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// $Id$
/****************************************************************************
* Copyright (C) 2006-2008 Adrien Saladin *
* adrien.saladin@gmail.com *
* Copyright (C) 2008 Pierre Poulain *
* Copyright (C) 2008 Sebastien Fiorucci *
* Copyright (C) 2008 Chantal Prevost *
* Copyright (C) 2008 Martin Zacharias *
* *
* This program 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. *
* *
* This program 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 this program. If not, see <http://www.gnu.org/licenses/>. *
* *
***************************************************************************/
#ifndef BASETYPES_H
#define BASETYPES_H
#include <vector>
#include <iostream>
#include <sstream>
// #include <iomanip> //setw, setprecision
#include <cassert>
#include <cstdio>
#include <boost/shared_array.hpp>
#include <stdexcept>
//switch to choose between automatic differenciation
//or normal double arithmetic
#include "derivify.h" //must be included in any cases
#ifdef AUTO_DIFF
typedef surreal dbl;
#else
typedef double dbl;
#endif
typedef unsigned int uint;
typedef std::vector<int> Vint;
typedef std::vector<uint> Vuint;
typedef std::vector<dbl> Vdouble;
#ifndef NDEBUG
#define Debug(func) func
#else
#define Debug(func)
#endif
// power (of int) faster much faster than pow()
// expands pow<6>(a) to a*a*a*a*a*a
template<size_t I,size_t N> struct metapow
{
static inline dbl Pow( dbl x )
{
return x*metapow<I+1,N>::Pow(x);
}
};
template<size_t N> struct metapow<N,N>
{
static inline dbl Pow( dbl x ) { return 1; }
};
template<size_t N> dbl pow(dbl x)
{
return metapow<0,N>::Pow(x);
}
/*! \brief 2-dimensional Object Oriented array
*
* this class provides a 2-dimensional OO array. Memory is managed automatically.
* The size of the array cannot be modified after creation.
* It should be compatible with functions that needs raw pointers (with few modifications of the object).
* WARNING: the assignemnt like 'Array2D array2=array1;' or 'Array2D array2(array1)' leads to two objects
* sharing the same memory (this reduce the cost of copying and transmission by value,
* like for Python objects). To make array2 independant of array1 (deep copy), use: array2.detach() after the
* copy.
* It should be reasonably fast for most usages
*/
template <class mytype>
class Array2D
{
public:
Array2D(){m_rows=0; m_columns=0;};
Array2D(int row, int columns)
:m_rows(row),
m_columns(columns)
{
m_size = row*columns;
msa_data = boost::shared_array<mytype>( new mytype[m_size]);
}
/// index operator (fortran-like syntax). a(0,2) gives raw 1, column 3.
mytype& operator() (int r, int c)
{
assert(r<m_rows);
assert(c<m_columns);
return msa_data[r*m_columns+c];
}
/// get or set an element of the array
const mytype& operator() (int r, int c) const
{
assert(r<m_rows);
assert(c<m_columns);
return msa_data[r*m_columns+c];
}
const void * id() {
return (void *) &msa_data[0];
}
/// "deep copy" of the array
void detach()
{
mytype * olddata = msa_data.get();
mytype * newdata = new mytype[m_size];
memcpy( newdata, olddata, m_size*sizeof(mytype) );
msa_data=boost::shared_array<mytype>(newdata);
}
std::string str()
{
std::ostringstream oss;
for (int r=0; r<m_rows; r++)
{
for (int c=0; c<m_columns; c++)
oss << (*this)(r,c) << " " ;
oss << "\n";
}
return oss.str();
}
///get size of the array
std::pair<int,int> getDim()
{
std::pair<int,int> out;
out.first = m_rows;
out.second = m_columns;
return out;
}
void Print()
{
std::cout << str();
}
bool almostEqual(const Array2D<mytype> & tocompare, dbl difference)
{
if (!( this-> m_rows == tocompare.m_rows && this-> m_columns==tocompare.m_columns))
throw std::invalid_argument("Arrays must have the same size to be compared !\n");
for (uint i=0; i<m_size; i++)
if ( fabs(real(msa_data[i] - tocompare.msa_data[i])) > real(difference)) return false;
return true;
}
private:
boost::shared_array<mytype> msa_data;
int m_rows;
int m_columns;
size_t m_size;
} ;
typedef Array2D<dbl> Matrix;
void MakeIdentity(Matrix & mat);
struct Superpose_t
{
dbl rmsd;
Matrix matrix;
};
#endif
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