added filter.shared command. fixed lci and uci for thetayc calc

[mothur.git] / aligncommand.h

diff --git a/aligncommand.h b/aligncommand.h
index 7eeaa1eb7e7bc3e2dc28d144d646b2190eb34983..cfded3819156764fc86e49e9cb1977af9bb2ef48 100644 (file)
--- 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