X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=consensusseqscommand.h;h=a69ddbf9197f6ca0264d467ff4c7428c79f56f02;hp=07a4c0816020ee0c9678f81dbdafe108c0f0f92d;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6

diff --git a/consensusseqscommand.h b/consensusseqscommand.h
index 07a4c08..a69ddbf 100644
--- 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:
@@ -23,26 +24,33 @@ 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;
+	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