hisat-3n/simple_func.h

/*
 * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
 *
 * This file is part of Bowtie 2.
 *
 * Bowtie 2 is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * Bowtie 2 is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with Bowtie 2.  If not, see <http://www.gnu.org/licenses/>.
 */

#ifndef SIMPLE_FUNC_H_
#define SIMPLE_FUNC_H_

#include <math.h>
#include <cassert>
#include <limits>
#include "tokenize.h"

#define SIMPLE_FUNC_CONST  1
#define SIMPLE_FUNC_LINEAR 2
#define SIMPLE_FUNC_SQRT   3
#define SIMPLE_FUNC_LOG    4

/**
 * A simple function of one argument, parmeterized by I, X, C and L: min
 * value, max value, constant term, and coefficient respectively:
 *
 * 1. Constant:    f(x) = max(I, min(X, C + L * 0))
 * 2. Linear:      f(x) = max(I, min(X, C + L * x))
 * 3. Square root: f(x) = max(I, min(X, C + L * sqrt(x)))
 * 4. Log:         f(x) = max(I, min(X, C + L * ln(x)))
 *
 * Clearly, the return value of the Constant function doesn't depend on x.
 */
class SimpleFunc {

public:

	SimpleFunc() : type_(0), I_(0.0), X_(0.0), C_(0.0), L_(0.0) { }

	SimpleFunc(int type, double I, double X, double C, double L) {
		init(type, I, X, C, L);
	}
	
	void init(int type, double I, double X, double C, double L) {
		type_ = type; I_ = I; X_ = X; C_ = C; L_ = L;
	}

	void init(int type, double C, double L) {
		type_ = type; C_ = C; L_ = L;
		I_ = -std::numeric_limits<double>::max();
		X_ = std::numeric_limits<double>::max();
	}
	
	void setType (int type ) { type_ = type; }
	void setMin  (double mn) { I_ = mn; }
	void setMax  (double mx) { X_ = mx; }
	void setConst(double co) { C_ = co; }
	void setCoeff(double ce) { L_ = ce; }

	int    getType () const { return type_; }
	double getMin  () const { return I_; }
	double getMax  () const { return X_; }
	double getConst() const { return C_; }
	double getCoeff() const { return L_; }
	
	void mult(double x) {
		if(I_ < std::numeric_limits<double>::max()) {
			I_ *= x; X_ *= x; C_ *= x; L_ *= x;
		}
	}
	
	bool initialized() const { return type_ != 0; }
	void reset() { type_ = 0; }
	
	template<typename T>
	T f(double x) const {
		assert(type_ >= SIMPLE_FUNC_CONST && type_ <= SIMPLE_FUNC_LOG);
		double X;
		if(type_ == SIMPLE_FUNC_CONST) {
			X = 0.0;
		} else if(type_ == SIMPLE_FUNC_LINEAR) {
			X = x;
		} else if(type_ == SIMPLE_FUNC_SQRT) {
			X = sqrt(x);
		} else if(type_ == SIMPLE_FUNC_LOG) {
			X = log(x);
		} else {
			throw 1;
		}
		double ret = std::max(I_, std::min(X_, C_ + L_ * X));
		if(ret == std::numeric_limits<double>::max()) {
			return std::numeric_limits<T>::max();
		} else if(ret == std::numeric_limits<double>::min()) {
			return std::numeric_limits<T>::min();
		} else {
			return (T)ret;
		}
	}
	
	static int parseType(const std::string& otype);
	
	static SimpleFunc parse(
		const std::string& s,
		double defaultConst = 0.0,
		double defaultLinear = 0.0,
		double defaultMin = 0.0,
		double defaultMax = std::numeric_limits<double>::max());

protected:

	int type_;
	double I_, X_, C_, L_;
};

#endif /*ndef SIMPLE_FUNC_H_*/