public class FluxBound extends SBase
The FluxBound
class of objects is used in Version 1 of the SBML
Level 3 Flux Balance Constraints (&ldquofbc&rdquo) package to express a single
(in)equality that provides the maximum or minimum value that a reaction
flux can obtain at steady state. (This same information is encoded
differently in Version 2 of &ldquofbc&rdquo see the
'upperFluxBound' and 'lowerFluxBound' attributes on FbcReactionPlugin
.)
FluxBound
In addition to the common optional attributes 'id' and 'name', FluxBound
takes three required attributes: 'reaction', 'operation' and 'value'.
These three attributes define the meaning of the FluxBound
, and are
interpreted using the following expression:
The 'reaction' attribute takes a value of SIdRef
. The value
must be the identifier of a Reaction
object defined within the enclosing
model.
The 'operation' attribute takes a value from an enumeration
(#FluxBoundOperation_t) of Boolean operations that represent mathemetical
inequalities. Possible values for 'operation' include
'greaterEqual'
, 'equal'
, and others.
The 'value' attribute takes a numerical value of type double
,
and represents the value of the flux bound. The permitted values include
positive infinity ('INF'
) and negative infinity
('-INF'
).
The following is an example of a set of flux bounds encoded in this form it
also demonstrates the use of ListOfFluxBounds
.
<fbc:listOfFluxBounds> <fbc:fluxBound fbc:id='R1b' fbc:reaction='R1' fbc:operation='greaterEqual' fbc:value='1.2'/> <fbc:fluxBound fbc:id='R2b' fbc:reaction='R2' fbc:operation='lessEqual' fbc:value='-1.2'/> <fbc:fluxBound fbc:id='R3b' fbc:reaction='R3' fbc:operation='greaterEqual' fbc:value='-INF'/> <fbc:fluxBound fbc:id='R4b' fbc:reaction='R4' fbc:operation='lessEqual' fbc:value='INF'/> <fbc:fluxBound fbc:id='R5b' fbc:reaction='R5' fbc:operation='equal' fbc:value='1'/> </fbc:listOfFluxBounds>
ListOfFluxBounds
Parameter
referenced by the 'upperFluxBound' or
'lowerFluxBound' attributes on an FbcReactionPlugin
. FluxBound
is
therefore not used for Version 2 &ldquofbc&rdquo models.
Constructor and Description |
---|
FluxBound()
Creates a new
FbcAssociation with the given SBML Level, Version, and
&ldquofbc&rdquopackage version. |
FluxBound(FbcPkgNamespaces fbcns)
Creates a new
FluxBound with the given FbcPkgNamespaces object. |
FluxBound(FluxBound source)
Copy constructor.
|
FluxBound(long level)
Creates a new
FbcAssociation with the given SBML Level, Version, and
&ldquofbc&rdquopackage version. |
FluxBound(long level,
long version)
Creates a new
FbcAssociation with the given SBML Level, Version, and
&ldquofbc&rdquopackage version. |
FluxBound(long level,
long version,
long pkgVersion)
Creates a new
FbcAssociation with the given SBML Level, Version, and
&ldquofbc&rdquopackage version. |
Modifier and Type | Method and Description |
---|---|
FluxBound |
cloneObject()
Creates and returns a deep copy of this
FluxBound object. |
void |
delete()
Explicitly deletes the underlying native object.
|
java.lang.String |
getElementName()
Returns the XML element name of this object.
|
int |
getFluxBoundOperation()
Returns the value of the 'operation' attribute of this
FluxBound object. |
java.lang.String |
getId()
Returns the value of the 'id' attribute of this
FluxBound object. |
java.lang.String |
getName()
Returns the value of the 'name' attribute of this
FluxBound object. |
java.lang.String |
getOperation()
Returns the value of the 'operation' attribute of this
FluxBound object. |
java.lang.String |
getReaction()
Returns the value of the 'reaction' attribute of this
FluxBound object. |
int |
getTypeCode()
Returns the libSBML type code of this object instance.
|
double |
getValue()
Returns the value of the 'value' attribute of this
FluxBound object. |
boolean |
isSetId()
Predicate returning
true if this FluxBound 's 'id' attribute is set. |
boolean |
isSetName()
Predicate returning
true if this FluxBound 's 'name' attribute is set. |
boolean |
isSetOperation()
Predicate returning
true if this FluxBound 's 'operation' attribute is
set. |
boolean |
isSetReaction()
Predicate returning
true if this FluxBound 's 'reaction' attribute is
set. |
boolean |
isSetValue()
Predicate returning
true if this FluxBound 's 'value' attribute is
set. |
void |
renameSIdRefs(java.lang.String oldid,
java.lang.String newid)
Replaces all uses of a given
SIdRef type attribute value with another
value. |
int |
setId(java.lang.String id)
Sets the value of the 'id' attribute of this
FluxBound object. |
int |
setName(java.lang.String name)
Sets the value of the 'name' attribute of this
FluxBound object. |
int |
setOperation(int operation)
Sets the value of the 'operation' attribute of this
FluxBound object. |
int |
setOperation(java.lang.String operation)
Sets the value of the 'operation' attribute of this
FluxBound object. |
int |
setReaction(java.lang.String reaction)
Sets the value of the 'reaction' attribute of this
FluxBound object. |
int |
setValue(double value)
Sets the value of the 'value' attribute of this
FluxBound object. |
int |
unsetId()
Unsets the value of the 'id' attribute of this
FluxBound object. |
int |
unsetName()
Unsets the value of the 'name' attribute of this
FluxBound object. |
int |
unsetOperation()
Unsets the value of the 'operation' attribute of this
FluxBound object. |
int |
unsetReaction()
Unsets the value of the 'reaction' attribute of this
FluxBound object. |
int |
unsetValue()
Unsets the value of the 'value' attribute of this
FluxBound object. |
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, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetMetaId, unsetModelHistory, unsetNotes, unsetSBOTerm, unsetUserData
public FluxBound(long level, long version, long pkgVersion) throws SBMLConstructorException
FbcAssociation
with the given SBML Level, Version, and
&ldquofbc&rdquopackage version.
level
- a long integer, the SBML Level to assign to this
FluxObjective
version
- a long integer, the SBML Version to assign to this
FluxObjective
pkgVersion
- a long integer, the SBML Fbc Version to assign to
this FluxObjective
SBMLConstructorException
public FluxBound(long level, long version) throws SBMLConstructorException
FbcAssociation
with the given SBML Level, Version, and
&ldquofbc&rdquopackage version.
level
- a long integer, the SBML Level to assign to this
FluxObjective
version
- a long integer, the SBML Version to assign to this
FluxObjective
pkgVersion
- a long integer, the SBML Fbc Version to assign to
this FluxObjective
SBMLConstructorException
public FluxBound(long level) throws SBMLConstructorException
FbcAssociation
with the given SBML Level, Version, and
&ldquofbc&rdquopackage version.
level
- a long integer, the SBML Level to assign to this
FluxObjective
version
- a long integer, the SBML Version to assign to this
FluxObjective
pkgVersion
- a long integer, the SBML Fbc Version to assign to
this FluxObjective
SBMLConstructorException
public FluxBound() throws SBMLConstructorException
FbcAssociation
with the given SBML Level, Version, and
&ldquofbc&rdquopackage version.
level
- a long integer, the SBML Level to assign to this
FluxObjective
version
- a long integer, the SBML Version to assign to this
FluxObjective
pkgVersion
- a long integer, the SBML Fbc Version to assign to
this FluxObjective
SBMLConstructorException
public FluxBound(FbcPkgNamespaces fbcns) throws SBMLConstructorException
FluxBound
with the given FbcPkgNamespaces
object.SBMLConstructorException
public FluxBound(FluxBound source) throws SBMLConstructorException
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 FluxBound.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 FluxBound.delete()
themselves.
public java.lang.String getId()
FluxBound
object.
public boolean isSetId()
true
if this FluxBound
's 'id' attribute is set.
public int setId(java.lang.String id)
FluxBound
object.
public int unsetId()
FluxBound
object.
public java.lang.String getName()
FluxBound
object.
public boolean isSetName()
true
if this FluxBound
's 'name' attribute is set.
public int setName(java.lang.String name)
FluxBound
object.
public int unsetName()
FluxBound
object.
public java.lang.String getReaction()
FluxBound
object.
FluxBound
object.public boolean isSetReaction()
true
if this FluxBound
's 'reaction' attribute is
set.
true
if this FluxBound
object's 'reaction' attribute has been
set, otherwise false
is returned.public int setReaction(java.lang.String reaction)
FluxBound
object.
public int unsetReaction()
FluxBound
object.
public java.lang.String getOperation()
FluxBound
object.
FluxBound
object.public int getFluxBoundOperation()
FluxBound
object.
FluxBound
object.public boolean isSetOperation()
true
if this FluxBound
's 'operation' attribute is
set.
true
if this FluxBound
object's 'operation' attribute has been set,
otherwise false
is returned.public int setOperation(java.lang.String operation)
FluxBound
object.
public int setOperation(int operation)
FluxBound
object.
public int unsetOperation()
FluxBound
object.
public double getValue()
FluxBound
object.
FluxBound
object.public boolean isSetValue()
true
if this FluxBound
's 'value' attribute is
set.
true
if this FluxBound
object's 'value' attribute has been set,
otherwise false
is returned.public int setValue(double value)
FluxBound
object.
public int unsetValue()
FluxBound
object.
public void renameSIdRefs(java.lang.String oldid, java.lang.String newid)
Replaces all uses of a given SIdRef
type attribute value with another
value.
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 in MathML content, comparing the referenced
identifiers to the value of oldid
. If any matches are found, the
matching values are replaced with newid
. The method does not
descend into child elements.
renameSIdRefs
 in class SBase
oldid
- the old identifiernewid
- the new identifierpublic java.lang.String getElementName()
For FluxBound
, the XML element name is always 'fluxBound'.
getElementName
 in class SBase
'fluxBound'.
public FluxBound cloneObject()
FluxBound
object.
cloneObject
 in class SBase
FluxBound
object.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_FBC_FLUXBOUND
FluxBound.getElementName()
,
SBase.getPackageName()