P
- NodeT
- ArcT
- LayoutBuilder<P>
, LayoutFactory<NodeT,ArcT>
public abstract class AbstractLayoutBuilder<P,NodeT,ArcT> extends java.lang.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.Constructor | Description |
---|---|
AbstractLayoutBuilder() |
Modifier and Type | Method | 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
|
buildCompartment, buildConnectingArc, buildCubicBezier, buildEntityPoolNode, builderEnd, builderStart, buildProcessNode, buildTextGlyph, getProduct
createAssociationNode, createCatalysis, createCompartment, createConsumption, createDissociationNode, createInhibition, createMacromolecule, createModulation, createNecessaryStimulation, createNucleicAcidFeature, createOmittedProcessNode, createPerturbingAgent, createProcessNode, createProduction, createReversibleConsumption, createSimpleChemical, createSourceSink, createStimulation, createUncertainProcessNode, createUnspecifiedNode
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()
LayoutBuilder
isProductReady
in interface LayoutBuilder<P>
true
, if product is not empty, else false