X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=consensusseqscommand.h;h=165d420f820d89c3015737e62cbda2226fbb07fc;hb=60928795782d8f8648ec373d6a96b53032a77429;hp=fd2f4f535dfa3ca7b4be2c99b2e323a2d4d0b49c;hpb=4de093e3b92bdab1579565cb2873553412f6671e;p=mothur.git

diff --git a/consensusseqscommand.h b/consensusseqscommand.h
index fd2f4f5..165d420 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:
@@ -23,27 +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;
-	int cutoff;
+	map<string, int> nameFileMap;
+	int seqLength;
+    float cutoff;
 	
 	int readFasta();
 	int readNames();
 	int processList(ListVector*&);
-	string getConsSeq(string, ofstream&, string&, int);
+	string getConsSeq(string, ofstream&, int);
 	char getBase(vector<int>, int);
 };