C D E F G H I L M O S U W

C

containsID(String) - Static method in class org.biopax.paxtools.io.sbgn.idmapping.EntrezGene

containsID(String) - Static method in class org.biopax.paxtools.io.sbgn.idmapping.HGNC

containsSymbol(String) - Static method in class org.biopax.paxtools.io.sbgn.idmapping.EntrezGene

containsSymbol(String) - Static method in class org.biopax.paxtools.io.sbgn.idmapping.HGNC

createSBGN(Model) - Method in class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter

Creates an Sbgn object from the given model.

createStateVar(EntityFeature, ObjectFactory) - Method in interface org.biopax.paxtools.io.sbgn.FeatureDecorator

Creates the State for the given EntityFeature.

D

doLayout - Variable in class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter

Flag to run a layout before writing down the sbgn.

E

EntrezGene - Class in org.biopax.paxtools.io.sbgn.idmapping

This class provides a mapping Entrez Gene IDs and gene symbols.

EntrezGene() - Constructor for class org.biopax.paxtools.io.sbgn.idmapping.EntrezGene

F

featStrGen - Variable in class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter

This class is used for generating short printable strings (text in info boxes) from recognized entity features.

FeatureDecorator - Interface in org.biopax.paxtools.io.sbgn

Generates a State class representing an entity feature.

flattenComplexContent - Variable in class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter

Option to flatten nested complexes.

G

getID(String) - Static method in class org.biopax.paxtools.io.sbgn.idmapping.EntrezGene

Provides Entrez Gene ID of the given gene symbol.

getID(String) - Static method in class org.biopax.paxtools.io.sbgn.idmapping.HGNC

Provides HGNC ID of the given approved gene symbol.

getSbgn2BPMap() - Method in class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter

Gets the mapping from SBGN IDs to BioPAX IDs.

getSymbol(String) - Static method in class org.biopax.paxtools.io.sbgn.idmapping.EntrezGene

getSymbol(String) - Static method in class org.biopax.paxtools.io.sbgn.idmapping.HGNC

getSymbols() - Static method in class org.biopax.paxtools.io.sbgn.idmapping.HGNC

H

HGNC - Class in org.biopax.paxtools.io.sbgn.idmapping

This class provides a mapping between HGNC IDs and approved gene symbols.

HGNC() - Constructor for class org.biopax.paxtools.io.sbgn.idmapping.HGNC

I

IS_UBIQUE - Static variable in class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter

Ubique label.

isFlattenComplexContent() - Method in class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter

isUbique(PhysicalEntity) - Method in class org.biopax.paxtools.io.sbgn.ListUbiqueDetector

Checks if the ID of the PhysicalEntity is in the set.

isUbique(PhysicalEntity) - Method in interface org.biopax.paxtools.io.sbgn.UbiqueDetector

Checks if the PhysicalEntity is a ubiquitous molecule.

isUseTwoGlyphsForReversibleConversion() - Method in class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter

Getter class for the parameter useTwoGlyphsForReversibleConversion.

L

L3ToSBGNPDConverter - Class in org.biopax.paxtools.io.sbgn

This class converts BioPAX L3 model into SBGN PD.

L3ToSBGNPDConverter() - Constructor for class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter

Empty constructor.

L3ToSBGNPDConverter(UbiqueDetector, FeatureDecorator, boolean) - Constructor for class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter

Constructor with parameters.

ListUbiqueDetector - Class in org.biopax.paxtools.io.sbgn

Detects ubiquitous molecules using a given ID set.

ListUbiqueDetector(Set<String>) - Constructor for class org.biopax.paxtools.io.sbgn.ListUbiqueDetector

Contructor with the Ubique IDs.

M

main(String[]) - Static method in class org.biopax.paxtools.io.sbgn.idmapping.EntrezGene

main(String[]) - Static method in class org.biopax.paxtools.io.sbgn.idmapping.HGNC

O

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.

S

sbgn2BPMap - Variable in class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter

Mapping from SBGN IDs to the IDs of the related objects in BioPAX.

setFlattenComplexContent(boolean) - Method in class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter

setUseTwoGlyphsForReversibleConversion(boolean) - Method in class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter

Sets the option to use two glyphs for the reversible conversion.

U

ubiqueDet - Variable in class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter

This class is used for detecting ubiques.

UbiqueDetector - Interface in org.biopax.paxtools.io.sbgn

Interface for ubiquitous molecule detection.

useTwoGlyphsForReversibleConversion - Variable in class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter

SBGN process glyph can be used to show reversible reactions.

W

writeSBGN(Model, String) - Method in class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter

Converts the given model to SBGN, and writes in the specified file.

writeSBGN(Model, OutputStream) - Method in class org.biopax.paxtools.io.sbgn.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