--- /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