public class SpeciesType extends SBase
The term species type refers to reacting entities independent of location. These include simple ions (e.g., protons, calcium), simple molecules (e.g., glucose, ATP), large molecules (e.g., RNA, polysaccharides, and proteins), and others.
SBML Level 2 Versions 2&ndash4 provide an explicit
SpeciesType
class of object to enable Species
objects of the same type
to be related together. SpeciesType
is a conceptual construct the
existence of SpeciesType
objects in a model has no effect on the model's
numerical interpretation. Except for the requirement for uniqueness of
species/species type combinations located in compartments, simulators
and other numerical analysis software may ignore SpeciesType
definitions
and references to them in a model.
There is no mechanism in SBML Level 2 for representing hierarchies of
species types. One SpeciesType
object cannot be the subtype of another
SpeciesType
object SBML provides no means of defining such
relationships.
As with other major structures in SBML, SpeciesType
has a mandatory
attribute, 'id', used to give the species type an identifier. The
identifier must be a text string conforming to the identifer syntax
permitted in SBML. SpeciesType
also has an optional 'name' attribute,
of type string.
The 'id' and 'name' must be used according to the
guidelines described in the SBML specification (e.g., Section 3.3 in
the Level 2 Version 4 specification).
SpeciesType
was introduced in SBML Level 2 Version 2. It is not
available in SBML Level 1 nor in Level 3.
Species
,
ListOfSpeciesTypes
,
CompartmentType
,
ListOfCompartmentTypes
Constructor and Description |
---|
SpeciesType(long level,
long version)
|
SpeciesType(SBMLNamespaces sbmlns)
|
SpeciesType(SpeciesType orig)
Copy constructor creates a copy of this
SpeciesType . |
Modifier and Type | Method and Description |
---|---|
SpeciesType |
cloneObject()
Creates and returns a deep copy of this
SpeciesType object. |
void |
delete()
Explicitly deletes the underlying native object.
|
java.lang.String |
getElementName()
Returns the XML element name of this object, which for
SpeciesType , is always 'compartmentType'. |
java.lang.String |
getId()
Returns the value of the 'id' attribute of this
SpeciesType . |
java.lang.String |
getName()
Returns the value of the 'name' attribute of this
SpeciesType . |
int |
getTypeCode()
Returns the libSBML type code for this SBML object.
|
boolean |
hasRequiredAttributes()
Predicate returning
true if
all the required attributes for this SpeciesType object
have been set. |
boolean |
isSetId()
Predicate returning
true if this
SpeciesType 's 'id' attribute is set. |
boolean |
isSetName()
Predicate returning
true if this
SpeciesType 's 'name' attribute is set. |
int |
setId(java.lang.String sid)
Sets the value of the 'id' attribute of this
SpeciesType . |
int |
setName(java.lang.String name)
Sets the value of the 'name' attribute of this
SpeciesType . |
int |
unsetName()
Unsets the value of the 'name' attribute of this
SpeciesType . |
addCVTerm, addCVTerm, appendAnnotation, appendAnnotation, appendNotes, appendNotes, connectToChild, deleteDisabledPlugins, deleteDisabledPlugins, disablePackage, enablePackage, equals, getAncestorOfType, getAncestorOfType, getAnnotation, getAnnotationString, getColumn, getCVTerm, getCVTerms, getDisabledPlugin, getElementByMetaId, getElementBySId, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumDisabledPlugins, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getPlugin, getPrefix, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getURI, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetMetaId, isSetModelHistory, isSetNotes, isSetSBOTerm, isSetUserData, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeFromParentAndDelete, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, renameSIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetId, unsetMetaId, unsetModelHistory, unsetNotes, unsetSBOTerm, unsetUserData
public SpeciesType(long level, long version) throws SBMLConstructorException
level
- a long integer, the SBML Level to assign to this SpeciesType
version
- a long integer, the SBML Version to assign to this
SpeciesType
SBMLConstructorException
- Thrown if the given level
and version
combination are invalid
or if this object is incompatible with the given level and version.
SBMLDocument
having a different
combination of SBML Level, Version and XML namespaces than the object
itself will result in an error at the time a caller attempts to make the
addition. A parent object must have compatible Level, Version and XML
namespaces. (Strictly speaking, a parent may also have more XML
namespaces than a child, but the reverse is not permitted.) The
restriction is necessary to ensure that an SBML model has a consistent
overall structure. This requires callers to manage their objects
carefully, but the benefit is increased flexibility in how models can be
created by permitting callers to create objects bottom-up if desired. In
situations where objects are not yet attached to parents (e.g.,
SBMLDocument
), knowledge of the intented SBML Level and Version help
libSBML determine such things as whether it is valid to assign a
particular value to an attribute.public SpeciesType(SBMLNamespaces sbmlns) throws SBMLConstructorException
SpeciesType
using the given SBMLNamespaces
object
sbmlns
.
The SBMLNamespaces
object encapsulates SBML Level/Version/namespaces
information. It is used to communicate the SBML Level, Version, and (in
Level 3) packages used in addition to SBML Level 3 Core. A
common approach to using libSBML's SBMLNamespaces
facilities is to create an
SBMLNamespaces
object somewhere in a program once, then hand that object
as needed to object constructors that accept SBMLNamespaces
as arguments.
It is worth emphasizing that although this constructor does not take
an identifier argument, in SBML Level 2 and beyond, the 'id'
(identifier) attribute of a SpeciesType
object is required to have a value.
Thus, callers are cautioned to assign a value after calling this
constructor. Setting the identifier can be accomplished using the
method SBase.setId(String)
.
sbmlns
- an SBMLNamespaces
object.
SBMLConstructorException
- Thrown if the given sbmlns
is inconsistent or incompatible
with this object.
SBMLDocument
having a different
combination of SBML Level, Version and XML namespaces than the object
itself will result in an error at the time a caller attempts to make the
addition. A parent object must have compatible Level, Version and XML
namespaces. (Strictly speaking, a parent may also have more XML
namespaces than a child, but the reverse is not permitted.) The
restriction is necessary to ensure that an SBML model has a consistent
overall structure. This requires callers to manage their objects
carefully, but the benefit is increased flexibility in how models can be
created by permitting callers to create objects bottom-up if desired. In
situations where objects are not yet attached to parents (e.g.,
SBMLDocument
), knowledge of the intented SBML Level and Version help
libSBML determine such things as whether it is valid to assign a
particular value to an attribute.public SpeciesType(SpeciesType orig) throws SBMLConstructorException
SpeciesType
.
orig
- the object to copy.SBMLConstructorException
public void delete()
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 SpeciesType.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 SpeciesType.delete()
themselves.
public SpeciesType cloneObject()
SpeciesType
object.
cloneObject
 in class SBase
SpeciesType
object.public java.lang.String getId()
SpeciesType
.
getId
 in class SBase
SpeciesType
.public java.lang.String getName()
SpeciesType
.
getName
 in class SBase
SpeciesType
.public boolean isSetId()
true
if this
SpeciesType
's 'id' attribute is set.
isSetId
 in class SBase
true
if the 'id' attribute of this SpeciesType
is
set, false
otherwise.public boolean isSetName()
true
if this
SpeciesType
's 'name' attribute is set.
isSetName
 in class SBase
true
if the 'name' attribute of this SpeciesType
is
set, false
otherwise.public int setId(java.lang.String sid)
SpeciesType
.
The string sid
is copied.
SBML has strict requirements for the syntax of identifiers, that is, the
values of the 'id' attribute present on most types of SBML objects.
The following is a summary of the definition of the SBML identifier type
SId
, which defines the permitted syntax of identifiers. We
express the syntax using an extended form of BNF notation:
letter .= 'a'..'z','A'..'Z' digit .= '0'..'9' idChar .= letter | digit | '_' SId .= ( letter | '_' ) idChar*The characters
(
and )
are used for grouping, the
character *
'zero or more times', and the character
|
indicates logical 'or'. The equality of SBML identifiers is
determined by an exact character sequence match i.e., comparisons must be
performed in a case-sensitive manner. In addition, there are a few
conditions for the uniqueness of identifiers in an SBML model. Please
consult the SBML specifications for the exact details of the uniqueness
requirements.
setId
 in class SBase
sid
- the string to use as the identifier of this SpeciesType
public int setName(java.lang.String name)
SpeciesType
.
The string in name
is copied.
setName
 in class SBase
name
- the new name for the SpeciesType
public int unsetName()
SpeciesType
.
public int getTypeCode()
LibSBML attaches an identifying code to every kind of SBML object. These
are integer constants known as SBML type codes. The names of all
the codes begin with the characters SBML_
.
In the Java language interface for libSBML, the
type codes are defined as static integer constants in the interface class
libsbmlConstants
. 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.
getTypeCode
 in class SBase
SBML_SPECIES_TYPE
(default).
SpeciesType.getElementName()
,
SBase.getPackageName()
public java.lang.String getElementName()
SpeciesType
, is always 'compartmentType'.
getElementName
 in class SBase
'compartmentType'.
public boolean hasRequiredAttributes()
true
if
all the required attributes for this SpeciesType
object
have been set.
The required attributes for a SpeciesType
object are:
hasRequiredAttributes
 in class SBase
true
if the required attributes have been set, false
otherwise.