libSBML Perl API
libSBML 5.10.0 Perl API
|
{core} Implementation of SBML's Unit construct.
The SBML unit definition facility uses two classes of objects, UnitDefinition and Unit. The approach to defining units in SBML is compositional; for example, meter second –2 is constructed by combining a Unit object representing meter with another Unit object representing second –2. The combination is wrapped inside a UnitDefinition, which provides for assigning an identifier and optional name to the combination. The identifier can then be referenced from elsewhere in a model. Thus, the UnitDefinition class is the container, and Unit instances are placed inside UnitDefinition instances.
A Unit has four attributes named "kind", "exponent", "scale" and "multiplier". It represents a (possibly transformed) reference to a base unit. The attribute "kind" on Unit indicates the chosen base unit. Its value must be one of the text strings listed below; this list corresponds to SBML Level 3 Version 1 Core:
ampere | farad | joule | lux | radian | volt |
avogadro | gram | katal | metre | second | watt |
becquerel | gray | kelvin | mole | siemens | weber |
candela | henry | kilogram | newton | sievert | |
coulomb | hertz | litre | ohm | steradian | |
dimensionless | item | lumen | pascal | tesla |
A few small differences exist between the Level 3 list of base units and the list defined in other Level/Version combinations of SBML. Specifically, Levels of SBML before Level 3 do not define avogadro
; conversely, Level 2 Version 1 defines Celsius
, and Level 1 defines celsius
, meter
, and liter
, none of which are available in Level 3. In libSBML, each of the predefined base unit names is represented by an enumeration value whose name begins with the characters UNIT_KIND_
, discussed in a separate section below.
The attribute named "exponent" on Unit represents an exponent on the unit. In SBML Level 2, the attribute is optional and has a default value of 1
(one); in SBML Level 3, the attribute is mandatory and there is no default value. A Unit also has an attribute called "scale"; its value must be an integer exponent for a power-of-ten multiplier used to set the scale of the unit. For example, a unit having a "kind" value of gram
and a "scale" value of -3
signifies 10 –3 gram, or milligrams. In SBML Level 2, the attribute is optional and has a default value of
0
(zero), because 10 0 = 1; in SBML Level 3, the attribute is mandatory and has no default value. Lastly, the attribute named "multiplier" can be used to multiply the unit by a real-numbered factor; this enables the definition of units that are not power-of-ten multiples of SI units. For instance, a multiplier of 0.3048 could be used to define foot
as a measure of length in terms of a metre
. The "multiplier" attribute is optional in SBML Level 2, where it has a default value of 1
(one); in SBML Level 3, the attribute is mandatory and has not default value.
As discussed above, SBML defines a set of base units which serves as the starting point for new unit definitions. This set of base units consists of the SI units and a small number of additional convenience units.
As a consequence of the fact that libSBML supports models in all Levels and Versions of SBML, libSBML's set of UNIT_KIND_
values is a union of all the possible base unit names defined in the different SBML specifications. However, not every base unit is allowed in every Level+Version combination of SBML. Note in particular the following exceptions:
The alternate spelling "meter"
is included in addition to the official SI spelling "metre"
. This spelling is only permitted in SBML Level 1 models.
The alternate spelling "liter"
is included in addition to the official SI spelling "litre"
. This spelling is only permitted in SBML Level 1 models.
The unit "Celsius"
is included because of its presence in specifications of SBML prior to SBML Level 2 Version 3.
avogadro
was introduced in SBML Level 3, and is only permitted for use in SBML Level 3 models. The table below lists the unit constants defined in libSBML, and their meanings.
Enumerator | Meaning |
---|---|
UNIT_KIND_AMPERE | The ampere unit. |
UNIT_KIND_AVOGADRO | The unit
dimensionless multiplied by the numerical value of Avogadro's
constant. (Only usable in SBML Level 3 models.) |
UNIT_KIND_BECQUEREL | The becquerel unit. |
UNIT_KIND_CANDELA | The candela unit. |
UNIT_KIND_CELSIUS | The Celsius unit. (Only usable in SBML Level 1 and SBML Level 2 Version 1 models.) |
UNIT_KIND_COULOMB | The coulomb unit. |
UNIT_KIND_DIMENSIONLESS | A pseudo-unit indicating a dimensionless quantity. |
UNIT_KIND_FARAD | The farad unit. |
UNIT_KIND_GRAM | The gram unit. |
UNIT_KIND_GRAY | The gray unit. |
UNIT_KIND_HENRY | The henry unit. |
UNIT_KIND_HERTZ | The hertz unit. |
UNIT_KIND_ITEM | A pseudo-unit representing a single "thing". |
UNIT_KIND_JOULE | The joule unit. |
UNIT_KIND_KATAL | The katal unit. |
UNIT_KIND_KELVIN | The kelvin unit. |
UNIT_KIND_KILOGRAM | The kilogram unit. |
UNIT_KIND_LITER | Alternate spelling of litre. |
UNIT_KIND_LITRE | The litre unit. |
UNIT_KIND_LUMEN | The lumen unit. |
UNIT_KIND_LUX | The lux unit. |
UNIT_KIND_METER | Alternate spelling of metre. |
UNIT_KIND_METRE | The metre unit. |
UNIT_KIND_MOLE | The mole unit. |
UNIT_KIND_NEWTON | The newton unit. |
UNIT_KIND_OHM | The ohm unit. |
UNIT_KIND_PASCAL | The pascal unit. |
UNIT_KIND_RADIAN | The radian unit. |
UNIT_KIND_SECOND | The second unit. |
UNIT_KIND_SIEMENS | The siemens unit. |
UNIT_KIND_SIEVERT | The sievert unit. |
UNIT_KIND_STERADIAN | The steradian unit. |
UNIT_KIND_TESLA | The tesla unit. |
UNIT_KIND_VOLT | The volt unit. |
UNIT_KIND_WATT | The watt unit. |
UNIT_KIND_WEBER | The weber unit. |
UNIT_KIND_INVALID | Marker used by libSBML to indicate an invalid or unset unit. |
Public Member Functions | |
virtual bool | accept (SBMLVisitor &v) const |
Accepts the given SBMLVisitor for this instance of Unit. More... | |
int | addCVTerm (CVTerm *term, bool newBag=false) |
Adds a copy of the given CVTerm object to this SBML object. More... | |
virtual int | appendAnnotation (const XMLNode *annotation) |
Appends the given annotation to the "annotation" subelement of this object. More... | |
virtual int | appendAnnotation (const std::string &annotation) |
Appends the given annotation to the "annotation" subelement of this object. More... | |
int | appendNotes (const XMLNode *notes) |
Appends the given notes to the "notes" subelement of this object. More... | |
int | appendNotes (const std::string ¬es) |
Appends the given notes to the "notes" subelement of this object. More... | |
virtual Unit * | clone () const |
Creates and returns a deep copy of this Unit. More... | |
int | disablePackage (const std::string &pkgURI, const std::string &pkgPrefix) |
Disables the given SBML Level 3 package on this object. More... | |
int | enablePackage (const std::string &pkgURI, const std::string &pkgPrefix, bool flag) |
Enables or disables the given SBML Level 3 package on this object. More... | |
virtual List * | getAllElements (ElementFilter *filter=NULL) |
Returns a List of all child SBase objects, including those nested to an arbitrary depth. More... | |
virtual List * | getAllElementsFromPlugins (ElementFilter *filter=NULL) |
Returns a List of all child SBase objects contained in SBML package plug-ins. More... | |
SBase * | getAncestorOfType (int type, const std::string pkgName="core") |
Returns the first ancestor object that has the given SBML type code from the given package. More... | |
const SBase * | getAncestorOfType (int type, const std::string pkgName="core") const |
Returns the first ancestor object that has the given SBML type code from the given package. More... | |
XMLNode * | getAnnotation () |
Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects. More... | |
XMLNode * | getAnnotation () const |
Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects. More... | |
std::string | getAnnotationString () |
Returns the content of the "annotation" subelement of this object as a character string. More... | |
std::string | getAnnotationString () const |
Returns the content of the "annotation" subelement of this object as a character string. More... | |
unsigned int | getColumn () const |
Returns the column number on which this object first appears in the XML representation of the SBML document. More... | |
CVTerm * | getCVTerm (unsigned int n) |
Returns the nth CVTerm in the list of CVTerms of this SBML object. More... | |
List * | getCVTerms () |
Returns a list of CVTerm objects in the annotations of this SBML object. More... | |
List * | getCVTerms () const |
Returns a list of CVTerm objects in the annotations of this SBML object. More... | |
virtual SBase * | getElementByMetaId (const std::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... | |
virtual SBase * | getElementBySId (const std::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... | |
virtual const std::string & | getElementName () const |
Returns the XML element name of this object, which for Unit, is always "unit" . More... | |
int | getExponent () const |
Returns the value of the "exponent" attribute of this unit. More... | |
double | getExponentAsDouble () const |
Returns the value of the "exponent" attribute of this unit. More... | |
UnitKind_t | getKind () const |
Returns the "kind" of Unit this is. More... | |
unsigned int | getLevel () const |
Returns the SBML Level of the SBMLDocument object containing this object. More... | |
unsigned int | getLine () const |
Returns the line number on which this object first appears in the XML representation of the SBML document. More... | |
const std::string & | getMetaId () const |
Returns the value of the "metaid" attribute of this object. More... | |
std::string & | getMetaId () |
Returns the value of the "metaid" attribute of this object. More... | |
const Model * | getModel () const |
Returns the Model object for the SBML Document in which the current object is located. More... | |
ModelHistory * | getModelHistory () const |
Returns the ModelHistory object, if any, attached to this object. More... | |
ModelHistory * | getModelHistory () |
Returns the ModelHistory object, if any, attached to this object. More... | |
double | getMultiplier () const |
Returns the value of the "multiplier" attribute of this Unit. More... | |
virtual XMLNamespaces * | getNamespaces () const |
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... | |
XMLNode * | getNotes () const |
Returns the content of the "notes" subelement of this object as a tree of XMLNode objects. More... | |
std::string | getNotesString () |
Returns the content of the "notes" subelement of this object as a string. More... | |
std::string | getNotesString () const |
Returns the content of the "notes" subelement of this object as a string. More... | |
unsigned int | getNumCVTerms () |
Returns the number of CVTerm objects in the annotations of this SBML object. More... | |
unsigned int | getNumPlugins () const |
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known. More... | |
double | getOffset () const |
Returns the value of the "offset" attribute of this Unit. More... | |
const std::string & | getPackageName () const |
Returns the name of the SBML Level 3 package in which this element is defined. More... | |
unsigned int | getPackageVersion () const |
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... | |
const SBase * | getParentSBMLObject () const |
Returns the parent SBML object containing this object. More... | |
SBasePlugin * | getPlugin (const std::string &package) |
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More... | |
const SBasePlugin * | getPlugin (const std::string &package) const |
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI. More... | |
SBasePlugin * | getPlugin (unsigned int n) |
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More... | |
const SBasePlugin * | getPlugin (unsigned int n) const |
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension. More... | |
std::string | getPrefix () const |
Returns the namespace prefix of this element. More... | |
BiolQualifierType_t | getResourceBiologicalQualifier (std::string resource) |
Returns the MIRIAM biological qualifier associated with the given resource. More... | |
ModelQualifierType_t | getResourceModelQualifier (std::string resource) |
Returns the MIRIAM model qualifier associated with the given resource. More... | |
const SBMLDocument * | getSBMLDocument () const |
Returns the SBMLDocument object containing this object instance. More... | |
SBMLDocument * | getSBMLDocument () |
Returns the SBMLDocument object containing this object instance. More... | |
int | getSBOTerm () const |
Returns the integer portion of the value of the "sboTerm" attribute of this object. More... | |
std::string | getSBOTermAsURL () const |
Returns the identifiers.org URL representation of the "sboTerm" attribute of this object. More... | |
std::string | getSBOTermID () const |
Returns the string representation of the "sboTerm" attribute of this object. More... | |
int | getScale () const |
Returns the value of the "scale" attribute of this unit. More... | |
virtual int | getTypeCode () const |
Returns the libSBML type code of this object instance. More... | |
std::string | getURI () const |
Gets the namespace URI to which this element belongs to. More... | |
void * | getUserData () const |
Returns the user data that has been previously set via setUserData(). More... | |
unsigned int | getVersion () const |
Returns the Version within the SBML Level of the SBMLDocument object containing this object. More... | |
virtual bool | hasRequiredAttributes () const |
Predicate returning true if all the required attributes for this Unit object have been set. 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 Unit object to "typical" default values. More... | |
bool | isAmpere () const |
Predicate for testing whether this Unit is of the kind ampere . More... | |
bool | isAvogadro () const |
Predicate for testing whether this Unit is of the kind avogadro . More... | |
bool | isBecquerel () const |
Predicate for testing whether this Unit is of the kind becquerel . More... | |
bool | isCandela () const |
Predicate for testing whether this Unit is of the kind candela . More... | |
bool | isCelsius () const |
Predicate for testing whether this Unit is of the kind Celsius . More... | |
bool | isCoulomb () const |
Predicate for testing whether this Unit is of the kind coulomb . More... | |
bool | isDimensionless () const |
Predicate for testing whether this Unit is of the kind dimensionless . More... | |
bool | isFarad () const |
Predicate for testing whether this Unit is of the kind farad . More... | |
bool | isGram () const |
Predicate for testing whether this Unit is of the kind gram . More... | |
bool | isGray () const |
Predicate for testing whether this Unit is of the kind gray . More... | |
bool | isHenry () const |
Predicate for testing whether this Unit is of the kind henry . More... | |
bool | isHertz () const |
Predicate for testing whether this Unit is of the kind hertz . More... | |
bool | isItem () const |
Predicate for testing whether this Unit is of the kind item . More... | |
bool | isJoule () const |
Predicate for testing whether this Unit is of the kind joule . More... | |
bool | isKatal () const |
Predicate for testing whether this Unit is of the kind katal . More... | |
bool | isKelvin () const |
Predicate for testing whether this Unit is of the kind kelvin . More... | |
bool | isKilogram () const |
Predicate for testing whether this Unit is of the kind kilogram . More... | |
bool | isLitre () const |
Predicate for testing whether this Unit is of the kind litre . More... | |
bool | isLumen () const |
Predicate for testing whether this Unit is of the kind lumen . More... | |
bool | isLux () const |
Predicate for testing whether this Unit is of the kind lux . More... | |
bool | isMetre () const |
Predicate for testing whether this Unit is of the kind metre . More... | |
bool | isMole () const |
Predicate for testing whether this Unit is of the kind mole . More... | |
bool | isNewton () const |
Predicate for testing whether this Unit is of the kind newton . More... | |
bool | isOhm () const |
Predicate for testing whether this Unit is of the kind ohm . More... | |
bool | isPackageEnabled (const std::string &pkgName) const |
Predicate returning true if the given SBML Level 3 package is enabled with this object. More... | |
bool | isPackageURIEnabled (const std::string &pkgURI) const |
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More... | |
bool | isPascal () const |
Predicate for testing whether this Unit is of the kind pascal . More... | |
bool | isPkgEnabled (const std::string &pkgName) const |
Predicate returning true if the given SBML Level 3 package is enabled with this object. More... | |
bool | isPkgURIEnabled (const std::string &pkgURI) const |
Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object. More... | |
bool | isRadian () const |
Predicate for testing whether this Unit is of the kind radian . More... | |
bool | isSecond () const |
Predicate for testing whether this Unit is of the kind second . More... | |
bool | isSetAnnotation () const |
Predicate returning true if this object's "annotation" subelement exists and has content. More... | |
bool | isSetExponent () const |
Predicate to test whether the "exponent" attribute of this Unit is set. More... | |
bool | isSetKind () const |
Predicate to test whether the "kind" attribute of this Unit is set. More... | |
bool | isSetMetaId () const |
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... | |
bool | isSetMultiplier () const |
Predicate to test whether the "multiplier" attribute of this Unit is set. More... | |
bool | isSetNotes () const |
Predicate returning true if this object's "notes" subelement exists and has content. More... | |
bool | isSetSBOTerm () const |
Predicate returning true if this object's "sboTerm" attribute is set. More... | |
bool | isSetScale () const |
Predicate to test whether the "scale" attribute of this Unit is set. More... | |
bool | isSiemens () const |
Predicate for testing whether this Unit is of the kind siemens . More... | |
bool | isSievert () const |
Predicate for testing whether this Unit is of the kind sievert . More... | |
bool | isSteradian () const |
Predicate for testing whether this Unit is of the kind steradian . More... | |
bool | isTesla () const |
Predicate for testing whether this Unit is of the kind tesla . More... | |
bool | isVolt () const |
Predicate for testing whether this Unit is of the kind volt . More... | |
bool | isWatt () const |
Predicate for testing whether this Unit is of the kind watt . More... | |
bool | isWeber () const |
Predicate for testing whether this Unit is of the kind weber . More... | |
bool | matchesRequiredSBMLNamespacesForAddition (const SBase *sb) |
Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More... | |
bool | matchesRequiredSBMLNamespacesForAddition (const SBase *sb) const |
Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces. More... | |
bool | matchesSBMLNamespaces (const SBase *sb) |
Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. More... | |
bool | matchesSBMLNamespaces (const SBase *sb) const |
Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces. More... | |
Unit & | operator= (const Unit &rhs) |
Assignment operator. More... | |
void | read (XMLNode &node, XMLErrorSeverityOverride_t flag=LIBSBML_OVERRIDE_DISABLED) |
Reads (initializes) this SBML object by reading from the given XMLNode. More... | |
virtual int | removeFromParentAndDelete () |
Removes this object from its parent. More... | |
int | removeTopLevelAnnotationElement (const std::string elementName, const std::string elementURI="", bool removeEmpty=true) |
Removes the top-level element within the "annotation" subelement of this SBML object with the given name and optional URI. More... | |
virtual void | renameMetaIdRefs (const std::string &oldid, const std::string &newid) |
Renames all the meta-identifier attributes on this element. More... | |
virtual void | renameSIdRefs (const std::string &oldid, const std::string &newid) |
Renames all the SIdRef attributes on this element, including any found in MathML content (if such exists). More... | |
virtual void | renameUnitSIdRefs (const std::string &oldid, const std::string &newid) |
Renames all the UnitSIdRef attributes on this element. More... | |
int | replaceTopLevelAnnotationElement (const 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 (const std::string &annotation) |
Replaces the given top-level element within the "annotation" subelement of this SBML object and with the annotation element supplied. More... | |
virtual int | setAnnotation (const XMLNode *annotation) |
Sets the value of the "annotation" subelement of this SBML object. More... | |
virtual int | setAnnotation (const std::string &annotation) |
Sets the value of the "annotation" subelement of this SBML object. More... | |
int | setExponent (int value) |
Sets the "exponent" attribute value of this Unit. More... | |
int | setExponent (double value) |
Sets the "exponent" attribute value of this Unit. More... | |
int | setKind (UnitKind_t kind) |
Sets the "kind" attribute value of this Unit. More... | |
int | setMetaId (const std::string &metaid) |
Sets the value of the meta-identifier attribute of this object. More... | |
int | setModelHistory (ModelHistory *history) |
Sets the ModelHistory of this object. More... | |
int | setMultiplier (double value) |
Sets the "multipler" attribute value of this Unit. More... | |
int | setNamespaces (XMLNamespaces *xmlns) |
Sets the namespaces relevant of this SBML object. More... | |
int | setNotes (const XMLNode *notes) |
Sets the value of the "notes" subelement of this SBML object. More... | |
int | setNotes (const std::string ¬es, bool addXHTMLMarkup=false) |
Sets the value of the "notes" subelement of this SBML object to a copy of the string notes . More... | |
int | setOffset (double value) |
Sets the "offset" attribute value of this Unit. More... | |
virtual int | setSBOTerm (int value) |
Sets the value of the "sboTerm" attribute. More... | |
virtual int | setSBOTerm (const std::string &sboid) |
Sets the value of the "sboTerm" attribute by string. More... | |
int | setScale (int value) |
Sets the "scale" attribute value of this Unit. More... | |
int | setUserData (void *userData) |
Sets the user data of this element. More... | |
char * | toSBML () |
Returns a string consisting of a partial SBML corresponding to just this object. More... | |
XMLNode * | toXMLNode () |
Returns this element as an XMLNode. More... | |
Unit (unsigned int level, unsigned int version) | |
Creates a new Unit using the given SBML level and version values. More... | |
Unit (SBMLNamespaces *sbmlns) | |
Creates a new Unit using the given SBMLNamespaces object sbmlns . More... | |
Unit (const Unit &orig) | |
Copy constructor; creates a copy of this Unit. More... | |
int | unsetAnnotation () |
Unsets the value of the "annotation" subelement of this SBML object. More... | |
int | unsetCVTerms () |
Clears the list of CVTerm objects attached to this SBML object. More... | |
virtual int | unsetId () |
Unsets the value of the "id" attribute of this SBML 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... | |
virtual int | unsetName () |
Unsets the value of the "name" attribute of this SBML 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... | |
virtual | ~Unit () |
Destroys this Unit. More... | |
Static Public Member Functions | |
static bool | areEquivalent (Unit *unit1, Unit *unit2) |
Predicate returning true if Unit objects are equivalent. More... | |
static bool | areIdentical (Unit *unit1, Unit *unit2) |
Predicate returning true if two Unit objects are identical. More... | |
static UnitDefinition * | convertToSI (const Unit *unit) |
Returns a UnitDefinition object containing the given unit converted to the appropriate SI unit. More... | |
static bool | isBuiltIn (const std::string &name, unsigned int level) |
Predicate to test whether a given string is the name of a predefined SBML unit. More... | |
static bool | isUnitKind (const std::string &name, unsigned int level, unsigned int version) |
Predicate to test whether a given string is the name of a valid base unit in SBML (such as "gram" or "mole" ). More... | |
static void | merge (Unit *unit1, Unit *unit2) |
Merges two Unit objects with the same "kind" attribute value into a single Unit. More... | |
static int | removeScale (Unit *unit) |
Manipulates the attributes of the Unit to express the unit with the value of the scale attribute reduced to zero. More... | |
Protected Member Functions | |
virtual void | setElementText (const std::string &text) |
When overridden allows SBase elements to use the text included in between the elements tags. More... | |
Unit::Unit | ( | unsigned int | level, |
unsigned int | version | ||
) |
Creates a new Unit using the given SBML level
and version
values.
level | an unsigned int, the SBML Level to assign to this Unit |
version | an unsigned int, the SBML Version to assign to this Unit |
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. |
Unit::Unit | ( | SBMLNamespaces * | sbmlns | ) |
Creates a new Unit using the given SBMLNamespaces object sbmlns
.
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. |
|
virtual |
Destroys this Unit.
Unit::Unit | ( | const Unit & | orig | ) |
Copy constructor; creates a copy of this Unit.
orig | the object to copy. |
SBMLConstructorException | Thrown if the argument orig is NULL . |
|
virtual |
Accepts the given SBMLVisitor for this instance of Unit.
v | the SBMLVisitor instance to be used. |
v.visit()
, which indicates whether the Visitor would like to visit the next Unit in the list of units within which this Unit is embedded (i.e., in the ListOfUnits located in the enclosing UnitDefinition instance). Implements SBase.
|
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. |
create
) for alternatives that do not lead to these issues.
|
virtualinherited |
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(const XMLNode* annotation) or SBase::setAnnotation(const std::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 |
Reimplemented in Model, and SpeciesReference.
|
virtualinherited |
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(const XMLNode* annotation) or SBase::setAnnotation(const std::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 |
Reimplemented in Model, and SpeciesReference.
|
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 |
Predicate returning true
if Unit objects are equivalent.
Two Unit objects are considered to be equivalent either if (1) both have a "kind" attribute value of dimensionless
, or (2) their "kind", "exponent" and (for SBML Level 2 Version 1) "offset" attribute values are equal. (Contrast this to the method areIdentical(), which compares Unit objects with respect to all attributes, not just the "kind" and "exponent".)
true
if the "kind" and "exponent" attributes of unit1 are identical to the kind and exponent attributes of unit2, false
otherwise.Predicate returning true
if two Unit objects are identical.
Two Unit objects are considered to be identical if they match in all attributes. (Contrast this to the method areEquivalent(), which compares Unit objects only with respect to certain attributes.)
true
if all the attributes of unit1 are identical to the attributes of unit2, false
otherwise.
|
virtual |
|
static |
Returns a UnitDefinition object containing the given unit
converted to the appropriate SI unit.
This method exists because some units can be expressed in terms of others when the same physical dimension is involved. For example, one hertz is identical to 1 sec-1, one litre is equivalent to 1 cubic decametre, and so on.
unit | the Unit object to convert to SI |
|
inherited |
Disables the given SBML Level 3 package on this object.
This method disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.
An example of when this may be useful is during construction of model components when mixing existing and new models. Suppose your application read an SBML document containing a model that used the SBML Hierarchical Model Composition (“comp”) package, and extracted parts of that model in order to construct a new model in memory. The new, in-memory model will not accept a component drawn from another SBMLDocument with different package namespace declarations. You could reconstruct the same namespaces in the in-memory model first, but as a shortcut, you could also disable the package namespace on the object being added. Here is a code example to help clarify this:
pkgURI | the URI of the package |
pkgPrefix | the XML prefix of the package |
|
inherited |
Enables or disables the given SBML Level 3 package on this object.
This method enables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object. This method is the converse of SBase::disablePackage(const std::string& pkgURI, const std::string& pkgPrefix).
pkgURI | the URI of the package. |
pkgPrefix | the XML prefix of the package |
flag | whether to enable (true ) or disable (false ) the package |
|
virtualinherited |
Returns a List of all child SBase objects, including those nested to an arbitrary depth.
Reimplemented in Layout, Transition, Model, ListOfFunctionTerms, SBMLDocument, Event, UnitDefinition, ReactionGlyph, Reaction, KineticLaw, GeneralGlyph, ListOf, Curve, Submodel, SBaseRef, SpeciesReferenceGlyph, BoundingBox, GraphicalObject, CubicBezier, Objective, LineSegment, and ReferenceGlyph.
|
virtualinherited |
Returns a List of all child SBase objects contained in SBML package plug-ins.
This method walks down the list of all SBML Level 3 packages used by this object and returns all child objects defined by those packages.
|
inherited |
Returns the first ancestor object that has the given SBML type code from the given package.
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 from the given pkgName
.
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.pkgName
must be used for all type codes from SBML Level 3 packages. Otherwise, the function will search the "core" namespace alone, not find any corresponding elements, and return NULL.
|
inherited |
Returns the first ancestor object that has the given SBML type code from the given package.
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 from the given pkgName
.
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.pkgName
must be used for all type codes from SBML Level 3 packages. Otherwise, the function will search the "core" namespace alone, not find any corresponding elements, and return NULL.
|
inherited |
Returns the content of the "annotation" subelement of this object as a tree of XMLNode objects.
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 tree of XMLNode objects.
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.
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. See the method getAnnotation() for a version that returns annotations in XML form.
|
inherited |
Returns the content of the "annotation" subelement of this object as a character string.
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. See the method getAnnotation() for a version that returns annotations in XML form.
|
inherited |
Returns the column number on which this object first appears in the XML representation of the SBML document.
|
inherited |
|
inherited |
Returns a list of CVTerm objects in the annotations of this SBML object.
|
inherited |
Returns a list of CVTerm objects in the annotations of this SBML object.
|
virtualinherited |
Returns the first child element it can find with a specific "metaid" attribute value, or NULL
if no such object is found.
ID
, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID
anywhere in the file, 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 the XML ID
type. Although SBML itself specifies the use of XML ID
only for the "metaid" attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML ID
data type; it uses ordinary character strings, which is easier for applications to support.metaid | string representing the "metaid" attribute value of the object to find. |
Reimplemented in Model, SBMLDocument, Event, UnitDefinition, Reaction, KineticLaw, ListOf, Submodel, SBaseRef, Transition, and Objective.
|
virtualinherited |
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. |
Reimplemented in ListOfUnitDefinitions, ListOfRules, ListOfEventAssignments, ListOfInitialAssignments, ListOfLocalParameters, Model, SBMLDocument, Event, UnitDefinition, Reaction, KineticLaw, ListOf, ListOfPorts, Submodel, SBaseRef, Transition, and Objective.
|
virtual |
int Unit::getExponent | ( | ) | const |
Returns the value of the "exponent" attribute of this unit.
double Unit::getExponentAsDouble | ( | ) | const |
Returns the value of the "exponent" attribute of this unit.
UnitKind_t Unit::getKind | ( | ) | const |
Returns the "kind" of Unit this is.
|
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 |
Returns the value of the "metaid" attribute of this object.
ID
, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID
anywhere in the file, 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 the XML ID
type. Although SBML itself specifies the use of XML ID
only for the "metaid" attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML ID
data type; it uses ordinary character strings, which is easier for applications to support.
|
inherited |
Returns the value of the "metaid" attribute of this object.
ID
, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID
anywhere in the file, 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 the XML ID
type. Although SBML itself specifies the use of XML ID
only for the "metaid" attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML ID
data type; it uses ordinary character strings, which is easier for applications to support.
|
inherited |
|
inherited |
Returns the ModelHistory object, if any, attached to this object.
NULL
if none exist.
|
inherited |
Returns the ModelHistory object, if any, attached to this object.
NULL
if none exist.double Unit::getMultiplier | ( | ) | const |
|
virtualinherited |
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 Level 3) packages used in addition to SBML Level 3 Core.
NULL
in certain very usual circumstances where a namespace is not set.Reimplemented in SBMLDocument.
|
inherited |
Returns the content of the "notes" subelement of this object as a tree of XMLNode objects.
The format of "notes" elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); The method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for "notes" and "message" structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using "notes" in SBML. 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 tree of XMLNode objects.
The format of "notes" elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); The method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for "notes" and "message" structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using "notes" in SBML. 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 format of "notes" elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); The method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for "notes" and "message" structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using "notes" in SBML. 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 content of the "notes" subelement of this object as a string.
The format of "notes" elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of "notes" content, libSBML provides the static utility method SyntaxChecker::hasExpectedXHTMLSyntax(); The method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for "notes" and "message" structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using "notes" in SBML. 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.
double Unit::getOffset | ( | ) | const |
Returns the value of the "offset" attribute of this Unit.
|
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 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 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 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 namespace prefix of this element.
|
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 values
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 value
resource | string representing the resource; e.g., "http://www.geneontology.org/#GO:0005892" . |
|
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 values
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 value
resource | string representing the resource; e.g., "http://www.geneontology.org/#GO:0005892" . |
|
inherited |
Returns the SBMLDocument object containing this object instance.
This method allows the caller to obtain the SBMLDocument for the current object.
|
inherited |
Returns the SBMLDocument object containing this object instance.
This method allows the caller to obtain the SBMLDocument for the current object.
|
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.
int Unit::getScale | ( | ) | const |
Returns the value of the "scale" attribute of this unit.
|
virtual |
Returns the libSBML type code of this object instance.
SBML_
”. Note that different Level 3 package plug-ins may use overlapping type codes; to identify the package to which a given object belongs, call the getPackageName()
method on the object.Reimplemented from SBase.
|
inherited |
Gets the namespace URI to which this element belongs to.
For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI "http://www.sbml.org/sbml/level3/version1/core"; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI "http://www.sbml.org/sbml/level3/version1/layout/version1/"
This function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. If not found, it willreturn the XML namespace to which this element belongs.
|
inherited |
Returns the user data that has been previously set via setUserData().
NULL
if no user data has been set.
|
inherited |
Returns the Version within the SBML Level of the SBMLDocument object containing this object.
|
virtual |
Predicate returning true
if all the required attributes for this Unit object have been set.
|
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 Unit::initDefaults | ( | ) |
Initializes the fields of this Unit object to "typical" default values.
The SBML Unit 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:
1
0
1.0
The "kind" attribute is left unchanged.
bool Unit::isAmpere | ( | ) | const |
bool Unit::isAvogadro | ( | ) | const |
bool Unit::isBecquerel | ( | ) | const |
|
static |
Predicate to test whether a given string is the name of a predefined SBML unit.
name | a string to be tested against the predefined unit names |
level | the Level of SBML for which the determination should be made. This is necessary because there are a few small differences in allowed units between SBML Level 1 and Level 2. |
true
if name
is one of the five SBML predefined unit identifiers ("substance"
, "volume"
, "area"
, "length"
or "time"
), false
otherwise."length"
and "area"
were added in Level 2 Version 1.bool Unit::isCandela | ( | ) | const |
bool Unit::isCelsius | ( | ) | const |
Predicate for testing whether this Unit is of the kind Celsius
.
true
if the kind of this Unit is Celsius
, false
otherwise.Celsius
was removed from the list of predefined units in SBML Level 2 Version 2 at the same time that the "offset" attribute was removed from Unit definitions. LibSBML methods such as this one related to Celsius
are retained in order to support SBML Level 2 Version 1, but their use is strongly discouraged. bool Unit::isCoulomb | ( | ) | const |
bool Unit::isDimensionless | ( | ) | const |
bool Unit::isFarad | ( | ) | const |
bool Unit::isGram | ( | ) | const |
bool Unit::isGray | ( | ) | const |
bool Unit::isHenry | ( | ) | const |
bool Unit::isHertz | ( | ) | const |
bool Unit::isItem | ( | ) | const |
bool Unit::isJoule | ( | ) | const |
bool Unit::isKatal | ( | ) | const |
bool Unit::isKelvin | ( | ) | const |
bool Unit::isKilogram | ( | ) | const |
bool Unit::isLitre | ( | ) | const |
bool Unit::isLumen | ( | ) | const |
bool Unit::isLux | ( | ) | const |
bool Unit::isMetre | ( | ) | const |
bool Unit::isMole | ( | ) | const |
bool Unit::isNewton | ( | ) | const |
bool Unit::isOhm | ( | ) | const |
|
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.bool Unit::isPascal | ( | ) | const |
|
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.bool Unit::isRadian | ( | ) | const |
bool Unit::isSecond | ( | ) | const |
|
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 Unit::isSetExponent | ( | ) | const |
bool Unit::isSetKind | ( | ) | const |
|
inherited |
Predicate returning true
if this object's "metaid" attribute is set.
ID
, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID
anywhere in the file, 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 the XML ID
type. Although SBML itself specifies the use of XML ID
only for the "metaid" attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML ID
data type; it uses ordinary character strings, which is easier for applications to support.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.bool Unit::isSetMultiplier | ( | ) | const |
|
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 Unit::isSetScale | ( | ) | const |
bool Unit::isSiemens | ( | ) | const |
bool Unit::isSievert | ( | ) | const |
bool Unit::isSteradian | ( | ) | const |
bool Unit::isTesla | ( | ) | const |
|
static |
Predicate to test whether a given string is the name of a valid base unit in SBML (such as "gram"
or "mole"
).
This method exists because prior to SBML Level 2 Version 3, an enumeration called UnitKind
was defined by SBML. This enumeration was removed in SBML Level 2 Version 3 and its values were folded into the space of values of a type called UnitSId
. This method therefore has less significance in SBML Level 2 Version 3 and Level 2 Version 4, but remains for backward compatibility and support for reading models in older Versions of Level 2.
name | a string to be tested |
level | an unsigned int representing the SBML specification Level |
version | an unsigned int representing the SBML specification Version |
true
if name is a valid SBML UnitKind, false
otherwisebool Unit::isVolt | ( | ) | const |
bool Unit::isWatt | ( | ) | const |
bool Unit::isWeber | ( | ) | const |
|
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 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 |
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. Merges two Unit objects with the same "kind" attribute value into a single Unit.
For example, the following,
<unit kind="metre" exponent="2"/> <unit kind="metre" exponent="1"/>
would be merged to become
<unit kind="metre" exponent="3"/>
unit1 | the first Unit object; the result of the operation is left as a new version of this unit, modified in-place. Not modified if the two units have different kinds. |
unit2 | the second Unit object to merge with the first |
Assignment operator.
rhs | The object whose values are used as the basis of the assignment. |
SBMLConstructorException | Thrown if the argument rhs is NULL . |
|
inherited |
Reads (initializes) this SBML object by reading from the given XMLNode.
node | The XMLNode to read from. |
flag | An optional flag that determines how how errors are logged during the reading process. |
|
virtualinherited |
Removes this object from its parent.
If the parent was storing this object as a pointer, it is deleted. If not, it is simply cleared (as in ListOf objects). This is a pure virtual method, 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.
Reimplemented in Model, KineticLaw, SBaseRef, StoichiometryMath, Trigger, Delay, Priority, ListOf, ModelDefinition, and ReplacedBy.
|
static |
Manipulates the attributes of the Unit to express the unit with the value of the scale attribute reduced to zero.
For example, 1 millimetre can be expressed as a Unit with kind="metre"
multiplier="1"
scale="-3"
exponent="1"
. It can also be expressed as a Unit with kind="metre"
multiplier="0.001"
scale="0"
exponent="1"
.
unit | the Unit object to manipulate. |
|
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 |
removeEmpty | if after removing of the element, the annotation is empty, and the removeEmpty argument is true, the annotation node will be deleted (default). |
|
virtualinherited |
Renames all the meta-identifier attributes on this element.
ID
; the SBML object attribute itself is typically named metaid
. All attributes that hold values referring to values of type ID
are of the XML data type IDREF
. They are also sometimes informally referred to as "metaid refs", in analogy to the SBML-defined type SIdRef
.This method works by looking at all meta-identifier 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 |
Reimplemented in Port, and GraphicalObject.
|
virtualinherited |
Renames all the SIdRef
attributes on this element, including any found in MathML content (if such exists).
In SBML, object identifiers are of a data type called SId
. In SBML Level 3, an explicit data type called SIdRef
was introduced for attribute values that refer to SId
values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as "referring to an identifier", but the effective data type was the same as SIdRef
in Level 3. These and other methods of libSBML refer to the type SIdRef
for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.
This method works by looking at all attributes and (if appropriate) mathematical formulas, 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 |
Reimplemented in Model, Species, Compartment, KineticLaw, ListOfObjectives, Rule, EventAssignment, Submodel, InitialAssignment, StoichiometryMath, Delay, SBaseRef, Trigger, Priority, Input, QualitativeSpecies, ReactionGlyph, Output, Constraint, Reaction, FluxBound, ReplacedElement, GeneralGlyph, SimpleSpeciesReference, Port, AssignmentRule, FluxObjective, RateRule, FunctionTerm, SpeciesReferenceGlyph, Replacing, CompartmentGlyph, ReferenceGlyph, TextGlyph, and SpeciesGlyph.
|
virtualinherited |
Renames all the UnitSIdRef
attributes on this element.
UnitSId
. In SBML Level 3, an explicit data type called UnitSIdRef
was introduced for attribute values that refer to UnitSId
values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as "referring to a unit identifier", but the effective data type was the same as UnitSIdRef
in Level 3. These and other methods of libSBML refer to the type UnitSIdRef
for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.This method works by looking at all unit identifier attribute values (including, if appropriate, inside mathematical formulas), comparing the unit 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 |
Reimplemented in Model, Species, Compartment, KineticLaw, Rule, Parameter, EventAssignment, InitialAssignment, StoichiometryMath, Delay, FunctionDefinition, Trigger, Priority, Constraint, and Port.
|
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)
followed by calling 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)
followed by calling 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 |
|
virtualinherited |
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(const XMLNode* annotation) or SBase::appendAnnotation(const std::string& annotation).
annotation | an XML structure that is to be used as the new content of the "annotation" subelement of this object |
Reimplemented in Model, and SpeciesReference.
|
virtualinherited |
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(const XMLNode* annotation) or SBase::appendAnnotation(const std::string& annotation).
annotation | an XML string that is to be used as the content of the "annotation" subelement of this object |
Reimplemented in Model, and SpeciesReference.
|
protectedvirtualinherited |
When overridden allows SBase elements to use the text included in between the elements tags.
The default implementation does nothing.
text | the text string found between the element tags. |
int Unit::setExponent | ( | int | value | ) |
Sets the "exponent" attribute value of this Unit.
value | the integer to which the attribute "exponent" should be set |
int Unit::setExponent | ( | double | value | ) |
Sets the "exponent" attribute value of this Unit.
value | the double to which the attribute "exponent" should be set |
int Unit::setKind | ( | UnitKind_t | kind | ) |
Sets the "kind" attribute value of this Unit.
|
inherited |
Sets the value of the meta-identifier attribute of this object.
ID
, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID
anywhere in the file, 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 the XML ID
type. Although SBML itself specifies the use of XML ID
only for the "metaid" attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML ID
data type; it uses ordinary character strings, which is easier for applications to support.The string metaid
is copied.
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. |
int Unit::setMultiplier | ( | double | value | ) |
Sets the "multipler" attribute value of this Unit.
value | the floating-point value to which the attribute "multiplier" should be set |
|
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.
notes | an XML string that is to be used as the content of the "notes" subelement of this object |
addXHTMLMarkup | a boolean 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. |
int Unit::setOffset | ( | double | value | ) |
Sets the "offset" attribute value of this Unit.
value | the float-point value to which the attribute "offset" should set |
|
virtualinherited |
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 |
|
virtualinherited |
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.
sboid | the SBO identifier string of the form "SBO:NNNNNNN" |
int Unit::setScale | ( | int | value | ) |
Sets the "scale" attribute value of this Unit.
value | the integer to which the attribute "scale" should be set |
|
inherited |
Sets the user data of this element.
userData | specifies the new user data. |
|
inherited |
Returns a string consisting of a partial SBML corresponding to just this object.
|
inherited |
|
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.
|
inherited |
Clears the list of CVTerm objects attached to this SBML object.
|
virtualinherited |
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.
Reimplemented in Model, Layout, Event, Input, QualitativeSpecies, Output, Objective, SimpleSpeciesReference, Submodel, Transition, GraphicalObject, ExternalModelDefinition, Point, Dimensions, Deletion, Port, BoundingBox, FluxBound, GeneAssociation, and FluxObjective.
|
inherited |
Unsets the value of the "metaid" attribute of this SBML object.
ID
, the XML identifier type, which means each "metaid" value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID
anywhere in the file, 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 the XML ID
type. Although SBML itself specifies the use of XML ID
only for the "metaid" attribute, SBML-compatible applications 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. Finally, note that LibSBML does not provide an explicit XML ID
data type; it uses ordinary character strings, which is easier for applications to support.
|
inherited |
Unsets the ModelHistory object attached to this object.
|
virtualinherited |
Unsets the value of the "name" attribute of this SBML object.
Most (but not all) objects in SBML include two common attributes: "id" and "name". In contrast to the "id" attribute, the "name" attribute is optional and is not intended to be used for cross-referencing purposes within a model. Its purpose instead is to provide a human-readable label for the component. The data type of "name" is the type string
defined in XML Schema. SBML imposes no restrictions as to the content of "name" attributes beyond those restrictions defined by the string
type in XML Schema.
The recommended practice for handling "name" is as follows. If a software tool has the capability for displaying the content of "name" attributes, it should display this content to the user as a component's label instead of the component's "id". If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the "name" attribute is missing on a given component, then the user interface should display the value of the "id" attribute instead. (Script language interpreters are especially likely to display "id" instead of "name".)
As a consequence of the above, authors of systems that automatically generate the values of "id" attributes should be aware some systems may display the "id"'s to the user. Authors therefore may wish to take some care to have their software create "id" values that are: (a) reasonably easy for humans to type and read; and (b) likely to be meaningful, for example by making the "id" attribute be an abbreviated form of the name attribute value.
An additional point worth mentioning is although there are restrictions on the uniqueness of "id" values, there are no restrictions on the uniqueness of "name" values in a model. This allows software applications leeway in assigning component identifiers.
Reimplemented in Species, Compartment, Model, Layout, Event, Reaction, Parameter, UnitDefinition, Input, QualitativeSpecies, FunctionDefinition, Output, CompartmentType, SpeciesType, Submodel, SimpleSpeciesReference, ExternalModelDefinition, Transition, Deletion, Port, FluxBound, Objective, and FluxObjective.
|
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.