ListOfQualitativeSpecies (LibSBML Java API)

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

```
public class ListOfQualitativeSpecies
extends ListOf
```
qual A list of QualitativeSpecies objects.
The ListOfQualitativeSpecies is a container for the QualitativeSpecies elements of a Model.

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):

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,
, QualitativeSpecies

Constructor Summary

Constructors
Constructor and Description
`ListOfQualitativeSpecies()` Creates a new `ListOfQualitativeSpecies` with the given level, version, and package version.
`ListOfQualitativeSpecies(long level)` Creates a new `ListOfQualitativeSpecies` with the given level, version, and package version.
`ListOfQualitativeSpecies(long level, long version)` Creates a new `ListOfQualitativeSpecies` with the given level, version, and package version.
`ListOfQualitativeSpecies(long level, long version, long pkgVersion)` Creates a new `ListOfQualitativeSpecies` with the given level, version, and package version.
`ListOfQualitativeSpecies(QualPkgNamespaces qualns)` Creates a new `ListOfQualitativeSpecies` with the given `QualPkgNamespaces` object.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`ListOfQualitativeSpecies`	`cloneObject()` Creates and returns a deep copy of this `ListOfQualitativeSpecies` object.
`void`	`delete()` Explicitly deletes the underlying native object.
`SBase`	`get(long n)` Get a `QualitativeSpecies` from the `ListOfQualitativeSpecies`.
`QualitativeSpecies`	`get(java.lang.String sid)` Get a `QualitativeSpecies` from the `ListOfQualitativeSpecies` based on its identifier.
`java.lang.String`	`getElementName()` Returns the XML name of this object.
`int`	`getItemTypeCode()` Returns the libSBML type code for the SBML objects contained in this `ListOf` object.
`SBase`	`remove(long n)` Removes the nth `QualitativeSpecies` from this `ListOfQualitativeSpecies` and returns a pointer to it.
`QualitativeSpecies`	`remove(java.lang.String sid)` Removes the `QualitativeSpecies` from this `ListOfQualitativeSpecies` 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, getTypeCode, 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, 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, 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, unsetName, unsetNotes, unsetSBOTerm, unsetUserData

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

- Constructor Detail
  - ListOfQualitativeSpecies
```
public ListOfQualitativeSpecies(long level,
                                long version,
                                long pkgVersion)
                         throws SBMLConstructorException
```
    Creates a new ListOfQualitativeSpecies with the given level, version, and package version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this ListOfQualitativeSpecies
    
    version - a long integer, the SBML Version to assign to this ListOfQualitativeSpecies
    
    pkgVersion - a long integer, the SBML Qual Version to assign to this ListOfQualitativeSpecies
    
    Throws:
    
    SBMLConstructorException
  - ListOfQualitativeSpecies
```
public ListOfQualitativeSpecies(long level,
                                long version)
                         throws SBMLConstructorException
```
    Creates a new ListOfQualitativeSpecies with the given level, version, and package version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this ListOfQualitativeSpecies
    
    version - a long integer, the SBML Version to assign to this ListOfQualitativeSpecies
    
    pkgVersion - a long integer, the SBML Qual Version to assign to this ListOfQualitativeSpecies
    
    Throws:
    
    SBMLConstructorException
  - ListOfQualitativeSpecies
```
public ListOfQualitativeSpecies(long level)
                         throws SBMLConstructorException
```
    Creates a new ListOfQualitativeSpecies with the given level, version, and package version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this ListOfQualitativeSpecies
    
    version - a long integer, the SBML Version to assign to this ListOfQualitativeSpecies
    
    pkgVersion - a long integer, the SBML Qual Version to assign to this ListOfQualitativeSpecies
    
    Throws:
    
    SBMLConstructorException
  - ListOfQualitativeSpecies
```
public ListOfQualitativeSpecies()
                         throws SBMLConstructorException
```
    Creates a new ListOfQualitativeSpecies with the given level, version, and package version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this ListOfQualitativeSpecies
    
    version - a long integer, the SBML Version to assign to this ListOfQualitativeSpecies
    
    pkgVersion - a long integer, the SBML Qual Version to assign to this ListOfQualitativeSpecies
    
    Throws:
    
    SBMLConstructorException
  - ListOfQualitativeSpecies
```
public ListOfQualitativeSpecies(QualPkgNamespaces qualns)
                         throws SBMLConstructorException
```
    Creates a new ListOfQualitativeSpecies with the given QualPkgNamespaces object.
    
    Parameters:
    
    qualns - the QualPkgNamespaces object
    
    Throws:
    
    SBMLConstructorException
- 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 ListOfQualitativeSpecies.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 ListOfQualitativeSpecies.delete() themselves.
    
    Overrides:
    
    delete in class ListOf
  - cloneObject
```
public ListOfQualitativeSpecies cloneObject()
```
    Creates and returns a deep copy of this ListOfQualitativeSpecies object.
    
    Overrides:
    
    cloneObject in class ListOf
    
    Returns:
    
    a (deep) copy of this ListOfQualitativeSpecies object.
  - get
```
public SBase get(long n)
```
    Get a QualitativeSpecies from the ListOfQualitativeSpecies.
    
    Overrides:
    
    get in class ListOf
    
    Parameters:
    
    n - the index number of the QualitativeSpecies to get.
    
    Returns:
    
    the nth QualitativeSpecies in this ListOfQualitativeSpecies.
    
    See Also:
    
    ListOf.size()
  - get
```
public QualitativeSpecies get(java.lang.String sid)
```
    Get a QualitativeSpecies from the ListOfQualitativeSpecies based on its identifier.
    
    Parameters:
    
    sid - a string representing the identifier of the QualitativeSpecies to get.
    
    Returns:
    
    QualitativeSpecies in this ListOfQualitativeSpecies with the given id or null if no such QualitativeSpecies exists.
    
    See Also:
    
    *, ListOf.size()
  - remove
```
public SBase remove(long n)
```
    Removes the nth QualitativeSpecies from this ListOfQualitativeSpecies 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 QualitativeSpecies to remove.
    
    See Also:
    
    ListOf.size()
  - remove
```
public QualitativeSpecies remove(java.lang.String sid)
```
    Removes the QualitativeSpecies from this ListOfQualitativeSpecies 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 QualitativeSpecies to remove.
    
    Returns:
    
    the QualitativeSpecies removed. As mentioned above, the caller owns the returned item.
  - getElementName
```
public java.lang.String getElementName()
```
    Returns the XML name of this object.
    
    Overrides:
    
    getElementName in class ListOf
    
    Returns:
    
    the name of this element.
  - getItemTypeCode
```
public int getItemTypeCode()
```
    Returns the libSBML type code for the SBML objects contained in this ListOf 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 getPackageName() method on the object.
    
    Overrides:
    
    getItemTypeCode in class ListOf
    
    Returns:
    
    the SBML type code for objects contained in this list: SBML_QUAL_QUALITATIVE_SPECIES (default).
    
    See Also:
    
    ListOfQualitativeSpecies.getElementName(), SBase.getPackageName()

Class ListOfQualitativeSpecies

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

ListOfQualitativeSpecies

ListOfQualitativeSpecies

ListOfQualitativeSpecies

ListOfQualitativeSpecies

ListOfQualitativeSpecies

Method Detail

delete

cloneObject

get

get

remove

remove

getElementName

getItemTypeCode