added count file to cluster.classic and cluster.split. modified splitting classes...

[mothur.git] / consensusseqscommand.h

diff --git a/consensusseqscommand.h b/consensusseqscommand.h
index 07a4c0816020ee0c9678f81dbdafe108c0f0f92d..1459b43d25bd54b525459721b5de55a5a1d6d9f6 100644 (file)
--- a/consensusseqscommand.h
+++ b/consensusseqscommand.h
@@ -1,6 +1,6 @@
 #ifndef CONSENSUSSEQSCOMMAND_H
 #define CONSENSUSSEQSCOMMAND_H
-
+//test
 /*
  *  consensusseqscommand.h
  *  Mothur
@@ -23,7 +23,11 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "consensus.seqs";              }
        string getCommandCategory()             { return "Sequence Processing"; }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
+       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()); }  
@@ -37,12 +41,13 @@ private:
        map<string, string> fastaMap;
        map<string, string> nameMap;
        map<string, string> nameFileMap;
+       int cutoff;
        
        int readFasta();
        int readNames();
        int processList(ListVector*&);
        string getConsSeq(string, ofstream&, string&, int);
-       char getBase(vector<int>);
+       char getBase(vector<int>, int);
 };
 
 #endif