X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=binsequencecommand.h;h=6ea7305265a6725a6a6290f6de028b307c5e8a0b;hb=cd4c86f68cb53017f0f98a82dd2c2e56a64c67bd;hp=e2ff648283a9c00569a8d2a4170a040b4a494902;hpb=81a77fdce5e9b060c71b162305ddd9fa4308f78a;p=mothur.git

diff --git a/binsequencecommand.h b/binsequencecommand.h
index e2ff648..6ea7305 100644
--- a/binsequencecommand.h
+++ b/binsequencecommand.h
@@ -24,9 +24,10 @@ class GlobalData;
 class BinSeqCommand : public Command {
 	
 public:
-	BinSeqCommand();	
+	BinSeqCommand(string);	
 	~BinSeqCommand();
-	int execute();	
+	int execute();
+	void help();	
 	
 private:
 	GlobalData* globaldata;
@@ -35,11 +36,15 @@ private:
 	InputData* input;
 	FastaMap* fasta;
 	GroupMap* groupMap;
-	string filename, fastafile, namesfile, groupfile;
+	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;
 	
 	void readNamesFile();
+	int process(ListVector*);
 };
 
 #endif