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C D E F G H I L M O S U W
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containsID(String) EntrezGene
containsID(String) HGNC
containsSymbol(String) EntrezGene
containsSymbol(String) HGNC
createSBGN(Model) L3ToSBGNPDConverter
Creates an SBGN object from the given BioPAX L3 model.
createStateVar(EntityFeature, ObjectFactory) FeatureDecorator
Creates the State for the given EntityFeature.
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doLayout L3ToSBGNPDConverter
Flag to run a layout before writing down the sbgn.(memberPhysicalEntity)
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EntrezGene org.biopax.paxtools.io.sbgn.idmapping
This class provides a mapping Entrez Gene IDs and gene symbols.
EntrezGene() EntrezGene
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featStrGen L3ToSBGNPDConverter
This class is used for generating short printable strings (text in info boxes) from
recognized entity features.
FeatureDecorator org.biopax.paxtools.io.sbgn
Generates a State class representing an entity feature.
flattenComplexContent L3ToSBGNPDConverter
Option to flatten nested complexes.
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getID(String) EntrezGene
Provides Entrez Gene ID of the given gene symbol.
getID(String) HGNC
Provides HGNC ID of the given approved gene symbol.
getSbgn2BPMap() L3ToSBGNPDConverter
Gets the mapping from SBGN IDs to BioPAX IDs.
getSymbol(String) EntrezGene
getSymbol(String) HGNC
getSymbols() HGNC
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HGNC org.biopax.paxtools.io.sbgn.idmapping
This class provides a mapping between HGNC IDs and approved gene symbols.
HGNC() HGNC
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isFlattenComplexContent() L3ToSBGNPDConverter
isUbique(Entity) ListUbiqueDetector
Checks if the ID of the PhysicalEntity is in the set.
isUbique(Entity) UbiqueDetector
Checks if the PhysicalEntity is a ubiquitous molecule.
isUseTwoGlyphsForReversibleConversion() L3ToSBGNPDConverter
Getter class for the parameter useTwoGlyphsForReversibleConversion.
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L3ToSBGNPDConverter org.biopax.paxtools.io.sbgn
This class converts BioPAX L3 model into SBGN PD (SBGN-ML XML).
L3ToSBGNPDConverter() L3ToSBGNPDConverter
Constructor.
L3ToSBGNPDConverter(UbiqueDetector, FeatureDecorator, boolean) L3ToSBGNPDConverter
Constructor with parameters.
ListUbiqueDetector org.biopax.paxtools.io.sbgn
Detects ubiquitous molecules using a given ID set.
ListUbiqueDetector(Set<String>) ListUbiqueDetector
Contructor.
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main(String[]) EntrezGene
main(String[]) HGNC
maxNodes L3ToSBGNPDConverter
If the number of nodes (biological processes and participants) in the model
is going to be greater than this maximum, then no layout (but a trivial one)
will be applied.
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org.biopax.paxtools.io.sbgn - package org.biopax.paxtools.io.sbgn
This package contains a BioPAX to SBGN-PD converter and associated classes.
org.biopax.paxtools.io.sbgn.idmapping - package org.biopax.paxtools.io.sbgn.idmapping
This package contains the SIF rules for BioPAX Level 3.
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sbgn2BPMap L3ToSBGNPDConverter
Mapping from SBGN IDs to the IDs of the related objects in BioPAX.
setDoLayout(boolean) L3ToSBGNPDConverter
setFlattenComplexContent(boolean) L3ToSBGNPDConverter
setUseTwoGlyphsForReversibleConversion(boolean) L3ToSBGNPDConverter
Sets the option to use two glyphs for the reversible conversion.
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ubiqueDet L3ToSBGNPDConverter
This class is used for detecting ubiques.
UbiqueDetector org.biopax.paxtools.io.sbgn
Interface for ubiquitous molecule detection.
useTwoGlyphsForReversibleConversion L3ToSBGNPDConverter
SBGN process glyph can be used to show reversible reactions.
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writeSBGN(Model, String) L3ToSBGNPDConverter
Converts the given model to SBGN, and writes in the specified file.
writeSBGN(Model, OutputStream) L3ToSBGNPDConverter
Converts the given model to SBGN, and writes in the specified output stream.
C D E F G H I L M O S U W Copyright © 2018 BioPAX . All rights reserved.