X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=binsequencecommand.h;fp=binsequencecommand.h;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=365fb3c3afdaf8cedd788b83e1ef2a29a4e9b00b;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/binsequencecommand.h b/binsequencecommand.h
deleted file mode 100644
index 365fb3c..0000000
--- a/binsequencecommand.h
+++ /dev/null
@@ -1,54 +0,0 @@
-#ifndef BINSEQCOMMAND_H
-#define BINSEQCOMMAND_H
-/*
- *  binsequencecommand.h
- *  Mothur
- *
- *  Created by Sarah Westcott on 4/3/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-/* The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name. */
-
-#include "command.hpp"
-#include "inputdata.h"
-#include "listvector.hpp"
-#include "fastamap.h"
-#include "groupmap.h"
-
-class BinSeqCommand : public Command {
-	
-public:
-	BinSeqCommand(string);	
-	BinSeqCommand();
-	~BinSeqCommand();
-	
-	vector<string> setParameters();
-	string getCommandName()			{ return "bin.seqs";			}
-	string getCommandCategory()		{ return "Sequence Processing"; }
-	string getHelpString();	
-	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:
-	
-	ListVector* list;
-	InputData* input;
-	FastaMap* fasta;
-	GroupMap* groupMap;
-	bool abort, allLines;
-	set<string> labels; //holds labels to be used
-	string filename, fastafile, listfile, namesfile, groupfile, label, outputDir;
-	ofstream out;
-	ifstream in, inNames;
-	vector<string> outputNames;
-	
-	void readNamesFile();
-	int process(ListVector*);
-};
-
-#endif