X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=binsequencecommand.h;fp=binsequencecommand.h;h=aceba65da17315de31515750a62fc53f4b7b9a48;hb=0470f6d037aacb3563c3f7010708120a4a67d4e6;hp=bc2f883fe5f3e232d935780f7660e5a53647b18b;hpb=bede5752eaeedb5a7e339439b6ba2f6670bca2b9;p=mothur.git

diff --git a/binsequencecommand.h b/binsequencecommand.h
index bc2f883..aceba65 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;
@@ -35,7 +36,13 @@ private:
 	InputData* input;
 	FastaMap* fasta;
 	GroupMap* groupMap;
-	string filename, fastafile, namesfile, groupfile;
+	OptionParser* parser;
+	map<string, string> parameters;
+	map<string, string>::iterator it;
+	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;
 	ofstream out;
 	ifstream in, inNames;