SBase (LibSBML Java API)

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org.sbml.libsbml
Class SBase

java.lang.Object
  org.sbml.libsbml.SBase

Direct Known Subclasses:: Compartment, CompartmentType, Constraint, Delay, Event, EventAssignment, FunctionDefinition, InitialAssignment, KineticLaw, ListOf, Model, Parameter, Priority, Reaction, Rule, SBMLDocument, SimpleSpeciesReference, Species, SpeciesType, StoichiometryMath, Trigger, Unit, UnitDefinition

public class SBase
extends Object
extends Object

Implementation of SBase, the base class of most SBML objects.

Most components in SBML are derived from a single abstract base type, SBase. In addition to serving as the parent class for most other classes of objects in SBML, this base type is designed to allow a modeler or a software package to attach arbitrary information to each major element or list in an SBML model.

SBase has an optional subelement called 'notes'. It is intended to serve 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. There are certain conditions on the XHTML content permitted inside the 'notes' element; please consult the SBML specification document corresponding to the SBML Level and Version of your model for more information about the requirements for 'notes' content.

SBase has another optional subelement called 'annotation'. Whereas the 'notes' element described above 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. The element's content type is XML type 'any', allowing essentially arbitrary data content. SBML places only a few restrictions on the organization of the content; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. As is the case with 'notes', it is important to refer to the SBML specification document corresponding to the SBML Level and Version of your model for more information about the requirements for 'annotation' content.

It is worth pointing out that the 'annotation' element in the definition of SBase exists in order that software developers may attach optional application-specific data to the elements in an SBML model. However, it is important that this facility not be misused. In particular, it is critical that data essential to a model definition or that can be encoded in existing SBML elements is not stored in 'annotation'. Parameter values, functional dependencies between model elements, etc., should not be recorded as annotations. It is crucial to keep in mind the fact that data placed in annotations can be freely ignored by software applications. If such data affects the interpretation of a model, then software interoperability is greatly impeded.

SBML Level 2 introduced an optional SBase attribute named 'metaid' for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.

Beginning with SBML Level 2 Version 3, SBase also has 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, SBase 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.

Finally, note that, in the list of methods on SBase, there is no public constructor because SBase is an abstract class. The constructors reside in the subclasses derived from SBase.

Standard format for annotations linking data resources

SBML Level 2 Versions 2, 3 and 4, and Level 3, define a proposed regular format for encoding two particular categories of annotations: (a) references to controlled vocabulary terms and database identifiers which define and describe biological and biochemical entities in a model; and (b) descriptions of the provenance of a model, including its author(s) and modification history.

Method Summary
`int`	`addCVTerm(CVTerm term)` Adds a copy of the given `CVTerm` object to this SBML object.
`int`	`addCVTerm(CVTerm term, boolean newBag)` Adds a copy of the given `CVTerm` object to this SBML object.
`int`	`appendAnnotation(String annotation)` Appends the given `annotation` to the 'annotation' subelement of this object.
`int`	`appendAnnotation(XMLNode annotation)` Appends the given `annotation` to the 'annotation' subelement of this object.
`int`	`appendNotes(String notes)` Appends the given `notes` to the 'notes' subelement of this object.
`int`	`appendNotes(XMLNode notes)` Appends the given `notes` to the 'notes' subelement of this object.
`SBase`	`cloneObject()` Creates and returns a deep copy of this `SBase` object.
`void`	`delete()` Explicitly deletes the underlying native object.
`int`	`disablePackage(String pkgURI, String pkgPrefix)` Disables the given SBML Level 3 package
`int`	`enablePackage(String pkgURI, String pkgPrefix, boolean flag)` Enables or disables the given SBML Level 3 package
`boolean`	`equals(Object sb)` Equality comparison method for SBase.
`SBase`	`getAncestorOfType(int type)` Returns the first ancestor object that has the given SBML type code.
`SBase`	`getAncestorOfType(int type, String pkgName)` Returns the first ancestor object that has the given SBML type code.
`XMLNode`	`getAnnotation()` Returns the content of the 'annotation' subelement of this object as a tree of `XMLNode` objects.
`String`	`getAnnotationString()` Returns the content of the 'annotation' subelement of this object as a character string.
`long`	`getColumn()` Returns the column number on which this object first appears in the XML representation of the SBML document.
`CVTerm`	`getCVTerm(long n)` Returns the nth `CVTerm` in the list of CVTerms of this SBML object.
`CVTermList`	`getCVTerms()` Returns a list of `CVTerm` objects in the annotations of this SBML object.
`SBase`	`getElementByMetaId(String metaid)` Returns the first child element it can find with a specific 'metaid' attribute value, or `null` if no such object is found.
`SBase`	`getElementBySId(String id)` Returns the first child element found that has the given `id` in the model-wide `SId` namespace, or `null` if no such object is found.
`String`	`getElementName()` Returns the XML element name of this object.
`long`	`getLevel()` Returns the SBML Level of the `SBMLDocument` object containing this object.
`long`	`getLine()` Returns the line number on which this object first appears in the XML representation of the SBML document.
`SBaseList`	`getListOfAllElements()` Returns an `SBaseList` of all child `SBase` objects, including those nested to an arbitrary depth.
`SBaseList`	`getListOfAllElementsFromPlugins()` Returns an `SBaseList` of all child `SBase` objects contained in SBML package plugins.
`String`	`getMetaId()` Returns the value of the 'metaid' attribute of this object.
`Model`	`getModel()` Returns the `Model` object in which the current object is located.
`ModelHistory`	`getModelHistory()` Returns the `ModelHistory` object, if any, attached to this object.
`XMLNamespaces`	`getNamespaces()` Returns a list of the XML Namespaces declared on this SBML document.
`XMLNode`	`getNotes()` Returns the content of the 'notes' subelement of this object as a tree of `XMLNode` objects.
`String`	`getNotesString()` Returns the content of the 'notes' subelement of this object as a string.
`long`	`getNumCVTerms()` Returns the number of `CVTerm` objects in the annotations of this SBML object.
`long`	`getNumPlugins()` Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.
`String`	`getPackageName()` Returns the name of the SBML Level 3 package in which this element is defined.
`long`	`getPackageVersion()` Returns the Version of the SBML Level 3 package to which this element belongs to.
`SBase`	`getParentSBMLObject()` Returns the parent SBML object containing this object.
`SBasePlugin`	`getPlugin(long n)` Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.
`SBasePlugin`	`getPlugin(String arg0)` Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.
`int`	`getResourceBiologicalQualifier(String resource)` Returns the MIRIAM biological qualifier associated with the given resource.
`int`	`getResourceModelQualifier(String resource)` Returns the MIRIAM model qualifier associated with the given resource.
`SBMLDocument`	`getSBMLDocument()` Returns the `SBMLDocument` object containing this object instance.
`int`	`getSBOTerm()` Returns the integer portion of the value of the 'sboTerm' attribute of this object.
`String`	`getSBOTermAsURL()` Returns the identifiers.org URL representation of the 'sboTerm' attribute of this object.
`String`	`getSBOTermID()` Returns the string representation of the 'sboTerm' attribute of this object.
`int`	`getTypeCode()` Returns the libSBML type code for this object.
`long`	`getVersion()` Returns the Version within the SBML Level of the `SBMLDocument` object containing this object.
`int`	`hashCode()` Returns a hashcode for this SBase object.
`boolean`	`hasValidLevelVersionNamespaceCombination()` Predicate returning `true` if this object's level/version and namespace values correspond to a valid SBML specification.
`boolean`	`isPackageEnabled(String pkgName)` Predicate returning `true` if the given SBML Level 3 package is enabled with this object.
`boolean`	`isPackageURIEnabled(String pkgURI)` Predicate returning `true` if an SBML Level 3 package with the given URI is enabled with this object.
`boolean`	`isPkgEnabled(String pkgName)` Deprecated. Replaced in libSBML 5.2.0 by isPackageEnabled(String pkgName)
`boolean`	`isPkgURIEnabled(String pkgURI)` Deprecated. Replaced in libSBML 5.2.0 by isPackageURIEnabled(String pkgURI)
`boolean`	`isSetAnnotation()` Predicate returning `true` if this object's 'annotation' subelement exists and has content.
`boolean`	`isSetMetaId()` Predicate returning `true` if this object's 'metaid' attribute is set.
`boolean`	`isSetModelHistory()` Predicate returning `true` if this object has a `ModelHistory` object attached to it.
`boolean`	`isSetNotes()` Predicate returning `true` if this object's 'notes' subelement exists and has content.
`boolean`	`isSetSBOTerm()` Predicate returning `true` if this object's 'sboTerm' attribute is set.
`boolean`	`matchesRequiredSBMLNamespacesForAddition(SBase sb)` Returns `true` if this object's set of XML namespaces are a subset of the given object's XML namespaces.
`boolean`	`matchesSBMLNamespaces(SBase sb)` Returns `true` if this object's set of XML namespaces are the same as the given object's XML namespaces.
`int`	`removeFromParentAndDelete()` Removes itself from its parent.
`int`	`removeTopLevelAnnotationElement(String elementName)` Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.
`int`	`removeTopLevelAnnotationElement(String elementName, String elementURI)` Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.
`void`	`renameMetaIdRefs(String oldid, String newid)` Renames all the `MetaIdRef` attributes on this element.
`void`	`renameSIdRefs(String oldid, String newid)` Renames all the `SIdRef` attributes on this element, including any found in MathML content (if such exists).
`void`	`renameUnitSIdRefs(String oldid, String newid)` Renames all the `UnitSIdRef` attributes on this element.
`int`	`replaceTopLevelAnnotationElement(String annotation)` Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.
`int`	`replaceTopLevelAnnotationElement(XMLNode annotation)` Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.
`int`	`setAnnotation(String annotation)` Sets the value of the 'annotation' subelement of this SBML object.
`int`	`setAnnotation(XMLNode annotation)` Sets the value of the 'annotation' subelement of this SBML object.
`int`	`setMetaId(String metaid)` Sets the value of the 'metaid' attribute of this object.
`int`	`setModelHistory(ModelHistory history)` Sets the `ModelHistory` of this object.
`int`	`setNamespaces(XMLNamespaces xmlns)` Sets the namespaces relevant of this SBML object.
`int`	`setNotes(String notes)` Sets the value of the 'notes' subelement of this SBML object to a copy of the string `notes`.
`int`	`setNotes(String notes, boolean addXHTMLMarkup)` Sets the value of the 'notes' subelement of this SBML object to a copy of the string `notes`.
`int`	`setNotes(XMLNode notes)` Sets the value of the 'notes' subelement of this SBML object.
`int`	`setSBOTerm(int value)` Sets the value of the 'sboTerm' attribute.
`int`	`setSBOTerm(String sboid)` Sets the value of the 'sboTerm' attribute by string.
`String`	`toSBML()` Returns a string consisting of a partial SBML corresponding to just this object.
`int`	`unsetAnnotation()` Unsets the value of the 'annotation' subelement of this SBML object.
`int`	`unsetCVTerms()` Clears the list of `CVTerm` objects attached to this SBML object.
`int`	`unsetId()` Unsets the value of the 'id' attribute of this SBML object.
`int`	`unsetMetaId()` Unsets the value of the 'metaid' attribute of this SBML object.
`int`	`unsetModelHistory()` Unsets the `ModelHistory` object attached to this object.
`int`	`unsetName()` Unsets the value of the 'name' attribute of this SBML object.
`int`	`unsetNotes()` Unsets the value of the 'notes' subelement of this SBML object.
`int`	`unsetSBOTerm()` Unsets the value of the 'sboTerm' attribute of this SBML object.

Methods inherited from class java.lang.Object
`getClass, notify, notifyAll, toString, wait, wait, wait`

Method Detail

delete

public void delete()

Explicitly deletes the underlying native object.

In general, application software will not need to call this method directly. The Java language binding for libSBML is implemented as a language wrapper that provides a Java interface to libSBML's underlying C++/C code. Some of the Java methods return objects that are linked to objects created not by Java code, but by C++ code. The Java objects wrapped around them will be deleted when the garbage collector invokes the corresponding C++ finalize() methods for the objects. The finalize() methods in turn call the SBase.delete() method on the libSBML object.

This method is exposed in case calling programs want to ensure that the underlying object is freed immediately, and not at some arbitrary time determined by the Java garbage collector. In normal usage, callers do not need to invoke SBase.delete() themselves.

equals

public boolean equals(Object sb)

Equality comparison method for SBase.

Because the Java methods for libSBML are actually wrappers around code implemented in C++ and C, certain operations will not behave as expected. Equality comparison is one such case. An instance of a libSBML object class is actually a proxy object wrapping the real underlying C/C++ object. The normal == equality operator in Java will only compare the Java proxy objects, not the underlying native object. The result is almost never what you want in practical situations. Unfortunately, Java does not provide a way to override ==.

The alternative that must be followed is to use the equals() method. The equals method on this class overrides the default java.lang.Object one, and performs an intelligent comparison of instances of objects of this class. The result is an assessment of whether two libSBML Java objects are truly the same underlying native-code objects.

The use of this method in practice is the same as the use of any other Java equals method. For example, a.equals(b) returns true if a and b are references to the same underlying object.

Overrides:: equals in class Object

Parameters:: sb - a reference to an object to which the current object instance will be compared
Returns:: true if sb refers to the same underlying native object as this one, false otherwise

hashCode

public int hashCode()

Returns a hashcode for this SBase object.

Overrides:: hashCode in class Object

Returns:: a hash code usable by Java methods that need them.

cloneObject

public SBase cloneObject()

Creates and returns a deep copy of this SBase object.

Returns:: a (deep) copy of this SBase object.

getElementBySId

public SBase getElementBySId(String id)

Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.

Parameters:: id - string representing the 'id' attribute value of the object to find.
Returns:: pointer to the first element found with the given identifier.

getElementByMetaId

public SBase getElementByMetaId(String metaid)

Returns the first child element it can find with a specific 'metaid' attribute value, or null if no such object is found.

Parameters:: metaid - string representing the 'metaid' attribute value of the object to find.
Returns:: pointer to the first element found with the given meta-identifier.

renameSIdRefs

public void renameSIdRefs(String oldid,
                          String newid)

Renames all the SIdRef attributes on this element, including any found in MathML content (if such exists).

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.

Parameters:: oldid - the old identifier; newid - the new identifier

renameMetaIdRefs

public void renameMetaIdRefs(String oldid,
                             String newid)

Renames all the MetaIdRef attributes on this element.

This method works by looking at all meta-attribute values, comparing the identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Parameters:: oldid - the old identifier; newid - the new identifier

renameUnitSIdRefs

public void renameUnitSIdRefs(String oldid,
                              String newid)

Renames all the UnitSIdRef attributes on this element.

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.

Parameters:: oldid - the old identifier; newid - the new identifier

getMetaId

public String getMetaId()

Returns the value of the 'metaid' attribute of this object.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.

Returns:: the meta-identifier of this SBML object.
See Also:: SBase.isSetMetaId(), SBase.setMetaId(String metaid)

getNotes

public XMLNode getNotes()

Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(XMLNode xhtml); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.

The 'notes' element content returned by this method will be in XML form, but libSBML does not provide an object model specifically for the content of notes. Callers will need to traverse the XML tree structure using the facilities available on XMLNode and related objects. For an alternative method of accessing the notes, see getNotesString().

Returns:: the content of the 'notes' subelement of this SBML object as a tree structure composed of XMLNode objects.
See Also:: SBase.getNotesString(), SBase.isSetNotes(), SBase.setNotes(XMLNode notes), SBase.setNotes(String notes), SBase.appendNotes(XMLNode notes), SBase.appendNotes(String notes), SBase.unsetNotes(), SyntaxChecker.hasExpectedXHTMLSyntax(XMLNode xhtml)

getNotesString

public String getNotesString()

Returns the content of the 'notes' subelement of this object as a string.

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.

Returns:: the content of the 'notes' subelement of this SBML object as a string.
See Also:: SBase.getNotes(), SBase.isSetNotes(), SBase.setNotes(XMLNode notes), SBase.setNotes(String notes), SBase.appendNotes(XMLNode notes), SBase.appendNotes(String notes), SBase.unsetNotes(), SyntaxChecker.hasExpectedXHTMLSyntax(XMLNode xhtml)

getAnnotation

public XMLNode getAnnotation()

Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects.

Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

The annotations returned by this method will be in XML form. LibSBML provides an object model and related interfaces for certain specific kinds of annotations, namely model history information and RDF content. See the ModelHistory, CVTerm and RDFAnnotationParser classes for more information about the facilities available.

Returns:: the annotation of this SBML object as a tree of XMLNode objects.
See Also:: SBase.getAnnotationString(), SBase.isSetAnnotation(), SBase.setAnnotation(XMLNode annotation), SBase.setAnnotation(String annotation), SBase.appendAnnotation(XMLNode annotation), SBase.appendAnnotation(String annotation), SBase.unsetAnnotation()

getAnnotationString

public String getAnnotationString()

Returns the content of the 'annotation' subelement of this object as a character string.

The annotations returned by this method will be in string form.

Returns:: the annotation of this SBML object as a character string.
See Also:: SBase.getAnnotation(), SBase.isSetAnnotation(), SBase.setAnnotation(XMLNode annotation), SBase.setAnnotation(String annotation), SBase.appendAnnotation(XMLNode annotation), SBase.appendAnnotation(String annotation), SBase.unsetAnnotation()

getNamespaces

public XMLNamespaces getNamespaces()

Returns a list of the XML Namespaces declared on this SBML document.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in SBML Level 3) packages used in addition to SBML Level 3 Core.

Returns:: the XML Namespaces associated with this SBML object
See Also:: SBase.getLevel(), SBase.getVersion()

getSBMLDocument

public SBMLDocument getSBMLDocument()

Returns the SBMLDocument object containing this object instance.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)

This method allows the caller to obtain the SBMLDocument for the current object.

Returns:: the parent SBMLDocument object of this SBML object.
See Also:: SBase.getParentSBMLObject(), SBase.getModel()

getParentSBMLObject

public SBase getParentSBMLObject()

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.

Returns:: the parent SBML object of this SBML object.
See Also:: SBase.getSBMLDocument(), SBase.getModel()

getAncestorOfType

public SBase getAncestorOfType(int type,
                               String pkgName)

Returns the first ancestor object that has the given SBML type code.

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In other languages, the set of type codes is stored in an enumeration; in the Java language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbmlConstants. The names of the type codes all begin with the characters SBML_.

This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code. If the optional argument pkgName is given, it will cause the search to be limited to the SBML Level 3 package given.

Parameters:: 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
Returns:: the ancestor SBML object of this SBML object that corresponds to the given SBML object type code, or null if no ancestor exists.

Documentation note:: The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.

getAncestorOfType

public SBase getAncestorOfType(int type)

Returns the first ancestor object that has the given SBML type code.

Parameters:: 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
Returns:: the ancestor SBML object of this SBML object that corresponds to the given SBML object type code, or null if no ancestor exists.

Documentation note:: The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.

getSBOTerm

public int getSBOTerm()

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.

Returns:: the value of the 'sboTerm' attribute as an integer, or -1 if the value is not set.

getSBOTermID

public String getSBOTermID()

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'.

Returns:: the value of the 'sboTerm' attribute as a string (its value will be of the form 'SBO:NNNNNNN'), or an empty string if the value is not set.

getSBOTermAsURL

public String getSBOTermAsURL()

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'.

Returns:: the value of the 'sboTerm' attribute as an identifiers.org URL (its value will be of the form 'http://identifiers.org/biomodels.sbo/SBO:NNNNNNN'), or an empty string if the value is not set.

getLine

public long getLine()

Returns the line number on which this object first appears in the XML representation of the SBML document.

Returns:: the line number of this SBML object.
See Also:: SBase.getColumn()
Note:: The line number for each construct in an SBML model is set upon reading the model. The accuracy of the line number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real line number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)

getColumn

public long getColumn()

Returns the column number on which this object first appears in the XML representation of the SBML document.

Returns:: the column number of this SBML object.
See Also:: SBase.getLine()
Note:: The column number for each construct in an SBML model is set upon reading the model. The accuracy of the column number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real column number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)

getModelHistory

public ModelHistory getModelHistory()

Returns the ModelHistory object, if any, attached to this object.

Returns:: the ModelHistory object attached to this object, or null if none exist.
Note:: In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.

isSetMetaId

public boolean isSetMetaId()

Predicate returning true if this object's 'metaid' attribute is set.

Returns:: true if the 'metaid' attribute of this SBML object is set, false otherwise.
See Also:: SBase.getMetaId(), SBase.setMetaId(String metaid)

isSetNotes

public boolean isSetNotes()

Predicate returning true if this object's 'notes' subelement exists and has content.

Returns:: true if a 'notes' subelement exists, false otherwise.
See Also:: SBase.getNotes(), SBase.getNotesString(), SBase.setNotes(XMLNode notes), SBase.setNotes(String notes), SBase.appendNotes(XMLNode notes), SBase.appendNotes(String notes), SBase.unsetNotes(), SyntaxChecker.hasExpectedXHTMLSyntax(XMLNode xhtml)

isSetAnnotation

public boolean isSetAnnotation()

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.

Returns:: true if a 'annotation' subelement exists, false otherwise.
See Also:: SBase.getAnnotation(), SBase.getAnnotationString(), SBase.setAnnotation(XMLNode annotation), SBase.setAnnotation(String annotation), SBase.appendAnnotation(XMLNode annotation), SBase.appendAnnotation(String annotation), SBase.unsetAnnotation()

isSetSBOTerm

public boolean isSetSBOTerm()

Predicate returning true if this object's 'sboTerm' attribute is set.

Returns:: true if the 'sboTerm' attribute of this SBML object is set, false otherwise.

setMetaId

public int setMetaId(String metaid)

Sets the value of the 'metaid' attribute of this object.

The string metaid is copied. The value of metaid must be an identifier conforming to the syntax defined by the XML 1.0 data type ID. Among other things, this type requires that a value is unique among all the values of type XML ID in an SBMLDocument. Although SBML only uses XML ID for the 'metaid' attribute, callers should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement.

Parameters:

metaid - the identifier string to use as the value of the 'metaid' attribute

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

isSetModelHistory

public boolean isSetModelHistory()

Predicate returning true if this object has a ModelHistory object attached to it.

Returns:: true if the ModelHistory of this object is set, false otherwise.
Note:: In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.

setAnnotation

public int setAnnotation(XMLNode annotation)

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.

Call this method will result in any existing content of the 'annotation' subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase.appendAnnotation(XMLNode annotation) or SBase.appendAnnotation(String annotation).

Parameters:

annotation - an XML structure that is to be used as the new content of the 'annotation' subelement of this object

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

setAnnotation

public int setAnnotation(String annotation)

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.

Parameters:

annotation - an XML string that is to be used as the content of the 'annotation' subelement of this object

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

appendAnnotation

public int appendAnnotation(XMLNode annotation)

Appends the given annotation to the 'annotation' subelement of this object.

Unlike SBase.setAnnotation(XMLNode annotation) or SBase.setAnnotation(String annotation), this method allows other annotations to be preserved when an application adds its own data.

Parameters:

annotation - an XML structure that is to be copied and appended to the content of the 'annotation' subelement of this object

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

appendAnnotation

public int appendAnnotation(String annotation)

Appends the given annotation to the 'annotation' subelement of this object.

Unlike SBase.setAnnotation(XMLNode annotation) or SBase.setAnnotation(String annotation), this method allows other annotations to be preserved when an application adds its own data.

Parameters:

annotation - an XML string that is to be copied and appended to the content of the 'annotation' subelement of this object

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

See Also:

removeTopLevelAnnotationElement

public int removeTopLevelAnnotationElement(String elementName,
                                           String elementURI)

Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.

Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.

Parameters:

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

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

removeTopLevelAnnotationElement

public int removeTopLevelAnnotationElement(String elementName)

Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.

Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.

Parameters:

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

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

replaceTopLevelAnnotationElement

public int replaceTopLevelAnnotationElement(XMLNode annotation)

Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.

This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name); appendAnnotation(annotation_with_name); with the exception that the placement of the annotation element remains the same.

Parameters:

annotation - XMLNode representing the replacement top level annotation

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

replaceTopLevelAnnotationElement

public int replaceTopLevelAnnotationElement(String annotation)

Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.

Parameters:

annotation - string representing the replacement top level annotation

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

setNotes

public int setNotes(XMLNode notes)

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.

Parameters:

notes - an XML structure that is to be used as the content of the 'notes' subelement of this object

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

setNotes

public int setNotes(String notes,
                    boolean addXHTMLMarkup)

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 following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component.

SBMLDocument s = new SBMLDocument(3, 1);
s.setNotes('<body xmlns='http://www.w3.org/1999/xhtml'>here is my note</p></body>');

Parameters:

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.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

setNotes

public int setNotes(String notes)

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.

SBMLDocument s = new SBMLDocument(3, 1);
s.setNotes('<body xmlns='http://www.w3.org/1999/xhtml'>here is my note</p></body>');

Parameters:

notes - an XML string that is to be used as the content of the 'notes' subelement of this object

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

See Also:

appendNotes

public int appendNotes(XMLNode notes)

Appends the given notes to the 'notes' subelement of this object.

The content of notes is copied.

Parameters:

notes - an XML node structure that is to appended to the content of the 'notes' subelement of this object

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

appendNotes

public int appendNotes(String notes)

Appends the given notes to the 'notes' subelement of this object.

The content of the parameter notes is copied.

Parameters:

notes - an XML string that is to appended to the content of the 'notes' subelement of this object

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

setModelHistory

public int setModelHistory(ModelHistory history)

Sets the ModelHistory of this object.

The content of history is copied, and this object's existing model history content is deleted.

Parameters:

history - ModelHistory of this object.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

Note:

In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.

setSBOTerm

public int setSBOTerm(int value)

Sets the value of the 'sboTerm' attribute.

Parameters:

value - the NNNNNNN integer portion of the SBO identifier

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

See Also:

SBase.setSBOTerm(String sbo_id)

setSBOTerm

public int setSBOTerm(String sboid)

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.

Parameters:

sboid - the SBO identifier string of the form 'SBO:NNNNNNN'

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

See Also:

SBase.setSBOTerm(int value)

setNamespaces

public int setNamespaces(XMLNamespaces xmlns)

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.

Parameters:

xmlns - the namespaces to set

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

unsetMetaId

public int unsetMetaId()

Unsets the value of the 'metaid' attribute of this SBML object.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

unsetId

public int unsetId()

Unsets the value of the 'id' attribute of this SBML object.

Most (but not all) objects in SBML include two common attributes: 'id' and 'name'. The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always either Sid or UnitSId, depending on the object in question. Both data types are defined as follows:

   letter .= 'a'..'z','A'..'Z'
   digit  .= '0'..'9'
   idChar .= letter | digit | '_'
   SId    .= ( letter | '_' ) idChar*

The equality of SId and UnitSId type values in SBML is determined by an exact character sequence match; i.e., comparisons of these identifiers must be performed in a case-sensitive manner. This applies to all uses of SId and UnitSId.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

unsetName

public int unsetName()

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.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

unsetNotes

public int unsetNotes()

Unsets the value of the 'notes' subelement of this SBML object.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

unsetAnnotation

public int unsetAnnotation()

Unsets the value of the 'annotation' subelement of this SBML object.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

unsetSBOTerm

public int unsetSBOTerm()

Unsets the value of the 'sboTerm' attribute of this SBML object.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

addCVTerm

public int addCVTerm(CVTerm term,
                     boolean newBag)

Adds a copy of the given CVTerm object to this SBML object.

Parameters:

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.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS
LIBSBML_OPERATION_FAILED
LIBSBML_UNEXPECTED_ATTRIBUTE , if this object lacks a 'metaid' attribute
LIBSBML_INVALID_OBJECT

Note:

Since the CV Term uses the 'metaid' attribute of the object as a reference, if the object has no 'metaid' attribute value set, then the CVTerm will not be added.

Warning:

The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained in this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance added here. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result.

Documentation note:: The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.

addCVTerm

public int addCVTerm(CVTerm term)

Adds a copy of the given CVTerm object to this SBML object.

Parameters:

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.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS
LIBSBML_OPERATION_FAILED
LIBSBML_UNEXPECTED_ATTRIBUTE , if this object lacks a 'metaid' attribute
LIBSBML_INVALID_OBJECT

Note:

Since the CV Term uses the 'metaid' attribute of the object as a reference, if the object has no 'metaid' attribute value set, then the CVTerm will not be added.

Warning:

Documentation note:: The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.

getCVTerms

public CVTermList getCVTerms()

Returns a list of CVTerm objects in the annotations of this SBML object.

Returns:: the list of CVTerms for this SBML object.

getNumCVTerms

public long getNumCVTerms()

Returns the number of CVTerm objects in the annotations of this SBML object.

Returns:: the number of CVTerms for this SBML object.

getCVTerm

public CVTerm getCVTerm(long n)

Returns the nth CVTerm in the list of CVTerms of this SBML object.

Parameters:: n - long the index of the CVTerm to retrieve
Returns:: the nth CVTerm in the list of CVTerms for this SBML object.

unsetCVTerms

public int unsetCVTerms()

Clears the list of CVTerm objects attached to this SBML object.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

unsetModelHistory

public int unsetModelHistory()

Unsets the ModelHistory object attached to this object.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

Note:

In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.

getResourceBiologicalQualifier

public int getResourceBiologicalQualifier(String resource)

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 whose names begin with BQB_ in the interface class libsbmlConstants.

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 whose name begins with BQB_ from the interface class libsbmlConstants.

Parameters:: resource - string representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'.
Returns:: the qualifier associated with the resource, or BQB_UNKNOWN if the resource does not exist.
Note:: The set of MIRIAM biological qualifiers grows over time, although relatively slowly. The values are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQB_ constants defined in libsbmlConstants may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.

getResourceModelQualifier

public int getResourceModelQualifier(String resource)

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 whose names begin with BQM_ in the interface class libsbmlConstants.

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 whose name begins with BQM_ from the interface class libsbmlConstants.

Parameters:: resource - string representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'.
Returns:: the model qualifier type associated with the resource, or BQM_UNKNOWN if the resource does not exist.
Note:: The set of MIRIAM model qualifiers grows over time, although relatively slowly. The values are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQM_ constants defined in libsbmlConstants may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.

getModel

public Model getModel()

Returns the Model object in which the current object is located.

Returns:: the parent Model of this SBML object.
See Also:: SBase.getParentSBMLObject(), SBase.getSBMLDocument()

getLevel

public long getLevel()

Returns the SBML Level of the SBMLDocument object containing this object.

Returns:: the SBML level of this SBML object.
See Also:: SBase.getVersion(), SBase.getNamespaces(), SBase.getPackageVersion()

getVersion

public long getVersion()

Returns the Version within the SBML Level of the SBMLDocument object containing this object.

Returns:: the SBML version of this SBML object.
See Also:: SBase.getLevel(), SBase.getNamespaces()

getPackageVersion

public long getPackageVersion()

Returns the Version of the SBML Level 3 package to which this element belongs to.

Returns:: the version of the SBML Level 3 package to which this element belongs. The value 0 will be returned if this element belongs to the SBML Level 3 Core package.
See Also:: SBase.getLevel(), SBase.getVersion()

getPackageName

public String getPackageName()

Returns the name of the SBML Level 3 package in which this element is defined.

Returns:: the name of the SBML package in which this element is defined. The string "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.

getTypeCode

public int getTypeCode()

Returns the libSBML type code for this object.

This method may return the type code of this SBML object, or it may return SBML_UNKNOWN. This is because subclasses of SBase are not required to implement this method to return a type code. This method is meant primarily for the LibSBML C interface, in which class and subclass information is not readily available.

Returns:: the SBML object type code of this SBML object or SBML_UNKNOWN (the default).
See Also:: SBase.getElementName(), SBase.getPackageName()

hasValidLevelVersionNamespaceCombination

public boolean hasValidLevelVersionNamespaceCombination()

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:

Level 1 Version 2: 'http://www.sbml.org/sbml/level1'
Level 2 Version 1: 'http://www.sbml.org/sbml/level2'
Level 2 Version 2: 'http://www.sbml.org/sbml/level2/version2'
Level 2 Version 3: 'http://www.sbml.org/sbml/level2/version3'
Level 2 Version 4: 'http://www.sbml.org/sbml/level2/version4'
Level 3 Version 1 Core: 'http://www.sbml.org/sbml/level3/version1/core'

Returns:: true if the level, version and namespace values of this SBML object correspond to a valid set of values, false otherwise.

getElementName

public String getElementName()

Returns the XML element name of this object.

This is overridden by subclasses to return a string appropriate to the SBML component. For example, Model defines it as returning 'model', CompartmentType defines it as returning 'compartmentType', and so on.

toSBML

public String toSBML()

Returns a string consisting of a partial SBML corresponding to just this object.

Returns:: the partial SBML that describes this SBML object.
Warning:: This is primarily provided for testing and debugging purposes. It may be removed in a future version of libSBML.

getPlugin

public SBasePlugin getPlugin(String arg0)

Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.

Parameters:: package - the name or URI of the package
Returns:: the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.

getPlugin

public SBasePlugin getPlugin(long n)

Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.

Parameters:: n - the index of the plug-in to return
Returns:: the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.

getNumPlugins

public long getNumPlugins()

Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.

Returns:: the number of plug-in objects (extension interfaces) of package extensions known by this instance of libSBML.

enablePackage

public int enablePackage(String pkgURI,
                         String pkgPrefix,
                         boolean flag)

Enables or disables the given SBML Level 3 package

This method enables or disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.

Parameters:

pkgURI - the URI of the package

pkgPrefix - the XML prefix of the package

flag - whether to enable (true) or disable (false) the package

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

disablePackage

public int disablePackage(String pkgURI,
                          String pkgPrefix)

Disables the given SBML Level 3 package

This method enables or disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.

Parameters:

pkgURI - the URI of the package

pkgPrefix - the XML prefix of the package

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

isPackageURIEnabled

public boolean isPackageURIEnabled(String pkgURI)

Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object.

Parameters:: pkgURI - the URI of the package
Returns:: true if the given package is enabled within this object, @c false otherwise.
See Also:: SBase.isPackageEnabled(String pkgName)

isPackageEnabled

public boolean isPackageEnabled(String pkgName)

Predicate returning true if the given SBML Level 3 package is enabled with this object.

The search ignores the package version.

Parameters:: pkgName - the name of the package
Returns:: true if the given package is enabled within this object, false otherwise.
See Also:: SBase.isPackageURIEnabled(String pkgURI)

isPkgURIEnabled

public boolean isPkgURIEnabled(String pkgURI)

Deprecated. Replaced in libSBML 5.2.0 by isPackageURIEnabled(String pkgURI)

Predicate returning true if an SBML Level 3 package with the given URI is enabled with this object.

Parameters:: pkgURI - the URI of the package
Returns:: true if the given package is enabled within this object, @c false otherwise.
See Also:

isPkgEnabled

public boolean isPkgEnabled(String pkgName)

Deprecated. Replaced in libSBML 5.2.0 by isPackageEnabled(String pkgName)

Predicate returning true if the given SBML Level 3 package is enabled with this object.

The search ignores the package version.

Parameters:: pkgName - the name of the package
Returns:: true if the given package is enabled within this object, false otherwise.
See Also:

removeFromParentAndDelete

public int removeFromParentAndDelete()

Removes itself from its parent. If the parent was storing it as a pointer, it is deleted. If not, it is simply cleared (as in ListOf objects). Pure virutal, as every SBase element has different parents, and therefore different methods of removing itself. Will fail (and not delete itself) if it has no parent object. This function is designed to be overridden, but for all objects whose parent is of the class ListOf, the default implementation will work.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

matchesSBMLNamespaces

public boolean matchesSBMLNamespaces(SBase sb)

Returns true if this object's set of XML namespaces are the same as the given object's XML namespaces.

Parameters:: sb - an object to compare with respect to namespaces
Returns:: boolean, true if this object's collection of namespaces is the same as sb's, false otherwise.

matchesRequiredSBMLNamespacesForAddition

public boolean matchesRequiredSBMLNamespacesForAddition(SBase sb)

Returns true if this object's set of XML namespaces are a subset of the given object's XML namespaces.

Parameters:: sb - an object to compare with respect to namespaces
Returns:: boolean, true if this object's collection of namespaces is a subset of sb's, false otherwise.

getListOfAllElements

public SBaseList getListOfAllElements()

Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth.

Returns:: a pointer to an SBaseList of pointers to all children objects.

getListOfAllElementsFromPlugins

public SBaseList getListOfAllElementsFromPlugins()

Returns an SBaseList of all child SBase objects contained in SBML package plugins. This method walks down the list of all packages used by the model and returns all objects contained in them.

Returns:: a pointer to a SBaseList of pointers to all children objects from plugins.

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org.sbml.libsbml Class SBase

Standard format for annotations linking data resources

delete

equals

hashCode

cloneObject

getElementBySId

getElementByMetaId

renameSIdRefs

renameMetaIdRefs

renameUnitSIdRefs

getMetaId

getNotes

getNotesString

getAnnotation

getAnnotationString

getNamespaces

getSBMLDocument

getParentSBMLObject

getAncestorOfType

getAncestorOfType

getSBOTerm

getSBOTermID

getSBOTermAsURL

getLine

getColumn

getModelHistory

isSetMetaId

isSetNotes

isSetAnnotation

isSetSBOTerm

setMetaId

isSetModelHistory

setAnnotation

setAnnotation

appendAnnotation

appendAnnotation

removeTopLevelAnnotationElement

removeTopLevelAnnotationElement

replaceTopLevelAnnotationElement

replaceTopLevelAnnotationElement

setNotes

setNotes

setNotes

appendNotes

appendNotes

setModelHistory

setSBOTerm

setSBOTerm

setNamespaces

unsetMetaId

unsetId

unsetName

unsetNotes

unsetAnnotation

unsetSBOTerm

addCVTerm

addCVTerm

getCVTerms

getNumCVTerms

getCVTerm

unsetCVTerms

unsetModelHistory

getResourceBiologicalQualifier

getResourceModelQualifier

getModel

getLevel

getVersion

getPackageVersion

getPackageName

getTypeCode

hasValidLevelVersionNamespaceCombination

getElementName

toSBML

getPlugin

getPlugin

getNumPlugins

enablePackage

disablePackage

isPackageURIEnabled

org.sbml.libsbml
Class SBase