Package | Description |
---|---|
org.sbml.jsbml |
Pure Java™ implementation of the data structures to represent all SBML
constructs.
|
org.sbml.jsbml.ext.arrays | |
org.sbml.jsbml.ext.distrib | |
org.sbml.jsbml.ext.qual |
Provides classes for the Qualitative Models package.
|
org.sbml.jsbml.ext.spatial |
Provides classes for the
Spatial Geometries and Processes package.
|
org.sbml.jsbml.math | |
org.sbml.jsbml.math.compiler | |
org.sbml.jsbml.util |
A collection of handy utilities when working with JSBML classes,
such as classes for String manipulation or mathematical operations.
|
org.sbml.jsbml.util.compilers |
The classes in this package can be used to evaluate the information
represented by abstract syntax trees (ASTNode objects).
|
org.sbml.jsbml.util.filters |
Filters are useful to decide whether or not to accept a certain item.
|
org.sbml.jsbml.validator.offline.constraints.helper |
Modifier and Type | Method | Description |
---|---|---|
static UnitDefinition |
UnitDefinition.area(int level,
int version) |
Returns the predefined unit for area.
|
UnitDefinition |
UnitDefinition.clone() |
|
static UnitDefinition |
Unit.convertToSI(Unit unit) |
Returns a UnitDefinition object which contains the argument Unit
converted to the appropriate SI unit.
|
UnitDefinition |
UnitDefinition.convertToSIAndSubstanceUnits() |
Converts this unit definition to using only SI units or valid SBML substance units.
|
UnitDefinition |
UnitDefinition.convertToSIUnits() |
Converts this unit definition to using only SI units and then call
simplify() . |
UnitDefinition |
UnitDefinition.convertToSIUnits(boolean simplify) |
Converts this unit definition to using only SI units.
|
UnitDefinition |
Model.createUnitDefinition() |
Creates a new
UnitDefinition inside this Model and returns
it. |
UnitDefinition |
Model.createUnitDefinition(java.lang.String id) |
Creates a new
UnitDefinition inside this Model and returns
it. |
UnitDefinition |
ASTNode.deriveUnit() |
Evaluates recursively this ASTNode and creates a new UnitDefinition with
respect of all referenced elements.
|
UnitDefinition |
UnitDefinition.divideBy(UnitDefinition definition) |
Divides this unit definition by the second unit definition.
|
UnitDefinition |
Model.findIdentical(UnitDefinition unitDefinition) |
Searches the first
UnitDefinition within this Model 's
Model.listOfUnitDefinitions that
is identical to the given UnitDefinition . |
UnitDefinition |
Model.findUnitDefinition(java.lang.String id) |
Returns a
UnitDefinition element that has the given 'id' within
this Model or null if no such element can be found. |
UnitDefinition |
Model.getAreaUnitsInstance() |
|
UnitDefinition |
Species.getDerivedSubstanceUnitDefinition() |
Returns the derived species substance units, never dividing by the compartment units.
|
UnitDefinition |
AbstractMathContainer.getDerivedUnitDefinition() |
|
UnitDefinition |
AbstractNamedSBaseWithUnit.getDerivedUnitDefinition() |
|
UnitDefinition |
Compartment.getDerivedUnitDefinition() |
|
UnitDefinition |
Event.getDerivedUnitDefinition() |
Deprecated.
|
UnitDefinition |
Reaction.getDerivedUnitDefinition() |
|
UnitDefinition |
SBaseWithDerivedUnit.getDerivedUnitDefinition() |
Derives the unit of this quantity and tries to identify an
equivalent
UnitDefinition within the corresponding Model . |
UnitDefinition |
Species.getDerivedUnitDefinition() |
|
UnitDefinition |
SpeciesReference.getDerivedUnitDefinition() |
|
UnitDefinition |
Model.getExtentUnitsInstance() |
Returns the
UnitDefinition instance which has the extent units ID
of this Model as id. |
UnitDefinition |
Model.getLengthUnitsInstance() |
Returns the length units of this
Model as a UnitDefinition . |
static UnitDefinition |
UnitDefinition.getPredefinedUnit(java.lang.String id,
int level,
int version) |
Returns the predefined unit with the given identifier for the
specified level and version combination or null if either for the given
combination of level and version there is no such predefined unit or the
identifier is not one of those belonging to the group of predefined unit
definitions.
|
UnitDefinition |
Model.getPredefinedUnitDefinition(java.lang.String unitKind) |
Returns a
UnitDefinition representing one of the predefined units
of SBML,
returns null if the given unit kind is not a valid one for the SBML
level
and version of this Model . |
UnitDefinition |
Species.getSpatialSizeUnitsInstance() |
Deprecated.
Only valid for SBML Level 2 Versions 1 and 2.
|
UnitDefinition |
KineticLaw.getSubstanceUnitsInstance() |
Deprecated.
|
UnitDefinition |
Model.getSubstanceUnitsInstance() |
|
UnitDefinition |
Species.getSubstanceUnitsInstance() |
Returns the substanceUnits of this Species as a
UnitDefinition instance. |
UnitDefinition |
Event.getTimeUnitsInstance() |
Deprecated.
|
UnitDefinition |
KineticLaw.getTimeUnitsInstance() |
Deprecated.
|
UnitDefinition |
Model.getTimeUnitsInstance() |
Gets the
UnitDefinition representing the time units of this
Model . |
UnitDefinition |
Model.getUnitDefinition(int n) |
Gets the nth
UnitDefinition object in this Model
. |
UnitDefinition |
Model.getUnitDefinition(java.lang.String id) |
Returns the
UnitDefinition of the Model.listOfUnitDefinitions
which has 'id' as id. |
UnitDefinition |
Model.getUnitDefinitionById(java.lang.String id) |
Returns a
UnitDefinition element that has the given 'id' within
this Model or null if no such element can be found. |
UnitDefinition |
AbstractNamedSBaseWithUnit.getUnitsInstance() |
|
UnitDefinition |
ASTNode.getUnitsInstance() |
Creates or obtains a
UnitDefinition corresponding to the unit
that has been set for this ASTNode and returns a pointer to it. |
UnitDefinition |
Compartment.getUnitsInstance() |
|
UnitDefinition |
Event.getUnitsInstance() |
Deprecated.
|
UnitDefinition |
ExplicitRule.getUnitsInstance() |
Deprecated.
This is a requirement for Level 1 Version 1 and Version 2,
but can only be used in conjunction with
Parameter s.
In this case this AssignmentRule represents the SBML
element ParameterRule. |
UnitDefinition |
KineticLaw.getUnitsInstance() |
Deprecated.
|
UnitDefinition |
SBaseWithUnit.getUnitsInstance() |
|
UnitDefinition |
Model.getVolumeUnitsInstance() |
|
static UnitDefinition |
UnitDefinition.length(int level,
int version) |
Returns the predefined unit for length.
|
UnitDefinition |
UnitDefinition.multiplyWith(UnitDefinition definition) |
Multiplies this unit with the given unit definition, i.e., adds a clone
of each unit object in the list of units of the given definition to the
list of this unit.
|
UnitDefinition |
UnitDefinition.raiseByThePowerOf(double exponent) |
Raises this unit definition by the power of the given exponent, i.e., the
exponents of every unit contained by this unit definition are multiplied
with the given exponent.
|
UnitDefinition |
Model.removeUnitDefinition(int n) |
Removes the n-th
UnitDefinition of the Model . |
UnitDefinition |
Model.removeUnitDefinition(java.lang.String id) |
Removes the
UnitDefinition of the Model with 'id' as id. |
UnitDefinition |
UnitDefinition.simplify() |
Simplifies the
UnitDefinition so that any Unit objects
occurring within the listOfUnits occurs only once. |
static UnitDefinition |
UnitDefinition.simplify(UnitDefinition ud) |
Returns a simplified version of the given
UnitDefinition . |
static UnitDefinition |
UnitDefinition.substance(int level,
int version) |
Returns the predefined unit for substance.
|
static UnitDefinition |
UnitDefinition.time(int level,
int version) |
Returns the predefined unit for time.
|
static UnitDefinition |
UnitDefinition.volume(int level,
int version) |
Returns the predefined unit for volume.
|
Modifier and Type | Method | Description |
---|---|---|
java.util.List<UnitDefinition> |
Model.getListOfPredefinedUnitDefinitions() |
Returns the list of predefined
UnitDefinition . |
ListOf<UnitDefinition> |
Model.getListOfUnitDefinitions() |
Returns the listOfUnitDefinitions of this
Model . |
ListOf<UnitDefinition> |
UnitDefinition.getParent() |
Modifier and Type | Method | Description |
---|---|---|
boolean |
Model.addUnitDefinition(UnitDefinition unitDefinition) |
|
static java.lang.String |
JSBML.addUnitDefinitionIfNotContained(Model model,
UnitDefinition units) |
Adds the given
UnitDefinition to the given model or returns the
identifier of an equivalent UnitDefinition that is already part
of the model. |
java.lang.String |
Model.addUnitDefinitionOrReturnIdenticalUnit(UnitDefinition units) |
Checks whether an identical
UnitDefinition like the given
UnitDefinition is already in this Model 's
Model.listOfUnitDefinitions . |
static boolean |
UnitDefinition.areCompatible(UnitDefinition ud1,
UnitDefinition ud2) |
Returns
true or false depending on
whether two UnitDefinition objects are compatible. |
static boolean |
UnitDefinition.areEquivalent(UnitDefinition ud,
java.lang.String units) |
Checks whether the given
UnitDefinition and the
UnitDefinition or Unit represented by the given
String are equivalent. |
static boolean |
UnitDefinition.areEquivalent(UnitDefinition ud1,
UnitDefinition ud2) |
Returns true or false depending on whether two
UnitDefinition objects are equivalent. |
static boolean |
UnitDefinition.areIdentical(UnitDefinition ud1,
UnitDefinition ud2) |
|
UnitDefinition |
UnitDefinition.divideBy(UnitDefinition definition) |
Divides this unit definition by the second unit definition.
|
UnitDefinition |
Model.findIdentical(UnitDefinition unitDefinition) |
Searches the first
UnitDefinition within this Model 's
Model.listOfUnitDefinitions that
is identical to the given UnitDefinition . |
static boolean |
UnitDefinition.isBuiltIn(UnitDefinition ud) |
Deprecated.
use
isPredefined() |
static boolean |
Unit.isPredefined(UnitDefinition ud) |
Tests whether the given
UnitDefinition belongs to the predefined
SBML units. |
static boolean |
UnitDefinition.isPredefined(UnitDefinition ud) |
Tests if the given unit is a predefined unit, meaning it is one of the five SBML predefined
unit identifiers ('substance', 'volume', 'area', 'length' or 'time').
|
UnitDefinition |
UnitDefinition.multiplyWith(UnitDefinition definition) |
Multiplies this unit with the given unit definition, i.e., adds a clone
of each unit object in the list of units of the given definition to the
list of this unit.
|
static java.lang.String |
UnitDefinition.printUnits(UnitDefinition ud) |
Returns a string that expresses the unit definition represented by this
UnitDefinition object.
|
static java.lang.String |
UnitDefinition.printUnits(UnitDefinition ud,
boolean compact) |
Returns a string that expresses the unit definition represented by this
UnitDefinition object.
|
boolean |
Model.removeUnitDefinition(UnitDefinition unitDefininition) |
Removes a
UnitDefinition of the Model . |
static void |
UnitDefinition.reorder(UnitDefinition ud) |
|
void |
Model.setAreaUnits(UnitDefinition areaUnits) |
Sets the areaUnitsID of this
Model to the id of the
UnitDefinition 'areaUnits'. |
void |
Model.setExtentUnits(UnitDefinition extentUnits) |
Sets the extentUnitsID of this
Model to the id of the
UnitDefinition 'extentUnits'. |
void |
Model.setLengthUnits(UnitDefinition lengthUnits) |
Sets the lengthUnitsID of this
Model to the id of the
UnitDefinition 'lengthUnits'. |
void |
Species.setSpatialSizeUnits(UnitDefinition spatialSizeUnits) |
Deprecated.
Only valid for SBML Level 2 Versions 1 and 2.
|
void |
Model.setSubstanceUnits(UnitDefinition substanceUnits) |
Sets the substanceUnitsID of this
Model to the id of
'substanceUnits'. |
void |
Species.setSubstanceUnits(UnitDefinition units) |
Sets the substanceUnitsID to the id of 'units'.
|
void |
Event.setTimeUnits(UnitDefinition timeUnits) |
Deprecated.
|
void |
KineticLaw.setTimeUnits(UnitDefinition timeUnits) |
Deprecated.
Only defined for Level 1 and Level 2 Version 1.
|
void |
Model.setTimeUnits(UnitDefinition timeUnits) |
Sets the timeUnitsID of this
Model to the id of the
UnitDefinition 'timeUnits'. |
void |
AbstractNamedSBaseWithUnit.setUnits(UnitDefinition units) |
|
void |
ASTNode.setUnits(UnitDefinition ud) |
|
void |
Compartment.setUnits(UnitDefinition unitDefinition) |
Set the unit attribute of this Compartment to the given unit definition.
|
void |
Event.setUnits(UnitDefinition timeUnits) |
Deprecated.
|
void |
ExplicitRule.setUnits(UnitDefinition units) |
Deprecated.
This is a requirement for Level 1 Version 1 and Version 2,
but can only be used in conjunction with
Parameter s.
In this case this AssignmentRule represents the SBML
element ParameterRule. |
void |
KineticLaw.setUnits(UnitDefinition units) |
Deprecated.
|
void |
SBaseWithUnit.setUnits(UnitDefinition units) |
Set the unit attribute of this
SBaseWithUnit to the given
unit definition. |
void |
Model.setVolumeUnits(UnitDefinition volumeUnits) |
Sets the volumeUnitsID of this
Model to the id of the
UnitDefinition 'volumeUnits'. |
static UnitDefinition |
UnitDefinition.simplify(UnitDefinition ud) |
Returns a simplified version of the given
UnitDefinition . |
Modifier and Type | Method | Description |
---|---|---|
void |
Model.setListOfUnitDefinitions(ListOf<UnitDefinition> listOfUnitDefinitions) |
Sets the listOfUnitDefinitions of this
Model to
'listOfUnitDefinitions'. |
Constructor | Description |
---|---|
UnitDefinition(UnitDefinition unitDefinition) |
Creates an
UnitDefinition instance from a given UnitDefinition. |
Modifier and Type | Method | Description |
---|---|---|
UnitDefinition |
Dimension.getDerivedUnitDefinition() |
Modifier and Type | Method | Description |
---|---|---|
UnitDefinition |
UncertParameter.getDerivedUnitDefinition() |
Modifier and Type | Method | Description |
---|---|---|
UnitDefinition |
Input.getDerivedUnitDefinition() |
|
UnitDefinition |
Output.getDerivedUnitDefinition() |
Modifier and Type | Method | Description |
---|---|---|
UnitDefinition |
CoordinateComponent.getDerivedUnitDefinition() |
|
UnitDefinition |
CoordinateComponent.getUnitsInstance() |
Modifier and Type | Method | Description |
---|---|---|
void |
CoordinateComponent.setUnits(UnitDefinition units) |
Modifier and Type | Method | Description |
---|---|---|
UnitDefinition |
ASTCnNumberNode.deriveUnit() |
Evaluates recursively this
ASTCnNumberNode and creates a new
UnitDefinition with respect to all referenced elements. |
UnitDefinition |
ASTCnNumberNode.getUnitsInstance() |
Creates or obtains a
UnitDefinition corresponding to the unit
that has been set for this ASTCnNumberNode and returns a pointer to it. |
Modifier and Type | Method | Description |
---|---|---|
UnitDefinition |
ASTNode2Value.getUnits() |
Modifier and Type | Method | Description |
---|---|---|
void |
ASTNode2Value.setUnits(UnitDefinition unit) |
|
static java.lang.String |
HTMLFormula.toHTML(UnitDefinition ud) |
Creates an HTML string representation of this UnitDefinition.
|
Constructor | Description |
---|---|
ASTNode2Value(UnitDefinition unit,
ASTNode2Compiler compiler) |
Modifier and Type | Method | Description |
---|---|---|
UnitDefinition |
ModelBuilder.buildUnitDefinition(java.lang.String id,
java.lang.String name,
Unit... units) |
Modifier and Type | Method | Description |
---|---|---|
Compartment |
ModelBuilder.buildCompartment(java.lang.String id,
boolean constant,
java.lang.String name,
double spatialDimensions,
double size,
UnitDefinition sizeUnits) |
|
Parameter |
ModelBuilder.buildParameter(java.lang.String id,
java.lang.String name,
double value,
boolean constant,
UnitDefinition units) |
|
Species |
ModelBuilder.buildSpecies(java.lang.String id,
java.lang.String name,
Compartment compartment,
boolean hasOnlySubstanceUnits,
boolean boundaryCondition,
boolean constant,
double initialConcentration,
UnitDefinition substanceUnits) |
|
static Unit |
ModelBuilder.buildUnit(UnitDefinition parent,
double multiplier,
int scale,
Unit.Kind kind,
double exponent) |
Modifier and Type | Method | Description |
---|---|---|
UnitDefinition |
ASTNodeValue.getUnits() |
Modifier and Type | Method | Description |
---|---|---|
void |
ASTNodeValue.setUnits(UnitDefinition unit) |
|
static java.lang.String |
HTMLFormula.toHTML(UnitDefinition ud) |
Creates an HTML string representation of this UnitDefinition.
|
Constructor | Description |
---|---|
ASTNodeValue(UnitDefinition unit,
ASTNodeCompiler compiler) |
Constructor | Description |
---|---|
IdenticalUnitDefinitionFilter(UnitDefinition ud) |
Initializes this
Filter with a UnitDefinition to be used in
the IdenticalUnitDefinitionFilter.accepts(Object) method for comparison. |
Modifier and Type | Method | Description |
---|---|---|
static boolean |
ValidationTools.areEquivalent(UnitDefinition ud1,
UnitDefinition ud2) |
Returns true or false depending on whether two
UnitDefinition objects are equivalent. |
static boolean |
ValidationTools.areIdentical(UnitDefinition ud1,
UnitDefinition ud2) |