public class FbcModelPlugin extends SBasePlugin
Model
.
The FbcModelPlugin
object is used to extend the standard SBML Model
object
with features used in the SBML Level 3 Flux Balance Constraints (&ldquofbc&rdquo)
package. In Version 1 of the &ldquofbc&rdquo specification, the
extended Model
class has two optional subobjects: ListOfObjectives
and
ListOfFluxBounds
. In Version 2 of the specification, the extended
Model
object is defined differently: it is extended with a new required
attribute named 'strict', and the two optional subobjects ListOfObjectives
and ListOfGeneProducts
. (ListOfFluxBounds is not used in Version 2.)
Model
class
The mandatory attribute 'strict', of type boolean
, in
Version 2 of this package, is used to
apply an additional set of restrictions to the model. The 'strict'
attribute helps ensure that the Flux Balance Constraints package can be
used to encode legacy flux-balance analysis models expressible as Linear
Programs (LP's) for software that is unable to analyze arbitrary
mathematical expressions that may appear in an SBML model. In addition, a
'strict' model is fully described and mathematically consistent, for
example, by ensuring that all fluxes have a valid upper or lower bound.
The following restrictions are in effect if an &ldquofbc&rdquo model
object has a value of 'true'
for the attribute 'strict' on
Model:
Reaction
in a Model
must define values for the attributes
'lowerFluxBound' and 'upperFluxBound', with each attribute pointing to a
valid Parameter
object defined in the current Model
.
Parameter
object referred to by the Reaction
attributes
'lowerFluxBound' and 'upperFluxBound' must have its 'constant' attribute
set to the value 'true'
and its 'value' attribute set to a
value of type double
. This value may not be
'NaN'
.
SpeciesReference
objects in Reaction
objects must have their
'stoichiometry' attribute set to a double
value that is not
'NaN'
, nor '-INF'
, nor 'INF'
. In
addition, the value of their 'constant' attribute must be set to
'true'
.
InitialAssignment
objects may not target the Parameter
objects
referenced by the Reaction
attributes 'lowerFluxBound' and
'upperFluxBound', nor any SpeciesReference
objects.
FluxObjective
objects must have their coefficient
attribute set to a double
value that is not
'NaN'
, nor '-INF'
, nor 'INF'
.
Reaction
'lowerFluxBound' attribute may not point to a Parameter
object that has a value of 'INF'
.
Reaction
'upperFluxBound' attribute may not point to a Parameter
object that has a value of '-INF'
.
Reaction
objects, the value of a 'lowerFluxBound' attribute
must be less than or equal to the value of the 'upperFluxBound' attribute.
While it is not compulsory for a 'strict' Flux Balance Constraints model
to define an Objective
, doing so does does allow the model to be
formulated as a Linear Program and optimized. However, this decision is
left to the modeler. Note that all other properties of the objects
referred to in the list above are to be set as specified in the relevant
SBML Level 3 Version 1 Core and Flux Balance Constraints (&ldquofbc&rdquo)
specifications.
Alternatively, if the value of the strict attribute is
'false'
, then none of these restrictions apply and the model
creator can choose to define &ldquofbc&rdquo models that are not
necessarily encodable as an LP. For example, if strict is
'false'
, the InitialAssignment
construct may be used to set
any valid numerical entity, including Parameter
values and stoichiometric
coefficients, with any value of type double
. In addition,
Parameter
elements are no longer required to be flagged as constant, thus
allowing for a Flux Balance Constraints model's use in alternative, hybrid
modeling strategies.
Model
class
The ListOfObjectives
is used to define the objectives of a given
&ldquofbc&rdquo model. Objectives generally consist of linear
combinations of model variables (fluxes) and a direction for the
optimality constraint (either maximization or minimization). Each
Objective
has a ListOfFluxObjectives
subobjects.
In Version 2 of &ldquofbc&rdquo, the ListOfGeneProducts
is used to
define the gene products represented by the &ldquofbc&rdquo model.
In Version 1 of &ldquofbc&rdquo, there is no ListOfGeneProducts
,
and instead, Model
can have an optional ListOfFluxBounds
.
Objective
,
FluxObjective
,
FluxBound
Constructor and Description |
---|
FbcModelPlugin(FbcModelPlugin orig)
Copy constructor for
FbcModelPlugin . |
FbcModelPlugin(java.lang.String uri,
java.lang.String prefix,
FbcPkgNamespaces fbcns)
Creates a new
FbcModelPlugin object using the given parameters. |
Modifier and Type | Method and Description |
---|---|
int |
addFluxBound(FluxBound bound)
Adds a copy of the given
FluxBound object to the list of FluxBounds. |
int |
addGeneAssociation(GeneAssociation association)
Adds a copy of the given
GeneAssociation annotation object to the list of GeneAssociations. |
int |
addGeneProduct(GeneProduct gp)
Adds a copy the given
GeneProduct to this FbcModelPlugin . |
int |
addObjective(Objective o)
Adds a copy the given
Objective to this FbcModelPlugin . |
SBasePlugin |
cloneObject()
Creates and returns a deep copy of this
FbcModelPlugin object. |
FluxBound |
createFluxBound()
|
GeneAssociation |
createGeneAssociation()
Creates a new
GeneAssociation annotation object and adds it to the list of GeneAssociation objects
and returns it. |
GeneProduct |
createGeneProduct()
Creates a new
GeneProduct object, adds it to this FbcModelPlugin 's
ListOfGeneProducts and returns the GeneProduct object created. |
Objective |
createObjective()
Creates a new
Objective object, adds it to this FbcModelPlugin 's
ListOfObjectives and returns the Objective object created. |
void |
delete()
Explicitly deletes the underlying native object.
|
Objective |
getActiveObjective()
Returns the current active objective.
|
java.lang.String |
getActiveObjectiveId()
Returns the id of the current active objective.
|
FluxBound |
getFluxBound(long n)
Returns the
FluxBound object that belongs to the given index. |
FluxBound |
getFluxBound(java.lang.String sid)
Returns the
FluxBound object based on its identifier. |
ListOfFluxBounds |
getFluxBoundsForReaction(java.lang.String reaction)
Creates a new
ListOfFluxBounds object that contains only the
FluxBound objects associated with the given Reaction . |
GeneAssociation |
getGeneAssociation(long n)
Returns the
GeneAssociation annotation object that belongs to the given index. |
GeneAssociation |
getGeneAssociation(java.lang.String sid)
Returns the
GeneAssociation annotation object based on its identifier. |
GeneProduct |
getGeneProduct(long n)
Get a
GeneProduct from the ListOfGeneProducts . |
GeneProduct |
getGeneProduct(java.lang.String sid)
Get a
GeneProduct from the ListOfGeneProducts
based on its identifier. |
GeneProduct |
getGeneProductByLabel(java.lang.String label)
Get a
GeneProduct from the ListOfGeneProducts
based on its label. |
ListOfFluxBounds |
getListOfFluxBounds()
Returns the
ListOfFluxBounds in this plugin object. |
ListOfGeneAssociations |
getListOfGeneAssociations()
Returns the
ListOfGeneAssociations annotation object for level 1 in this plugin object. |
ListOfGeneProducts |
getListOfGeneProducts()
Returns the 'ListOfGeneProducts' in this
FbcModelPlugin object. |
ListOfObjectives |
getListOfObjectives()
Returns the
ListOfObjectives in this FbcModelPlugin object. |
long |
getNumFluxBounds()
Returns the number of
FluxBound object in this plugin object. |
int |
getNumGeneAssociations()
Returns the number of
GeneAssociation annotation object in this plugin object. |
long |
getNumGeneProducts()
Get the number of
GeneProduct objects in this FbcModelPlugin . |
long |
getNumObjectives()
Get the number of
Objective objects in this FbcModelPlugin . |
Objective |
getObjective(long n)
Get an
Objective from the ListOfObjectives . |
Objective |
getObjective(java.lang.String sid)
Get an
Objective from the ListOfObjectives
based on its identifier. |
boolean |
getStrict()
Returns the value of the 'strict' attribute of this
FbcModelPlugin . |
boolean |
isSetStrict()
Predicate returning
true if this FbcModelPlugin 's 'strict' attribute
is set. |
FluxBound |
removeFluxBound(long n)
Removes the nth
FluxBound object from this plugin object and
returns a pointer to it. |
FluxBound |
removeFluxBound(java.lang.String sid)
Removes the
FluxBound object with the given sid attribute from
this plugin object and returns a pointer to it. |
GeneAssociation |
removeGeneAssociation(long n)
Removes the nth
GeneAssociation annotation object from this plugin object and
returns a pointer to it. |
GeneAssociation |
removeGeneAssociation(java.lang.String sid)
Removes the
GeneAssociation annotation object with the given sid attribute from
this plugin object and returns a pointer to it. |
GeneProduct |
removeGeneProduct(long n)
|
GeneProduct |
removeGeneProduct(java.lang.String sid)
Removes the
GeneProduct with the given identifier from the ListOfGeneProducts within this FbcModelPlugin
and returns a pointer to it. |
Objective |
removeObjective(long n)
|
Objective |
removeObjective(java.lang.String sid)
Removes the
Objective with the given identifier from the ListOfObjectives within this FbcModelPlugin
and returns a pointer to it. |
int |
setActiveObjectiveId(java.lang.String objectiveId)
Sets the id of the active objective.
|
int |
setStrict(boolean strict)
Sets the value of the 'strict' attribute of this
FbcModelPlugin . |
int |
unsetActiveObjectiveId()
Unsets the 'activeObjective' attribute of the
ListOfObjectives . |
int |
unsetStrict()
Unsets the value of the 'strict' attribute of this
FbcModelPlugin . |
getElementByMetaId, getElementBySId, getElementNamespace, getLevel, getListOfAllElements, getListOfAllElements, getPackageName, getPackageVersion, getParentSBMLObject, getPrefix, getSBMLDocument, getURI, getVersion, isValidTypeForList, renameMetaIdRefs, renameSIdRefs, renameUnitSIdRefs, setElementNamespace
public FbcModelPlugin(java.lang.String uri, java.lang.String prefix, FbcPkgNamespaces fbcns)
FbcModelPlugin
object using the given parameters.
In the XML representation of an SBML document, XML namespaces are used to
identify the origin of each XML construct used. XML namespaces are
identified by their unique resource identifiers (URIs). The core SBML
specifications stipulate the namespaces that must be used for core SBML
constructs for example, all XML elements that belong to SBML Level 3
Version 1 Core must be placed in the XML namespace identified by the URI
'http://www.sbml.org/sbml/level3/version1/core'
. Individual
SBML Level 3 packages define their own XML namespaces for example,
all elements belonging to the SBML Level 3 Layout Version 1
package must be placed in the XML namespace
'http://www.sbml.org/sbml/level3/version1/layout/version1/'
.
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.
uri
- the URI of the SBML Level 3 package implemented by
this libSBML package extension.
prefix
- the XML namespace prefix being used for the package.
fbcns
- the namespaces object for the package.public FbcModelPlugin(FbcModelPlugin orig)
FbcModelPlugin
.
orig
- the FbcModelPlugin
instance to copy.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 FbcModelPlugin.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 FbcModelPlugin.delete()
themselves.
delete
 in class SBasePlugin
public SBasePlugin cloneObject()
FbcModelPlugin
object.
cloneObject
 in class SBasePlugin
FbcModelPlugin
object.public boolean getStrict()
FbcModelPlugin
.
FbcModelPlugin
as a boolean.FbcModelPlugin
is only defined for
version 2 of the 'Flux Balance Constraints' specification, and has no
equivalent in version 1 of the specification.
public boolean isSetStrict()
true
if this FbcModelPlugin
's 'strict' attribute has been set,
otherwise false
is returned.FbcModelPlugin
is only defined for
version 2 of the 'Flux Balance Constraints' specification, and has no
equivalent in version 1 of the specification.
public int setStrict(boolean strict)
FbcModelPlugin
.
strict
- boolean value of the 'strict' attribute to be set.
FbcModelPlugin
is only defined for
version 2 of the 'Flux Balance Constraints' specification, and has no
equivalent in version 1 of the specification.
public int unsetStrict()
FbcModelPlugin
.
FbcModelPlugin
is only defined for
version 2 of the 'Flux Balance Constraints' specification, and has no
equivalent in version 1 of the specification.
public ListOfFluxBounds getListOfFluxBounds()
ListOfFluxBounds
in this plugin object.
ListOfFluxBounds
object in this plugin object.FluxBound
objects are only defined for version 1
of the 'Flux Balance Constraints' specification, and are
replaced in version 2 by the 'upperFluxBound' and
'lowerFluxBound' attributes of the FbcReactionPlugin
.
public FluxBound getFluxBound(long n)
FluxBound
object that belongs to the given index. If the
index is invalid, null
is returned.
n
- the index number of the FluxBound
to get.
FluxBound
in the ListOfFluxBounds
.FluxBound
objects are only defined for version 1
of the 'Flux Balance Constraints' specification, and are
replaced in version 2 by the 'upperFluxBound' and
'lowerFluxBound' attributes of the FbcReactionPlugin
.
public FluxBound getFluxBound(java.lang.String sid)
FluxBound
object based on its identifier.
sid
- a string representing the identifier
of the FluxBound
to get.
FluxBound
in the ListOfFluxBounds
with the given sid
or null if no such FluxBound
exists.
FbcModelPlugin.getFluxBound(long n)
,
FbcModelPlugin.getListOfFluxBounds()
FluxBound
objects are only defined for version 1
of the 'Flux Balance Constraints' specification, and are
replaced in version 2 by the 'upperFluxBound' and
'lowerFluxBound' attributes of the FbcReactionPlugin
.
public ListOfFluxBounds getFluxBoundsForReaction(java.lang.String reaction)
ListOfFluxBounds
object that contains only the
FluxBound
objects associated with the given Reaction
. If no such
Reaction
can be found, or if there are no FluxBound
objects associated
with it, returns null.
reaction
- the id of an reaction to find FluxBound
objects for.
ListOfFluxBounds
for the given reaction id.FluxBound
objects are only defined for version 1
of the 'Flux Balance Constraints' specification, and are
replaced in version 2 by the 'upperFluxBound' and
'lowerFluxBound' attributes of the FbcReactionPlugin
.
public int addFluxBound(FluxBound bound)
FluxBound
object to the list of FluxBounds.
bound
- the FluxBound
object to be added to the list of FluxBounds.
FluxBound
objects are only defined for version 1
of the 'Flux Balance Constraints' specification, and are
replaced in version 2 by the 'upperFluxBound' and
'lowerFluxBound' attributes of the FbcReactionPlugin
.
public FluxBound createFluxBound()
FluxBound
object.FluxBound
objects are only defined for version 1
of the 'Flux Balance Constraints' specification, and are
replaced in version 2 by the 'upperFluxBound' and
'lowerFluxBound' attributes of the FbcReactionPlugin
.
public FluxBound removeFluxBound(long n)
FluxBound
object from this plugin object and
returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n
- the index of the FluxBound
object to remove.
FluxBound
object removed. As mentioned above, the
caller owns the returned object. null
is returned if the
given index is out of range.FluxBound
objects are only defined for version 1
of the 'Flux Balance Constraints' specification, and are
replaced in version 2 by the 'upperFluxBound' and
'lowerFluxBound' attributes of the FbcReactionPlugin
.
public FluxBound removeFluxBound(java.lang.String sid)
FluxBound
object with the given sid
attribute from
this plugin object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
sid
- the id attribute of the FluxBound
object to remove.
FluxBound
object removed. As mentioned above, the
caller owns the returned object. null
is returned if the
given index is out of range.FluxBound
objects are only defined for version 1
of the 'Flux Balance Constraints' specification, and are
replaced in version 2 by the 'upperFluxBound' and
'lowerFluxBound' attributes of the FbcReactionPlugin
.
public long getNumFluxBounds()
FluxBound
object in this plugin object.
FluxBound
object in this plugin object.FluxBound
objects are only defined for version 1
of the 'Flux Balance Constraints' specification, and are
replaced in version 2 by the 'upperFluxBound' and
'lowerFluxBound' attributes of the FbcReactionPlugin
.
public ListOfObjectives getListOfObjectives()
ListOfObjectives
in this FbcModelPlugin
object.
ListOfObjectives
child of this FbcModelPlugin
.public Objective getObjective(long n)
Objective
from the ListOfObjectives
.
n
- the index number of the Objective
to get.
Objective
in the ListOfObjectives
within this FbcModelPlugin
.
FbcModelPlugin.getNumObjectives()
public Objective getObjective(java.lang.String sid)
Objective
from the ListOfObjectives
based on its identifier.
sid
- a string representing the identifier
of the Objective
to get.
Objective
in the ListOfObjectives
with the given id or null if no such
Objective
exists.
,
FbcModelPlugin.getObjective(long n)
public int addObjective(Objective o)
Objective
to this FbcModelPlugin
.
o
- the Objective
object to add.
public long getNumObjectives()
Objective
objects in this FbcModelPlugin
.
Objective
objects in this FbcModelPlugin
.public Objective createObjective()
Objective
object, adds it to this FbcModelPlugin
's
ListOfObjectives
and returns the Objective
object created.
Objective
object instance.
FbcModelPlugin.addObjective(Objective o)
public Objective removeObjective(long n)
Objective
from the ListOfObjectives
within this FbcModelPlugin
.
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
n
- the index of the Objective
to remove.
FbcModelPlugin.getNumObjectives()
public Objective removeObjective(java.lang.String sid)
Objective
with the given identifier from the ListOfObjectives
within this FbcModelPlugin
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier sid
, then
null
is returned.
public Objective getActiveObjective()
public int setActiveObjectiveId(java.lang.String objectiveId)
public java.lang.String getActiveObjectiveId()
ListOfObjectives
.public int unsetActiveObjectiveId()
ListOfObjectives
.
public ListOfGeneProducts getListOfGeneProducts()
FbcModelPlugin
object.
FbcModelPlugin
.GeneProduct
objects are only defined for version 2
of the 'Flux Balance Constraints' specification, and have no
equivalent in version 1 of the specification.
public GeneProduct getGeneProduct(long n)
n
- the index number of the GeneProduct
to get.
GeneProduct
in the ListOfGeneProducts
within this FbcModelPlugin
.
FbcModelPlugin.getNumGeneProducts()
GeneProduct
objects are only defined for version 2
of the 'Flux Balance Constraints' specification, and have no
equivalent in version 1 of the specification.
public GeneProduct getGeneProduct(java.lang.String sid)
sid
- a string representing the identifier
of the GeneProduct
to get.
GeneProduct
in the ListOfGeneProducts
with the given id or null if no such
GeneProduct
exists.
,
FbcModelPlugin.getGeneProduct(long n)
GeneProduct
objects are only defined for version 2
of the 'Flux Balance Constraints' specification, and have no
equivalent in version 1 of the specification.
public GeneProduct getGeneProductByLabel(java.lang.String label)
label
- a string representing the label
of the GeneProduct
to get.
GeneProduct
in the ListOfGeneProducts
with the given label or null if no such
GeneProduct
exists.
,
FbcModelPlugin.getGeneProduct(long n)
GeneProduct
objects are only defined for version 2
of the 'Flux Balance Constraints' specification, and have no
equivalent in version 1 of the specification.
public int addGeneProduct(GeneProduct gp)
gp
- the GeneProduct
object to add.
GeneProduct
objects are only defined for version 2
of the 'Flux Balance Constraints' specification, and have no
equivalent in version 1 of the specification.
public long getNumGeneProducts()
GeneProduct
objects in this FbcModelPlugin
.GeneProduct
objects are only defined for version 2
of the 'Flux Balance Constraints' specification, and have no
equivalent in version 1 of the specification.
public GeneProduct createGeneProduct()
GeneProduct
object, adds it to this FbcModelPlugin
's
ListOfGeneProducts
and returns the GeneProduct
object created.
GeneProduct
object instance.
FbcModelPlugin.addGeneProduct(GeneProduct gp)
GeneProduct
objects are only defined for version 2
of the 'Flux Balance Constraints' specification, and have no
equivalent in version 1 of the specification.
public GeneProduct removeGeneProduct(long n)
GeneProduct
from the ListOfGeneProducts
within this FbcModelPlugin
.
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
n
- the index of the GeneProduct
to remove.
FbcModelPlugin.getNumGeneProducts()
GeneProduct
objects are only defined for version 2
of the 'Flux Balance Constraints' specification, and have no
equivalent in version 1 of the specification.
public GeneProduct removeGeneProduct(java.lang.String sid)
GeneProduct
with the given identifier from the ListOfGeneProducts
within this FbcModelPlugin
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier sid
, then
null
is returned.
sid
- the identifier of the GeneProduct
to remove.
GeneProduct
removed. As mentioned above, the caller owns the
returned item.GeneProduct
objects are only defined for version 2
of the 'Flux Balance Constraints' specification, and have no
equivalent in version 1 of the specification.
public ListOfGeneAssociations getListOfGeneAssociations()
ListOfGeneAssociations
annotation object for level 1 in this plugin object.
ListOfGeneAssociations
annotation object for level 1 in this plugin object.GeneAssociation
objects are not defined in any version of the
'Flux Balance Constraints' specification, and can only be used for
annotation purposes. Version 2 instead defines the
GeneProduct
and GeneProductAssociation
classes to cover the information
otherwise encoded here.
public GeneAssociation getGeneAssociation(long n)
GeneAssociation
annotation object that belongs to the given index. If the
index is invalid, null
is returned.
n
- the index number of the GeneAssociation
annotation to get.
GeneAssociation
annotation in the ListOfGeneAssociations
.GeneAssociation
objects are not defined in any version of the
'Flux Balance Constraints' specification, and can only be used for
annotation purposes. Version 2 instead defines the
GeneProduct
and GeneProductAssociation
classes to cover the information
otherwise encoded here.
public GeneAssociation getGeneAssociation(java.lang.String sid)
GeneAssociation
annotation object based on its identifier.
sid
- a string representing the identifier
of the GeneAssociation
annotation to get.
GeneAssociation
annotation in the ListOfGeneAssociations
with the given sid
or null if no such GeneAssociation
annotation exists.
FbcModelPlugin.getGeneAssociation(long n)
,
FbcModelPlugin.getListOfGeneAssociations()
GeneAssociation
objects are not defined in any version of the
'Flux Balance Constraints' specification, and can only be used for
annotation purposes. Version 2 instead defines the
GeneProduct
and GeneProductAssociation
classes to cover the information
otherwise encoded here.
public int addGeneAssociation(GeneAssociation association)
GeneAssociation
annotation object to the list of GeneAssociations.
association
- the GeneAssociation
annotation object to be added to the list of GeneAssociations.
GeneAssociation
objects are not defined in any version of the
'Flux Balance Constraints' specification, and can only be used for
annotation purposes. Version 2 instead defines the
GeneProduct
and GeneProductAssociation
classes to cover the information
otherwise encoded here.
public GeneAssociation createGeneAssociation()
GeneAssociation
annotation object and adds it to the list of GeneAssociation
objects
and returns it.
GeneAssociation
annotation object.public GeneAssociation removeGeneAssociation(long n)
GeneAssociation
annotation object from this plugin object and
returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n
- the index of the GeneAssociation
annotation object to remove.
GeneAssociation
annotation object removed. As mentioned above, the
caller owns the returned object. null
is returned if the
given index is out of range.GeneAssociation
objects are not defined in any version of the
'Flux Balance Constraints' specification, and can only be used for
annotation purposes. Version 2 instead defines the
GeneProduct
and GeneProductAssociation
classes to cover the information
otherwise encoded here.
public GeneAssociation removeGeneAssociation(java.lang.String sid)
GeneAssociation
annotation object with the given sid
attribute from
this plugin object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
sid
- the id attribute of the GeneAssociation
annotation object to remove.
GeneAssociation
annotation object removed. As mentioned above, the
caller owns the returned object. null
is returned if the
given index is out of range.GeneAssociation
objects are not defined in any version of the
'Flux Balance Constraints' specification, and can only be used for
annotation purposes. Version 2 instead defines the
GeneProduct
and GeneProductAssociation
classes to cover the information
otherwise encoded here.
public int getNumGeneAssociations()
GeneAssociation
annotation object in this plugin object.
GeneAssociation
annotation object in this plugin object.GeneAssociation
objects are not defined in any version of the
'Flux Balance Constraints' specification, and can only be used for
annotation purposes. Version 2 instead defines the
GeneProduct
and GeneProductAssociation
classes to cover the information
otherwise encoded here.