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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/njn__matrix_8hpp_source.html below:

NCBI C++ ToolKit: src/algo/blast/gumbel_params/njn_matrix.hpp Source File

1 #ifndef ALGO_BLAST_GUMBEL_PARAMS__INCLUDED_NJN_MATRIX 2 #define ALGO_BLAST_GUMBEL_PARAMS__INCLUDED_NJN_MATRIX 55 template

typename

60 static inline Matrix <T>

matrix

(

size_t

k_,

size_t

m_,

size_t

n_,

a_ =

static_cast <T>

(0));

72 inline Matrix

(

size_t

m_,

size_t

n_,

const T

*vector_);

73 inline Matrix

(

size_t

m_,

size_t

n_,

a_ =

static_cast <T>

(0));

77 virtual inline void

create

(

bool

isCopy_ =

false

)

const

;

78 virtual inline void copy

(

size_t

m_,

size_t

n_,

const T

const

*matrix_);

79 virtual inline void copy

(

size_t

m_,

size_t

n_,

const T

*vector_);

80 virtual inline void copy

(

size_t

m_,

size_t

n_,

a_ =

static_cast <T>

(0));

82 virtual inline operator bool

()

const

;

84 virtual inline

std::ostream &

out

(std::ostream &ostr_)

const

;

85 virtual inline

std::istream &

(std::istream &istr_);

90 virtual inline const T

operator []

(

size_t

i_)

const

;

94 virtual inline size_t getM

()

const

{

return d_m

;}

95 virtual inline size_t getN

()

const

{

return d_n

;}

106 virtual inline void init

(

size_t

m_,

size_t

n_);

107 virtual inline void free

();

128 template

typename

129 bool operator==

(

const

Njn::Matrix <T> &matrix_,

const

Njn::Matrix <T> &matrix0_);

131 template

typename

132 void copy

(Njn::Matrix <S> *matrix_,

const

Njn::Matrix <T> &matrix0_);

134 template

typename

135

std::ostream &

operator<<

(std::ostream &ostr_,

const

Njn::Matrix <T> &matrix_);

137 template

typename

138

std::istream &

operator>>

(std::istream &istr_, Njn::Matrix <T> &matrix_);

149 template

typename

157 for

(

size_t i

= 0;

< k_;

++)

158

matrix [

copy

(m_, n_, a_);

163 template

typename

166 assert

(x_.getM () == y_.getM ());

167 assert

(x_.getN () == y_.getN ());

169 for

(

size_t i

= 0;

< x_.getM ();

++) {

170 for

(

size_t

j = 0; j < x_.getN (); j++) {

178 template

typename

181 assert

(x_.getM () == y_.getM ());

182 assert

(x_.getN () == y_.getN ());

184 for

(

size_t i

= 0;

< x_.getM ();

++) {

185 for

(

size_t

j = 0; j < x_.getN (); j++) {

193 template

typename

196 assert

(x_.getM () == y_.getM ());

197 assert

(x_.getN () == y_.getN ());

199 for

(

size_t i

= 0;

< x_.getM ();

++) {

200 for

(

size_t

j = 0; j < x_.getN (); j++) {

208 template

typename

211 if

(x_.getM () != x_.getN ())

return false

;

213 for

(

size_t i

= 0;

< x_.getM ();

++) {

214 for

(

size_t

j = 0; j <

; j++) {

215 if

(x_ [

][j] != x_ [j][

])

return false

;

222 template

typename

224

: d_m (0), d_n (0), d_matrix_p (0), d_value (0)

227 template

typename

229

: d_m (0), d_n (0), d_matrix_p (0), d_value (0)

234 template

typename

239

: d_m (0), d_n (0), d_matrix_p (0), d_value (0)

241 copy

(m_, n_, vector_);

244 template

typename

249

: d_m (0), d_n (0), d_matrix_p (0), d_value (0)

254 template

typename

257 template

typename

260 if

(

this

!= &matrix_)

262 copy

(matrix_.getM (), matrix_.getN (), matrix_.getMatrix ());

263

this->setValue () = matrix_.getValue ();

268 template

typename

272 if

(isCopy_) matrix->operator= (*this);

276 template

typename

279 template

typename

296 for

(

= 0;

< getM ();

++) {

298 if

(

!= 0) ostr_ << endl;

300 for

(

size_t

j = 0; j < getN (); j++) {

302 if

(j != 0) ostr_ <<

'\t'

;

303

ostr_ << getMatrix () [

][j];

312

ostr_ << getM () <<

"\t! row dimension of matrix\n"

;

313

ostr_ << getN () <<

"\t! column dimension of matrix\n"

;

315 for

(

= 0;

< getM ();

++) {

317 if

(

!= 0) ostr_ <<

"\t! matrix elements\n"

;

319 for

(j = 0; j < getN (); j++) {

321 if

(j != 0) ostr_ <<

'\t'

;

322

ostr_ << getMatrix () [

][j];

326

ostr_ <<

"\t! matrix elements"

;

333 if

(! isSymmetric (*

this

))

IoUtil::abort

(

"Matrix::out : matrix is not symmetric"

);

335 for

(

= 0;

< getM ();

++)

337 if

(

!= 0) ostr_ << endl;

339 for

(

size_t

j =

; j < getN (); j++)

341 if

(j !=

) ostr_ <<

'\t'

;

342

ostr_ << getMatrix () [

][j];

346 else IoUtil::abort

(

"Matrix::out : impossible MatrixIO::getFormat ()"

);

354 template

typename

369

stringstream sstream;

372 T value

= this->getValue ();

384 while

(sstream >>

value

) v.push_back (

value

);

386 if

(! sstream.eof ())

IoUtil::abort

(

"Njn::Matrix::in : bad value for the MACHINE"

);

389 if

(

== 0)

IoUtil::abort

(

"Njn::Matrix::in : bad n for the MACHINE"

);

391 while

(istr_ >>

value

) v.push_back (

value

);

392 if

(! sstream.eof ())

IoUtil::abort

(

"Njn::Matrix::in : bad value for the MACHINE"

);

395 if

(m *

!= v.size ())

IoUtil::abort

(

"Njn::Matrix::in : rows for the MACHINE have different lengths."

);

397 if

(m != this->getM () ||

!= this->getN ()) {

403 for

(

= 0;

< m;

++) {

405 for

(j = 0; j <

; j++) d_matrix_p [

][j] = v [k++];

414

stringstream sstream;

421 if

(sstream.fail ())

IoUtil::abort

(

"Njn::Matrix::in : bad m"

);

428 if

(sstream.fail ())

IoUtil::abort

(

"Njn::Matrix::in : bad n"

);

430 if

(m != this->getM () ||

!= this->getN ()) {

436 for

(

= 0;

< this->getM ();

++) {

443 for

(j = 0; j < this->getN (); j++) {

445

sstream >> d_matrix_p [

][j];

447 if

(sstream.fail ()) {

449

ostringstream sistream;

451

ostringstream sjstream;

453 IoUtil::abort

(

"Njn::Matrix::in : bad d_matrix_p ["

+ sistream.str () +

"]["

+ sjstream.str () +

"]"

);

467 while

(sstream >>

value

)

469

v.push_back (

value

);

471 if

(! sstream.eof ())

IoUtil::abort

(

"Njn::Matrix::in : bad value for the MatrixIO::SYMMETRIC"

);

474 if

(

== 0)

IoUtil::abort

(

"Njn::Matrix::in : bad n for the MatrixIO::SYMMETRIC"

);

476 while

(istr_ >>

value

) v.push_back (

value

);

477 if

(! istr_.eof ())

IoUtil::abort

(

"Njn::Matrix::in : bad value for the MatrixIO::SYMMETRIC"

);

480 if

(m * (m + 1) / 2 != v.size ())

IoUtil::abort

(

"Njn::Matrix::in : rows for the MatrixIO::SYMMETRIC have incorrect lengths."

);

482 if

(m != this->getM () ||

!= this->getN ()) {

488 for

(

= 0;

< m;

++)

490 for

(j = 0; j <

; j++) d_matrix_p [

][j] = d_matrix_p [j][

];

491 for

(j =

; j <

; j++) d_matrix_p [

][j] = v [k++];

494 else IoUtil::abort

(

"Matrix::in : impossible MatrixIO::getFormat ()"

);

502 template

typename

505 copy

(this->getM (), this->getN (), a_);

509 template

typename

512 return

d_matrix_p [i_];

515 template

typename

518 return

d_matrix_p [i_];

521 template

typename

525 const T

const

*matrix_)

527 if

(m_ != this->getM () || n_ != this->getN ()) {

529

this->

init

(m_, n_);

532 for

(

size_t i

= 0;

< this->getM ();

++)

534 for

(

size_t

j = 0; j < this->getN (); j++)

536

d_matrix_p [

][j] = matrix_ [

][j];

541 template

typename

547 if

(m_ != this->getM () || n_ != this->getN ()) {

549

this->

init

(m_, n_);

553 for

(

size_t i

= 0;

< this->getM ();

++)

555 for

(

size_t

j = 0; j < this->getN (); j++)

557

d_matrix_p [

][j] = vector_ [k++];

562 template

typename

568 if

(m_ != this->getM () || n_ != this->getN ())

571

this->

init

(m_, n_);

574 for

(

size_t i

= 0;

< this->getM ();

++)

576 for

(

size_t

j = 0; j < this->getN (); j++)

578

d_matrix_p [

][j] = a_;

583 template

typename

586 if

(m_ > 0) d_matrix_p =

new T

* [m_];

588 for

(

size_t i

= 0;

< m_;

++)

590

d_matrix_p [

] =

new T

[n_];

597 template

typename

600 for

(

size_t i

= 0;

< this->getM ();

++) {

601 delete

[] d_matrix_p [

]; d_matrix_p [

] = 0;

603 if

(this->getM () > 0)

delete

[] d_matrix_p;

612 template

typename

613 void copy

(Njn::Matrix <S> *matrix_,

const

Njn::Matrix <T> &matrix0_)

615

matrix_->copy (matrix0_.getM (), matrix0_.getN ());

617 for

(

size_t i

= 0;

< matrix0_.getM ();

++) {

618 for

(

size_t

j = 0; j < matrix0_.getN (); j++) {

619

(*matrix_) [

][j] =

static_cast <S>

(matrix0_ [

][j]);

625 template

typename

626 bool operator==

(

const

Njn::Matrix <T> &matrix_,

const

Njn::Matrix <T> &matrix0_)

628 if

(matrix_.getM () != matrix0_.getM ())

return false

;

629 if

(matrix_.getN () != matrix0_.getN ())

return false

;

630 for

(

size_t i

= 0;

< matrix_.getM ();

++) {

631 for

(

size_t

j = 0; j < matrix_.getN (); j++) {

632 if

(matrix_.getMatrix () [

][j] != matrix0_.getMatrix () [

][j])

return false

;

639 template

typename

640

std::ostream &

operator<<

(std::ostream &ostr_,

const

Njn::Matrix <T> &matrix_)

641

{

return

matrix_.out (ostr_);}

643 template

typename

644

std::istream &

operator>>

(std::istream &istr_, Njn::Matrix <T> &matrix_)

645

{

return

matrix_.in (istr_);}

static bool absRelApprox(const Matrix< T > &x_, const Matrix< T > &y_, T tol_, T rtol_)

virtual void * create(bool isCopy_=false) const

virtual T * operator[](size_t i_)

virtual const T getValue() const

virtual size_t getN() const

virtual const T *const * getMatrix() const

static bool approx(const Matrix< T > &x_, const Matrix< T > &y_, T eps_)

static bool relApprox(const Matrix< T > &x_, const Matrix< T > &y_, T eps_)

virtual std::istream & in(std::istream &istr_)

virtual std::ostream & out(std::ostream &ostr_) const

virtual void copy(size_t m_, size_t n_, const T *const *matrix_)

static bool isSymmetric(const Matrix< T > &x_)

Matrix & operator=(const Matrix &matrix_)

static Matrix< T > * matrix(size_t k_, size_t m_, size_t n_, T a_=static_cast< T >(0))

virtual void init(size_t m_, size_t n_)

virtual size_t getM() const

static void DLIST_NAME() init(DLIST_LIST_TYPE *list)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define USING_SCOPE(ns)

Use the specified namespace.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

const GenericPointer< typename T::ValueType > T2 value

Defines Limits for the types used in NCBI C/C++ toolkit.

bool relApprox(T x_, T y_, T eps_)

bool approx(T x_, T y_, T eps_)

bool absRelApprox(T x_, T y_, T tol_, T rtol_)

std::istream & getLine(std::istream &in_, std::string &str_, const char t_=getTerminator())

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

bool operator==(const Njn::Matrix< T > &matrix_, const Njn::Matrix< T > &matrix0_)

std::istream & operator>>(std::istream &istr_, Njn::Matrix< T > &matrix_)

void setFormat(Format format_)

std::ostream & operator<<(std::ostream &ostr_, const Njn::Matrix< T > &matrix_)

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