libSBML C# API
libSBML 5.8.0 C# API
|
Implementation of SBML's Species construct.
A species in SBML refers to a pool of entities that (a) are considered indistinguishable from each other for the purposes of the model, (b) participate in reactions, and (c) are located in a specific compartment. The SBML Species object class is intended to represent these pools.
As with other major constructs in SBML, Species has a mandatory attribute, 'id', used to give the species type an identifier in the model. The identifier must be a text string conforming to the identifer syntax permitted in SBML. Species also has an optional 'name' attribute, of type string
. The 'id' and 'name' must be used according to the guidelines described in the SBML specifications.
The required attribute 'compartment' is used to identify the compartment in which the species is located. The attribute's value must be the identifier of an existing Compartment object. It is important to note that there is no default value for the 'compartment' attribute on Species; every species in an SBML model must be assigned a compartment explicitly. (This also implies that every model with one or more Species objects must define at least one Compartment object.)
The optional attributes 'initialAmount' and 'initialConcentration', both having a data type of double
, can be used to set the initial quantity of the species in the compartment where the species is located. These attributes are mutually exclusive; i.e., only one can have a value on any given instance of a Species object. Missing 'initialAmount' and 'initialConcentration' values implies that their values either are unknown, or to be obtained from an external source, or determined by an InitialAssignment or other SBML construct elsewhere in the model.
A species' initial quantity in SBML is set by the 'initialAmount' or 'initialConcentration' attribute exactly once. If the 'constant' attribute is true
, then the value of the species' quantity is fixed and cannot be changed except by an InitialAssignment. These methods differ in that the 'initialAmount' and 'initialConcentration' attributes can only be used to set the species quantity to a literal floating-point number, whereas the use of an InitialAssignment object allows the value to be set using an arbitrary mathematical expression (which, thanks to MathML's expressiveness, may evaluate to a rational number). If the species' 'constant' attribute is false
, the species' quantity value may be overridden by an InitialAssignment or changed by AssignmentRule or AlgebraicRule, and in addition, for t > 0, it may also be changed by a RateRule, Event objects, and as a result of being a reactant or product in one or more Reaction objects. (However, some constructs are mutually exclusive; see the SBML specifications for the precise details.) It is not an error to define 'initialAmount' or 'initialConcentration' on a species and also redefine the value using an InitialAssignment, but the 'initialAmount' or 'initialConcentration' setting in that case is ignored. The SBML specifications provide additional information about the semantics of assignments, rules and values for simulation time t <= 0.
SBML Level 2 additionally stipulates that in cases where a species' compartment has a 'spatialDimensions' value of 0
(zero), the species cannot have a value for 'initialConcentration' because the concepts of concentration and density break down when a container has zero dimensions.
When the attribute 'initialAmount' is set, the unit of measurement associated with the value of 'initialAmount' is specified by the Species attribute 'substanceUnits'. When the 'initialConcentration' attribute is set, the unit of measurement associated with this concentration value is {unit of amount} divided by {unit of size}, where the {unit of amount} is specified by the Species 'substanceUnits' attribute, and the {unit of size} is specified by the 'units' attribute of the Compartment object in which the species is located. Note that in either case, a unit of amount is involved and determined by the 'substanceUnits' attribute. Note these two attributes alone do not determine the units of the species when the species identifier appears in a mathematical expression; that aspect is determined by the attribute 'hasOnlySubstanceUnits' discussed below.
In SBML Level 3, if the 'substanceUnits' attribute is not set on a given Species object instance, then the unit of amount for that species is inherited from the 'substanceUnits' attribute on the enclosing Model object instance. If that attribute on Model is not set either, then the unit associated with the species' quantity is undefined.
In SBML Level 2, if the 'substanceUnits' attribute is not set on a given Species object instance, then the unit of amount for that species is taken from the predefined SBML unit identifier 'substance'
. The value assigned to 'substanceUnits' must be chosen from one of the following possibilities: one of the base unit identifiers defined in SBML, the built-in unit identifier 'substance'
, or the identifier of a new unit defined in the list of unit definitions in the enclosing Model object. The chosen units for 'substanceUnits' must be be 'dimensionless'
, 'mole'
, 'item'
, 'kilogram'
, 'gram'
, or units derived from these.
As noted at the beginning of this section, simply setting 'initialAmount' or 'initialConcentration' alone does not determine whether a species identifier represents an amount or a concentration when it appears elsewhere in an SBML model. The role of the attribute 'hasOnlySubstanceUnits' is to indicate whether the units of the species, when the species identifier appears in mathematical formulas, are intended to be concentration or amount. The attribute takes on a bool value. In SBML Level 3, the attribute has no default value and must always be set in a model; in SBML Level 2, it has a default value of false
.
The units of the species are used in the following ways:
When the species' identifier appears in a MathML formula, it represents the species' quantity, and the unit of measurement associated with the quantity is as described above.
The 'math' elements of AssignmentRule, InitialAssignment and EventAssignment objects referring to this species should all have the same units as the unit of measurement associated with the species quantity.
In a RateRule object that defines the rate of change of the species' quantity, the unit associated with the rule's 'math' element should be equal to the unit of the species' quantity divided by the model-wide unit of time; in other words, {unit of species quantity}/{unit of time}.
The Species object class has two bool attributes named 'constant' and 'boundaryCondition', used to indicate whether and how the quantity of that species can vary during a simulation. In SBML Level 2 they are optional; in SBML Level 3 they are mandatory. The following table shows how to interpret the combined values of these attributes.
constant value |
boundaryCondition value |
Can have assignment or rate rule? |
Can be reactant or product? |
Species' quantity can be changed by |
---|---|---|---|---|
true |
true |
no | yes | (never changes) |
false |
true |
yes | yes | rules and events |
true |
false |
no | no | (never changes) |
false |
false |
yes | yes | reactions or rules (but not both at the same time), and events |
By default, when a species is a product or reactant of one or more reactions, its quantity is determined by those reactions. In SBML, it is possible to indicate that a given species' quantity is not determined by the set of reactions even when that species occurs as a product or reactant; i.e., the species is on the boundary of the reaction system, and its quantity is not determined by the reactions. The bool attribute 'boundaryCondition' can be used to indicate this. A value of false
indicates that the species is part of the reaction system. In SBML Level 2, the attribute has a default value of false
, while in SBML Level 3, it has no default.
The 'constant' attribute indicates whether the species' quantity can be changed at all, regardless of whether by reactions, rules, or constructs other than InitialAssignment. A value of false
indicates that the species' quantity can be changed. (This is also a common value because the purpose of most simulations is precisely to calculate changes in species quantities.) In SBML Level 2, the attribute has a default value of false
, while in SBML Level 3, it has no default. Note that the initial quantity of a species can be set by an InitialAssignment irrespective of the value of the 'constant' attribute.
In practice, a 'boundaryCondition' value of true
means a differential equation derived from the reaction definitions should not be generated for the species. However, the species' quantity may still be changed by AssignmentRule, RateRule, AlgebraicRule, Event, and InitialAssignment constructs if its 'constant' attribute is false
. Conversely, if the species' 'constant' attribute is true
, then its value cannot be changed by anything except InitialAssignment.
A species having 'boundaryCondition'=false
and 'constant'=false
can appear as a product and/or reactant of one or more reactions in the model. If the species is a reactant or product of a reaction, it must not also appear as the target of any AssignmentRule or RateRule object in the model. If instead the species has 'boundaryCondition'=false
and 'constant'=true
, then it cannot appear as a reactant or product, or as the target of any AssignmentRule, RateRule or EventAssignment object in the model.
In SBML Level 3, Species has an additional optional attribute, 'conversionFactor', that defines a conversion factor that applies to a particular species. The value must be the identifier of a Parameter object instance defined in the model. That Parameter object must be a constant, meaning its 'constant' attribute must be set to true
. If a given Species object definition defines a value for its 'conversionFactor' attribute, it takes precedence over any factor defined by the Model object's 'conversionFactor' attribute.
The unit of measurement associated with a species' quantity can be different from the unit of extent of reactions in the model. SBML Level 3 avoids implicit unit conversions by providing an explicit way to indicate any unit conversion that might be required. The use of a conversion factor in computing the effects of reactions on a species' quantity is explained in detail in the SBML Level 3 specification document. Because the value of the 'conversionFactor' attribute is the identifier of a Parameter object, and because parameters can have units attached to them, the transformation from reaction extent units to species units can be completely specified using this approach.
Note that the unit conversion factor is only applied when calculating the effect of a reaction on a species. It is not used in any rules or other SBML constructs that affect the species, and it is also not used when the value of the species is referenced in a mathematical expression.
In SBML Level 2 Versions 2–4, each species in a model may optionally be designated as belonging to a particular species type. The optional attribute 'speciesType' is used to identify the species type of the chemical entities that make up the pool represented by the Species objects. The attribute's value must be the identifier of an existing SpeciesType object in the model. If the 'speciesType' attribute is not present on a particular species definition, it means the pool contains chemical entities of a type unique to that pool; in effect, a virtual species type is assumed for that species, and no other species can belong to that species type. The value of 'speciesType' attributes on species have no effect on the numerical interpretation of a model; simulators and other numerical analysis software may ignore 'speciesType' attributes.
There can be only one species of a given species type in any given compartment of a model. More specifically, for all Species objects having a value for the 'speciesType' attribute, the pair
must be unique across the set of all Species object in a model.
In versions of SBML Level 2 before Version 3, the class Species included an attribute called 'spatialSizeUnits', which allowed explicitly setting the units of size for initial concentration. LibSBML retains this attribute for compatibility with older definitions of Level 2, but its use is strongly discouraged because many software tools do no properly interpret this unit declaration and it is incompatible with all SBML specifications after Level 2 Version 3.
Species are unique in SBML in that they have a kind of duality: a species identifier may stand for either substance amount (meaning, a count of the number of individual entities) or a concentration or density (meaning, amount divided by a compartment size). The previous sections explain the meaning of a species identifier when it is referenced in a mathematical formula or in rules or other SBML constructs; however, it remains to specify what happens to a species when the compartment in which it is located changes in size.
When a species definition has a 'hasOnlySubstanceUnits' attribute value of false
and the size of the compartment in which the species is located changes, the default in SBML is to assume that it is the concentration that must be updated to account for the size change. This follows from the principle that, all other things held constant, if a compartment simply changes in size, the size change does not in itself cause an increase or decrease in the number of entities of any species in that compartment. In a sense, the default is that the amount of a species is preserved across compartment size changes. Upon such size changes, the value of the concentration or density must be recalculated from the simple relationship concentration = amount / size if the value of the concentration is needed (for example, if the species identifier appears in a mathematical formula or is otherwise referenced in an SBML construct). There is one exception: if the species' quantity is determined by an AssignmentRule, RateRule, AlgebraicRule, or an EventAssignment and the species has a 'hasOnlySubstanceUnits' attribute value of false
, it means that the concentration is assigned by the rule or event; in that case, the amount must be calculated when the compartment size changes. (Events also require additional care in this situation, because an event with multiple assignments could conceivably reassign both a species quantity and a compartment size simultaneously. Please refer to the SBML specifications for the details.)
Note that the above only matters if a species has a 'hasOnlySubstanceUnits' attribute value of false
, meaning that the species identifier refers to a concentration wherever the identifier appears in a mathematical formula. If instead the attribute's value is true
, then the identifier of the species always stands for an amount wherever it appears in a mathematical formula or is referenced by an SBML construct. In that case, there is never a question about whether an assignment or event is meant to affect the amount or concentration: it is always the amount.
A particularly confusing situation can occur when the species has 'constant' attribute value of true
in combination with a 'hasOnlySubstanceUnits' attribute value of false
. Suppose this species is given a value for 'initialConcentration'. Does a 'constant' value of true
mean that the concentration is held constant if the compartment size changes? No; it is still the amount that is kept constant across a compartment size change. The fact that the species was initialized using a concentration value is irrelevant.
Public Member Functions | |
int | addCVTerm (CVTerm term, bool newBag) |
Adds a copy of the given CVTerm object to this SBML object. More... | |
int | addCVTerm (CVTerm term) |
Adds a copy of the given CVTerm object to this SBML object. More... | |
int | appendAnnotation (XMLNode annotation) |
Appends the given annotation to the 'annotation' subelement of this object. More... | |
int | appendAnnotation (string annotation) |
Appends the given annotation to the 'annotation' subelement of this object. More... | |
int | appendNotes (XMLNode notes) |
Appends the given notes to the 'notes' subelement of this object. More... | |
int | appendNotes (string notes) |
Appends the given notes to the 'notes' subelement of this object. More... | |
int | checkCompatibility (SBase arg0) |
Subclasses should override this method to write out their contained SBML objects as XML elements. More... | |
string | checkMathMLNamespace (XMLToken elem) |
Subclasses should override this method to write out their contained SBML objects as XML elements. More... | |
new Species | clone () |
Creates and returns a deep copy of this Species object. More... | |
void | connectToChild () |
Sets this SBML object to child SBML objects (if any). More... | |
void | connectToParent (SBase parent) |
Sets the parent SBML object of this SBML object. More... | |
int | disablePackage (string pkgURI, string pkgPrefix) |
Disables the given SBML Level 3 package. More... | |
override void | Dispose () |
void | divideAssignmentsToSIdByFunction (string id, ASTNode function) |
If the function of this object is to assign a value has a child 'math' object (or anything with ASTNodes in general), replace the 'math' object with the function (existing/function). More... | |
int | enablePackage (string pkgURI, string pkgPrefix, bool flag) |
Enables or disables the given SBML Level 3 package. More... | |
void | enablePackageInternal (string pkgURI, string pkgPrefix, bool flag) |
Enables/Disables the given package with this element and child elements (if any). More... | |
override bool | Equals (Object sb) |
SBase | getAncestorOfType (int type, string pkgName) |
Returns the first ancestor object that has the given SBML type code. More... | |
SBase | getAncestorOfType (int type) |
Returns the first ancestor object that has the given SBML type code. More... | |
XMLNode | getAnnotation () |
Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects. More... | |
string | getAnnotationString () |
Returns the content of the 'annotation' subelement of this object as a character string. More... | |
bool | getBoundaryCondition () |
Get the value of the 'boundaryCondition' attribute. More... | |
int | getCharge () |
Get the value of the 'charge' attribute. More... | |
long | getColumn () |
Returns the column number on which this object first appears in the XML representation of the SBML document. More... | |
string | getCompartment () |
Get the compartment in which this species is located. More... | |
bool | getConstant () |
Get the value of the 'constant' attribute. More... | |
string | getConversionFactor () |
Get the value of the 'conversionFactor' attribute. More... | |
CVTerm | getCVTerm (long n) |
Returns the nth CVTerm in the list of CVTerms of this SBML object. More... | |
CVTermList | getCVTerms () |
Returns a list of CVTerm objects in the annotations of this SBML object. More... | |
UnitDefinition | getDerivedUnitDefinition () |
Constructs and returns a UnitDefinition that corresponds to the units of this Species' amount or concentration. More... | |
SBase | getElementByMetaId (string metaid) |
Returns the first child element it can find with a specific 'metaid' attribute value, or null if no such object is found. More... | |
SBase | getElementBySId (string id) |
Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found. More... | |
SBase | getElementFromPluginsByMetaId (string metaid) |
Returns the first child element it can find with the given metaid from all plug-ins associated with this element, or null if no such object is found. More... | |
SBase | getElementFromPluginsBySId (string id) |
Returns the first child element found that has the given id in the model-wide SId namespace from all plug-ins associated with this element, or null if no such object is found. More... | |
new string | getElementName () |
Returns the XML element name of this object, which for Species, is always 'species' . More... | |
override int | GetHashCode () |
bool | getHasOnlySubstanceUnits () |
Get the value of the 'hasOnlySubstanceUnits' attribute. More... | |
new string | getId () |
Returns the value of the 'id' attribute of this Species object. More... | |
double | getInitialAmount () |
Get the value of the 'initialAmount' attribute. More... | |
double | getInitialConcentration () |
Get the value of the 'initialConcentration' attribute. More... | |
long | getLevel () |
Returns the SBML Level of the SBMLDocument object containing this object. More... | |
long | getLine () |
Returns the line number on which this object first appears in the XML representation of the SBML document. More... | |
SBaseList | getListOfAllElements () |
SBaseList | getListOfAllElementsFromPlugins () |
string | getMetaId () |
Returns the value of the 'metaid' attribute of this object. More... | |
Model | getModel () |
Returns the Model object in which the current object is located. More... | |
ModelHistory | getModelHistory () |
Returns the ModelHistory object, if any, attached to this object. More... | |
new string | getName () |
Returns the value of the 'name' attribute of this Species object. More... | |
XMLNamespaces | getNamespaces () |
Returns a list of the XML Namespaces declared on this SBML document. More... | |
XMLNode | getNotes () |
Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects. More... | |
string | getNotesString () |
Returns the content of the 'notes' subelement of this object as a string. More... | |
long | getNumCVTerms () |
Returns the number of CVTerm objects in the annotations of this SBML object. More... | |
long | getNumPlugins () |
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More... | |
string | getPackageName () |
Returns the name of the SBML Level 3 package in which this element is defined. More... | |
long | getPackageVersion () |
Returns the Version of the SBML Level 3 package to which this element belongs to. More... | |
SBase | getParentSBMLObject () |
Returns the parent SBML object containing this object. More... | |
SBasePlugin | getPlugin (string package) |
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More... | |
SBasePlugin | getPlugin (long n) |
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More... | |
int | getResourceBiologicalQualifier (string resource) |
Returns the MIRIAM biological qualifier associated with the given resource. More... | |
int | getResourceModelQualifier (string resource) |
Returns the MIRIAM model qualifier associated with the given resource. More... | |
SBMLDocument | getSBMLDocument () |
Returns the SBMLDocument object containing this object instance. More... | |
SBMLNamespaces | getSBMLNamespaces () |
Subclasses should override this method to write out their contained SBML objects as XML elements. More... | |
int | getSBOTerm () |
Returns the integer portion of the value of the 'sboTerm' attribute of this object. More... | |
string | getSBOTermAsURL () |
Returns the identifiers.org URL representation of the 'sboTerm' attribute of this object. More... | |
string | getSBOTermID () |
Returns the string representation of the 'sboTerm' attribute of this object. More... | |
string | getSpatialSizeUnits () |
Get the value of the 'spatialSizeUnits' attribute. More... | |
string | getSpeciesType () |
Get the type of this Species object object. More... | |
string | getSubstanceUnits () |
Get the value of the 'substanceUnits' attribute. More... | |
new int | getTypeCode () |
Returns the libSBML type code for this SBML object. More... | |
string | getUnits () |
Get the value of the 'units' attribute. More... | |
long | getVersion () |
Returns the Version within the SBML Level of the SBMLDocument object containing this object. More... | |
bool | hasNonstandardIdentifierBeginningWith (string prefix) |
Check to see if the given prefix is used by any of the IDs defined by extension elements *excluding* 'id' and 'metaid' attributes (as, for example, the spatial id attributes 'spid'). More... | |
new bool | hasRequiredAttributes () |
Predicate returning true if all the required attributes for this Species object have been set. More... | |
bool | hasRequiredElements () |
Subclasses should override this method to write out their contained SBML objects as XML elements. More... | |
bool | hasValidLevelVersionNamespaceCombination () |
Predicate returning true if this object's level/version and namespace values correspond to a valid SBML specification. More... | |
void | initDefaults () |
Initializes the fields of this Species object to 'typical' defaults values. More... | |
bool | isPackageEnabled (string pkgName) |
Predicate returning true if the given SBML Level 3 package is enabled with this object. More... | |
bool | isPackageURIEnabled (string pkgURI) |
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More... | |
bool | isPkgEnabled (string pkgName) |
Predicate returning true if the given SBML Level 3 package is enabled with this object. More... | |
bool | isPkgURIEnabled (string pkgURI) |
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More... | |
bool | isSetAnnotation () |
Predicate returning true if this object's 'annotation' subelement exists and has content. More... | |
bool | isSetBoundaryCondition () |
Predicate returning true if this Species object's 'boundaryCondition' attribute is set. More... | |
bool | isSetCharge () |
Predicate returning true if this Species object's 'charge' attribute is set. More... | |
bool | isSetCompartment () |
Predicate returning true if this Species object's 'compartment' attribute is set. More... | |
bool | isSetConstant () |
Predicate returning true if this Species object's 'constant' attribute is set. More... | |
bool | isSetConversionFactor () |
Predicate returning true if this Species object's 'conversionFactor' attribute is set. More... | |
bool | isSetHasOnlySubstanceUnits () |
Predicate returning true if this Species object's 'hasOnlySubstanceUnits' attribute is set. More... | |
new bool | isSetId () |
Predicate returning true if this Species object's 'id' attribute is set. More... | |
bool | isSetInitialAmount () |
Predicate returning true if this Species object's 'initialAmount' attribute is set. More... | |
bool | isSetInitialConcentration () |
Predicate returning true if this Species object's 'initialConcentration' attribute is set. More... | |
bool | isSetMetaId () |
Predicate returning true if this object's 'metaid' attribute is set. More... | |
bool | isSetModelHistory () |
Predicate returning true if this object has a ModelHistory object attached to it. More... | |
new bool | isSetName () |
Predicate returning true if this Species object's 'name' attribute is set. More... | |
bool | isSetNotes () |
Predicate returning true if this object's 'notes' subelement exists and has content. More... | |
bool | isSetSBOTerm () |
Predicate returning true if this object's 'sboTerm' attribute is set. More... | |
bool | isSetSpatialSizeUnits () |
Predicate returning true if this Species object's 'spatialSizeUnits' attribute is set. More... | |
bool | isSetSpeciesType () |
Predicate returning true if this Species object's 'speciesType' attribute is set. More... | |
bool | isSetSubstanceUnits () |
Predicate returning true if this Species object's 'substanceUnits' attribute is set. More... | |
bool | isSetUnits () |
Predicate returning true if this Species object's 'units' attribute is set. More... | |
bool | matchesRequiredSBMLNamespacesForAddition (SBase sb) |
Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More... | |
bool | matchesSBMLNamespaces (SBase sb) |
Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. More... | |
void | multiplyAssignmentsToSIdByFunction (string id, ASTNode function) |
If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing*function). More... | |
int | prependStringToAllIdentifiers (string prefix) |
Add the given string to all identifiers in the object. More... | |
int | removeFromParentAndDelete () |
Removes itself from its parent. More... | |
int | removeTopLevelAnnotationElement (string elementName, string elementURI) |
Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI. More... | |
int | removeTopLevelAnnotationElement (string elementName) |
Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI. More... | |
void | renameMetaIdRefs (string oldid, string newid) |
Renames all the MetaIdRef attributes on this element. More... | |
void | renameSIdRefs (string oldid, string newid) |
Renames all the SIdRef attributes on this element, including any found in MathML. More... | |
void | renameUnitSIdRefs (string oldid, string newid) |
Renames all the UnitSIdRef attributes on this element. More... | |
void | replaceSIDWithFunction (string id, ASTNode function) |
If this object has a child 'math' object (or anything with ASTNodes in general), replace all nodes with the name 'id' with the provided function. More... | |
int | replaceTopLevelAnnotationElement (XMLNode annotation) |
Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied. More... | |
int | replaceTopLevelAnnotationElement (string annotation) |
Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied. More... | |
int | setAnnotation (XMLNode annotation) |
Sets the value of the 'annotation' subelement of this SBML object. More... | |
int | setAnnotation (string annotation) |
Sets the value of the 'annotation' subelement of this SBML object. More... | |
int | setBoundaryCondition (bool value) |
Sets the 'boundaryCondition' attribute of this Species object. More... | |
int | setCharge (int value) |
Sets the 'charge' attribute of this Species object. More... | |
int | setCompartment (string sid) |
Sets the 'compartment' attribute of this Species object. More... | |
int | setConstant (bool value) |
Sets the 'constant' attribute of this Species object. More... | |
int | setConversionFactor (string sid) |
Sets the value of the 'conversionFactor' attribute of this Species object. More... | |
int | setHasOnlySubstanceUnits (bool value) |
Sets the 'hasOnlySubstanceUnits' attribute of this Species object. More... | |
new int | setId (string sid) |
Sets the value of the 'id' attribute of this Species object. More... | |
int | setInitialAmount (double value) |
Sets the 'initialAmount' attribute of this Species and marks the field as set. More... | |
int | setInitialConcentration (double value) |
Sets the 'initialConcentration' attribute of this Species and marks the field as set. More... | |
int | setMetaId (string metaid) |
Sets the value of the 'metaid' attribute of this object. More... | |
int | setModelHistory (ModelHistory history) |
Sets the ModelHistory of this object. More... | |
new int | setName (string name) |
Sets the value of the 'name' attribute of this Species object. More... | |
int | setNamespaces (XMLNamespaces xmlns) |
Sets the namespaces relevant of this SBML object. More... | |
int | setNotes (XMLNode notes) |
Sets the value of the 'notes' subelement of this SBML object. More... | |
int | setNotes (string notes, bool addXHTMLMarkup) |
Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes . More... | |
int | setNotes (string notes) |
Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes . More... | |
void | setSBMLNamespacesAndOwn (SBMLNamespaces sbmlns) |
Subclasses should override this method to write out their contained SBML objects as XML elements. More... | |
int | setSBOTerm (int value) |
Sets the value of the 'sboTerm' attribute. More... | |
int | setSBOTerm (string sboid) |
Sets the value of the 'sboTerm' attribute by string. More... | |
int | setSpatialSizeUnits (string sid) |
(SBML Level 2 Versions 1–2) Sets the 'spatialSizeUnits' attribute of this Species object. More... | |
int | setSpeciesType (string sid) |
Sets the 'speciesType' attribute of this Species object. More... | |
int | setSubstanceUnits (string sid) |
Sets the 'substanceUnits' attribute of this Species object. More... | |
int | setUnits (string sname) |
(SBML Level 1 only) Sets the units of this Species object. More... | |
Species (long level, long version) | |
Creates a new Species using the given SBML level and version values. More... | |
Species (SBMLNamespaces sbmlns) | |
Creates a new Species using the given SBMLNamespaces object sbmlns . More... | |
Species (Species orig) | |
Copy constructor; creates a copy of this Species object. More... | |
string | toSBML () |
Returns a string consisting of a partial SBML corresponding to just this object. More... | |
int | unsetAnnotation () |
Unsets the value of the 'annotation' subelement of this SBML object. More... | |
int | unsetCharge () |
Unsets the 'charge' attribute value of this Species object. More... | |
int | unsetConversionFactor () |
Unsets the 'conversionFactor' attribute value of this Species object. More... | |
int | unsetCVTerms () |
Clears the list of CVTerm objects attached to this SBML object. More... | |
int | unsetId () |
Unsets the value of the 'id' attribute of this SBML object. More... | |
int | unsetInitialAmount () |
Unsets the 'initialAmount' attribute value of this Species object. More... | |
int | unsetInitialConcentration () |
Unsets the 'initialConcentration' attribute value of this Species object. More... | |
int | unsetMetaId () |
Unsets the value of the 'metaid' attribute of this SBML object. More... | |
int | unsetModelHistory () |
Unsets the ModelHistory object attached to this object. More... | |
new int | unsetName () |
Unsets the value of the 'name' attribute of this Species object. More... | |
int | unsetNotes () |
Unsets the value of the 'notes' subelement of this SBML object. More... | |
int | unsetSBOTerm () |
Unsets the value of the 'sboTerm' attribute of this SBML object. More... | |
int | unsetSpatialSizeUnits () |
Unsets the 'spatialSizeUnits' attribute value of this Species object. More... | |
int | unsetSpeciesType () |
Unsets the 'speciesType' attribute value of this Species object. More... | |
int | unsetSubstanceUnits () |
Unsets the 'substanceUnits' attribute value of this Species object. More... | |
int | unsetUnits () |
Unsets the 'units' attribute value of this Species object. More... | |
void | writeExtensionElements (XMLOutputStream stream) |
Writes out contained SBML objects of package extensions (if any) as XML elements. More... | |
Static Public Member Functions | |
static bool | operator!= (SBase lhs, SBase rhs) |
static bool | operator== (SBase lhs, SBase rhs) |
Protected Attributes | |
bool | swigCMemOwn |
libsbmlcs.Species.Species | ( | long | level, |
long | version | ||
) |
Creates a new Species using the given SBML level
and version
values.
level | a long integer, the SBML Level to assign to this Species |
version | a long integer, the SBML Version to assign to this Species |
SBMLConstructorException | Thrown if the given level and version combination, or this kind of SBML object, are either invalid or mismatched with respect to the parent SBMLDocument object. |
libsbmlcs.Species.Species | ( | SBMLNamespaces | sbmlns | ) |
Creates a new Species using the given SBMLNamespaces object sbmlns
.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using this class constructor is to create an SBMLNamespaces object somewhere in a program, once, then pass it to object constructors such as this one when needed.
It is worth emphasizing that although this constructor does not take an identifier argument, in SBML Level 2 and beyond, the 'id' (identifier) attribute of a Species is required to have a value. Thus, callers are cautioned to assign a value after calling this constructor. Setting the identifier can be accomplished using the method Species::setId().
sbmlns | an SBMLNamespaces object. |
SBMLConstructorException | Thrown if the given level and version combination, or this kind of SBML object, are either invalid or mismatched with respect to the parent SBMLDocument object. |
libsbmlcs.Species.Species | ( | Species | orig | ) |
Copy constructor; creates a copy of this Species object.
orig | the object to copy. |
SBMLConstructorException | Thrown if the argument orig is null . |
|
inherited |
Adds a copy of the given CVTerm object to this SBML object.
term | the CVTerm to assign. |
newBag | if true , creates a new RDF bag with the same identifier as a previous bag, and if false , adds the term to an existing RDF bag with the same type of qualifier as the term being added. |
|
inherited |
Adds a copy of the given CVTerm object to this SBML object.
term | the CVTerm to assign. |
newBag | if true , creates a new RDF bag with the same identifier as a previous bag, and if false , adds the term to an existing RDF bag with the same type of qualifier as the term being added. |
|
inherited |
Appends the given annotation
to the 'annotation' subelement of this object.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Unlike SBase::setAnnotation(XMLNode annotation) or SBase::setAnnotation(string annotation), this method allows other annotations to be preserved when an application adds its own data.
annotation | an XML structure that is to be copied and appended to the content of the 'annotation' subelement of this object |
|
inherited |
Appends the given annotation
to the 'annotation' subelement of this object.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Unlike SBase::setAnnotation(XMLNode annotation) or SBase::setAnnotation(string annotation), this method allows other annotations to be preserved when an application adds its own data.
annotation | an XML string that is to be copied and appended to the content of the 'annotation' subelement of this object |
|
inherited |
Appends the given notes
to the 'notes' subelement of this object.
The content of notes
is copied.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
notes | an XML node structure that is to appended to the content of the 'notes' subelement of this object |
|
inherited |
Appends the given notes
to the 'notes' subelement of this object.
The content of the parameter notes
is copied.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
notes | an XML string that is to appended to the content of the 'notes' subelement of this object |
|
inherited |
Subclasses should override this method to write out their contained SBML objects as XML elements.
Be sure to call your parents implementation of this method as well. For example:
|
inherited |
Subclasses should override this method to write out their contained SBML objects as XML elements.
Be sure to call your parents implementation of this method as well. For example:
new Species libsbmlcs.Species.clone | ( | ) |
|
inherited |
Sets this SBML object to child SBML objects (if any).
(Creates a child-parent relationship by the parent)
Subclasses must override this function if they define one ore more child elements. Basically, this function needs to be called in constructor, copy constructor, assignment operator.
|
inherited |
Sets the parent SBML object of this SBML object.
(Creates a child-parent relationship by the child) This function is called when a child element is set/added/created by its parent element (e.g. by setXXX, addXXX, createXXX, and connectToChild functions of the parent element).
parent | the SBML object to use |
|
inherited |
Disables the given SBML Level 3 package.
This method enables or disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.
pkgURI | the URI of the package |
pkgPrefix | the XML prefix of the package |
|
virtual |
Reimplemented from libsbmlcs.SBase.
|
inherited |
If the function of this object is to assign a value has a child 'math' object (or anything with ASTNodes in general), replace the 'math' object with the function (existing/function).
|
inherited |
Enables or disables the given SBML Level 3 package.
This method enables or disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.
pkgURI | the URI of the package |
pkgPrefix | the XML prefix of the package |
flag | whether to enable (true ) or disable (false ) the package |
|
inherited |
Enables/Disables the given package with this element and child elements (if any).
(This is an internal implementation for enablePackage function)
|
inherited |
|
inherited |
Returns the first ancestor object that has the given SBML type code.
LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_
.
This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code. If the optional argument pkgName
is given, it will cause the search to be limited to the SBML Level 3 package given.
type | the SBML type code of the object sought |
pkgName | (optional) the short name of an SBML Level 3 package to which the sought-after object must belong |
null
if no ancestor exists.
|
inherited |
Returns the first ancestor object that has the given SBML type code.
LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_
.
This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code. If the optional argument pkgName
is given, it will cause the search to be limited to the SBML Level 3 package given.
type | the SBML type code of the object sought |
pkgName | (optional) the short name of an SBML Level 3 package to which the sought-after object must belong |
null
if no ancestor exists.
|
inherited |
Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects.
Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
The annotations returned by this method will be in XML form. LibSBML provides an object model and related interfaces for certain specific kinds of annotations, namely model history information and RDF content. See the ModelHistory, CVTerm and RDFAnnotationParser classes for more information about the facilities available.
|
inherited |
Returns the content of the 'annotation' subelement of this object as a character string.
Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
The annotations returned by this method will be in string form.
bool libsbmlcs.Species.getBoundaryCondition | ( | ) |
Get the value of the 'boundaryCondition' attribute.
true
if this Species' 'boundaryCondition' attribute value is nonzero, false
otherwise. int libsbmlcs.Species.getCharge | ( | ) |
Get the value of the 'charge' attribute.
|
inherited |
Returns the column number on which this object first appears in the XML representation of the SBML document.
string libsbmlcs.Species.getCompartment | ( | ) |
Get the compartment in which this species is located.
The compartment is designated by its identifier.
bool libsbmlcs.Species.getConstant | ( | ) |
string libsbmlcs.Species.getConversionFactor | ( | ) |
|
inherited |
|
inherited |
Returns a list of CVTerm objects in the annotations of this SBML object.
UnitDefinition libsbmlcs.Species.getDerivedUnitDefinition | ( | ) |
Constructs and returns a UnitDefinition that corresponds to the units of this Species' amount or concentration.
Species in SBML have an attribute ('substanceUnits') for declaring the units of measurement intended for the species' amount or concentration (depending on which one applies). In the absence of a value given for 'substanceUnits', the units are taken from the enclosing Model's definition of 'substance'
or 'substance'/
(size of the compartment) in which the species is located, or finally, if these are not redefined by the Model, the relevant SBML default units for those quantities. Following that procedure, the method getDerivedUnitDefinition() returns a UnitDefinition based on the interpreted units of this species's amount or concentration.
Note that the functionality that facilitates unit analysis depends on the model as a whole. Thus, in cases where the object has not been added to a model or the model itself is incomplete, unit analysis is not possible and this method will return null
.
Note also that unit declarations for Species are in terms of the identifier of a unit, but this method returns a UnitDefinition object, not a unit identifier. It does this by constructing an appropriate UnitDefinition. Callers may find this particularly useful when used in conjunction with the helper methods on UnitDefinition for comparing different UnitDefinition objects.
In SBML Level 2 specifications prior to Version 3, Species includes an additional attribute named 'spatialSizeUnits', which allows explicitly setting the units of size for initial concentration. The getDerivedUnitDefinition() takes this into account for models expressed in SBML Level 2 Versions 1 and 2.
null
if one cannot be constructed.
|
inherited |
Returns the first child element it can find with a specific 'metaid' attribute value, or null
if no such object is found.
metaid | string representing the 'metaid' attribute value of the object to find. |
|
inherited |
Returns the first child element found that has the given id
in the model-wide SId
namespace, or null
if no such object is found.
id | string representing the 'id' attribute value of the object to find. |
|
inherited |
Returns the first child element it can find with the given metaid
from all plug-ins associated with this element, or null
if no such object is found.
metaid | string representing the metaid of objects to find |
metaid
.
|
inherited |
Returns the first child element found that has the given id
in the model-wide SId namespace from all plug-ins associated with this element, or null
if no such object is found.
id | string representing the id of objects to find |
id
. new string libsbmlcs.Species.getElementName | ( | ) |
Returns the XML element name of this object, which for Species, is always 'species'
.
'species'
.
|
inherited |
bool libsbmlcs.Species.getHasOnlySubstanceUnits | ( | ) |
Get the value of the 'hasOnlySubstanceUnits' attribute.
true
if this Species' 'hasOnlySubstanceUnits' attribute value is nonzero, false
otherwise.new string libsbmlcs.Species.getId | ( | ) |
double libsbmlcs.Species.getInitialAmount | ( | ) |
Get the value of the 'initialAmount' attribute.
double libsbmlcs.Species.getInitialConcentration | ( | ) |
|
inherited |
Returns the SBML Level of the SBMLDocument object containing this object.
|
inherited |
Returns the line number on which this object first appears in the XML representation of the SBML document.
|
inherited |
|
inherited |
|
inherited |
Returns the value of the 'metaid' attribute of this object.
The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.
|
inherited |
|
inherited |
Returns the ModelHistory object, if any, attached to this object.
null
if none exist.new string libsbmlcs.Species.getName | ( | ) |
|
inherited |
Returns a list of the XML Namespaces declared on this SBML document.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in SBML Level 3) packages used in addition to SBML Level 3 Core.
|
inherited |
Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
The 'notes' element content returned by this method will be in XML form, but libSBML does not provide an object model specifically for the content of notes. Callers will need to traverse the XML tree structure using the facilities available on XMLNode and related objects. For an alternative method of accessing the notes, see getNotesString().
|
inherited |
Returns the content of the 'notes' subelement of this object as a string.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.
|
inherited |
Returns the number of CVTerm objects in the annotations of this SBML object.
|
inherited |
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.
|
inherited |
Returns the name of the SBML Level 3 package in which this element is defined.
"core"
will be returned if this element is defined in SBML Level 3 Core. The string "unknown"
will be returned if this element is not defined in any SBML package.
|
inherited |
Returns the Version of the SBML Level 3 package to which this element belongs to.
0
will be returned if this element belongs to the SBML Level 3 Core package.
|
inherited |
Returns the parent SBML object containing this object.
This returns the immediately-containing object. This method is convenient when holding an object nested inside other objects in an SBML model.
|
inherited |
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.
package | the name or URI of the package |
|
inherited |
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.
n | the index of the plug-in to return |
|
inherited |
Returns the MIRIAM biological qualifier associated with the given resource.
In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The latter kind is used to qualify the relationship between a model component and a biological entity which it represents. Examples of relationships include 'is' and 'has part', but many others are possible. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify biological annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM biological qualifiers are represented using valueswhose names begin with BQB_
in the interface class libsbml.
This method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have biological qualifiers, looks for an annotation to the given resource
. If such an annotation is found, it returns the type of biological qualifier associated with that resource as a valuewhose names begin with BQB_
in the interface class libsbml.
resource | string representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892' . |
BQB_
constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
|
inherited |
Returns the MIRIAM model qualifier associated with the given resource.
In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The former kind is used to qualify the relationship between a model component and another modeling object. An example qualifier is 'isDerivedFrom', to indicate that a given component of the model is derived from the modeling object represented by the referenced resource. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify model annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM model qualifiers are represented using valueswhose names begin with BQB_
in the interface class libsbml.
This method method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have model qualifiers, looks for an annotation to the given resource
. If such an annotation is found, it returns the type of type of model qualifier associated with that resource as a valuewhose names begin with BQB_
in the interface class libsbml.
resource | string representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892' . |
BQM_
constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
|
inherited |
Returns the SBMLDocument object containing this object instance.
LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
This method allows the caller to obtain the SBMLDocument for the current object.
|
inherited |
Subclasses should override this method to write out their contained SBML objects as XML elements.
Be sure to call your parents implementation of this method as well. For example:
|
inherited |
Returns the integer portion of the value of the 'sboTerm' attribute of this object.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int
, and SBO identifiers are stored simply as integers. (For convenience, libSBML offers methods for returning both the integer form and a text-string form of the SBO identifier.)
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
-1
if the value is not set.
|
inherited |
Returns the identifiers.org URL representation of the 'sboTerm' attribute of this object.
This method returns the entire SBO identifier as a text string in the form 'http://identifiers.org/biomodels.sbo/SBO:NNNNNNN'.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
|
inherited |
Returns the string representation of the 'sboTerm' attribute of this object.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int
, and SBO identifiers are stored simply as integers. This method returns the entire SBO identifier as a text string in the form 'SBO:NNNNNNN'.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
string libsbmlcs.Species.getSpatialSizeUnits | ( | ) |
Get the value of the 'spatialSizeUnits' attribute.
string libsbmlcs.Species.getSpeciesType | ( | ) |
string libsbmlcs.Species.getSubstanceUnits | ( | ) |
Get the value of the 'substanceUnits' attribute.
dimensionless
. In SBML, default units are never
attributed to numbers, and numbers without units are not automatically
assumed to have the unit dimensionless
. Please consult the
relevant SBML specification document for a more in-depth explanation of
this topic and the SBML unit system.
new int libsbmlcs.Species.getTypeCode | ( | ) |
Returns the libSBML type code for this SBML object.
LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the C# language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbmlcs.libsbml. The names of the type codes all begin with the characters SBML_
.
string libsbmlcs.Species.getUnits | ( | ) |
Get the value of the 'units' attribute.
|
inherited |
Returns the Version within the SBML Level of the SBMLDocument object containing this object.
|
inherited |
Check to see if the given prefix is used by any of the IDs defined by extension elements *excluding* 'id' and 'metaid' attributes (as, for example, the spatial id attributes 'spid').
new bool libsbmlcs.Species.hasRequiredAttributes | ( | ) |
Predicate returning true
if all the required attributes for this Species object have been set.
|
inherited |
Subclasses should override this method to write out their contained SBML objects as XML elements.
Be sure to call your parents implementation of this method as well. For example:
|
inherited |
Predicate returning true
if this object's level/version and namespace values correspond to a valid SBML specification.
The valid combinations of SBML Level, Version and Namespace as of this release of libSBML are the following:
'http://www.sbml.org/sbml/level1'
'http://www.sbml.org/sbml/level2'
'http://www.sbml.org/sbml/level2/version2'
'http://www.sbml.org/sbml/level2/version3'
'http://www.sbml.org/sbml/level2/version4'
'http://www.sbml.org/sbml/level3/version1/core'
true
if the level, version and namespace values of this SBML object correspond to a valid set of values, false
otherwise. void libsbmlcs.Species.initDefaults | ( | ) |
Initializes the fields of this Species object to 'typical' defaults values.
The SBML Species component has slightly different aspects and default attribute values in different SBML Levels and Versions. This method sets the values to certain common defaults, based mostly on what they are in SBML Level 2. Specifically:
false
false
false
mole
|
inherited |
Predicate returning true
if the given SBML Level 3 package is enabled with this object.
The search ignores the package version.
pkgName | the name of the package |
true
if the given package is enabled within this object, false
otherwise.
|
inherited |
Predicate returning true
if an SBML Level 3 package with the given URI is enabled with this object.
pkgURI | the URI of the package |
true
if the given package is enabled within this object, false
otherwise.
|
inherited |
Predicate returning true
if the given SBML Level 3 package is enabled with this object.
The search ignores the package version.
pkgName | the name of the package |
true
if the given package is enabled within this object, false
otherwise.
|
inherited |
Predicate returning true
if an SBML Level 3 package with the given URI is enabled with this object.
pkgURI | the URI of the package |
true
if the given package is enabled within this object, false
otherwise.
|
inherited |
Predicate returning true
if this object's 'annotation' subelement exists and has content.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
true
if a 'annotation' subelement exists, false
otherwise.bool libsbmlcs.Species.isSetBoundaryCondition | ( | ) |
bool libsbmlcs.Species.isSetCharge | ( | ) |
Predicate returning true
if this Species object's 'charge' attribute is set.
true
if the 'charge' attribute of this Species is set, false
otherwise.bool libsbmlcs.Species.isSetCompartment | ( | ) |
bool libsbmlcs.Species.isSetConstant | ( | ) |
bool libsbmlcs.Species.isSetConversionFactor | ( | ) |
bool libsbmlcs.Species.isSetHasOnlySubstanceUnits | ( | ) |
new bool libsbmlcs.Species.isSetId | ( | ) |
bool libsbmlcs.Species.isSetInitialAmount | ( | ) |
Predicate returning true
if this Species object's 'initialAmount' attribute is set.
true
if the 'initialAmount' attribute of this Species is set, false
otherwise.true
until a value has been assigned.) In SBML Level 2, 'initialAmount' is optional and as such may or may not be set. bool libsbmlcs.Species.isSetInitialConcentration | ( | ) |
Predicate returning true
if this Species object's 'initialConcentration' attribute is set.
true
if the 'initialConcentration' attribute of this Species is set, false
otherwise.
|
inherited |
Predicate returning true
if this object's 'metaid' attribute is set.
The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.
true
if the 'metaid' attribute of this SBML object is set, false
otherwise.
|
inherited |
Predicate returning true
if this object has a ModelHistory object attached to it.
true
if the ModelHistory of this object is set, false
otherwise.new bool libsbmlcs.Species.isSetName | ( | ) |
|
inherited |
Predicate returning true
if this object's 'notes' subelement exists and has content.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
true
if a 'notes' subelement exists, false
otherwise.
|
inherited |
Predicate returning true
if this object's 'sboTerm' attribute is set.
true
if the 'sboTerm' attribute of this SBML object is set, false
otherwise. bool libsbmlcs.Species.isSetSpatialSizeUnits | ( | ) |
Predicate returning true
if this Species object's 'spatialSizeUnits' attribute is set.
true
if the 'spatialSizeUnits' attribute of this Species is set, false
otherwise.bool libsbmlcs.Species.isSetSpeciesType | ( | ) |
bool libsbmlcs.Species.isSetSubstanceUnits | ( | ) |
bool libsbmlcs.Species.isSetUnits | ( | ) |
|
inherited |
Returns true
if this object's set of XML namespaces are a subset of the given object's XML namespaces.
sb | an object to compare with respect to namespaces |
true
if this object's collection of namespaces is a subset of sb's
, false
otherwise.
|
inherited |
Returns true
if this object's set of XML namespaces are the same as the given object's XML namespaces.
sb | an object to compare with respect to namespaces |
true
if this object's collection of namespaces is the same as sb's
, false
otherwise.
|
inherited |
If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing*function).
|
inherited |
Add the given string to all identifiers in the object.
If the string is added to anything other than an id or a metaid, this code is responsible for tracking down and renaming all *idRefs in the package extention that identifier comes from.
|
inherited |
Removes itself from its parent.
If the parent was storing it as a pointer, it is deleted. If not, it is simply cleared (as in ListOf objects). Pure virutal, as every SBase element has different parents, and therefore different methods of removing itself. Will fail (and not delete itself) if it has no parent object. This function is designed to be overridden, but for all objects whose parent is of the class ListOf, the default implementation will work.
|
inherited |
Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.
elementName | a string representing the name of the top level annotation element that is to be removed |
elementURI | an optional string that is used to check both the name and URI of the top level element to be removed |
|
inherited |
Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.
elementName | a string representing the name of the top level annotation element that is to be removed |
elementURI | an optional string that is used to check both the name and URI of the top level element to be removed |
|
inherited |
Renames all the MetaIdRef
attributes on this element.
This method works by looking at all meta-attribute values, comparing the identifiers to the value of oldid
. If any matches are found, the matching identifiers are replaced with newid
. The method does not descend into child elements.
oldid | the old identifier |
newid | the new identifier |
void libsbmlcs.Species.renameSIdRefs | ( | string | oldid, |
string | newid | ||
) |
Renames all the SIdRef attributes on this element, including any found in MathML.
void libsbmlcs.Species.renameUnitSIdRefs | ( | string | oldid, |
string | newid | ||
) |
Renames all the UnitSIdRef attributes on this element.
|
inherited |
If this object has a child 'math' object (or anything with ASTNodes in general), replace all nodes with the name 'id' with the provided function.
|
inherited |
Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name); appendAnnotation(annotation_with_name);
with the exception that the placement of the annotation element remains the same.
annotation | XMLNode representing the replacement top level annotation |
|
inherited |
Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name); appendAnnotation(annotation_with_name);
with the exception that the placement of the annotation element remains the same.
annotation | string representing the replacement top level annotation |
|
inherited |
Sets the value of the 'annotation' subelement of this SBML object.
The content of annotation
is copied, and any previous content of this object's 'annotation' subelement is deleted.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Call this method will result in any existing content of the 'annotation' subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation
that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase::appendAnnotation(XMLNode annotation) or SBase::appendAnnotation(string annotation).
annotation | an XML structure that is to be used as the new content of the 'annotation' subelement of this object |
|
inherited |
Sets the value of the 'annotation' subelement of this SBML object.
The content of annotation
is copied, and any previous content of this object's 'annotation' subelement is deleted.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Call this method will result in any existing content of the 'annotation' subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation
that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase::appendAnnotation(XMLNode annotation) or SBase::appendAnnotation(string annotation).
annotation | an XML string that is to be used as the content of the 'annotation' subelement of this object |
int libsbmlcs.Species.setBoundaryCondition | ( | bool | value | ) |
Sets the 'boundaryCondition' attribute of this Species object.
value | bool value for the 'boundaryCondition' attribute. |
int libsbmlcs.Species.setCharge | ( | int | value | ) |
Sets the 'charge' attribute of this Species object.
value | an integer to which to set the 'charge' to. |
int libsbmlcs.Species.setCompartment | ( | string | sid | ) |
Sets the 'compartment' attribute of this Species object.
sid | the identifier of a Compartment object defined elsewhere in this Model. |
int libsbmlcs.Species.setConstant | ( | bool | value | ) |
Sets the 'constant' attribute of this Species object.
value | a bool value for the 'constant' attribute |
int libsbmlcs.Species.setConversionFactor | ( | string | sid | ) |
Sets the value of the 'conversionFactor' attribute of this Species object.
The string in sid
is copied.
sid | the new conversionFactor for the Species |
int libsbmlcs.Species.setHasOnlySubstanceUnits | ( | bool | value | ) |
Sets the 'hasOnlySubstanceUnits' attribute of this Species object.
value | bool value for the 'hasOnlySubstanceUnits' attribute. |
new int libsbmlcs.Species.setId | ( | string | sid | ) |
Sets the value of the 'id' attribute of this Species object.
The string sid
is copied. Note that SBML has strict requirements for the syntax of identifiers. The following is a summary of the definition of the SBML identifier type
SId
, which defines the permitted syntax of identifiers. We
express the syntax using an extended form of BNF notation:
letter ::= 'a'..'z','A'..'Z' digit ::= '0'..'9' idChar ::= letter | digit | '_' SId ::= ( letter | '_' ) idChar*The characters
(
and )
are used for grouping, the
character *
"zero or more times", and the character
|
indicates logical "or". The equality of SBML identifiers is
determined by an exact character sequence match; i.e., comparisons must be
performed in a case-sensitive manner. In addition, there are a few
conditions for the uniqueness of identifiers in an SBML model. Please
consult the SBML specifications for the exact formulations.
sid | the string to use as the identifier of this Species |
int libsbmlcs.Species.setInitialAmount | ( | double | value | ) |
Sets the 'initialAmount' attribute of this Species and marks the field as set.
This method also unsets the 'initialConcentration' attribute.
value | the value to which the 'initialAmount' attribute should be set. |
int libsbmlcs.Species.setInitialConcentration | ( | double | value | ) |
Sets the 'initialConcentration' attribute of this Species and marks the field as set.
This method also unsets the 'initialAmount' attribute.
value | the value to which the 'initialConcentration' attribute should be set. |
|
inherited |
Sets the value of the 'metaid' attribute of this object.
The string metaid
is copied. The value of metaid
must be an identifier conforming to the syntax defined by the XML 1.0 data type ID. Among other things, this type requires that a value is unique among all the values of type XML ID in an SBMLDocument. Although SBML only uses XML ID for the 'metaid' attribute, callers should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement.
metaid | the identifier string to use as the value of the 'metaid' attribute |
|
inherited |
Sets the ModelHistory of this object.
The content of history
is copied, and this object's existing model history content is deleted.
history | ModelHistory of this object. |
new int libsbmlcs.Species.setName | ( | string | name | ) |
|
inherited |
Sets the namespaces relevant of this SBML object.
The content of xmlns
is copied, and this object's existing namespace content is deleted.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.
xmlns | the namespaces to set |
|
inherited |
Sets the value of the 'notes' subelement of this SBML object.
The content of notes
is copied, and any existing content of this object's 'notes' subelement is deleted.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
notes | an XML structure that is to be used as the content of the 'notes' subelement of this object |
|
inherited |
Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes
.
The content of notes
is copied, and any existing content of this object's 'notes' subelement is deleted.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component. SBMLDocument s = new SBMLDocument(3, 1); s.setNotes('<body xmlns="http://www.w3.org/1999/xhtml">
here is my note
</body>');
notes | an XML string that is to be used as the content of the 'notes' subelement of this object |
addXHTMLMarkup | a bool indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p> ) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup. |
|
inherited |
Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes
.
The content of notes
is copied, and any existing content of this object's 'notes' subelement is deleted.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component. SBMLDocument s = new SBMLDocument(3, 1); s.setNotes('<body xmlns="http://www.w3.org/1999/xhtml">
here is my note
</body>');
notes | an XML string that is to be used as the content of the 'notes' subelement of this object |
addXHTMLMarkup | a bool indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p> ) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup. |
|
inherited |
Subclasses should override this method to write out their contained SBML objects as XML elements.
Be sure to call your parents implementation of this method as well. For example:
|
inherited |
Sets the value of the 'sboTerm' attribute.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int
, and SBO identifiers are stored simply as integers.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
value | the NNNNNNN integer portion of the SBO identifier |
|
inherited |
Sets the value of the 'sboTerm' attribute by string.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int
, and SBO identifiers are stored simply as integers. This method lets you set the value of 'sboTerm' as a complete string of the form 'SBO:NNNNNNN', whereas setSBOTerm(int value) allows you to set it using the integer form.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
int libsbmlcs.Species.setSpatialSizeUnits | ( | string | sid | ) |
(SBML Level 2 Versions 1–2) Sets the 'spatialSizeUnits' attribute of this Species object.
sid | the identifier of the unit to use. |
int libsbmlcs.Species.setSpeciesType | ( | string | sid | ) |
Sets the 'speciesType' attribute of this Species object.
sid | the identifier of a SpeciesType object defined elsewhere in this Model. |
int libsbmlcs.Species.setSubstanceUnits | ( | string | sid | ) |
Sets the 'substanceUnits' attribute of this Species object.
sid | the identifier of the unit to use. |
int libsbmlcs.Species.setUnits | ( | string | sname | ) |
(SBML Level 1 only) Sets the units of this Species object.
sname | the identifier of the unit to use. |
|
inherited |
Returns a string consisting of a partial SBML corresponding to just this object.
|
inherited |
Unsets the value of the 'annotation' subelement of this SBML object.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
int libsbmlcs.Species.unsetCharge | ( | ) |
Unsets the 'charge' attribute value of this Species object.
int libsbmlcs.Species.unsetConversionFactor | ( | ) |
Unsets the 'conversionFactor' attribute value of this Species object.
|
inherited |
Clears the list of CVTerm objects attached to this SBML object.
|
inherited |
Unsets the value of the 'id' attribute of this SBML object.
Most (but not all) objects in SBML include two common attributes: 'id' and 'name'. The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always either Sid
or UnitSId
, depending on the object in question. Both data types are defined as follows:
letter ::= 'a'..'z','A'..'Z' digit ::= '0'..'9' idChar ::= letter | digit | '_' SId ::= ( letter | '_' ) idChar*
The equality of SId
and UnitSId
type values in SBML is determined by an exact character sequence match; i.e., comparisons of these identifiers must be performed in a case-sensitive manner. This applies to all uses of SId
and UnitSId
.
int libsbmlcs.Species.unsetInitialAmount | ( | ) |
Unsets the 'initialAmount' attribute value of this Species object.
int libsbmlcs.Species.unsetInitialConcentration | ( | ) |
Unsets the 'initialConcentration' attribute value of this Species object.
|
inherited |
Unsets the value of the 'metaid' attribute of this SBML object.
The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.
|
inherited |
Unsets the ModelHistory object attached to this object.
new int libsbmlcs.Species.unsetName | ( | ) |
Unsets the value of the 'name' attribute of this Species object.
|
inherited |
Unsets the value of the 'notes' subelement of this SBML object.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
|
inherited |
Unsets the value of the 'sboTerm' attribute of this SBML object.
int libsbmlcs.Species.unsetSpatialSizeUnits | ( | ) |
Unsets the 'spatialSizeUnits' attribute value of this Species object.
int libsbmlcs.Species.unsetSpeciesType | ( | ) |
Unsets the 'speciesType' attribute value of this Species object.
int libsbmlcs.Species.unsetSubstanceUnits | ( | ) |
Unsets the 'substanceUnits' attribute value of this Species object.
int libsbmlcs.Species.unsetUnits | ( | ) |
Unsets the 'units' attribute value of this Species object.
|
inherited |
Writes out contained SBML objects of package extensions (if any) as XML elements.
|
protectedinherited |