removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / classifyseqscommand.h

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index 16549135aacbe25e36d89f21c503f1baae2fe659..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
@@ -31,12 +30,16 @@ public:
        ClassifySeqsCommand(string);
        ClassifySeqsCommand();
        ~ClassifySeqsCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
+       
+       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 {
@@ -53,7 +56,6 @@ private:
        vector<string> outputNames;
        map<string, vector<string> > nameMap;
        map<string,  vector<string> >::iterator itNames;
-       map<string, vector<string> > outputTypes;
        
        Classify* classify;