sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / consensusseqscommand.h

diff --git a/consensusseqscommand.h b/consensusseqscommand.h
index fd2f4f535dfa3ca7b4be2c99b2e323a2d4d0b49c..a69ddbf9197f6ca0264d467ff4c7428c79f56f02 100644 (file)
--- a/consensusseqscommand.h
+++ b/consensusseqscommand.h
@@ -1,6 +1,6 @@
 #ifndef CONSENSUSSEQSCOMMAND_H
 #define CONSENSUSSEQSCOMMAND_H
-
+//test
 /*
  *  consensusseqscommand.h
  *  Mothur
@@ -13,6 +13,7 @@
 
 #include "command.hpp"
 #include "listvector.hpp"
+#include "counttable.h"
 
 class ConsensusSeqsCommand : public Command {
 public:
@@ -23,27 +24,32 @@ public:
        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, string> fastaMap;
        map<string, string> nameMap;
-       map<string, string> nameFileMap;
-       int cutoff;
+       map<string, int> nameFileMap;
+       int cutoff, seqLength;
        
        int readFasta();
        int readNames();
        int processList(ListVector*&);
-       string getConsSeq(string, ofstream&, string&, int);
+       string getConsSeq(string, ofstream&, int);
        char getBase(vector<int>, int);
 };