X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=consensusseqscommand.h;h=e0c97150bfb0bc3e5baafcea911c4ba1c6c60dcb;hb=e10c72304ee071c0c40e0218a06d89dc4731cbc2;hp=423c4e48796a2a9294dc8373fd29823b3418abb0;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;p=mothur.git

diff --git a/consensusseqscommand.h b/consensusseqscommand.h
index 423c4e4..e0c9715 100644
--- a/consensusseqscommand.h
+++ b/consensusseqscommand.h
@@ -13,6 +13,7 @@
 
 #include "command.hpp"
 #include "listvector.hpp"
+#include "counttable.h"
 
 class ConsensusSeqsCommand : public Command {
 public:
@@ -23,6 +24,7 @@ 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"; }
@@ -33,19 +35,20 @@ public:
 	
 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);
 };