fr.curie.BiNoM.pathways
Class BioPAXToSBMLConverter

java.lang.Object
  fr.curie.BiNoM.pathways.BioPAXToSBMLConverter

Direct Known Subclasses:

BioPAXToCytoscapeConverter, parseBioPAX

public class BioPAXToSBMLConverter
extends java.lang.Object

Converts BioPAX (represented by BioPAX object) to SBML (represented by org.sbml.x2001.ns.celldesigner.SbmlDocument object)

Nested Class Summary

class

BioPAXToSBMLConverter.BioPAXSpecies Represents BioPAX physicalEntityParticipants grouped into distinctive chemical species (entity, characterized by a definite location and a definite modification).

Field Summary

static boolean	alwaysMentionCompartment Check to show compartment information in species names
BioPAX	biopax Input for conversion
java.util.HashMap	bioPAXreactions Map from cutted uris (after # separator) to BioPAX 'conversion' objects
BioPAXNamingService	bpnm BioPAX Naming service used for conversion
java.util.Vector	compartments List of compartments (represented as openControlledVocabulary objects)
java.util.HashMap	complexList Map from cutted uris (after # separator) to 'complex' entities
static boolean	considerCompartmentNameRatherThanId Check off if you want to use compartment id and not name
java.util.HashMap	controls Map from cutted uris (after # separator) to BioPAX 'control' objects
java.util.HashMap	dnaList Map from cutted uris (after # separator) to 'dna' entities
java.util.HashMap	includedSpecies Map from cutted uris (after # separator) to BioPAXSpecies included into entities (these species group complex components, for example)
java.util.HashMap	independentSpecies Auxilary map
java.util.HashMap	independentSpeciesIds Map from cutted uris (after # separator) to BioPAXSpecies
java.util.HashMap	proteinList Map from cutted uris (after # separator) to 'protein' entities
java.util.HashMap	reactions Map from BioPAX conversion (cutted) uris to SBML reactions (represented by ReactionDocument.Reaction objects)
java.util.HashMap	rnaList Map from cutted uris (after # separator) to 'rna' entities
org.sbml.x2001.ns.celldesigner.SbmlDocument	sbmlDoc Result of conversion
java.util.HashMap	smallMoleculeList Map from cutted uris (after # separator) to 'smallMolecule' entities
java.util.HashMap	species Map from SBML species ids to SpeciesDocument.Species objects
static boolean	useBiopaxModelOntology not used

Constructor Summary

BioPAXToSBMLConverter()

Method Summary

void	addControl(control cntrl)
void	addConversionReaction(conversion conv, org.sbml.x2001.ns.celldesigner.ListOfReactionsDocument.ListOfReactions lr)
void	addIncludedParticipant(physicalEntityParticipant part) Adds included physicalEntityParticipant (such as complex components)
void	findIndependentSpecies() Procedure of groupping physicalEntityParticipants into BioPAXSpecies (chemical species)
java.util.Vector	getAllCompartments()
java.lang.String	getTypeForParticipant(physicalEntityParticipant part)
java.lang.String	makeComment(java.util.Iterator comments)
void	makeLists() Fills all maps for needed conversion
void	populateSbml() Performs actual BioPAX->SBML conversion Requires this.biopax object to be specified

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

sbmlDoc

public org.sbml.x2001.ns.celldesigner.SbmlDocument sbmlDoc

Result of conversion

biopax

public BioPAX biopax

Input for conversion

bpnm

public BioPAXNamingService bpnm

BioPAX Naming service used for conversion

alwaysMentionCompartment

public static boolean alwaysMentionCompartment

Check to show compartment information in species names

useBiopaxModelOntology

public static boolean useBiopaxModelOntology

not used

considerCompartmentNameRatherThanId

public static boolean considerCompartmentNameRatherThanId

Check off if you want to use compartment id and not name

independentSpeciesIds

public java.util.HashMap independentSpeciesIds

Map from cutted uris (after # separator) to BioPAXSpecies

independentSpecies

public java.util.HashMap independentSpecies

Auxilary map

includedSpecies

public java.util.HashMap includedSpecies

Map from cutted uris (after # separator) to BioPAXSpecies included into entities (these species group complex components, for example)

complexList

public java.util.HashMap complexList

Map from cutted uris (after # separator) to 'complex' entities

proteinList

public java.util.HashMap proteinList

Map from cutted uris (after # separator) to 'protein' entities

dnaList

public java.util.HashMap dnaList

Map from cutted uris (after # separator) to 'dna' entities

rnaList

public java.util.HashMap rnaList

Map from cutted uris (after # separator) to 'rna' entities

smallMoleculeList

public java.util.HashMap smallMoleculeList

Map from cutted uris (after # separator) to 'smallMolecule' entities

compartments

public java.util.Vector compartments

List of compartments (represented as openControlledVocabulary objects)

reactions

public java.util.HashMap reactions

Map from BioPAX conversion (cutted) uris to SBML reactions (represented by ReactionDocument.Reaction objects)

bioPAXreactions

public java.util.HashMap bioPAXreactions

Map from cutted uris (after # separator) to BioPAX 'conversion' objects

controls

public java.util.HashMap controls

Map from cutted uris (after # separator) to BioPAX 'control' objects

species

public java.util.HashMap species

Map from SBML species ids to SpeciesDocument.Species objects

Constructor Detail

BioPAXToSBMLConverter

public BioPAXToSBMLConverter()

Method Detail

populateSbml

public void populateSbml()
                  throws java.lang.Exception

Performs actual BioPAX->SBML conversion Requires this.biopax object to be specified

Throws:

java.lang.Exception

findIndependentSpecies

public void findIndependentSpecies()
                            throws java.lang.Exception

Procedure of groupping physicalEntityParticipants into BioPAXSpecies (chemical species)

Throws:

java.lang.Exception

addIncludedParticipant

public void addIncludedParticipant(physicalEntityParticipant part)
                            throws java.lang.Exception

Adds included physicalEntityParticipant (such as complex components)

Throws:

java.lang.Exception

getAllCompartments

public java.util.Vector getAllCompartments()
                                    throws java.lang.Exception

Throws:

java.lang.Exception

addConversionReaction

public void addConversionReaction(conversion conv,
                                  org.sbml.x2001.ns.celldesigner.ListOfReactionsDocument.ListOfReactions lr)
                           throws java.lang.Exception

Throws:

java.lang.Exception

addControl

public void addControl(control cntrl)
                throws java.lang.Exception

Throws:

java.lang.Exception

makeComment

public java.lang.String makeComment(java.util.Iterator comments)

getTypeForParticipant

public java.lang.String getTypeForParticipant(physicalEntityParticipant part)
                                       throws java.lang.Exception

Throws:

java.lang.Exception

makeLists

public void makeLists()
               throws java.lang.Exception

Fills all maps for needed conversion

Throws:

java.lang.Exception