A B C D E F G H I L M O P R S U V W

A

assignProcessAndLogicOpNodesToCompartment(Sbgn) - Method in class org.biopax.paxtools.io.sbgn.SBGNLayoutManager

This method finds process nodes and logical operator nodes in sbgn map and assigns them to a compartment by using majority rule.

B

Bound(float, float) - Constructor for class org.biopax.paxtools.io.sbgn.VNode.Bound

C

calcReqWidthByStateAndInfos(List<Glyph>) - Method in class org.biopax.paxtools.io.sbgn.VNode

Calculates required width according to the given list state and info glyphs of this VNode.

children - Variable in class org.biopax.paxtools.io.sbgn.VCompound

clusterID - Variable in class org.biopax.paxtools.io.sbgn.VNode

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

Prepares displayable Stat class to generate labels like "pY@123" for modification features and like x[30 - 122] for fragment features.

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

connectArcToPort(SbgnPDNode, Port) - Method in class org.biopax.paxtools.io.sbgn.SBGNLayoutManager

This method connects the existing arcs to the newly created ports which are created by ChiLay and SBGNPD Layout.

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

createLayout(Sbgn) - Method in class org.biopax.paxtools.io.sbgn.SBGNLayoutManager

Applies CoSE layout to the given SBGN model.

createLEdges(List<Arc>, Layout) - Method in class org.biopax.paxtools.io.sbgn.SBGNLayoutManager

Creates LNodes from Arcs of Sbgn and adds it to the passed layout object.

createLNode(VNode, VNode, Layout) - Method in class org.biopax.paxtools.io.sbgn.SBGNLayoutManager

Helper function for creating LNode objects from VNode objects and adds them to the given layout.

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

Creates an Sbgn object from the given model.

createStateVar(EntityFeature, ObjectFactory) - Method in class org.biopax.paxtools.io.sbgn.CommonFeatureStringGenerator

Creates State to represent the entity feature.

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

Creates the State for the given EntityFeature.

createVNodes(VCompound, List<Glyph>) - Method in class org.biopax.paxtools.io.sbgn.SBGNLayoutManager

Recursively creates VNodes from Glyphs of Sbgn.

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

getChildren() - Method in class org.biopax.paxtools.io.sbgn.VCompound

Returns the child list of this VCompound

getHeight() - Method in class org.biopax.paxtools.io.sbgn.VNode.Bound

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

getWidth() - Method in class org.biopax.paxtools.io.sbgn.VNode.Bound

glyph - Variable in class org.biopax.paxtools.io.sbgn.VNode

H

height - Variable in class org.biopax.paxtools.io.sbgn.VNode.Bound

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

initPortIdToGlyphMap(List<Glyph>) - Method in class org.biopax.paxtools.io.sbgn.SBGNLayoutManager

This method initializes map for glyphs and their respective ports.

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

Ubique label.

isChildless(Glyph) - Method in class org.biopax.paxtools.io.sbgn.SBGNLayoutManager

Returns true if a glyph includes child glyphs (state and info glyphs are out of count!)

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.

P

placeStateAndInfoGlyphs() - Method in class org.biopax.paxtools.io.sbgn.VNode

Places state and info glyphs of this node

populateCompartmentOccurencesMap(Glyph, HashMap<String, Integer>) - Method in class org.biopax.paxtools.io.sbgn.SBGNLayoutManager

Updates a hashmap by incrementing the number of nodes in the compartment glyph that includes targetGlyph.

R

removePortsFromArcs(List<Arc>) - Method in class org.biopax.paxtools.io.sbgn.SBGNLayoutManager

This method replaces ports of arc objects with their owners.

S

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

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

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

SBGNLayoutManager Class: Applies layout by using ChiLay to Sbgn graph generated by paxtools.

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

setBounds(float, float) - Method in class org.biopax.paxtools.io.sbgn.VNode

Sets the bound of this VNode by given width and height

setCompartmentRefForComplexMembers(Glyph, Glyph) - Method in class org.biopax.paxtools.io.sbgn.SBGNLayoutManager

This method recursively set compartmentRef fields of members of any complex glyphs as same as complex's compartmentRef

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

setHeight(float) - Method in class org.biopax.paxtools.io.sbgn.VNode.Bound

setSizeAccordingToClass() - Method in class org.biopax.paxtools.io.sbgn.VNode

Chooses a proper bound for this VNode according to its class.

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

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

setWidth(float) - Method in class org.biopax.paxtools.io.sbgn.VNode.Bound

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.

update(LGraphObject) - Method in class org.biopax.paxtools.io.sbgn.VNode

Function that will take place when VNode objects will update in layout process of ChiLay

updateCompoundBounds(Glyph, List<Glyph>) - Method in class org.biopax.paxtools.io.sbgn.SBGNLayoutManager

Updates bounds of a compound node ( i.e.

updateSizeForStateAndInfo() - Method in class org.biopax.paxtools.io.sbgn.VNode

If glyph attribute of this VNode object includes any "state of information" or "unit of information" glyphs, this method updates the size of VNode accordingly.

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

SBGN process glyph can be used to show reversible reactions.

V

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

VCompound Class

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

Default Constructor, creates a VCompound node by given glyph

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

VNode Class

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

Default Constructor, sets the geometry of the bounds which are attributes of this class

VNode.Bound - Class in org.biopax.paxtools.io.sbgn

Inner Class for glyph bounds

W

width - Variable in class org.biopax.paxtools.io.sbgn.VNode.Bound

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.

A B C D E F G H I L M O P R S U V W