X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=binsequencecommand.h;h=c93041f348505d7482e9a18d2658d29919eae309;hp=1fb5664b0c018c4120881055014ec08a4e6d5559;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=f687723a8357916e86a05116978e6869b039ce36

diff --git a/binsequencecommand.h b/binsequencecommand.h
index 1fb5664..c93041f 100644
--- a/binsequencecommand.h
+++ b/binsequencecommand.h
@@ -16,6 +16,7 @@
 #include "listvector.hpp"
 #include "fastamap.h"
 #include "groupmap.h"
+#include "counttable.h"
 
 class BinSeqCommand : public Command {
 	
@@ -27,8 +28,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "bin.seqs";			}
 	string getCommandCategory()		{ return "Sequence Processing"; }
-	string getOutputFileNameTag(string, string);
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Bin.seqs"; }
 	string getDescription()		{ return "maps sequences to otus"; }
 	
@@ -36,14 +38,14 @@ public:
 	void help() { m->mothurOut(getHelpString()); }		
 	
 private:
-	
+	CountTable ct;
 	ListVector* list;
 	InputData* input;
 	FastaMap* fasta;
 	GroupMap* groupMap;
 	bool abort, allLines;
 	set<string> labels; //holds labels to be used
-	string filename, fastafile, listfile, namesfile, groupfile, label, outputDir;
+	string filename, fastafile, listfile, namesfile, groupfile, countfile, label, outputDir;
 	ofstream out;
 	ifstream in, inNames;
 	vector<string> outputNames;