org.sbml.jsbml.util

Class SubModel

java.lang.Object

org.sbml.jsbml.util.SubModel

public class SubModel
extends java.lang.Object

Generates a sub-Model containing the elements passed as argument and all the necessary dependencies.

You do not need to fill all of the parameter arrays. Here is how the sub-Model generation works:

• If you give some Compartment ids, all the species inside these Compartment are included.
• If you give some Species ids (and all added Species from the Compartments), all the Reactions where one of these Species is present are included
• All the Species involved in the Reactions given as parameter or added automatically from the given Species are included.
• All Compartments where one of the included species is present is included.
• All needed UnitDefinitions, SpeciesTypes and CompartmentTypes are included.
• All the Rules and events passed as parameter along the one needed are included.
• All the global Parameters are added automatically at the moment, without checking if there are used or not.
• All the FunctionDefinitions used in the included MathML are added automatically.

Since:

0.8

Version:

$Rev$

Author:

Nicolas Rodriguez, chenli

Constructor Summary

Constructors

Constructor and Description
SubModel()

Method Summary

Modifier and Type	Method and Description
private static boolean	contains(ListOf<? extends SimpleSpeciesReference> speciesReferences, Species species)
static SBMLDocument	generateSubModel(Model model, java.lang.String[] compartmentsIds, java.lang.String[] speciesIds, java.lang.String[] reactsIds) Generates a sub-model containing the elements passed as argument and all the necessary dependencies.
static SBMLDocument	generateSubModel(Model model, java.lang.String[] compartmentsIds, java.lang.String[] speciesIds, java.lang.String[] reactsIds, java.lang.String[] rulesIds, java.lang.String[] eventsIds) Generates a sub-model containing the elements passed as argument and all the necessary dependencies.
private static SBMLDocument	generateSubModel(Model model, java.lang.String[] compartmentsIds, java.lang.String[] speciesIds, java.lang.String[] reactsIds, java.lang.String[] rulesIds, java.lang.String[] eventsIds, boolean inclComp, boolean inclSpecies, boolean inclReact, boolean inclRules, boolean inclEvents) Creates a sub-model with the option to ignore certain items.
static java.lang.String[]	getRelatedCompartments(Model model, java.lang.String[] compartmentsIds, java.lang.String[] speciesIds)
private static java.lang.String[]	getRelatedEvents(Model model, java.lang.String[] eventsIds, java.lang.String[] compartmentsIds, java.lang.String[] speciesIds)
private static void	getRelatedFunctions(java.util.Set<java.lang.String> relatedFunctionsSet, java.util.Set<java.lang.String> allFunctionsIdSet, ASTNode mathNode)
private static void	getRelatedFunctionsId(java.util.Set<java.lang.String> relatedFunctionsSet, java.util.Set<java.lang.String> allFunctionsIdSet, ASTNode mathNode)
static java.lang.String[]	getRelatedReactions(Model model, java.lang.String[] reactsIds, java.lang.String[] speciesIds) Returns an array of reaction id related to the reactsIds or speciesIds.
private static java.lang.String[]	getRelatedRules(Model model, java.lang.String[] rulesIds, java.lang.String[] compartmentsIds, java.lang.String[] speciesIds)
static java.lang.String[]	getRelatedSpecies(Model model, java.lang.String[] reactsIds, java.lang.String[] compartmentsIds, java.lang.String[] speciesIds)
private static void	processUnitsMap(java.util.Map<java.lang.String,UnitDefinition> unitsMap, Model model, KineticLaw kineticLaw)
private static void	processUnitsMap(java.util.Map<java.lang.String,UnitDefinition> unitsMap, Model model, java.lang.String elementUnits)

Methods inherited from class java.lang.Object

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

Constructor Detail

SubModel

public SubModel()

Method Detail

generateSubModel

public static SBMLDocument generateSubModel(Model model,
                                            java.lang.String[] compartmentsIds,
                                            java.lang.String[] speciesIds,
                                            java.lang.String[] reactsIds)

Generates a sub-model containing the elements passed as argument and all the necessary dependencies.

Parameters:

model -

compartmentsIds -

speciesIds -

reactsIds -

Returns:

generateSubModel

public static SBMLDocument generateSubModel(Model model,
                                            java.lang.String[] compartmentsIds,
                                            java.lang.String[] speciesIds,
                                            java.lang.String[] reactsIds,
                                            java.lang.String[] rulesIds,
                                            java.lang.String[] eventsIds)

Generates a sub-model containing the elements passed as argument and all the necessary dependencies.

You do not need to fill all of the parameter arrays. Here is how the sub-Model generation works:

• If you give some Compartment ids, all the species inside these Compartment are included.
• If you give some Species ids (and all added Species from the Compartments), all the Reactions where one of these Species is present are included
• All the Species involved in the Reactions given as parameter or added automatically from the given Species are included.
• All Compartments where one of the included species is present is included.
• All needed UnitDefinitions, SpeciesTypes and CompartmentTypes are included.
• All the Rules and events passed as parameter along the one needed are included.
• All the global Parameters are added automatically at the moment, without checking if there are used or not.
• All the FunctionDefinitions used in the included MathML are added automatically.

Parameters:

model - the SBML model where we want to extract a sub-model.

compartmentsIds - the list of compartment to keep

speciesIds - the list of species to keep

reactsIds - the list of reactions to keep

rulesIds - the list of rules to keep

eventsIds - the list of events to keep

Returns:

a sub-model containing the elements passed as argument and all the necessary dependencies.

generateSubModel

private static SBMLDocument generateSubModel(Model model,
                                             java.lang.String[] compartmentsIds,
                                             java.lang.String[] speciesIds,
                                             java.lang.String[] reactsIds,
                                             java.lang.String[] rulesIds,
                                             java.lang.String[] eventsIds,
                                             boolean inclComp,
                                             boolean inclSpecies,
                                             boolean inclReact,
                                             boolean inclRules,
                                             boolean inclEvents)

Creates a sub-model with the option to ignore certain items.

Parameters:

model -

compartmentsIds -

speciesIds -

reactsIds -

rulesIds -

eventsIds -

inclComp -

inclSpecies -

inclReact -

inclRules -

inclEvents -

Returns:

processUnitsMap

private static void processUnitsMap(java.util.Map<java.lang.String,UnitDefinition> unitsMap,
                                    Model model,
                                    java.lang.String elementUnits)

Parameters:

unitsMap -

model - the original model from which a sub-model is to be created.

elementUnits -

processUnitsMap

private static void processUnitsMap(java.util.Map<java.lang.String,UnitDefinition> unitsMap,
                                    Model model,
                                    KineticLaw kineticLaw)

Parameters:

unitsMap -

model - the original model from which a sub-model is to be created.

kineticLaw -

contains

private static boolean contains(ListOf<? extends SimpleSpeciesReference> speciesReferences,
                                Species species)

Parameters:

speciesReferences -

species -

Returns:

getRelatedCompartments

public static java.lang.String[] getRelatedCompartments(Model model,
                                                        java.lang.String[] compartmentsIds,
                                                        java.lang.String[] speciesIds)

Parameters:

model - the original model from which a sub-model is to be created.

compartmentsIds -

speciesIds -

Returns:

getRelatedSpecies

public static java.lang.String[] getRelatedSpecies(Model model,
                                                   java.lang.String[] reactsIds,
                                                   java.lang.String[] compartmentsIds,
                                                   java.lang.String[] speciesIds)

Parameters:

model - the original model from which a sub-model is to be created.

reactsIds -

compartmentsIds -

speciesIds -

Returns:

an array of related species id or null if no related species are found.

getRelatedRules

private static java.lang.String[] getRelatedRules(Model model,
                                                  java.lang.String[] rulesIds,
                                                  java.lang.String[] compartmentsIds,
                                                  java.lang.String[] speciesIds)

Parameters:

model - the original model from which a sub-model is to be created.

rulesIds -

compartmentsIds -

speciesIds -

Returns:

getRelatedEvents

private static java.lang.String[] getRelatedEvents(Model model,
                                                   java.lang.String[] eventsIds,
                                                   java.lang.String[] compartmentsIds,
                                                   java.lang.String[] speciesIds)

Parameters:

model - the original model from which a sub-model is to be created.

eventsIds -

compartmentsIds -

speciesIds -

Returns:

getRelatedReactions

public static java.lang.String[] getRelatedReactions(Model model,
                                                     java.lang.String[] reactsIds,
                                                     java.lang.String[] speciesIds)

Returns an array of reaction id related to the reactsIds or speciesIds. All the reactions in reactsIds should be part of the result if the function is called properly with valid reacionId.
The Reactions, where the Species in the speciesIds array are involved as reactant, product or modifier, are added in the returned reaction id array.

Parameters:

model - the original model from which a sub-model is to be created.

reactsIds - the list of Reactions selected by the user to create a sub-model

speciesIds - the list of Species selected by the user to create a sub-model

Returns:

an array of related Reactions id or null if no related reactions are found.

getRelatedFunctionsId

private static void getRelatedFunctionsId(java.util.Set<java.lang.String> relatedFunctionsSet,
                                          java.util.Set<java.lang.String> allFunctionsIdSet,
                                          ASTNode mathNode)

Parameters:

relatedFunctionsSet -

allFunctionsIdSet -

mathNode -

getRelatedFunctions

private static void getRelatedFunctions(java.util.Set<java.lang.String> relatedFunctionsSet,
                                        java.util.Set<java.lang.String> allFunctionsIdSet,
                                        ASTNode mathNode)

Parameters:

relatedFunctionsSet -

allFunctionsIdSet -

mathNode -