fixed sub.sample so that it will eliminate samples with abundances that are less...

[mothur.git] / classifyseqscommand.h

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index 84f5f9f04d6752728c5f3bf72d5688cafd73b723..115360f7d5c3015130b0beef8a704f7669a382b5 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 +28,18 @@ class ClassifySeqsCommand : public Command {
        
 public:
        ClassifySeqsCommand(string);
+       ClassifySeqsCommand();
        ~ClassifySeqsCommand();
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "classify.seqs";               }
+       string getCommandCategory()             { return "Phylotype Analysis";  }
+       string getHelpString(); 
+       
        int execute(); 
-       void help();    
+       void help() { m->mothurOut(getHelpString()); }  
+       
+       
        
 private:
        struct linePair {
@@ -45,6 +53,7 @@ private:
        vector<string> fastaFileNames;
        vector<string> namefileNames;
        vector<string> groupfileNames;
+       vector<string> outputNames;
        map<string, vector<string> > nameMap;
        map<string,  vector<string> >::iterator itNames;