1.21.0

[mothur.git] / aligncommand.h

diff --git a/aligncommand.h b/aligncommand.h
index 1e1ebdc71188644f62dda2f1c2dbcb0d5226b29a..75b9c2ba8ffa727b84dadbc4ebdd25479e11674c 100644 (file)
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -27,7 +27,8 @@ public:
        string getCommandName()                 { return "align.seqs";                  }
        string getCommandCategory()             { return "Sequence Processing"; }
        string getHelpString(); 
-       string getCitation() { return "http://www.mothur.org/wiki/Align.seqs"; }
+       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"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
@@ -60,7 +61,7 @@ private:
        vector<string> candidateFileNames;
        vector<string> outputNames;
        
-       bool abort, flip, calledHelp;
+       bool abort, flip, calledHelp, save;
 
 };