X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.h;h=cfded3819156764fc86e49e9cb1977af9bb2ef48;hb=deba0af0ccdcb6005ed5b2b82649b137c63fbdf7;hp=7eeaa1eb7e7bc3e2dc28d144d646b2190eb34983;hpb=05c52893c6c2467381fe7e7b769d86b6209af2e1;p=mothur.git

diff --git a/aligncommand.h b/aligncommand.h
index 7eeaa1e..cfded38 100644
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -34,7 +34,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "align.seqs";			}
 	string getCommandCategory()		{ return "Sequence Processing"; }
+	
 	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"; }
 	
@@ -55,7 +57,6 @@ private:
 	
 	int driver(linePair*, string, string, string, string);
 	int createProcesses(string, string, string, string);
-	void appendAlignFiles(string, string); 
 	void appendReportFiles(string, string);
 	
 	#ifdef USE_MPI