Package psidev.psi.mi.jami.binary.expansion

Interface ComplexExpansionMethod<T extends Interaction,B extends BinaryInteraction>

All Known Implementing Classes:

AbstractBipartiteExpansion, AbstractComplexExpansionMethod, AbstractMatrixExpansion, AbstractSpokeExpansion, BipartiteExpansion, InteractionEvidenceBipartiteExpansion, InteractionEvidenceMatrixExpansion, InteractionEvidenceSpokeExpansion, MatrixExpansion, ModelledInteractionBipartiteExpansion, ModelledInteractionMatrixExpansion, ModelledInteractionSpokeExpansion, SpokeExpansion

public interface ComplexExpansionMethod<T extends Interaction,B extends BinaryInteraction>

The method by which complex n-ary data is expanded into binary data. This may be performed manually on data input, or computationally on data export.

Since:

04/06/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

Fields

Modifier and Type	Field	Description
static String	BIPARTITE	Constant BIPARTITE="bipartite"
static String	BIPARTITE_EXPANSION	Constant BIPARTITE_EXPANSION="bipartite expansion"
static String	BIPARTITE_EXPANSION_MI	Constant BIPARTITE_EXPANSION_MI="MI:1062"
static String	MATRIX	Constant MATRIX="matrix expansion"
static String	MATRIX_EXPANSION	Constant MATRIX_EXPANSION="matrix expansion"
static String	MATRIX_EXPANSION_MI	Constant MATRIX_EXPANSION_MI="MI:1061"
static String	SPOKE	Constant SPOKE="spoke"
static String	SPOKE_EXPANSION	Constant SPOKE_EXPANSION="spoke expansion"
static String	SPOKE_EXPANSION_MI	Constant SPOKE_EXPANSION_MI="MI:1060"

Method Summary

Modifier and Type	Method	Description
Collection<B>	expand(T interaction)	Expand the interaction in a collection of BinaryInteraction.
BinaryInteractionFactory	getBinaryInteractionFactory()	getBinaryInteractionFactory
CvTerm	getMethod()	The method represented by the ComplexExpansionMethod object.
boolean	isInteractionExpandable(T interaction)	Method to know if this ComplexExpansionMethod can expand the given Interaction
void	setBinaryInteractionFactory(BinaryInteractionFactory factory)	Sets the binary interaction factory

Field Detail

BIPARTITE_EXPANSION_MI

static final String BIPARTITE_EXPANSION_MI

Constant BIPARTITE_EXPANSION_MI="MI:1062"

See Also:

Constant Field Values

BIPARTITE_EXPANSION

static final String BIPARTITE_EXPANSION

Constant BIPARTITE_EXPANSION="bipartite expansion"

See Also:

Constant Field Values

BIPARTITE

static final String BIPARTITE

Constant BIPARTITE="bipartite"

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Constant Field Values

SPOKE_EXPANSION_MI

static final String SPOKE_EXPANSION_MI

Constant SPOKE_EXPANSION_MI="MI:1060"

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Constant Field Values

SPOKE_EXPANSION

static final String SPOKE_EXPANSION

Constant SPOKE_EXPANSION="spoke expansion"

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Constant Field Values

SPOKE

static final String SPOKE

Constant SPOKE="spoke"

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Constant Field Values

MATRIX_EXPANSION_MI

static final String MATRIX_EXPANSION_MI

Constant MATRIX_EXPANSION_MI="MI:1061"

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Constant Field Values

MATRIX_EXPANSION

static final String MATRIX_EXPANSION

Constant MATRIX_EXPANSION="matrix expansion"

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Constant Field Values

MATRIX

static final String MATRIX

Constant MATRIX="matrix expansion"

See Also:

Constant Field Values

Method Detail

getMethod

CvTerm getMethod()

The method represented by the ComplexExpansionMethod object. It is a controlled vocabulary term and cannot be null.

Returns:

the complex expansion method

isInteractionExpandable

boolean isInteractionExpandable(T interaction)

Method to know if this ComplexExpansionMethod can expand the given Interaction

Parameters:

interaction - a T object.

Returns:

true if this interaction can be expanded with this ComplexExpansionMethod

expand

Collection<B> expand(T interaction)
              throws ComplexExpansionException

Expand the interaction in a collection of BinaryInteraction. The collection cannot be null.

Parameters:

interaction - a T object.

Returns:

collection of binary interactions expanded from the original interaction object

Throws:

ComplexExpansionException - if the interaction cannot be expanded with this method

getBinaryInteractionFactory

BinaryInteractionFactory getBinaryInteractionFactory()

getBinaryInteractionFactory

Returns:

the factory used to create new BinaryInteractions

setBinaryInteractionFactory

void setBinaryInteractionFactory(BinaryInteractionFactory factory)

Sets the binary interaction factory

Parameters:

factory - a BinaryInteractionFactory object.