+++ /dev/null
-/*
- McCaskill's Algorithm -- The algorithm calculates a base paring probability matrix from the input of one sequence.
-
- $Id: nrutil.h,v 1.0 2005/10/20 14:22 $;
-
- Copyright (C) 2005 Yasuo Tabei <tabei@cb.k.u-tokyo.ac.jp>
-
- This is free software with ABSOLUTELY NO WARRANTY.
-
- This library is free software; you can redistribute it and/or
- modify it under the terms of the GNU Lesser General Public
- License as published by the Free Software Foundation; either
- version 2.1 of the License, or (at your option) any later version.
-
- This library 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
- Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public
- License along with this library; if not, write to the Free Software
- Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-*/
-
-#ifndef _NR_UTIL_H_
-#define _NR_UTIL_H_
-#include <string>
-#include <cmath>
-#include <complex>
-#include <iostream>
-#include <cstdlib> // by katoh
-
-using namespace std;
-
-typedef double DP;
-
-template<class T>
-inline const T SQR(const T a) {return a*a;}
-
-template<class T>
-inline const T MAX(const T &a, const T &b)
-{return b > a ? (b) : (a);}
-
-inline float MAX(const double &a, const float &b)
-{return b > a ? (b) : float(a);}
-
-inline float MAX(const float &a, const double &b)
-{return b > a ? float(b) : (a);}
-
-template<class T>
-inline const T MIN(const T &a, const T &b)
-{return b < a ? (b) : (a);}
-
-inline float MIN(const double &a, const float &b)
-{return b < a ? (b) : float(a);}
-
-inline float MIN(const float &a, const double &b)
-{return b < a ? float(b) : (a);}
-
-template<class T>
-inline const T SIGN(const T &a, const T &b)
-{return b >= 0 ? (a >= 0 ? a : -a) : (a >= 0 ? -a : a);}
-
-inline float SIGN(const float &a, const double &b)
-{return b >= 0 ? (a >= 0 ? a : -a) : (a >= 0 ? -a : a);}
-
-inline float SIGN(const double &a, const float &b)
-{return b >= 0 ? (a >= 0 ? a : -a) : (a >= 0 ? -a : a);}
-
-template<class T>
-inline void SWAP(T &a, T &b)
-{T dum=a; a=b; b=dum;}
-namespace NR {
- inline void nrerror(const string error_text)
-// Numerical Recipes standard error handler
- {
- cerr << "Numerical Recipes run-time error..." << endl;
- cerr << error_text << endl;
- cerr << "...now exiting to system..." << endl;
- exit(1);
- }
-}
-
-template <class T>
-class NRVec {
- private:
- int nn; // size of array. upper index is nn-1
- T *v;
- public:
- NRVec();
- explicit NRVec(int n); // Zero-based array
- NRVec(const T &a, int n); //initialize to constant value
- NRVec(const T *a, int n); // Initialize to array
- NRVec(const NRVec &rhs); // Copy constructor
- NRVec & operator=(const NRVec &rhs); //assignment
- NRVec & operator=(const T &a); //assign a to every element
- inline T & operator[](const int i); //i¡Çth element
- inline const T & operator[](const int i) const;
- void Allocator(int i);
- inline int size() const;
- ~NRVec();
-};
-
-template <class T>
-NRVec<T>::NRVec() : nn(0), v(0) {}
-
-template <class T>
-NRVec<T>::NRVec(int n) : nn(n), v(new T[n]) {}
-
-template <class T>
-NRVec<T>::NRVec(const T& a, int n) : nn(n), v(new T[n])
-{
- for(int i=0; i<n; i++)
- v[i] = a;
-}
-
-template <class T>
-NRVec<T>::NRVec(const T *a, int n) : nn(n), v(new T[n])
-{
-for(int i=0; i<n; i++)
- v[i] = *a++;
-}
-
-template <class T>
-void NRVec<T>::Allocator(int n = 0)
-{
- v = new T[n];
-}
-
-template <class T>
-NRVec<T>::NRVec(const NRVec<T> &rhs) : nn(rhs.nn), v(new T[nn])
-{
- for(int i=0; i<nn; i++)
- v[i] = rhs[i];
-}
-
-template <class T>
-NRVec<T> & NRVec<T>::operator=(const NRVec<T> &rhs)
-// postcondition: normal assignment via copying has been performed;
-// if vector and rhs were different sizes, vector
-// has been resized to match the size of rhs
-{
- if (this != &rhs)
-{
- if (nn != rhs.nn) {
- if (v != 0) delete [] (v);
- nn=rhs.nn;
- v= new T[nn];
- }
- for (int i=0; i<nn; i++)
- v[i]=rhs[i];
-}
- return *this;
-}
-
-template <class T>
-NRVec<T> & NRVec<T>::operator=(const T &a) //assign a to every element
-{
- for (int i=0; i<nn; i++)
- v[i]=a;
- return *this;
-}
-
-template <class T>
-inline T & NRVec<T>::operator[](const int i) //subscripting
-{
- return v[i];
-}
-
-template <class T>
-inline const T & NRVec<T>::operator[](const int i) const //subscripting
-{
- return v[i];
-}
-
-template <class T>
-inline int NRVec<T>::size() const
-{
- return nn;
-}
-
-template <class T>
-NRVec<T>::~NRVec()
-{
- if (v != 0)
- delete[] (v);
-}
-
-template <class T>
-class NRMat {
- private:
- int nn;
- int mm;
- T **v;
- public:
- NRMat();
- NRMat(int n, int m); // Zero-based array
- NRMat(const T &a, int n, int m); //Initialize to constant
- NRMat(const T *a, int n, int m); // Initialize to array
- NRMat(const NRMat &rhs); // Copy constructor
- void Allocator(int n, int m);
- void Allocator(const T &a, int n, int m);
- void Allocator(const T *a, int n, int m);
- NRMat & operator=(const NRMat &rhs); //assignment
- NRMat & operator=(const T &a); //assign a to every element
- inline T* operator[](const int i); //subscripting: pointer to row i
- inline const T* operator[](const int i) const;
- inline T & ref(const int i, const int j);
- inline const T ref(const int i, const int j) const;
- inline int nrows() const;
- inline int ncols() const;
- ~NRMat();
-};
-
-template <class T>
-NRMat<T>::NRMat() : nn(0), mm(0), v(0) {}
-
-template <class T>
-NRMat<T>::NRMat(int n, int m) : nn(n), mm(m), v(new T*[n])
-{
- v[0] = new T[m*n];
- for (int i=1; i< n; i++)
- v[i] = v[i-1] + m;
-}
-
-template <class T>
-NRMat<T>::NRMat(const T &a, int n, int m) : nn(n), mm(m), v(new T*[n])
-{
- int i,j;
- v[0] = new T[m*n];
- for (i=1; i< n; i++)
- v[i] = v[i-1] + m;
- for (i=0; i< n; i++)
- for (j=0; j<m; j++)
- v[i][j] = a;
-}
-
-template <class T>
-NRMat<T>::NRMat(const T *a, int n, int m) : nn(n), mm(m), v(new T*[n])
-{
- int i,j;
- v[0] = new T[m*n];
- for (i=1; i< n; i++)
- v[i] = v[i-1] + m;
- for (i=0; i< n; i++)
- for (j=0; j<m; j++)
- v[i][j] = *a++;
-}
-
-template <class T>
-void NRMat<T>::Allocator(int n, int m)
-{
- if( v != 0 ) {
- delete[] (v[0]); delete (v);
- }
-
- nn = n; mm = m; v = new T*[n];
-
- v[0] = new T[m*n];
- for (int i=1; i< n; i++)
- v[i] = v[i-1] + m;
-}
-
-template <class T>
-void NRMat<T>::Allocator(const T &a, int n, int m)
-{
- if( v != 0 ) {
- delete[] (v[0]); delete (v);
- }
-
- int i,j;
-
- nn = n; mm = m; v = new T*[n];
-
- v[0] = new T[m*n];
- for (i=1; i< n; i++)
- v[i] = v[i-1] + m;
- for (i=0; i< n; i++)
- for (j=0; j<m; j++)
- v[i][j] = a;
-}
-
-template <class T>
-void NRMat<T>::Allocator(const T *a, int n, int m)
-{
- if( v != 0 ) {
- delete[] (v[0]); delete (v);
- }
-
- int i,j;
-
- nn = n; mm = m; v = new T*[n];
-
- v[0] = new T[m*n];
- for (i=1; i< n; i++)
- v[i] = v[i-1] + m;
- for (i=0; i< n; i++)
- for (j=0; j<m; j++)
- v[i][j] = *a++;
-}
-
-template <class T>
-NRMat<T>::NRMat(const NRMat &rhs) : nn(rhs.nn), mm(rhs.mm), v(new T*[nn])
-{
- int i,j;
- v[0] = new T[mm*nn];
- for (i=1; i< nn; i++)
- v[i] = v[i-1] + mm;
- for (i=0; i< nn; i++)
- for (j=0; j<mm; j++)
- v[i][j] = rhs[i][j];
-}
-template <class T>
-NRMat<T> & NRMat<T>::operator=(const NRMat<T> &rhs)
-// postcondition: normal assignment via copying has been performed;
-// if matrix and rhs were different sizes, matrix
-// has been resized to match the size of rhs
-{
- if (this != &rhs) {
- int i,j;
- if (nn != rhs.nn || mm != rhs.mm) {
- if (v != 0) {
- delete[] (v[0]);
- delete[] (v);
- }
- nn=rhs.nn;
- mm=rhs.mm;
- v = new T*[nn];
- v[0] = new T[mm*nn];
- }
- for (i=1; i< nn; i++)
- v[i] = v[i-1] + mm;
- for (i=0; i< nn; i++)
- for (j=0; j<mm; j++)
- v[i][j] = rhs[i][j];
- }
- return *this;
-}
-
-template <class T>
-NRMat<T> & NRMat<T>::operator=(const T &a) //assign a to every element
-{
- for (int i=0; i< nn; i++)
- for (int j=0; j<mm; j++)
- v[i][j] = a;
- return *this;
-}
-
-template <class T>
-inline T* NRMat<T>::operator[](const int i) //subscripting: pointer to row i
-{
- return v[i];
-}
-
-template <class T>
-inline const T* NRMat<T>::operator[](const int i) const
-{
- return v[i];
-}
-
-template <class T>
-inline T & NRMat<T>::ref(const int i, const int j)
-{
- return v[i][j];
-}
-
-template <class T>
-inline const T NRMat<T>::ref(const int i, const int j) const
-{
- return v[i][j];
-}
-
-template <class T>
-inline int NRMat<T>::nrows() const
-{
- return nn;
-}
-
-template <class T>
-inline int NRMat<T>::ncols() const
-{
- return mm;
-}
-
-template <class T>
-NRMat<T>::~NRMat()
-{
- if (v != 0) {
- delete[] (v[0]);
- delete[] (v);
- }
-}
-
-template <class T>
-class NRMat3d {
- private:
- int nn;
- int mm;
- int kk;
- T ***v;
- public:
- NRMat3d();
- NRMat3d(int n, int m, int k);
- inline void Allocator(int n, int m, int k);
- inline T** operator[](const int i); //subscripting: pointer to row i
- inline const T* const * operator[](const int i) const;
- inline int dim1() const;
- inline int dim2() const;
- inline int dim3() const;
- ~NRMat3d();
-};
-
-template <class T>
-NRMat3d<T>::NRMat3d(): nn(0), mm(0), kk(0), v(0) {}
-template <class T>
-NRMat3d<T>::NRMat3d(int n, int m, int k) : nn(n), mm(m), kk(k), v(new T**[n])
-{
- int i,j;
- v[0] = new T*[n*m];
- v[0][0] = new T[n*m*k];
- for(j=1; j<m; j++)
- v[0][j] = v[0][j-1] + k;
- for(i=1; i<n; i++) {
- v[i] = v[i-1] + m;
- v[i][0] = v[i-1][0] + m*k;
- for(j=1; j<m; j++)
- v[i][j] = v[i][j-1] + k;
- }
-}
-
-template <class T>
-inline void NRMat3d<T>::Allocator(int n, int m, int k)
-{
- int i,j;
- v[0] = new T*[n*m];
- v[0][0] = new T[n*m*k];
- for(j=1; j<m; j++)
- v[0][j] = v[0][j-1] + k;
- for(i=1; i<n; i++) {
- v[i] = v[i-1] + m;
- v[i][0] = v[i-1][0] + m*k;
- for(j=1; j<m; j++)
- v[i][j] = v[i][j-1] + k;
- }
-}
-
-template <class T>
-inline T** NRMat3d<T>::operator[](const int i) //subscripting: pointer to row i
-{
- return v[i];
-}
-
-template <class T>
-inline const T* const * NRMat3d<T>::operator[](const int i) const
-{
- return v[i];
-}
-
-template <class T>
-inline int NRMat3d<T>::dim1() const
-{
- return nn;
-}
-
-template <class T>
-inline int NRMat3d<T>::dim2() const
-{
- return mm;
-}
-
-template <class T>
-inline int NRMat3d<T>::dim3() const
-{
- return kk;
-}
-
-template <class T>
-NRMat3d<T>::~NRMat3d()
-{
- if (v != 0) {
- delete[] (v[0][0]);
- delete[] (v[0]);
- delete[] (v);
- }
-}
-
-//The next 3 classes are used in artihmetic coding, Huffman coding, and
-//wavelet transforms respectively. This is as good a place as any to put them!
-class arithcode {
- private:
- NRVec<unsigned long> *ilob_p,*iupb_p,*ncumfq_p;
- public:
- NRVec<unsigned long> &ilob,&iupb,&ncumfq;
- unsigned long jdif,nc,minint,nch,ncum,nrad;
- arithcode(unsigned long n1, unsigned long n2, unsigned long n3)
- : ilob_p(new NRVec<unsigned long>(n1)),
- iupb_p(new NRVec<unsigned long>(n2)),
- ncumfq_p(new NRVec<unsigned long>(n3)),
- ilob(*ilob_p),iupb(*iupb_p),ncumfq(*ncumfq_p) {}
- ~arithcode() {
- if (ilob_p != 0) delete ilob_p;
- if (iupb_p != 0) delete iupb_p;
- if (ncumfq_p != 0) delete ncumfq_p;
- }
-};
-
-class huffcode {
- private:
- NRVec<unsigned long> *icod_p,*ncod_p,*left_p,*right_p;
- public:
- NRVec<unsigned long> &icod,&ncod,&left,&right;
- int nch,nodemax;
- huffcode(unsigned long n1, unsigned long n2, unsigned long n3,
- unsigned long n4) :
- icod_p(new NRVec<unsigned long>(n1)),
- ncod_p(new NRVec<unsigned long>(n2)),
- left_p(new NRVec<unsigned long>(n3)),
- right_p(new NRVec<unsigned long>(n4)),
- icod(*icod_p),ncod(*ncod_p),left(*left_p),right(*right_p) {}
- ~huffcode() {
- if (icod_p != 0) delete icod_p;
- if (ncod_p != 0) delete ncod_p;
- if (left_p != 0) delete left_p;
- if (right_p != 0) delete right_p;
- }
-};
-
-class wavefilt {
- private:
- NRVec<DP> *cc_p,*cr_p;
- public:
- int ncof,ioff,joff;
- NRVec<DP> &cc,&cr;
- wavefilt() : cc(*cc_p),cr(*cr_p) {}
- wavefilt(const DP *a, const int n) : //initialize to array
- cc_p(new NRVec<DP>(n)),cr_p(new NRVec<DP>(n)),
- ncof(n),ioff(-(n >> 1)),joff(-(n >> 1)),cc(*cc_p),cr(*cr_p) {
- int i;
- for (i=0; i<n; i++)
- cc[i] = *a++;
- DP sig = -1.0;
- for (i=0; i<n; i++) {
- cr[n-1-i]=sig*cc[i];
- sig = -sig;
- }
- }
- ~wavefilt() {
- if (cc_p != 0) delete cc_p;
- if (cr_p != 0) delete cr_p;
- }
-};
-
-
-/* Triangle Matrix Class
- ---------------------------------------------------------
- |v[0][0]|v[0][1]| | | |v[0][n-1]|
- |-------|-------|------|------------|---------|---------|
- |v[1][1]|v[1][2]| | |v[1][n-2]| |
- |-------|-------|------|------------|---------|---------|
- | | | | | | |
- |-------|-------|------|------------|---------|---------|
- | | |
- | | |
- | | |
- |-------|-----------------------------------------------|
- | | |
- |-------|-----------------------------------------------|
- |v[n-2][0]|v[n-2][1]| |
- |-------|-----------------------------------------------|
- |v[n-1][0]| |
- |-------------------------------------------------------|
- */
-template <class T>
-class Trimat {
- private:
- int nn;
- T **v;
- inline T* operator[](const int i); //subscripting: pointer to row i
- inline const T* operator[](const int i) const;
- public:
- Trimat();
- Trimat(int n); // Zero-based array
- Trimat(const T &a, int n); //Initialize to constant
- Trimat(const T *a, int n); // Initialize to array
- Trimat(const Trimat &rhs); // Copy constructor
- void Allocator(int n);
- void Allocator(const T &a, int n);
- void Allocator(const T *a, int n);
- Trimat & operator=(const Trimat &rhs); //assignment
- Trimat & operator=(const T &a); //assign a to every element
- inline T & ref(const int i, const int j);
- inline T * getPointer(const int i, const int j);
- inline T * begin() const;
- inline T * end() const;
- inline const T ref(const int i, const int j) const;
- inline int nrows() const;
- ~Trimat();
-};
-
-template <class T>
-Trimat<T>::Trimat() : nn(0), v(0) {}
-
-template <class T>
-Trimat<T>::Trimat(int n) : nn(n), v(new T*[n])
-{
- v[0] = new T[n*(n+1)/2];
- for (int i=1; i< n; i++)
- v[i] = v[i-1] + (n-i+1);
-
- for (int i=0; i< n; i++)
- for (int j=0; j<(n-i); j++)
- v[i][j] = 0;
-}
-template <class T>
-Trimat<T>::Trimat(const T &a, int n) : nn(n), v(new T*[n])
-{
- int i,j;
- v[0] = new T[n*(n+1)/2];
- for (i=1; i< n; i++)
- v[i] = v[i-1] + (n-i+1);
- for (i=0; i< n; i++)
- for (j=0; j<(n-i); j++)
- v[i][j] = a;
-}
-
-template <class T>
-Trimat<T>::Trimat(const T *a, int n) : nn(n), v(new T*[n])
-{
- int i,j;
- v[0] = new T[n*(n+1)/2];
- for (i=1; i< n; i++)
- v[i] = v[i-1] + (n-i+1);
- for (i=0; i< n; i++)
- for (j=0; j<(n-i); j++)
- v[i][j] = *a++;
-}
-
-
-template <class T>
-void Trimat<T>::Allocator(int n)
-{
- nn = n; v = new T*[n];
-
- v[0] = new T[n*(n+1)/2];
- for (int i=1; i< n; i++)
- v[i] = v[i-1] + (n-i+1);
-}
-
-template <class T>
-void Trimat<T>::Allocator(const T &a, int n)
-{
- nn = n; v = new T*[n];
-
- int i,j;
- v[0] = new T[n*(n+1)/2];
- for (i=1; i < n; i++)
- v[i] = v[i-1] + (n-i+1);
- for (i=0; i < n; i++)
- for (j=0; j < (n-i); j++)
- v[i][j] = a;
-}
-
-template <class T>
-void Trimat<T>::Allocator(const T *a, int n)
-{
- nn = n; v = new T*[n];
- int i,j;
- v[0] = new T[n*(n+1)/2];
- for (i=1; i< n; i++)
- v[i] = v[i-1] + (n-i+1);
- for (i=0; i< n; i++)
- for (j=0; j<(n-i); j++)
- v[i][j] = *a++;
-}
-
-
-template <class T>
-Trimat<T>::Trimat(const Trimat &rhs) : nn(rhs.nn), v(new T*[nn])
-{
- int i,j;
- v[0] = new T[nn*(nn+1)/2];
- for (i=1; i< nn; i++)
- v[i] = v[i-1] + (nn-i+1);
- for (i=0; i< nn; i++)
- for (j=0; j<(nn-i); j++)
- v[i][j] = rhs[i][j];
-}
-template <class T>
-Trimat<T> & Trimat<T>::operator=(const Trimat<T> &rhs)
-// postcondition: normal assignment via copying has been performed;
-// if matrix and rhs were different sizes, matrix
-// has been resized to match the size of rhs
-{
- if (this != &rhs) {
- int i,j;
- if (nn != rhs.nn) {
- if (v != 0) {
- delete[] (v[0]);
- delete[] (v);
- }
- nn=rhs.nn;
- v = new T*[nn];
- v[0] = new T[nn*(nn+1)/2];
- }
- for (i=1; i< nn; i++)
- v[i] = v[i-1] + (nn-i+1);
- for (i=0; i< nn; i++)
- for (j=0; j<(nn-i); j++)
- v[i][j] = rhs[i][j];
- }
- return *this;
-}
-
-template <class T>
-Trimat<T> & Trimat<T>::operator=(const T &a) //assign a to every element
-{
- for (int i=0; i< nn; i++)
- for (int j=0; j<nn-i; j++)
- v[i][j] = a;
- return *this;
-}
-
-template <class T>
-inline T & Trimat<T>::ref(const int i, const int j)
-{
- return v[i][j-i];
-}
-
-template <class T>
-inline const T Trimat<T>::ref(const int i, const int j) const
-{
- return v[i][j-i];
-}
-
-template <class T>
-inline T * Trimat<T>::getPointer(const int i, const int j)
-{
- return &v[i][j-i];
-}
-
-template <class T>
-inline T * Trimat<T>::begin() const
-{
- return &v[0][0];
-}
-
-template <class T>
-inline T * Trimat<T>::end() const
-{
- return (&v[nn-1][0] + 1);
-}
-
-template <class T>
-inline int Trimat<T>::nrows() const
-{
- return nn;
-}
-
-template <class T>
-Trimat<T>::~Trimat()
-{
- if (v != 0) {
- delete[] (v[0]);
- delete[] (v);
- }
-}
-
-
-/* Triangle Vertical Matrix Class
- ---------------------------------------------------------
- |v[0][0]|v[1][0]| | | |v[n-1][0]|
- |-------|-------|------|------------|---------|---------|
- |v[0][1]|v[1][1]| | |v[n-2][1]| |
- |-------|-------|------|------------|---------|---------|
- | | | | | | |
- |-------|-------|------|------------|---------|---------|
- | | |
- | | |
- | | |
- |-------|-----------------------------------------------|
- | | |
- |-------|-----------------------------------------------|
- |v[0][n-2]|v[n-2][n-2]| |
- |-------|-----------------------------------------------|
- |v[0][n-1]| |
- |-------------------------------------------------------|
- */
-template <class T>
-class TriVertMat {
- private:
- int nn;
- T **v;
- inline T* operator[](const int i); //subscripting: pointer to row i
- inline const T* operator[](const int i) const;
- public:
- TriVertMat();
- TriVertMat(int n); // Zero-based array
- TriVertMat(const T &a, int n); //Initialize to constant
- TriVertMat(const T *a, int n); // Initialize to array
- TriVertMat(const TriVertMat &rhs); // Copy constructor
- void Allocator(int n);
- void Allocator(const T &a, int n);
- void Allocator(const T *a, int n);
- TriVertMat & operator=(const TriVertMat &rhs); //assignment
- TriVertMat & operator=(const T &a); //assign a to every element
- inline T & ref(const int i, const int j);
- inline T * getPointer(const int i, const int j);
- inline const T ref(const int i, const int j) const;
- inline int nrows() const;
- ~TriVertMat();
-};
-
-template <class T>
-TriVertMat<T>::TriVertMat() : nn(0), v(0) {}
-
-template <class T>
-TriVertMat<T>::TriVertMat(int n) : nn(n), v(new T*[n])
-{
- v[0] = new T[n*(n+1)/2];
- for (int i=1; i< n; i++)
- v[i] = v[i-1] + i;
-}
-
-template <class T>
-TriVertMat<T>::TriVertMat(const T &a, int n) : nn(n), v(new T*[n])
-{
- int i,j;
- v[0] = new T[n*(n+1)/2];
- for (i=1; i< n; i++)
- v[i] = v[i-1] + i;
- for (i=0; i< n; i++)
- for (j=0; j<(n-i); j++)
- v[i][j] = a;
-}
-
-template <class T>
-TriVertMat<T>::TriVertMat(const T *a, int n) : nn(n), v(new T*[n])
-{
- int i,j;
- v[0] = new T[n*(n+1)/2];
- for (i=1; i< n; i++)
- v[i] = v[i-1] + i;
- for (i=0; i< n; i++)
- for (j=0; j<(n-i); j++)
- v[i][j] = *a++;
-}
-
-
-template <class T>
-void TriVertMat<T>::Allocator(int n)
-{
- nn = n; v = new T*[n];
-
- v[0] = new T[n*(n+1)/2];
- for (int i=1; i< n; i++)
- v[i] = v[i-1] + i;
-}
-
-template <class T>
-void TriVertMat<T>::Allocator(const T &a, int n)
-{
- nn = n; v = new T*[n];
-
- int i,j;
- v[0] = new T[n*(n+1)/2];
- for (i=1; i< n; i++)
- v[i] = v[i-1] + i;
- for (i=0; i< n; i++)
- for (j=0; j<(n-i); j++)
- v[i][j] = a;
-}
-
-template <class T>
-void TriVertMat<T>::Allocator(const T *a, int n)
-{
- nn = n; v = new T*[n];
- int i,j;
- v[0] = new T[n*(n+1)/2];
- for (i=1; i< n; i++)
- v[i] = v[i-1] + i;
- for (i=0; i< n; i++)
- for (j=0; j<(n-i); j++)
- v[i][j] = *a++;
-}
-
-
-template <class T>
-TriVertMat<T>::TriVertMat(const TriVertMat &rhs) : nn(rhs.nn), v(new T*[nn])
-{
- int i,j;
- v[0] = new T[nn*(nn+1)/2];
- for (i=1; i< nn; i++)
- v[i] = v[i-1] + i;
- for (i=0; i< nn; i++)
- for (j=0; j<(nn-i); j++)
- v[i][j] = rhs[i][j];
-}
-template <class T>
-TriVertMat<T> & TriVertMat<T>::operator=(const TriVertMat<T> &rhs)
-// postcondition: normal assignment via copying has been performed;
-// if matrix and rhs were different sizes, matrix
-// has been resized to match the size of rhs
-{
- if (this != &rhs) {
- int i,j;
- if (nn != rhs.nn) {
- if (v != 0) {
- delete[] (v[0]);
- delete[] (v);
- }
- nn=rhs.nn;
- v = new T*[nn];
- v[0] = new T[nn*(nn+1)/2];
- }
- for (i=1; i< nn; i++)
- v[i] = v[i-1] + i;
- for (i=0; i< nn; i++)
- for (j=0; j<(nn-i); j++)
- v[i][j] = rhs[i][j];
- }
- return *this;
-}
-
-template <class T>
-TriVertMat<T> & TriVertMat<T>::operator=(const T &a) //assign a to every element
-{
- for (int i=0; i< nn; i++)
- for (int j=0; j<nn-i; j++)
- v[i][j] = a;
- return *this;
-}
-
-template <class T>
-inline T & TriVertMat<T>::ref(const int i, const int j)
-{
- return v[j][i];
-}
-
-template <class T>
-inline const T TriVertMat<T>::ref(const int i, const int j) const
-{
- return v[j][i];
-}
-
-template <class T>
-inline T * TriVertMat<T>::getPointer(const int i, const int j)
-{
- return &v[j][i];
-}
-
-template <class T>
-inline int TriVertMat<T>::nrows() const
-{
- return nn;
-}
-
-template <class T>
-TriVertMat<T>::~TriVertMat()
-{
- if (v != 0) {
- delete[] (v[0]);
- delete[] (v);
- }
-}
-
-
-//Overloaded complex operations to handle mixed float and double
-//This takes care of e.g. 1.0/z, z complex<float>
-inline const complex<float> operator+(const double &a,
- const complex<float> &b) { return float(a)+b; }
-inline const complex<float> operator+(const complex<float> &a,
- const double &b) { return a+float(b); }
-inline const complex<float> operator-(const double &a,
- const complex<float> &b) { return float(a)-b; }
-inline const complex<float> operator-(const complex<float> &a,
- const double &b) { return a-float(b); }
-inline const complex<float> operator*(const double &a,
- const complex<float> &b) { return float(a)*b; }
-inline const complex<float> operator*(const complex<float> &a,
- const double &b) { return a*float(b); }
-inline const complex<float> operator/(const double &a,
- const complex<float> &b) { return float(a)/b; }
-inline const complex<float> operator/(const complex<float> &a,
- const double &b) { return a/float(b); }
-//some compilers choke on pow(float,double) in single precision. also atan2
-inline float pow (float x, double y) {return pow(double(x),y);}
-inline float pow (double x, float y) {return pow(x,double(y));}
-inline float atan2 (float x, double y) {return atan2(double(x),y);}
-inline float atan2 (double x, float y) {return atan2(x,double(y));}
-
-#endif /* _NR_UTIL_H_ */
git://source.jalview.org / jabaws.git / blobdiff