fixed bug with trim.seqs allfiles=t

[mothur.git] / aligncommand.h

diff --git a/aligncommand.h b/aligncommand.h
index 169b43512375aef99a22029b35425d87d6360afb..c0147512df11740241e9d4bd611a34b37a2d00b8 100644 (file)
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -22,12 +22,15 @@ public:
        AlignCommand(string);   
        AlignCommand();
        ~AlignCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "align.seqs";                  }
+       string getCommandCategory()             { return "Sequence Processing"; }
+       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"; }
+       
        int execute(); 
-       void help();    
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
        struct linePair {
@@ -38,7 +41,6 @@ private:
        vector<int> processIDS;   //processid
        vector<linePair*> lines;
        bool MPIWroteAccnos;
-       map<string, vector<string> > outputTypes;
        
        AlignmentDB* templateDB;
        Alignment* alignment;