ListOfGeneProducts (LibSBML Java API)

java.lang.Object
- org.sbml.libsbml.SBase
- - org.sbml.libsbml.ListOf
  - - org.sbml.libsbml.ListOfGeneProducts

```
public class ListOfGeneProducts
extends ListOf
```
fbc A list of GeneProduct objects.
The ListOfGeneProducts is a container for the SBML extended Model that lists all the possible GeneProduct elements in the model. These GeneProduct elements are referenced in the GeneProductAssociation child of an extended Reaction.

The various ListOf___ classes in SBML are merely containers used for organizing the main components of an SBML model. In libSBML's implementation, ListOf___ classes are derived from the intermediate utility class ListOf, which is not defined by the SBML specifications but serves as a useful programmatic construct. ListOf is itself is in turn derived from SBase, which provides all of the various ListOf___ classes with common features defined by the SBML specification, such as 'metaid' attributes and annotations.
The relationship between the lists and the rest of an SBML model is illustrated by the following (for SBML Level 2 Version 4):

SBML Level 3 Version 1 has essentially the same structure as Level 2 Version 4, depicted above, but SBML Level 3 Version 2 allows containers to contain zero or more of the relevant object, instead of requiring at least one. As such, libsbml will write out an otherwise-empty ListOf___ element that has any optional attribute set (such as 'id' or 'metaid'), that has an optional child (such as a 'notes' or 'annotation'), or that has attributes or children set from any SBML Level 3 package, whether or not the ListOf___ has any other children.
Readers may wonder about the motivations for using the ListOf___ containers in SBML. A simpler approach in XML might be to place the components all directly at the top level of the model definition. The choice made in SBML is to group them within XML elements named after ListOfClassname, in part because it helps organize the components. More importantly, the fact that the container classes are derived from SBase means that software tools can add information about the lists themselves into each list container's 'annotation'.

See Also:

ListOfFunctionDefinitions, ListOfUnitDefinitions, ListOfCompartmentTypes, ListOfSpeciesTypes, ListOfCompartments, ListOfSpecies, ListOfParameters, ListOfInitialAssignments, ListOfRules, ListOfConstraints, ListOfReactions,
, GeneProduct, FbcModelPlugin

"Note:"

This class of objects was introduced in Version 2 of the SBML Level 3 Flux Balance Constraints (&ldquofbc&rdquo) specification. In Version 1 of &ldquofbc&rdquo, the information encoded by this class can be stored instead using the Association and GeneAssociation annotation classes. Please see the Version 1 and Version 2 &ldquofbc&rdquo specifications for more details.

Constructor Summary

Constructors
Constructor and Description
`ListOfGeneProducts()` Creates a new `GeneProduct` with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
`ListOfGeneProducts(FbcPkgNamespaces fbcns)` Creates a new `ListOfGeneProducts` with the given `FbcPkgNamespaces` object.
`ListOfGeneProducts(long level)` Creates a new `GeneProduct` with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
`ListOfGeneProducts(long level, long version)` Creates a new `GeneProduct` with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
`ListOfGeneProducts(long level, long version, long pkgVersion)` Creates a new `GeneProduct` with the given SBML Level, Version, and &ldquofbc&rdquopackage version.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`addGeneProduct(GeneProduct gp)` Adds a copy the given `GeneProduct` to this `ListOfGeneProducts`.
`ListOfGeneProducts`	`cloneObject()` Creates and returns a deep copy of this `ListOfGeneProducts` object.
`GeneProduct`	`createGeneProduct()` Creates a new `GeneProduct` object, adds it to the `ListOfGeneProducts` and returns the `GeneProduct` object created.
`void`	`delete()` Explicitly deletes the underlying native object.
`GeneProduct`	`get(long n)` Get a `GeneProduct` from the `ListOfGeneProducts`.
`GeneProduct`	`get(java.lang.String sid)` Get a `GeneProduct` from the `ListOfGeneProducts` based on its identifier.
`java.lang.String`	`getElementName()` Returns the XML element name of this object.
`int`	`getItemTypeCode()` Returns the libSBML type code for the objects contained in this `ListOf`.
`long`	`getNumGeneProducts()` Get the number of `GeneProduct` objects in this `ListOfGeneProducts`.
`int`	`getTypeCode()` Returns the libSBML type code for this SBML object.
`GeneProduct`	`remove(long n)` Removes the nth `GeneProduct` from this `ListOfGeneProducts` and returns a pointer to it.
`GeneProduct`	`remove(java.lang.String sid)` Removes the `GeneProduct` from this `ListOfGeneProducts` with the given identifier and returns a pointer to it.

Methods inherited from class org.sbml.libsbml.ListOf
append, appendAndOwn, appendFrom, clear, clear, connectToChild, getElementByMetaId, getElementBySId, insert, insertAndOwn, removeFromParentAndDelete, size

Methods inherited from class org.sbml.libsbml.SBase
addCVTerm, addCVTerm, appendAnnotation, appendAnnotation, appendNotes, appendNotes, deleteDisabledPlugins, deleteDisabledPlugins, disablePackage, enablePackage, equals, getAncestorOfType, getAncestorOfType, getAnnotation, getAnnotationString, getColumn, getCVTerm, getCVTerms, getDisabledPlugin, getId, getIdAttribute, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getName, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumDisabledPlugins, getNumPlugins, getPackageCoreVersion, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getPlugin, getPrefix, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getURI, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetId, isSetIdAttribute, isSetMetaId, isSetModelHistory, isSetName, isSetNotes, isSetSBOTerm, isSetUserData, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, renameSIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setId, setIdAttribute, setMetaId, setModelHistory, setName, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetId, unsetIdAttribute, unsetMetaId, unsetModelHistory, unsetName, unsetNotes, unsetSBOTerm, unsetUserData

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

- Constructor Detail
  - ListOfGeneProducts
```
public ListOfGeneProducts(long level,
                          long version,
                          long pkgVersion)
                   throws SBMLConstructorException
```
    Creates a new GeneProduct with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this ListOfGeneProducts.
    
    version - a long integer, the SBML Version to assign to this ListOfGeneProducts.
    
    pkgVersion - a long integer, the SBML Fbc Version to assign to this ListOfGeneProducts.
    
    Throws:
    
    SBMLConstructorException
    
    "Note:"
    
    Attempting to add an object to an 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. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
  - ListOfGeneProducts
```
public ListOfGeneProducts(long level,
                          long version)
                   throws SBMLConstructorException
```
    Creates a new GeneProduct with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this ListOfGeneProducts.
    
    version - a long integer, the SBML Version to assign to this ListOfGeneProducts.
    
    pkgVersion - a long integer, the SBML Fbc Version to assign to this ListOfGeneProducts.
    
    Throws:
    
    SBMLConstructorException
    
    "Note:"
    
    Attempting to add an object to an 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. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
  - ListOfGeneProducts
```
public ListOfGeneProducts(long level)
                   throws SBMLConstructorException
```
    Creates a new GeneProduct with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this ListOfGeneProducts.
    
    version - a long integer, the SBML Version to assign to this ListOfGeneProducts.
    
    pkgVersion - a long integer, the SBML Fbc Version to assign to this ListOfGeneProducts.
    
    Throws:
    
    SBMLConstructorException
    
    "Note:"
    
    Attempting to add an object to an 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. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
  - ListOfGeneProducts
```
public ListOfGeneProducts()
                   throws SBMLConstructorException
```
    Creates a new GeneProduct with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this ListOfGeneProducts.
    
    version - a long integer, the SBML Version to assign to this ListOfGeneProducts.
    
    pkgVersion - a long integer, the SBML Fbc Version to assign to this ListOfGeneProducts.
    
    Throws:
    
    SBMLConstructorException
    
    "Note:"
    
    Attempting to add an object to an 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. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
  - ListOfGeneProducts
```
public ListOfGeneProducts(FbcPkgNamespaces fbcns)
                   throws SBMLConstructorException
```
    Creates a new ListOfGeneProducts with the given FbcPkgNamespaces object.
    
    The package namespaces object used in this constructor is derived from a SBMLNamespaces object, which encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and package version and name information used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an package namespace object somewhere in a program once, then hand that object as needed to object constructors of that package that accept it as and argument, such as this one.
    
    Parameters:
    
    fbcns - the FbcPkgNamespaces object.
    
    Throws:
    
    SBMLConstructorException
    
    "Note:"
    
    Attempting to add an object to an 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. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
- 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 ListOfGeneProducts.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 ListOfGeneProducts.delete() themselves.
    
    Overrides:
    
    delete in class ListOf
  - cloneObject
```
public ListOfGeneProducts cloneObject()
```
    Creates and returns a deep copy of this ListOfGeneProducts object.
    
    Overrides:
    
    cloneObject in class ListOf
    
    Returns:
    
    a (deep) copy of this ListOfGeneProducts object.
  - get
```
public GeneProduct get(long n)
```
    Get a GeneProduct from the ListOfGeneProducts.
    
    Overrides:
    
    get in class ListOf
    
    Parameters:
    
    n - the index number of the GeneProduct to get.
    
    Returns:
    
    the nth GeneProduct in this ListOfGeneProducts.
    
    See Also:
    
    ListOf.size()
  - get
```
public GeneProduct get(java.lang.String sid)
```
    Get a GeneProduct from the ListOfGeneProducts based on its identifier.
    
    Parameters:
    
    sid - a string representing the identifier of the GeneProduct to get.
    
    Returns:
    
    GeneProduct in this ListOfGeneProducts with the given id or null if no such GeneProduct exists.
    
    See Also:
    
    ListOfGeneProducts.get(long n), ListOf.size()
  - addGeneProduct
```
public int addGeneProduct(GeneProduct gp)
```
    Adds a copy the given GeneProduct to this ListOfGeneProducts.
    Parameters:
    
    gp - the GeneProduct object to add.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - getNumGeneProducts
```
public long getNumGeneProducts()
```
    Get the number of GeneProduct objects in this ListOfGeneProducts.
    
    Returns:
    
    the number of GeneProduct objects in this ListOfGeneProducts.
  - createGeneProduct
```
public GeneProduct createGeneProduct()
```
    Creates a new GeneProduct object, adds it to the ListOfGeneProducts and returns the GeneProduct object created.
    
    Returns:
    
    a new GeneProduct object instance.
    
    See Also:
    
    ListOfGeneProducts.addGeneProduct(GeneProduct gp)
  - remove
```
public GeneProduct remove(long n)
```
    Removes the nth GeneProduct from this ListOfGeneProducts and returns a pointer to it.
    The caller owns the returned item and is responsible for deleting it.
    
    Overrides:
    
    remove in class ListOf
    
    Parameters:
    
    n - the index of the GeneProduct to remove.
    
    See Also:
    
    ListOf.size()
  - remove
```
public GeneProduct remove(java.lang.String sid)
```
    Removes the GeneProduct from this ListOfGeneProducts with the given identifier 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.
    
    Parameters:
    
    sid - the identifier of the GeneProduct to remove.
    
    Returns:
    
    the GeneProduct removed. As mentioned above, the caller owns the returned item.
  - getElementName
```
public java.lang.String getElementName()
```
    Returns the XML element name of this object.
    For ListOfGeneProducts, the XML element name is always 'listOfGeneProducts'.
    
    Overrides:
    
    getElementName in class ListOf
    
    Returns:
    
    the name of this element, i.e. 'listOfGeneProducts'.
  - getTypeCode
```
public int getTypeCode()
```
    Returns the libSBML type code for this SBML object.
    
    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 SBase.getPackageName() method on the object.
    
    Overrides:
    
    getTypeCode in class ListOf
    
    Returns:
    
    the SBML type code for this object: SBML_LIST_OF (default).
    
    See Also:
    
    ListOfGeneProducts.getElementName(), SBase.getPackageName()
    
    "Warning:"
    
    The specific integer values of the possible type codes may be reused by different libSBML plug-ins for SBML Level 3. packages, To fully identify the correct code, it is necessary to invoke both getTypeCode() and getPackageName().
  - getItemTypeCode
```
public int getItemTypeCode()
```
    Returns the libSBML type code for the objects contained in this ListOf.
    
    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 SBase.getPackageName() method on the object.
    
    Overrides:
    
    getItemTypeCode in class ListOf
    
    Returns:
    
    the SBML type code for the objects contained in this ListOf instance: SBML_FBC_GENEPRODUCT (default).
    
    See Also:
    
    ListOfGeneProducts.getElementName(), SBase.getPackageName()

Class ListOfGeneProducts

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.ListOf

Methods inherited from class org.sbml.libsbml.SBase

Methods inherited from class java.lang.Object

Constructor Detail

ListOfGeneProducts

ListOfGeneProducts

ListOfGeneProducts

ListOfGeneProducts

ListOfGeneProducts

Method Detail

delete

cloneObject

get

get

addGeneProduct

getNumGeneProducts

createGeneProduct

remove

remove

getElementName

getTypeCode

getItemTypeCode