output.h

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//output.h
 //Copyright (c) 2007-2012 Paul C Lott 
 //University of California, Davis
 //Genome and Biomedical Sciences Facility
 //UC Davis Genome Center
 //Ian Korf Lab
 //Website: www.korflab.ucdavis.edu
 //Email: lottpaul@gmail.com
 //
 //Permission is hereby granted, free of charge, to any person obtaining a copy of
 //this software and associated documentation files (the "Software"), to deal in
 //the Software without restriction, including without limitation the rights to
 //use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
 //the Software, and to permit persons to whom the Software is furnished to do so,
 //subject to the following conditions:
 //
 //The above copyright notice and this permission notice shall be included in all
 //copies or substantial portions of the Software.
 //
 //THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 //IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
 //FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
 //COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
 //IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
 //CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

#ifndef OUTPUT_H_
#define OUTPUT_H_
namespace StochHMM{


//Deprecate functions in this code.  Leave it up to user to format the output how they want 
//
//#include <vector>
//#include <iostream>
//#include <stdio.h>
//#include "table.h"
//#include "trellis.h"
//#include "hmm.h"
//#include "options.h"
//#include "decoding.h"
//#include "traceback_path.h"
//#define WIDTH 80
//using namespace std;
//
//extern const char usage[];
//
////----------------------------------------------------------------------------//
//// Description: Defines a couple output formats.                                                          
////
//// Label only outputs state label from the traceback path
//// Path only outputs the state traceback path
//// Heat only outputs a hit table for states
//// GFF outputs the gff entries (for only those states that have GFF_DESC defined
////----------------------------------------------------------------------------//
//
//void map_label(trellis&, const HMM&,options&);
//void map_path (trellis&, const HMM&,options&); 
//void map_heat (trellis&, const HMM&,options&);
//void map_gff (trellis&, const HMM&, options&);
//
//void convert_label( map<char,string> , vector<char> ,options, int, int , double);
//

}
#endif