DistanceMatrix< Value > Class Template Reference [Datastructures]

A two-dimensional distance matrix, similar to OpenMS::Matrix. More...

#include <OpenMS/DATASTRUCTURES/DistanceMatrix.h>

List of all members.

Public Types
STL compliance type definitions
typedef Value	value_type
OpenMS compliance type definitions
typedef Size	SizeType
typedef value_type	ValueType
Public Member Functions
	DistanceMatrix ()
	default constructor
	DistanceMatrix (SizeType dimensionsize, Value value=Value())
	detailed constructor
	DistanceMatrix (const DistanceMatrix &source)
	copy constructor
	~DistanceMatrix ()
	destructor
const ValueType	operator() (SizeType i, SizeType j) const
	gets a value at a given position (read only):
ValueType	operator() (SizeType i, SizeType j)
	gets a value at a given position (read only):
const ValueType	getValue (SizeType i, SizeType j) const
	gets a value at a given position:
ValueType	getValue (SizeType i, SizeType j)
	gets a value at a given position:
void	setValue (SizeType i, SizeType j, ValueType value)
	sets a value at a given position:
void	setValueQuick (SizeType i, SizeType j, ValueType value)
	sets a value at a given position:
void	clear ()
	reset all
void	resize (SizeType dimensionsize, Value value=Value())
	resizing the container
void	reduce (SizeType j)
	reduces DistanceMatrix by one dimension. first the jth row, then jth column
SizeType	dimensionsize () const
	gives the number of rows (i.e. number of columns)
void	updateMinElement ()
	keep track of the actual minimum element after altering the matrix
bool	operator== (DistanceMatrix< ValueType > const &rhs) const
	Equality comparator.
std::pair< SizeType, SizeType >	getMinElementCoordinates () const
	Indexpair of minimal element.
Protected Attributes
ValueType **	matrix_
	sparse element not to be included in base container
SizeType	init_size_
	number of actually stored rows
SizeType	dimensionsize_
	number of accessably stored rows (i.e. number of columns)
std::pair< SizeType, SizeType >	min_element_
	index of minimal element(i.e. number in underlying SparseVector)
Private Member Functions
DistanceMatrix &	operator= (const DistanceMatrix &rhs)
	assignment operator (unsafe)
Related Functions
(Note that these are not member functions.)
template<typename Value >
std::ostream &	operator<< (std::ostream &os, const DistanceMatrix< Value > &matrix)
	Print the contents to a stream.

---

Detailed Description

template<typename Value>
class OpenMS::DistanceMatrix< Value >

A two-dimensional distance matrix, similar to OpenMS::Matrix.

similar to OpenMS::Matrix, but contains only elements above the main diagonal, hence translating access with operator(,) for elements of above the main diagonal to corresponing elements below the main diagonal and returning 0 for requested elements in the main diagonal, since selfdistance is assumed to be 0. Keeps track of the minimal element in the Matrix with OpenMS::DistanceMatrix::min_element_ if only for setting a value OpenMS::DistanceMatrix::setValue is used. Other OpenMS::DistanceMatrix altering methods may require a maual update by call of OpenMS::DistanceMatrix::updateMinElement, see the respective methods documentation.

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Member Typedef Documentation

typedef Size SizeType

typedef Value value_type

typedef value_type ValueType

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Constructor & Destructor Documentation

DistanceMatrix

(

)

[inline]

default constructor

DistanceMatrix	(	SizeType	dimensionsize,
		Value	value = Value()
	)			[inline]

detailed constructor

Parameters:

	dimensionsize	the number of rows (and therewith cols)
	value	DistanceMatrix will be filled with this element (main diagonal will still "hold" only zeros)

Exceptions:

Exception::OutOfMemory

if requested dimensionsize is to big to fit into memory

References DistanceMatrix< Value >::dimensionsize_, DistanceMatrix< Value >::init_size_, DistanceMatrix< Value >::matrix_, DistanceMatrix< Value >::min_element_, and NULL.

DistanceMatrix

(

const DistanceMatrix< Value > &

source

)

[inline]

copy constructor

Parameters:

source

this DistanceMatrix will be copied

Exceptions:

Exception::OutOfMemory

if requested dimensionsize is to big to fit into memory

References DistanceMatrix< Value >::dimensionsize_, DistanceMatrix< Value >::init_size_, DistanceMatrix< Value >::matrix_, DistanceMatrix< Value >::min_element_, and NULL.

~DistanceMatrix

(

)

[inline]

destructor

References DistanceMatrix< Value >::init_size_, and DistanceMatrix< Value >::matrix_.

---

Member Function Documentation

void clear

(

)

[inline]

reset all

References DistanceMatrix< Value >::dimensionsize_, DistanceMatrix< Value >::init_size_, DistanceMatrix< Value >::matrix_, and DistanceMatrix< Value >::min_element_.

Referenced by ClusterHierarchical::cluster().

SizeType dimensionsize

(

)

const [inline]

gives the number of rows (i.e. number of columns)

References DistanceMatrix< Value >::dimensionsize_.

Referenced by ClusterHierarchical::cluster(), and DistanceMatrix< Value >::operator==().

std::pair<SizeType, SizeType> getMinElementCoordinates

(

)

const [inline]

Indexpair of minimal element.

Exceptions:

Exception::OutOfRange

thrown if there is no element to access

References DistanceMatrix< Value >::dimensionsize_, and DistanceMatrix< Value >::min_element_.

ValueType getValue	(	SizeType	i,
		SizeType	j
	)			[inline]

gets a value at a given position:

Parameters:

	i	the i-th row
	j	the j-th col

Exceptions:

Exception::OutOfRange

if given coordinates are out of range

References DistanceMatrix< Value >::dimensionsize_, and DistanceMatrix< Value >::matrix_.

const ValueType getValue	(	SizeType	i,
		SizeType	j
	)			const [inline]

gets a value at a given position:

Parameters:

	i	the i-th row
	j	the j-th col

Exceptions:

Exception::OutOfRange

if given coordinates are out of range

References DistanceMatrix< Value >::dimensionsize_, and DistanceMatrix< Value >::matrix_.

Referenced by DistanceMatrix< Value >::operator()().

ValueType operator()	(	SizeType	i,
		SizeType	j
	)			[inline]

gets a value at a given position (read only):

Parameters:

	i	the i-th row
	j	the j-th col

References DistanceMatrix< Value >::getValue().

const ValueType operator()	(	SizeType	i,
		SizeType	j
	)			const [inline]

gets a value at a given position (read only):

Parameters:

	i	the i-th row
	j	the j-th col

References DistanceMatrix< Value >::getValue().

DistanceMatrix& operator=

(

const DistanceMatrix< Value > &

rhs

)

[inline, private]

assignment operator (unsafe)

References DistanceMatrix< Value >::dimensionsize_, DistanceMatrix< Value >::init_size_, DistanceMatrix< Value >::matrix_, and DistanceMatrix< Value >::min_element_.

bool operator==

(

DistanceMatrix< ValueType > const &

rhs

)

const [inline]

Equality comparator.

Exceptions:

Exception::Precondition

thrown if given DistanceMatrix is not compatible in size

References DistanceMatrix< Value >::dimensionsize(), DistanceMatrix< Value >::dimensionsize_, DistanceMatrix< Value >::matrix_, and OPENMS_PRECONDITION.

void reduce

(

SizeType

j

)

[inline]

reduces DistanceMatrix by one dimension. first the jth row, then jth column

Parameters:

j

the jth row (and therewith also jth col) to be removed

Exceptions:

Exception::OutOfRange

if j is grater than the greatest row number

may invalidates min_element_, make sure to update min_element_ if neccessary before used

References DistanceMatrix< Value >::dimensionsize_, DistanceMatrix< Value >::matrix_, and NULL.

void resize	(	SizeType	dimensionsize,
		Value	value = Value()
	)			[inline]

resizing the container

Parameters:

	dimensionsize	the desired number of rows (and therewith cols)
	value	which the matrix will be filled with

Exceptions:

Exception::OutOfMemory

thrown if size of DistanceMatrix requested does not fit into memory

invalidates all content

References DistanceMatrix< Value >::dimensionsize_, DistanceMatrix< Value >::init_size_, OpenMS::Constants::k, DistanceMatrix< Value >::matrix_, DistanceMatrix< Value >::min_element_, and NULL.

Referenced by ClusterHierarchical::cluster().

void setValue	(	SizeType	i,
		SizeType	j,
		ValueType	value
	)			[inline]

sets a value at a given position:

Parameters:

	i	the i-th row
	j	the j-th col
	value	the set-value

Exceptions:

Exception::OutOfRange

if given coordinates are out of range

References DistanceMatrix< Value >::dimensionsize_, DistanceMatrix< Value >::matrix_, DistanceMatrix< Value >::min_element_, and DistanceMatrix< Value >::updateMinElement().

Referenced by ClusterHierarchical::cluster().

void setValueQuick	(	SizeType	i,
		SizeType	j,
		ValueType	value
	)			[inline]

sets a value at a given position:

Parameters:

	i	the i-th row
	j	the j-th col
	value	the set-value

Exceptions:

Exception::OutOfRange

if given coordinates are out of range

possible invalidation of min_element_ - make sure to update before further usage of matrix

References DistanceMatrix< Value >::dimensionsize_, and DistanceMatrix< Value >::matrix_.

Referenced by ClusterHierarchical::cluster().

void updateMinElement

(

)

[inline]

keep track of the actual minimum element after altering the matrix

Exceptions:

Exception::OutOfRange

thrown if there is no element to access

References DistanceMatrix< Value >::dimensionsize_, DistanceMatrix< Value >::matrix_, and DistanceMatrix< Value >::min_element_.

Referenced by DistanceMatrix< Value >::setValue().

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Friends And Related Function Documentation

std::ostream & operator<<	(	std::ostream &	os,
		const DistanceMatrix< Value > &	matrix
	)			[related]

Print the contents to a stream.

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Member Data Documentation

SizeType dimensionsize_ [protected]

number of accessably stored rows (i.e. number of columns)

Referenced by DistanceMatrix< Value >::clear(), DistanceMatrix< Value >::dimensionsize(), DistanceMatrix< Value >::DistanceMatrix(), DistanceMatrix< Value >::getMinElementCoordinates(), DistanceMatrix< Value >::getValue(), DistanceMatrix< Value >::operator=(), DistanceMatrix< Value >::operator==(), DistanceMatrix< Value >::reduce(), DistanceMatrix< Value >::resize(), DistanceMatrix< Value >::setValue(), DistanceMatrix< Value >::setValueQuick(), and DistanceMatrix< Value >::updateMinElement().

SizeType init_size_ [protected]

number of actually stored rows

Referenced by DistanceMatrix< Value >::clear(), DistanceMatrix< Value >::DistanceMatrix(), DistanceMatrix< Value >::operator=(), DistanceMatrix< Value >::resize(), and DistanceMatrix< Value >::~DistanceMatrix().

ValueType** matrix_ [protected]

sparse element not to be included in base container

Referenced by DistanceMatrix< Value >::clear(), DistanceMatrix< Value >::DistanceMatrix(), DistanceMatrix< Value >::getValue(), DistanceMatrix< Value >::operator=(), DistanceMatrix< Value >::operator==(), DistanceMatrix< Value >::reduce(), DistanceMatrix< Value >::resize(), DistanceMatrix< Value >::setValue(), DistanceMatrix< Value >::setValueQuick(), DistanceMatrix< Value >::updateMinElement(), and DistanceMatrix< Value >::~DistanceMatrix().

std::pair<SizeType, SizeType> min_element_ [protected]

index of minimal element(i.e. number in underlying SparseVector)

Referenced by DistanceMatrix< Value >::clear(), DistanceMatrix< Value >::DistanceMatrix(), DistanceMatrix< Value >::getMinElementCoordinates(), DistanceMatrix< Value >::operator=(), DistanceMatrix< Value >::resize(), DistanceMatrix< Value >::setValue(), and DistanceMatrix< Value >::updateMinElement().