org.sbml.jsbml.ext.render.director

Class AbstractLayoutBuilder<P,NodeT,ArcT>

java.lang.Object

org.sbml.jsbml.ext.render.director.AbstractLayoutBuilder<P,NodeT,ArcT>

Type Parameters:

P -

NodeT -

ArcT -

All Implemented Interfaces:

LayoutBuilder<P>, LayoutFactory<NodeT,ArcT>

public abstract class AbstractLayoutBuilder<P,NodeT,ArcT>
extends Object
implements LayoutBuilder<P>, LayoutFactory<NodeT,ArcT>

This abstract class combines the interfaces LayoutBuilder and LayoutFactory. It implements the methods getSBGNNode(int), getSBGNArc(int) and getSBGNReactionNode(int) to get the node, arc or process node for a specific SBO term or a specific species reference role.

Since:

1.4

Author:

Andreas Dräger

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	terminated Indicates whether graph generation has finished or not.

Constructor Summary

Constructors

Constructor and Description
AbstractLayoutBuilder()

Method Summary

Modifier and Type	Method and Description
SBGNArc<ArcT>	createArc(SpeciesReferenceGlyph srg, ReactionGlyph reactionGlyph) Create a SBGNArc for the given SpeciesReferenceGlyph and ReactionGlyph.
SBGNArc<ArcT>	getSBGNArc(int sboTerm) Creates the correct SBGNArc according to the given SBO term.
SBGNArc<ArcT>	getSBGNArc(SpeciesReferenceRole speciesReferenceRole) Creates the correct SBGNArc according to the given SpeciesReferenceRole.
SBGNNode<NodeT>	getSBGNNode(int sboTerm) Create the correct SBGNNode according to the given SBO term.
SBGNProcessNode<NodeT>	getSBGNReactionNode(int sboTerm) Create the correct process node according to the SBO term of the reaction.
boolean	isProductReady() method to check if the builder has produced a complete product

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.sbml.jsbml.ext.render.director.LayoutBuilder

buildCompartment, buildConnectingArc, buildCubicBezier, buildEntityPoolNode, builderEnd, builderStart, buildProcessNode, buildTextGlyph, getProduct

Methods inherited from interface org.sbml.jsbml.ext.render.director.LayoutFactory

createAssociationNode, createCatalysis, createCompartment, createConsumption, createDissociationNode, createInhibition, createMacromolecule, createModulation, createNecessaryStimulation, createNucleicAcidFeature, createOmittedProcessNode, createPerturbingAgent, createProcessNode, createProduction, createReversibleConsumption, createSimpleChemical, createSourceSink, createStimulation, createUncertainProcessNode, createUnspecifiedNode

Field Detail

terminated

protected boolean terminated

Indicates whether graph generation has finished or not.

Constructor Detail

AbstractLayoutBuilder

public AbstractLayoutBuilder()

Method Detail

createArc

public SBGNArc<ArcT> createArc(SpeciesReferenceGlyph srg,
                               ReactionGlyph reactionGlyph)

Create a SBGNArc for the given SpeciesReferenceGlyph and ReactionGlyph. The decision which arc to produce is based on the role (priority) or the SBO term of the SpeciesReferenceGlyph.

Parameters:

srg - the SpeciesReferenceGlyph of the arc

reactionGlyph - the ReactionGlyph of the arc

Returns:

a SBGNArc for the two given objects

getSBGNNode

public SBGNNode<NodeT> getSBGNNode(int sboTerm)

Create the correct SBGNNode according to the given SBO term.

Parameters:

sboTerm - of the corresponding species

Returns:

correct SBGNNode according to the SBO term

getSBGNArc

public SBGNArc<ArcT> getSBGNArc(int sboTerm)

Creates the correct SBGNArc according to the given SBO term.

Parameters:

sboTerm - of the corresponding connecting arc

Returns:

correct SBGNArc according to the SBO term

getSBGNArc

public SBGNArc<ArcT> getSBGNArc(SpeciesReferenceRole speciesReferenceRole)

Creates the correct SBGNArc according to the given SpeciesReferenceRole. The conversion of SpeciesReferenceRole to SBO term is performed by the class SpeciesReferenceRole.

Parameters:

speciesReferenceRole - of the corresponding connecting arc

Returns:

correct SBGNArc according to the SBO term

getSBGNReactionNode

public SBGNProcessNode<NodeT> getSBGNReactionNode(int sboTerm)

Create the correct process node according to the SBO term of the reaction.

Parameters:

sboTerm - of the reaction

Returns:

correct SBGNProcessNode for the process

isProductReady

public boolean isProductReady()

Description copied from interface: LayoutBuilder

method to check if the builder has produced a complete product

Specified by:

isProductReady in interface LayoutBuilder<P>

Returns:

true, if product is not empty, else false