X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=binsequencecommand.h;h=c93041f348505d7482e9a18d2658d29919eae309;hb=a0f1fca79d2ddfa7ad36b4485039c68b5704fe8d;hp=fe83f20f59b0e6f4db7d765f9b1aa5dc17618252;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/binsequencecommand.h b/binsequencecommand.h
index fe83f20..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 {
 	
@@ -27,20 +28,24 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "bin.seqs";			}
 	string getCommandCategory()		{ return "Sequence Processing"; }
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
+	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:
-	
+	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;