added count.seqs command and made some modifcations to the uchime code to allow it...

[mothur.git] / classifyseqscommand.h

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index 84f5f9f04d6752728c5f3bf72d5688cafd73b723..f075b41495afc9002e2a695d47972d4d947eafc9 100644 (file)
--- a/classifyseqscommand.h
+++ b/classifyseqscommand.h
@@ -12,7 +12,6 @@
 
 #include "mothur.h"
 #include "command.hpp"
-//#include "alignment.hpp"
 #include "classify.h"
 
 //KNN and Bayesian methods modeled from algorithms in
@@ -29,9 +28,20 @@ class ClassifySeqsCommand : public Command {
        
 public:
        ClassifySeqsCommand(string);
+       ClassifySeqsCommand();
        ~ClassifySeqsCommand();
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "classify.seqs";               }
+       string getCommandCategory()             { return "Phylotype Analysis";  }
+       string getHelpString(); 
+       string getCitation() { return "Wang Q, Garrity GM, Tiedje JM, Cole JR (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-7. [ for Bayesian classifier ] \nAltschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-402. [ for BLAST ] \nDeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-72. [ for kmer ] \nhttp://www.mothur.org/wiki/Classify.seqs"; }
+
+       
        int execute(); 
-       void help();    
+       void help() { m->mothurOut(getHelpString()); }  
+       
+       
        
 private:
        struct linePair {
@@ -45,6 +55,7 @@ private:
        vector<string> fastaFileNames;
        vector<string> namefileNames;
        vector<string> groupfileNames;
+       vector<string> outputNames;
        map<string, vector<string> > nameMap;
        map<string,  vector<string> >::iterator itNames;