public class CellDesignerToBioPAXConverter
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
static boolean |
alwaysMentionCompartment
Check to include compartment label in the name
|
java.util.HashMap<java.lang.String,CelldesignerAntisenseRNADocument.CelldesignerAntisenseRNA> |
asrnas |
BioPAX |
biopax
The result of the conversion
|
java.util.HashMap |
cellDesignerTerms
Map from CellDesigner terms (strings) to OpenControlledVocabulary objects
|
java.util.HashMap<java.lang.String,CellularLocationVocabulary> |
cellularLocationVocabularyHash |
java.util.HashMap<java.lang.String,CompartmentDocument.Compartment> |
compartmentHash
Map from compartment ids to CompartmentDocument.Compartment objects
|
java.util.HashMap<java.lang.String,CelldesignerComplexSpeciesAliasDocument.CelldesignerComplexSpeciesAlias> |
complexes
Map of CellDesigner CelldesignerComplexSpeciesAliasDocument.CelldesignerComplexSpeciesAlias objects
|
java.util.HashMap<java.lang.String,PhysicalEntity> |
entities |
java.util.HashMap<java.lang.String,EntityReference> |
entityReferences |
java.lang.String |
filename
Name of CellDesigner file
|
java.util.HashMap<java.lang.String,CelldesignerGeneDocument.CelldesignerGene> |
genes |
java.util.HashMap<java.lang.String,CelldesignerSpeciesDocument.CelldesignerSpecies> |
includedSpecies |
java.util.HashMap<java.lang.String,CelldesignerProteinDocument.CelldesignerProtein> |
proteins
Map of CellDesigner Celldesigner entity objects
|
java.util.HashMap |
pubmedrefsHash
Map from Pubmed ids to publicationXref objects
|
java.util.HashMap<java.lang.String,ReactionDocument.Reaction> |
reactions
Map of CellDesigner ReactionDocument.Reaction objects
|
java.util.HashMap<java.lang.String,CelldesignerRNADocument.CelldesignerRNA> |
rnas |
org.sbml.x2001.ns.celldesigner.SbmlDocument |
sbml
Java xml-beans mapping of CellDesigner file
|
java.util.HashMap<java.lang.String,SpeciesDocument.Species> |
species
Map of CellDesigner SpeciesDocument.Species objects
|
static boolean |
useBiopaxModelOntology
not used
|
Constructor and Description |
---|
CellDesignerToBioPAXConverter() |
Modifier and Type | Method and Description |
---|---|
void |
addModification(java.lang.String sp_id,
PhysicalEntity pep,
CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity si) |
void |
addPublicationXrefsToEntity(Entity ent,
java.util.Vector v) |
void |
addPublicationXrefsToEntityReference(EntityReference ent,
java.util.Vector v) |
BioPAX |
convert()
The main conversion function to be used from outside
|
static java.lang.String |
correctName(java.lang.String s)
Eliminates spaces, stars, dashes from the string
|
void |
createCellDesignerTerms()
Encodes a list of standard terms (protein modification types (GOs) and
influence types) by controlledVocabulary terms
|
PhysicalEntity |
createEntityForHomodimer(java.lang.String id,
java.util.HashMap<java.lang.String,SpeciesDocument.Species> species,
java.util.Vector complexes_list,
java.util.HashMap<java.lang.String,PhysicalEntity> entities,
java.util.HashMap<java.lang.String,EntityReference> entityReferences,
SbmlDocument.Sbml sbml,
BioPAX biopax,
java.lang.String rId) |
PhysicalEntity |
createEntityForSpecies(java.lang.String id,
java.util.HashMap<java.lang.String,SpeciesDocument.Species> species,
java.util.Vector complexes_list,
java.util.HashMap<java.lang.String,PhysicalEntity> entities,
java.util.HashMap<java.lang.String,EntityReference> entityReferences,
SbmlDocument.Sbml sbml,
BioPAX biopax,
java.lang.String rId) |
PhysicalEntity |
createEntityForSpecies(java.lang.String id,
SbmlDocument.Sbml sbml,
BioPAX biopax)
Makes a physical entity from CellDesigner species
|
PhysicalEntity |
createEntityForSpecies(java.lang.String id,
SbmlDocument.Sbml sbml,
BioPAX biopax,
boolean complexComponent) |
java.util.Vector |
extractPubMedReferenceFromComment(java.lang.String comment)
Extracts pubmed ids from a string in the form PMID: xxxxxx and creates publicationXref list
|
CelldesignerAntisenseRNADocument.CelldesignerAntisenseRNA |
getAntisenseRNAById(java.lang.String pid) |
static java.util.HashMap<java.lang.String,CelldesignerAntisenseRNADocument.CelldesignerAntisenseRNA> |
getAntisenseRNAs(SbmlDocument.Sbml sbml) |
static java.util.HashMap |
getCompartmentHash(SbmlDocument.Sbml sbml)
Creates the map of compartments
|
CelldesignerComplexSpeciesAliasDocument.CelldesignerComplexSpeciesAlias |
getComplexById(java.lang.String id) |
static java.util.HashMap<java.lang.String,CelldesignerComplexSpeciesAliasDocument.CelldesignerComplexSpeciesAlias> |
getComplexes(SbmlDocument.Sbml sbml)
Creates the list of complexes
|
static java.util.HashMap<java.lang.String,CelldesignerGeneDocument.CelldesignerGene> |
getGenes(SbmlDocument.Sbml sbml)
Creates the list of genes
|
static java.util.HashMap<java.lang.String,CelldesignerSpeciesDocument.CelldesignerSpecies> |
getIncludedSpecies(SbmlDocument.Sbml sbml) |
CelldesignerProteinDocument.CelldesignerProtein |
getProteinById(java.lang.String pid) |
static java.util.HashMap<java.lang.String,CelldesignerProteinDocument.CelldesignerProtein> |
getProteins(SbmlDocument.Sbml sbml)
Creates the list of proteins
|
ReactionDocument.Reaction |
getReactionById(java.lang.String id) |
static java.util.HashMap<java.lang.String,ReactionDocument.Reaction> |
getReactions(SbmlDocument.Sbml sbml)
Creates the list of reactions
|
CelldesignerRNADocument.CelldesignerRNA |
getRNAById(java.lang.String pid) |
static java.util.HashMap<java.lang.String,CelldesignerRNADocument.CelldesignerRNA> |
getRNAs(SbmlDocument.Sbml sbml) |
static java.util.HashMap<java.lang.String,SpeciesDocument.Species> |
getSpecies(SbmlDocument.Sbml sbml)
Creates the list of species
|
SpeciesDocument.Species |
getSpeciesById(java.lang.String id) |
static boolean |
isRealReaction(ReactionDocument.Reaction r,
SbmlDocument.Sbml sbml)
Returns true if the reaction r describes real interaction (not influence on a phenotype, for example)
|
void |
populateModel() |
void |
populateModelnew()
The converter itself
|
public static boolean alwaysMentionCompartment
public static boolean useBiopaxModelOntology
public java.util.HashMap<java.lang.String,SpeciesDocument.Species> species
public java.util.HashMap<java.lang.String,CelldesignerSpeciesDocument.CelldesignerSpecies> includedSpecies
public java.util.HashMap<java.lang.String,ReactionDocument.Reaction> reactions
public java.util.HashMap<java.lang.String,CelldesignerComplexSpeciesAliasDocument.CelldesignerComplexSpeciesAlias> complexes
public java.util.HashMap<java.lang.String,CelldesignerProteinDocument.CelldesignerProtein> proteins
public java.util.HashMap<java.lang.String,CelldesignerGeneDocument.CelldesignerGene> genes
public java.util.HashMap<java.lang.String,CelldesignerRNADocument.CelldesignerRNA> rnas
public java.util.HashMap<java.lang.String,CelldesignerAntisenseRNADocument.CelldesignerAntisenseRNA> asrnas
public java.util.HashMap<java.lang.String,EntityReference> entityReferences
public java.util.HashMap<java.lang.String,PhysicalEntity> entities
public java.lang.String filename
public org.sbml.x2001.ns.celldesigner.SbmlDocument sbml
public BioPAX biopax
public java.util.HashMap<java.lang.String,CompartmentDocument.Compartment> compartmentHash
public java.util.HashMap<java.lang.String,CellularLocationVocabulary> cellularLocationVocabularyHash
public java.util.HashMap pubmedrefsHash
public java.util.HashMap cellDesignerTerms
public BioPAX convert()
public void populateModelnew()
public void populateModel()
public static java.util.HashMap<java.lang.String,CelldesignerProteinDocument.CelldesignerProtein> getProteins(SbmlDocument.Sbml sbml)
public static java.util.HashMap<java.lang.String,CelldesignerGeneDocument.CelldesignerGene> getGenes(SbmlDocument.Sbml sbml)
public static java.util.HashMap<java.lang.String,CelldesignerRNADocument.CelldesignerRNA> getRNAs(SbmlDocument.Sbml sbml)
public static java.util.HashMap<java.lang.String,CelldesignerAntisenseRNADocument.CelldesignerAntisenseRNA> getAntisenseRNAs(SbmlDocument.Sbml sbml)
public CelldesignerProteinDocument.CelldesignerProtein getProteinById(java.lang.String pid)
public CelldesignerRNADocument.CelldesignerRNA getRNAById(java.lang.String pid)
public CelldesignerAntisenseRNADocument.CelldesignerAntisenseRNA getAntisenseRNAById(java.lang.String pid)
public static java.util.HashMap<java.lang.String,ReactionDocument.Reaction> getReactions(SbmlDocument.Sbml sbml)
public ReactionDocument.Reaction getReactionById(java.lang.String id)
public static java.util.HashMap<java.lang.String,SpeciesDocument.Species> getSpecies(SbmlDocument.Sbml sbml)
public static java.util.HashMap<java.lang.String,CelldesignerSpeciesDocument.CelldesignerSpecies> getIncludedSpecies(SbmlDocument.Sbml sbml)
public SpeciesDocument.Species getSpeciesById(java.lang.String id)
public static java.util.HashMap<java.lang.String,CelldesignerComplexSpeciesAliasDocument.CelldesignerComplexSpeciesAlias> getComplexes(SbmlDocument.Sbml sbml)
public CelldesignerComplexSpeciesAliasDocument.CelldesignerComplexSpeciesAlias getComplexById(java.lang.String id)
public static java.util.HashMap getCompartmentHash(SbmlDocument.Sbml sbml)
public PhysicalEntity createEntityForSpecies(java.lang.String id, SbmlDocument.Sbml sbml, BioPAX biopax) throws java.lang.Exception
java.lang.Exception
public PhysicalEntity createEntityForSpecies(java.lang.String id, SbmlDocument.Sbml sbml, BioPAX biopax, boolean complexComponent) throws java.lang.Exception
java.lang.Exception
public PhysicalEntity createEntityForSpecies(java.lang.String id, java.util.HashMap<java.lang.String,SpeciesDocument.Species> species, java.util.Vector complexes_list, java.util.HashMap<java.lang.String,PhysicalEntity> entities, java.util.HashMap<java.lang.String,EntityReference> entityReferences, SbmlDocument.Sbml sbml, BioPAX biopax, java.lang.String rId)
public void addModification(java.lang.String sp_id, PhysicalEntity pep, CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity si) throws java.lang.Exception
java.lang.Exception
public PhysicalEntity createEntityForHomodimer(java.lang.String id, java.util.HashMap<java.lang.String,SpeciesDocument.Species> species, java.util.Vector complexes_list, java.util.HashMap<java.lang.String,PhysicalEntity> entities, java.util.HashMap<java.lang.String,EntityReference> entityReferences, SbmlDocument.Sbml sbml, BioPAX biopax, java.lang.String rId)
public java.util.Vector extractPubMedReferenceFromComment(java.lang.String comment)
public void addPublicationXrefsToEntity(Entity ent, java.util.Vector v)
public void addPublicationXrefsToEntityReference(EntityReference ent, java.util.Vector v)
public static java.lang.String correctName(java.lang.String s)
public void createCellDesignerTerms()
public static boolean isRealReaction(ReactionDocument.Reaction r, SbmlDocument.Sbml sbml)