ListOfSpeciesGlyphs (LibSBML Java API)

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

```
public class ListOfSpeciesGlyphs
extends ListOf
```
layout A list of SpeciesGlyph objects.
The ListOfSpeciesGlyphs is a container for the SpeciesGlyph elements of a Layout.

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,
, SpeciesGlyph

Constructor Summary

Constructors
Constructor and Description
`ListOfSpeciesGlyphs()` Ctor.
`ListOfSpeciesGlyphs(LayoutPkgNamespaces layoutns)` Ctor.
`ListOfSpeciesGlyphs(long level)` Ctor.
`ListOfSpeciesGlyphs(long level, long version)` Ctor.
`ListOfSpeciesGlyphs(long level, long version, long pkgVersion)` Ctor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`ListOfSpeciesGlyphs`	`cloneObject()` Creates and returns a deep copy of this `ListOfSpeciesGlyphs`.
`void`	`delete()` Explicitly deletes the underlying native object.
`SpeciesGlyph`	`get(long n)` Get a `SpeciesGlyph` from the `ListOfSpeciesGlyphs`.
`SpeciesGlyph`	`get(java.lang.String sid)` Get a `SpeciesGlyph` from the `ListOfSpeciesGlyphs` based on its identifier.
`java.lang.String`	`getElementName()` Returns the XML element name of this SBML object.
`int`	`getItemTypeCode()` Returns the libSBML type code for the SBML objects contained in this `ListOf` object.
`SpeciesGlyph`	`remove(long n)` Removes the nth item from this `ListOfSpeciesGlyphs` items and returns a pointer to it.
`SpeciesGlyph`	`remove(java.lang.String sid)` Removes item in this `ListOfSpeciesGlyphs` items with the given identifier.
`XMLNode`	`toXML()` Creates an `XMLNode` object from this.

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
  - ListOfSpeciesGlyphs
```
public ListOfSpeciesGlyphs(long level,
                           long version,
                           long pkgVersion)
                    throws SBMLConstructorException
```
    Ctor.
    
    Throws:
    
    SBMLConstructorException
  - ListOfSpeciesGlyphs
```
public ListOfSpeciesGlyphs(long level,
                           long version)
                    throws SBMLConstructorException
```
    Ctor.
    
    Throws:
    
    SBMLConstructorException
  - ListOfSpeciesGlyphs
```
public ListOfSpeciesGlyphs(long level)
                    throws SBMLConstructorException
```
    Ctor.
    
    Throws:
    
    SBMLConstructorException
  - ListOfSpeciesGlyphs
```
public ListOfSpeciesGlyphs()
                    throws SBMLConstructorException
```
    Ctor.
    
    Throws:
    
    SBMLConstructorException
  - ListOfSpeciesGlyphs
```
public ListOfSpeciesGlyphs(LayoutPkgNamespaces layoutns)
                    throws SBMLConstructorException
```
    Ctor.
    
    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 ListOfSpeciesGlyphs.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 ListOfSpeciesGlyphs.delete() themselves.
    
    Overrides:
    
    delete in class ListOf
  - cloneObject
```
public ListOfSpeciesGlyphs cloneObject()
```
    Creates and returns a deep copy of this ListOfSpeciesGlyphs.
    
    Overrides:
    
    cloneObject in class ListOf
    
    Returns:
    
    a (deep) copy of this ListOfSpeciesGlyphs.
  - 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_LAYOUT_SPECIESGLYPH (default).
    
    See Also:
    
    ListOfSpeciesGlyphs.getElementName(), SBase.getPackageName()
  - getElementName
```
public java.lang.String getElementName()
```
    Returns the XML element name of this SBML object.
    
    Overrides:
    
    getElementName in class ListOf
    
    Returns:
    
    the string of the name of this element
  - get
```
public SpeciesGlyph get(long n)
```
    Get a SpeciesGlyph from the ListOfSpeciesGlyphs.
    
    Overrides:
    
    get in class ListOf
    
    Parameters:
    
    n - the index number of the SpeciesGlyph to get.
    
    Returns:
    
    the nth SpeciesGlyph in this ListOfSpeciesGlyphs.
    
    See Also:
    
    ListOf.size()
  - get
```
public SpeciesGlyph get(java.lang.String sid)
```
    Get a SpeciesGlyph from the ListOfSpeciesGlyphs based on its identifier.
    
    Parameters:
    
    sid - a string representing the identifier of the SpeciesGlyph to get.
    
    Returns:
    
    SpeciesGlyph in this ListOfSpeciesGlyphs with the given sid or null if no such SpeciesGlyph exists.
    
    See Also:
    
    ListOfSpeciesGlyphs.get(long n), ListOf.size()
  - remove
```
public SpeciesGlyph remove(long n)
```
    Removes the nth item from this ListOfSpeciesGlyphs items 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 item to remove
    
    See Also:
    
    ListOf.size()
  - remove
```
public SpeciesGlyph remove(java.lang.String sid)
```
    Removes item in this ListOfSpeciesGlyphs items with the given identifier.
    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 item to remove
    
    Returns:
    
    the item removed. As mentioned above, the caller owns the returned item.
  - toXML
```
public XMLNode toXML()
```
    Creates an XMLNode object from this.

Class ListOfSpeciesGlyphs

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

ListOfSpeciesGlyphs

ListOfSpeciesGlyphs

ListOfSpeciesGlyphs

ListOfSpeciesGlyphs

ListOfSpeciesGlyphs

Method Detail

delete

cloneObject

getItemTypeCode

getElementName

get

get

remove

remove

toXML