X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=binsequencecommand.h;h=5bdd401f9411e4abb21aa6a12284bfa98f4b5bda;hb=e10c72304ee071c0c40e0218a06d89dc4731cbc2;hp=25f52160e6c314e300e0abd6f303c378881cf2af;hpb=c5c7502f435e1413c19e373dab1dfebcaa67588d;p=mothur.git

diff --git a/binsequencecommand.h b/binsequencecommand.h
index 25f5216..5bdd401 100644
--- a/binsequencecommand.h
+++ b/binsequencecommand.h
@@ -14,30 +14,43 @@
 #include "command.hpp"
 #include "inputdata.h"
 #include "listvector.hpp"
-#include "readmatrix.hpp"
 #include "fastamap.h"
-
-
-class GlobalData;
+#include "groupmap.h"
+#include "counttable.h"
 
 class BinSeqCommand : public Command {
 	
 public:
-	BinSeqCommand();	
+	BinSeqCommand(string);	
+	BinSeqCommand();
 	~BinSeqCommand();
-	int execute();	
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "bin.seqs";			}
+	string getCommandCategory()		{ return "Sequence Processing"; }
+	string getOutputFileNameTag(string, string);
+	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Bin.seqs"; }
+	string getDescription()		{ return "maps sequences to otus"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }		
 	
 private:
-	GlobalData* globaldata;
+	CountTable ct;
 	ListVector* list;
-	ReadMatrix* read;
 	InputData* input;
 	FastaMap* fasta;
-	string filename, fastafile, namesfile;
+	GroupMap* groupMap;
+	bool abort, allLines;
+	set<string> labels; //holds labels to be used
+	string filename, fastafile, listfile, namesfile, groupfile, countfile, label, outputDir;
 	ofstream out;
 	ifstream in, inNames;
+	vector<string> outputNames;
 	
 	void readNamesFile();
+	int process(ListVector*);
 };
 
 #endif