public class ModelBuilder
extends java.lang.Object
Modifier and Type | Field | Description |
---|---|---|
static java.lang.String |
F_L |
Typical size scale of a cell, hence needed as default volume unit in CBM.
|
static java.lang.String |
HOUR |
Default time unit in constraint-based modeling (CBM), 3,600 seconds.
|
static java.lang.String |
MMOL_PER_G_DW |
Millimoles per gram of dry weight of a probe, used as extend units of
reactions.
|
static java.lang.String |
MMOL_PER_G_DW_PER_HR |
Extend units per time unit, millimoles per gram of dry weight.
|
Constructor | Description |
---|---|
ModelBuilder(int level,
int version) |
|
ModelBuilder(SBMLDocument doc) |
Modifier and Type | Method | Description |
---|---|---|
void |
buildCBMunits() |
Creates the default units needed in a constraint-based modeling context
|
Compartment |
buildCompartment(java.lang.String id,
boolean constant,
java.lang.String name,
double spatialDimensions,
double size,
java.lang.String sizeUnits) |
|
Compartment |
buildCompartment(java.lang.String id,
boolean constant,
java.lang.String name,
double spatialDimensions,
double size,
Unit.Kind sizeUnits) |
|
Compartment |
buildCompartment(java.lang.String id,
boolean constant,
java.lang.String name,
double spatialDimensions,
double size,
UnitDefinition sizeUnits) |
|
static KineticLaw |
buildKineticLaw(Reaction reaction,
java.lang.String formula,
Pair<java.lang.String,java.lang.Double>... localParameters) |
|
Model |
buildModel(java.lang.String id,
java.lang.String name) |
|
static void |
buildModifiers(Reaction reaction,
Pair<Species,java.lang.Integer>... modifiers) |
A convenient method to create multiple modifiers in one single step by
passing the
Species along with its role (SBO term) to this method. |
Parameter |
buildParameter(java.lang.String id,
java.lang.String name,
double value,
boolean constant,
java.lang.String units) |
|
Parameter |
buildParameter(java.lang.String id,
java.lang.String name,
double value,
boolean constant,
Unit.Kind units) |
|
Parameter |
buildParameter(java.lang.String id,
java.lang.String name,
double value,
boolean constant,
UnitDefinition units) |
|
static void |
buildProducts(Reaction reaction,
Pair<java.lang.Double,Species>... products) |
Convenient method to build multiple products together with their
stoichiometry in one step.
|
static void |
buildReactants(Reaction reaction,
Pair<java.lang.Double,Species>... reactants) |
Convenient method to build multiple reactants together with their
stoichiometry in one step.
|
Reaction |
buildReaction(java.lang.String id,
java.lang.String name,
java.lang.String compartment,
boolean fast,
boolean reversible) |
|
Reaction |
buildReaction(java.lang.String id,
java.lang.String name,
Compartment compartment,
boolean fast,
boolean reversible) |
|
Species |
buildSpecies(java.lang.String id,
java.lang.String name,
java.lang.String compartmentId,
boolean hasOnlySubstanceUnits,
boolean boundaryCondition,
boolean constant,
double initialConcentration,
java.lang.String substanceUnits) |
|
Species |
buildSpecies(java.lang.String id,
java.lang.String name,
Compartment compartment,
boolean hasOnlySubstanceUnits,
boolean boundaryCondition,
boolean constant,
double initialConcentration,
java.lang.String substanceUnits) |
|
Species |
buildSpecies(java.lang.String id,
java.lang.String name,
Compartment compartment,
boolean hasOnlySubstanceUnits,
boolean boundaryCondition,
boolean constant,
double initialConcentration,
Unit.Kind substanceUnits) |
|
Species |
buildSpecies(java.lang.String id,
java.lang.String name,
Compartment compartment,
boolean hasOnlySubstanceUnits,
boolean boundaryCondition,
boolean constant,
double initialConcentration,
UnitDefinition substanceUnits) |
|
Unit |
buildUnit(double multiplier,
int scale,
Unit.Kind kind,
double exponent) |
|
static Unit |
buildUnit(UnitDefinition parent,
double multiplier,
int scale,
Unit.Kind kind,
double exponent) |
|
UnitDefinition |
buildUnitDefinition(java.lang.String id,
java.lang.String name,
Unit... units) |
|
Model |
getModel() |
|
SBMLDocument |
getSBMLDocument() |
public static final java.lang.String HOUR
public static final java.lang.String F_L
public static final java.lang.String MMOL_PER_G_DW
public static final java.lang.String MMOL_PER_G_DW_PER_HR
public ModelBuilder(int level, int version)
level
- version
- public ModelBuilder(SBMLDocument doc)
doc
- public static KineticLaw buildKineticLaw(Reaction reaction, java.lang.String formula, Pair<java.lang.String,java.lang.Double>... localParameters) throws ParseException
reaction
- formula
- localParameters
- ParseException
public static void buildModifiers(Reaction reaction, Pair<Species,java.lang.Integer>... modifiers)
Species
along with its role (SBO term) to this method.public static void buildProducts(Reaction reaction, Pair<java.lang.Double,Species>... products)
true
for
convenience (as this is a required attribute).@SafeVarargs public static void buildReactants(Reaction reaction, Pair<java.lang.Double,Species>... reactants)
true
for
convenience (as this is a required attribute).public static Unit buildUnit(UnitDefinition parent, double multiplier, int scale, Unit.Kind kind, double exponent)
parent
- multiplier
- scale
- kind
- exponent
- public void buildCBMunits()
public Compartment buildCompartment(java.lang.String id, boolean constant, java.lang.String name, double spatialDimensions, double size, java.lang.String sizeUnits)
id
- constant
- name
- spatialDimensions
- size
- sizeUnits
- public Compartment buildCompartment(java.lang.String id, boolean constant, java.lang.String name, double spatialDimensions, double size, Unit.Kind sizeUnits)
id
- constant
- name
- spatialDimensions
- size
- sizeUnits
- public Compartment buildCompartment(java.lang.String id, boolean constant, java.lang.String name, double spatialDimensions, double size, UnitDefinition sizeUnits)
id
- constant
- name
- spatialDimensions
- size
- sizeUnits
- public Model buildModel(java.lang.String id, java.lang.String name)
id
- name
- public Parameter buildParameter(java.lang.String id, java.lang.String name, double value, boolean constant, java.lang.String units)
id
- name
- value
- constant
- units
- public Parameter buildParameter(java.lang.String id, java.lang.String name, double value, boolean constant, Unit.Kind units)
id
- name
- value
- constant
- units
- public Parameter buildParameter(java.lang.String id, java.lang.String name, double value, boolean constant, UnitDefinition units)
id
- name
- value
- constant
- units
- public Reaction buildReaction(java.lang.String id, java.lang.String name, Compartment compartment, boolean fast, boolean reversible)
id
- name
- compartment
- fast
- reversible
- public Reaction buildReaction(java.lang.String id, java.lang.String name, java.lang.String compartment, boolean fast, boolean reversible)
id
- name
- compartment
- fast
- reversible
- public Species buildSpecies(java.lang.String id, java.lang.String name, Compartment compartment, boolean hasOnlySubstanceUnits, boolean boundaryCondition, boolean constant, double initialConcentration, java.lang.String substanceUnits)
id
- name
- compartment
- hasOnlySubstanceUnits
- boundaryCondition
- constant
- initialConcentration
- substanceUnits
- public Species buildSpecies(java.lang.String id, java.lang.String name, Compartment compartment, boolean hasOnlySubstanceUnits, boolean boundaryCondition, boolean constant, double initialConcentration, Unit.Kind substanceUnits)
id
- name
- compartment
- hasOnlySubstanceUnits
- boundaryCondition
- constant
- initialConcentration
- substanceUnits
- public Species buildSpecies(java.lang.String id, java.lang.String name, Compartment compartment, boolean hasOnlySubstanceUnits, boolean boundaryCondition, boolean constant, double initialConcentration, UnitDefinition substanceUnits)
id
- name
- compartment
- hasOnlySubstanceUnits
- boundaryCondition
- constant
- initialConcentration
- substanceUnits
- public Species buildSpecies(java.lang.String id, java.lang.String name, java.lang.String compartmentId, boolean hasOnlySubstanceUnits, boolean boundaryCondition, boolean constant, double initialConcentration, java.lang.String substanceUnits)
id
- name
- compartmentId
- hasOnlySubstanceUnits
- boundaryCondition
- constant
- initialConcentration
- substanceUnits
- public UnitDefinition buildUnitDefinition(java.lang.String id, java.lang.String name, Unit... units)
id
- name
- public Model getModel()
public SBMLDocument getSBMLDocument()