X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=binsequencecommand.h;h=df7ea7593dd266c71a3a1b7a49c03c70596a368f;hb=257eaa172451ede9d63a0715f6cdb7336a52996b;hp=617f5ec7ac98f17f358c383ca424ebd817cb3227;hpb=154e089bcd37c2c2f773e53ffb88a20170b27037;p=mothur.git

diff --git a/binsequencecommand.h b/binsequencecommand.h
index 617f5ec..df7ea75 100644
--- a/binsequencecommand.h
+++ b/binsequencecommand.h
@@ -16,6 +16,7 @@
 #include "listvector.hpp"
 #include "readotu.h"
 #include "fastamap.h"
+#include "groupmap.h"
 
 
 class GlobalData;
@@ -23,9 +24,15 @@ class GlobalData;
 class BinSeqCommand : public Command {
 	
 public:
-	BinSeqCommand();	
+	BinSeqCommand(string);	
+	BinSeqCommand();
 	~BinSeqCommand();
-	int execute();	
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
+	int execute();
+	void help();	
 	
 private:
 	GlobalData* globaldata;
@@ -33,11 +40,17 @@ private:
 	ReadOTUFile* 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, namesfile, groupfile, label, outputDir;
 	ofstream out;
 	ifstream in, inNames;
+	vector<string> outputNames;
+	map<string, vector<string> > outputTypes;
 	
 	void readNamesFile();
+	int process(ListVector*);
 };
 
 #endif