changed random forest output filename

[mothur.git] / consensusseqscommand.h

diff --git a/consensusseqscommand.h b/consensusseqscommand.h
index 555b62c63f263526917a388a6e03b62359cc1db3..a69ddbf9197f6ca0264d467ff4c7428c79f56f02 100644 (file)
--- a/consensusseqscommand.h
+++ b/consensusseqscommand.h
@@ -1,6 +1,6 @@
 #ifndef CONSENSUSSEQSCOMMAND_H
 #define CONSENSUSSEQSCOMMAND_H
-
+//test
 /*
  *  consensusseqscommand.h
  *  Mothur
@@ -13,35 +13,44 @@
 
 #include "command.hpp"
 #include "listvector.hpp"
+#include "counttable.h"
 
 class ConsensusSeqsCommand : public Command {
 public:
        ConsensusSeqsCommand(string);
        ConsensusSeqsCommand();
-       ~ConsensusSeqsCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~ConsensusSeqsCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "consensus.seqs";              }
+       string getCommandCategory()             { return "Sequence Processing"; }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "http://www.mothur.org/wiki/Consensus.seqs"; }
+       string getDescription()         { return "create a consensus sequence for each OTU or for a fasta file"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
        
+    CountTable ct;
        bool abort, allLines;
-       string fastafile, listfile, namefile, label, outputDir;
+       string fastafile, listfile, namefile, countfile, label, outputDir;
        set<string> labels;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
        map<string, string> fastaMap;
        map<string, string> nameMap;
-       map<string, string> nameFileMap;
+       map<string, int> nameFileMap;
+       int cutoff, seqLength;
        
        int readFasta();
        int readNames();
        int processList(ListVector*&);
-       string getConsSeq(string, ofstream&, string&, int);
-       char getBase(vector<int>);
+       string getConsSeq(string, ofstream&, int);
+       char getBase(vector<int>, int);
 };
 
 #endif