X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=binsequencecommand.h;h=df7ea7593dd266c71a3a1b7a49c03c70596a368f;hb=e6c4a7223199d800d496356604eb34dfe273673d;hp=8ea88cbfcff767eec8461df493cea50217675404;hpb=71b2121662daae3f9044252887d1c16eeddd85bb;p=mothur.git

diff --git a/binsequencecommand.h b/binsequencecommand.h
index 8ea88cb..df7ea75 100644
--- a/binsequencecommand.h
+++ b/binsequencecommand.h
@@ -25,7 +25,12 @@ class BinSeqCommand : public Command {
 	
 public:
 	BinSeqCommand(string);	
+	BinSeqCommand();
 	~BinSeqCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();
 	void help();	
 	
@@ -37,11 +42,12 @@ private:
 	FastaMap* fasta;
 	GroupMap* groupMap;
 	bool abort, allLines;
-	set<int> lines; //hold lines to be used
 	set<string> labels; //holds labels to be used
-	string filename, fastafile, namesfile, groupfile, line, label;
+	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*);