public class BioPAXToSBMLConverter
extends java.lang.Object
Converts BioPAX (represented by BioPAX object) to SBML (represented by org.sbml.x2001.ns.celldesigner.SbmlDocument object)
Modifier and Type | Class and Description |
---|---|
class |
BioPAXToSBMLConverter.BioPAXSpecies
Represents BioPAX physicalEntityParticipants grouped into
distinctive chemical species (entity, characterized by
a definite location and a definite modification).
|
Modifier and Type | Field and Description |
---|---|
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 cut 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 cut uris (after # separator) to 'dna' entities
|
java.util.HashMap |
dnaRegionList
Map from cut uris (after # separator) to 'dnaRegion' entities
|
java.util.HashMap |
includedSpecies
Map from cut uris (after # separator) to BioPAXSpecies
included into entities (these species group complex
components, for example)
|
java.util.HashMap |
independentSpecies
Auxiliary map
|
java.util.HashMap |
independentSpeciesIds
Map from cut uris (after # separator) to BioPAXSpecies
|
java.util.HashMap |
proteinList
Map from cut 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 cut uris (after # separator) to 'rna' entities
|
java.util.HashMap |
rnaRegionList
Map from cut uris (after # separator) to 'rnaRegion' entities
|
SbmlDocument |
sbmlDoc
Result of conversion
|
java.util.HashMap |
smallMoleculeList
Map from cut 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 and Description |
---|
BioPAXToSBMLConverter() |
Modifier and Type | Method and Description |
---|---|
void |
addControl(Control cntrl) |
void |
addConversionReaction(Conversion conv,
ListOfReactionsDocument.ListOfReactions lr) |
void |
addIncludedParticipant(PhysicalEntity pe)
Adds included PhysicalEntity (such as the components of a complex)
|
void |
addInteractionReaction(Interaction inter,
ListOfReactionsDocument.ListOfReactions lr) |
void |
addModifierToReaction(java.lang.String reaction_id,
BioPAXToSBMLConverter.BioPAXSpecies part) |
void |
findIndependentSpecies()
Procedure of grouping physicalEntityParticipants into
BioPAXSpecies (chemical species)
|
java.util.Vector |
getAllCompartments() |
java.lang.String |
getTypeForParticipant(PhysicalEntity pe)
Determine the type (Complex, Protein, Dna, etc.) of a given Physical Entity
|
java.lang.String |
makeComment(java.util.Iterator comments)
Compile comments in a string from an iterator, with each comment on a different line.
|
void |
makeLists()
Fills hashmaps(URI, Object) with Protein, Dna, Rna and SmallMolecule Objects for needed conversion.
|
void |
populateSbml()
Performs actual BioPAX->SBML conversion
Requires this.biopax object to be specified
|
public SbmlDocument sbmlDoc
public BioPAX biopax
public BioPAXNamingService bpnm
public static boolean alwaysMentionCompartment
public static boolean useBiopaxModelOntology
public static boolean considerCompartmentNameRatherThanId
public java.util.HashMap independentSpeciesIds
public java.util.HashMap independentSpecies
public java.util.HashMap includedSpecies
public java.util.HashMap complexList
public java.util.HashMap proteinList
public java.util.HashMap dnaList
public java.util.HashMap dnaRegionList
public java.util.HashMap rnaList
public java.util.HashMap rnaRegionList
public java.util.HashMap smallMoleculeList
public java.util.Vector compartments
public java.util.HashMap reactions
public java.util.HashMap bioPAXreactions
public java.util.HashMap controls
public java.util.HashMap species
public void populateSbml() throws java.lang.Exception
java.lang.Exception
public void findIndependentSpecies() throws java.lang.Exception
java.lang.Exception
public void addIncludedParticipant(PhysicalEntity pe) throws java.lang.Exception
java.lang.Exception
public java.util.Vector getAllCompartments() throws java.lang.Exception
java.lang.Exception
public void addConversionReaction(Conversion conv, ListOfReactionsDocument.ListOfReactions lr) throws java.lang.Exception
java.lang.Exception
public void addInteractionReaction(Interaction inter, ListOfReactionsDocument.ListOfReactions lr) throws java.lang.Exception
java.lang.Exception
public void addModifierToReaction(java.lang.String reaction_id, BioPAXToSBMLConverter.BioPAXSpecies part)
public void addControl(Control cntrl) throws java.lang.Exception
java.lang.Exception
public java.lang.String makeComment(java.util.Iterator comments)
Iterator
- of Stringpublic java.lang.String getTypeForParticipant(PhysicalEntity pe) throws java.lang.Exception
pe
- PhysicalEntity Objectjava.lang.Exception
public void makeLists() throws java.lang.Exception
java.lang.Exception