// SeqWeight.h
// Kevin Karplus
// 23 Oct 1995

// Sequence weighting techniques applied to blocks (no insertions)
// 
// Note: linking SeqWeight.o into an executable makes the table of
//	SequenceWeightObject available, preloaded with three methods
//		FlatWeight
//		HenikoffWeight
//		EntropyWeight
//	See the .cc file for details

#ifndef SeqWeight_H
#define SeqWeight_H

class alignment;	// forward reference, use readBlocks.h to get full spec
#include "Utilities/log2.h"
#include "Regularizer/Regularizer.h"
#include "NamedClass/NameToPtr.h"	// for look up table for named sequence weight methods

    typedef void (*SequenceWeightFcn)(alignment&b, float bits_to_save, 
	ostream *weight_file,
	Regularizer* r, float extra_param, float clip_total_to);
	// function for setting the weights of sequences in a block
	// specifies number of bits to save
	// takes an arbitrary "float" parameter, and an optional
	//	target regularizer (if weighting depends on regularizer)
	// The optional weight_file gets the weights in a format suitable
	// for SAM's sequeince weight input.

class SequenceWeightObject: public NamedObject
{
    SequenceWeightFcn Function;
    
    static NameToPtr* WeighterTable;
    
    private:
    	inline void AddName(OptionIfOld opt=ErrorIfOld)
	{   if (!WeighterTable) 
	    {	WeighterTable=new NameToPtr(79);
		WeighterTable->ignore_case();
	    }
	    WeighterTable->AddName(this, opt);
	}

    public:
	SequenceWeightObject(const char *nm, SequenceWeightFcn fun,
		const char* hlp) : NamedObject(nm,hlp)
	{   Function=fun;
	    AddName();
	}
    
	inline static const SequenceWeightObject* find_name(const char* name)
	{   return dynamic_cast<SequenceWeightObject*>
		(WeighterTable->FindOldName(name, ZeroIfNew));
	}
	
	inline static NameToPtr* weighter_table(void) 
	{   return WeighterTable;
	}
	
	inline SequenceWeightFcn fcn(void) const {return Function;}
	
	void execute(alignment&b, int interface_num=0, ostream* weight_file=0) const;
	// picks up paramters from Globals
};

// For both HenikoffWeight and EntropyWeight, only normal characters 
//	(not wildcards or gaps) are used.
// There are ways to handle wildcards in both schemes, but it wasn't
// thought to be worth the effort for the relatively few wildcards
// found in the databases.

// CHANGE LOG:
// 9 April 2004 Kevin Karplus
//	Changed include for move of log2.h to Utilities/
// 24 May 2004 Kevin Karplus
//	inlined simple functions


#endif