, Andersen GL (2006). NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res 34: W394-9.\nSchloss PD (2009). A high-throughput DNA sequence aligner for microbial ecology studies. PLoS ONE 4: e8230.\nSchloss PD (2010). The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 6: e1000844.\nhttp://www.mothur.org/wiki/Align.seqs http://www.mothur.org/wiki/Align.seqs"; }
 	string getDescription()		{ return "align sequences"; }