P - NodeT - ArcT - public abstract class AbstractLayoutBuilder<P,NodeT,ArcT> extends Object implements LayoutBuilder<P>, LayoutFactory<NodeT,ArcT>
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.| Modifier and Type | Field and Description |
|---|---|
protected boolean |
terminated
Indicates whether graph generation has finished or not.
|
| Constructor and Description |
|---|
AbstractLayoutBuilder() |
| Modifier and Type | Method and Description |
|---|---|
SBGNArc<ArcT> |
createArc(SpeciesReferenceGlyph srg,
ReactionGlyph 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
|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitbuildCompartment, buildConnectingArc, buildCubicBezier, buildEntityPoolNode, builderEnd, builderStart, buildProcessNode, buildTextGlyph, getProductcreateAssociationNode, createCatalysis, createCompartment, createConsumption, createDissociationNode, createInhibition, createMacromolecule, createModulation, createNecessaryStimulation, createNucleicAcidFeature, createOmittedProcessNode, createPerturbingAgent, createProcessNode, createProduction, createReversibleConsumption, createSimpleChemical, createSourceSink, createStimulation, createUncertainProcessNode, createUnspecifiedNodeprotected boolean terminated
public SBGNArc<ArcT> createArc(SpeciesReferenceGlyph srg, ReactionGlyph reactionGlyph)
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.srg - the SpeciesReferenceGlyph of the arcreactionGlyph - the ReactionGlyph of the arcSBGNArc for the two given objectspublic SBGNNode<NodeT> getSBGNNode(int sboTerm)
SBGNNode according to the given SBO term.sboTerm - of the corresponding speciesSBGNNode according to the SBO termpublic SBGNArc<ArcT> getSBGNArc(int sboTerm)
SBGNArc according to the given SBO term.sboTerm - of the corresponding connecting arcSBGNArc according to the SBO termpublic SBGNArc<ArcT> getSBGNArc(SpeciesReferenceRole speciesReferenceRole)
SBGNArc according to the given
SpeciesReferenceRole. The conversion of
SpeciesReferenceRole to SBO term is performed by the class
SpeciesReferenceRole.speciesReferenceRole - of the corresponding connecting arcSBGNArc according to the SBO termpublic SBGNProcessNode<NodeT> getSBGNReactionNode(int sboTerm)
sboTerm - of the reactionSBGNProcessNode for the processpublic boolean isProductReady()
LayoutBuilderisProductReady in interface LayoutBuilder<P>true, if product is not empty, else falseCopyright © 2009–2018. All rights reserved.