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

#include <OpenMS/DATASTRUCTURES/DistanceMatrix.h>

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 More...

	DistanceMatrix (SizeType dimensionsize, Value value=Value())
	detailed constructor More...

	DistanceMatrix (const DistanceMatrix &source)
	copy constructor More...

	~DistanceMatrix ()
	destructor More...

const ValueType	operator() (SizeType i, SizeType j) const
	gets a value at a given position (read only): More...

ValueType	operator() (SizeType i, SizeType j)
	gets a value at a given position (read only): More...

const ValueType	getValue (SizeType i, SizeType j) const
	gets a value at a given position: More...

ValueType	getValue (SizeType i, SizeType j)
	gets a value at a given position: More...

void	setValue (SizeType i, SizeType j, ValueType value)
	sets a value at a given position: More...

void	setValueQuick (SizeType i, SizeType j, ValueType value)
	sets a value at a given position: More...

void	clear ()
	reset all More...

void	resize (SizeType dimensionsize, Value value=Value())
	resizing the container More...

void	reduce (SizeType j)
	reduces DistanceMatrix by one dimension. first the jth row, then jth column More...

SizeType	dimensionsize () const
	gives the number of rows (i.e. number of columns) More...

void	updateMinElement ()
	keep track of the actual minimum element after altering the matrix More...

bool	operator== (DistanceMatrix< ValueType > const &rhs) const
	Equality comparator. More...

std::pair< SizeType, SizeType >	getMinElementCoordinates () const
	Indexpair of minimal element. More...

Protected Attributes
ValueType **	matrix_
	sparse element not to be included in base container More...

SizeType	init_size_
	number of actually stored rows More...

SizeType	dimensionsize_
	number of accessibly stored rows (i.e. number of columns) More...

std::pair< SizeType, SizeType >	min_element_
	index of minimal element(i.e. number in underlying SparseVector) More...

Private Member Functions
DistanceMatrix &	operator= (const DistanceMatrix &rhs)
	assignment operator (unsafe) More...

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. More...

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 corresponding elements below the main diagonal and returning 0 for requested elements in the main diagonal, since self-distance 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 manual update by call of OpenMS::DistanceMatrix::updateMinElement, see the respective methods documentation.

Member Typedef Documentation

◆ SizeType

typedef Size SizeType

◆ value_type

typedef Value value_type

◆ ValueType

typedef value_type ValueType

Constructor & Destructor Documentation

◆ DistanceMatrix() [1/3]

DistanceMatrix ( )

inline

default constructor

◆ DistanceMatrix() [2/3]

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

◆ DistanceMatrix() [3/3]

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_, and DistanceMatrix< Value >::min_element_.

◆ ~DistanceMatrix()

~DistanceMatrix ( )

inline

destructor

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

Member Function Documentation

◆ clear()

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().

◆ dimensionsize()

SizeType dimensionsize ( ) const

inline

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

References DistanceMatrix< Value >::dimensionsize_.

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

◆ getMinElementCoordinates()

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_.

◆ getValue() [1/2]

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()().

◆ getValue() [2/2]

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_.

◆ operator()() [1/2]

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().

◆ operator()() [2/2]

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().

◆ operator=()

DistanceMatrix& operator= ( const DistanceMatrix< Value > & rhs )

inlineprivate

assignment operator (unsafe)

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

◆ operator==()

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.

◆ reduce()

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 necessary before used

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

◆ resize()

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

Referenced by ClusterHierarchical::cluster().

◆ setValue()

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().

◆ setValueQuick()

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().

◆ updateMinElement()

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().

Friends And Related Function Documentation

◆ operator<<()

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

Member Data Documentation

◆ dimensionsize_

SizeType dimensionsize_

protected

number of accessibly 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().

◆ init_size_

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().

◆ matrix_

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().

◆ min_element_

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().

Public Types

Public Member Functions

Protected Attributes

Private Member Functions

Related Functions

Detailed Description

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

Member Typedef Documentation

◆ SizeType

◆ value_type

◆ ValueType

Constructor & Destructor Documentation

◆ DistanceMatrix() [1/3]

◆ DistanceMatrix() [2/3]

◆ DistanceMatrix() [3/3]

◆ ~DistanceMatrix()

Member Function Documentation

◆ clear()

◆ dimensionsize()

◆ getMinElementCoordinates()

◆ getValue() [1/2]

◆ getValue() [2/2]

◆ operator()() [1/2]

◆ operator()() [2/2]

◆ operator=()

◆ operator==()

◆ reduce()

◆ resize()

◆ setValue()

◆ setValueQuick()

◆ updateMinElement()

Friends And Related Function Documentation

◆ operator<<()

Member Data Documentation

◆ dimensionsize_

◆ init_size_

◆ matrix_

◆ min_element_

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