X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=consensusseqscommand.h;h=a69ddbf9197f6ca0264d467ff4c7428c79f56f02;hb=372fb21ea66ced432b109225851a1b80ef0491a3;hp=555b62c63f263526917a388a6e03b62359cc1db3;hpb=3fd6dd6e4f19a458ac2966ee5458787e998a1bde;p=mothur.git

diff --git a/consensusseqscommand.h b/consensusseqscommand.h
index 555b62c..a69ddbf 100644
--- a/consensusseqscommand.h
+++ b/consensusseqscommand.h
@@ -1,6 +1,6 @@
 #ifndef CONSENSUSSEQSCOMMAND_H
 #define CONSENSUSSEQSCOMMAND_H
-
+//test
 /*
  *  consensusseqscommand.h
  *  Mothur
@@ -13,35 +13,44 @@
 
 #include "command.hpp"
 #include "listvector.hpp"
+#include "counttable.h"
 
 class ConsensusSeqsCommand : public Command {
 public:
 	ConsensusSeqsCommand(string);
 	ConsensusSeqsCommand();
-	~ConsensusSeqsCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();
+	~ConsensusSeqsCommand(){}
+	
+	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, vector<string> > outputTypes;
 	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