X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.h;fp=aligncommand.h;h=cfded3819156764fc86e49e9cb1977af9bb2ef48;hb=1a5c2356c1b955c6ec024b2baf9f46377ee7c72e;hp=5432d00564b2151fabaf09e9d16258dff0d298ae;hpb=79a7d3273749b08d4f9f8dfe350c964ff0c4351e;p=mothur.git

diff --git a/aligncommand.h b/aligncommand.h
index 5432d00..cfded38 100644
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -34,8 +34,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "align.seqs";			}
 	string getCommandCategory()		{ return "Sequence Processing"; }
-	string getOutputFileNameTag(string, string);
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	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"; }