X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=binsequencecommand.h;h=c93041f348505d7482e9a18d2658d29919eae309;hp=aceba65da17315de31515750a62fc53f4b7b9a48;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6

diff --git a/binsequencecommand.h b/binsequencecommand.h
index aceba65..c93041f 100644
--- a/binsequencecommand.h
+++ b/binsequencecommand.h
@@ -14,40 +14,44 @@
 #include "command.hpp"
 #include "inputdata.h"
 #include "listvector.hpp"
-#include "readotu.h"
 #include "fastamap.h"
 #include "groupmap.h"
-
-
-class GlobalData;
+#include "counttable.h"
 
 class BinSeqCommand : public Command {
 	
 public:
 	BinSeqCommand(string);	
+	BinSeqCommand();
 	~BinSeqCommand();
-	int execute();
-	void help();	
+	
+	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:
-	GlobalData* globaldata;
+	CountTable ct;
 	ListVector* list;
-	ReadOTUFile* read;
 	InputData* input;
 	FastaMap* fasta;
 	GroupMap* groupMap;
-	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;
+	string filename, fastafile, listfile, namesfile, groupfile, countfile, label, outputDir;
 	ofstream out;
 	ifstream in, inNames;
+	vector<string> outputNames;
 	
 	void readNamesFile();
-	int process(ListVector*, int);
+	int process(ListVector*);
 };
 
 #endif