SpeciesReferenceGlyph (LibSBML Java API)

java.lang.Object
- org.sbml.libsbml.SBase
- - org.sbml.libsbml.GraphicalObject
  - - org.sbml.libsbml.SpeciesReferenceGlyph

```
public class SpeciesReferenceGlyph
extends GraphicalObject
```
layout A SpeciesReferenceGlyph represents a reactant or product from a Reaction in the &ldquolayout&rdquo package.
The SpeciesReferenceGlyph element describes the graphical connection between a SpeciesGlyph and a ReactionGlyph (which would be an arrow or some curve in most cases). A SpeciesReferenceGlyph inherits from GraphicalObject, and adds a mandatory attribute 'speciesGlyph' and two optional attributes 'speciesReference' and 'role'. Optionally, the SpeciesReferenceGlyph also has a child element 'curve'.
If the curve is specified, it overrides the inherited bounding box.

Constructor Summary

Constructors
Constructor and Description
`SpeciesReferenceGlyph()` Creates a new `SpeciesReferenceGlyph` with the given SBML level, version and package version.
`SpeciesReferenceGlyph(LayoutPkgNamespaces layoutns)` Ctor.
`SpeciesReferenceGlyph(LayoutPkgNamespaces layoutns, java.lang.String sid, java.lang.String speciesGlyphId, java.lang.String speciesReferenceId, int role)` Creates a new `SpeciesReferenceGlyph`.
`SpeciesReferenceGlyph(long level)` Creates a new `SpeciesReferenceGlyph` with the given SBML level, version and package version.
`SpeciesReferenceGlyph(long level, long version)` Creates a new `SpeciesReferenceGlyph` with the given SBML level, version and package version.
`SpeciesReferenceGlyph(long level, long version, long pkgVersion)` Creates a new `SpeciesReferenceGlyph` with the given SBML level, version and package version.
`SpeciesReferenceGlyph(SpeciesReferenceGlyph source)` Copy constructor.
`SpeciesReferenceGlyph(XMLNode node)` Creates a new `SpeciesReferenceGlyph` from the given `XMLNode`
`SpeciesReferenceGlyph(XMLNode node, long l2version)` Creates a new `SpeciesReferenceGlyph` from the given `XMLNode`

Method Summary

Methods
Modifier and Type	Method and Description
`SpeciesReferenceGlyph`	`cloneObject()` Creates and returns a deep copy of this `SpeciesReferenceGlyph`.
`CubicBezier`	`createCubicBezier()` Creates a new `CubicBezier` object, adds it to the end of the list of curve segment objects of the curve and returns a reference to the newly created object.
`LineSegment`	`createLineSegment()` Creates a new `LineSegment` object, adds it to the end of the list of curve segment objects of the curve and returns a reference to the newly created object.
`void`	`delete()` Explicitly deletes the underlying native object.
`Curve`	`getCurve()` Returns the curve object for the species reference glyph
`boolean`	`getCurveExplicitlySet()`
`java.lang.String`	`getElementName()` Returns the XML element name of this SBML object.
`int`	`getRole()` Returns the role.
`java.lang.String`	`getRoleString()` Returns a string representation of the role.
`java.lang.String`	`getSpeciesGlyphId()` Returns the id of the associated `SpeciesGlyph`.
`java.lang.String`	`getSpeciesReferenceId()` Returns the id of the associated species reference.
`int`	`getTypeCode()` Returns the libSBML type code of this object instance.
`void`	`initDefaults()` Calls initDefaults on `GraphicalObject` and sets role to SPECIES_ROLE_UNDEFINED.
`boolean`	`isSetCurve()` Returns true if the curve consists of one or more segments.
`boolean`	`isSetRole()` Returns true of role is different from SPECIES_ROLE_UNDEFINED.
`boolean`	`isSetSpeciesGlyphId()` Returns true if the id of the associated species glyph is not the empty string.
`boolean`	`isSetSpeciesReferenceId()` Returns true if the id of the associated species reference is not the empty string.
`void`	`renameSIdRefs(java.lang.String oldid, java.lang.String newid)` Renames all the `SIdRef` attributes on this element, including any found in MathML content (if such exists).
`void`	`setCurve(Curve curve)` Sets the curve object for the species reference glyph.
`void`	`setRole(int role)` Sets the role.
`void`	`setRole(java.lang.String role)` Sets the role based on a string.
`void`	`setSpeciesGlyphId(java.lang.String speciesGlyphId)` Sets the id of the associated species glyph.
`void`	`setSpeciesReferenceId(java.lang.String id)` Sets the id of the associated species reference.
`XMLNode`	`toXML()` Creates an `XMLNode` object from this.

Methods inherited from class org.sbml.libsbml.GraphicalObject
getBoundingBox, getBoundingBoxExplicitlySet, getId, getMetaIdRef, isSetId, isSetMetaIdRef, renameMetaIdRefs, setBoundingBox, setId, setMetaIdRef, unsetId, unsetMetaIdRef

Methods inherited from class org.sbml.libsbml.SBase
addCVTerm, addCVTerm, appendAnnotation, appendAnnotation, appendNotes, appendNotes, disablePackage, enablePackage, equals, getAncestorOfType, getAncestorOfType, getAnnotation, getAnnotationString, getColumn, getCVTerm, getCVTerms, getElementByMetaId, getElementBySId, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getPlugin, getPrefix, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getURI, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isSetAnnotation, isSetMetaId, isSetModelHistory, isSetNotes, isSetSBOTerm, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeFromParentAndDelete, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetMetaId, unsetModelHistory, unsetName, unsetNotes, unsetSBOTerm

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

- Constructor Detail
  - SpeciesReferenceGlyph
```
public SpeciesReferenceGlyph()
                      throws SBMLConstructorException
```
    Creates a new SpeciesReferenceGlyph with the given SBML level, version and package version. The id if the associated species reference and the id of the associated species glyph are set to the empty string. The role is set to SPECIES_ROLE_UNDEFINED.
    
    Throws:
    
    SBMLConstructorException
  - SpeciesReferenceGlyph
```
public SpeciesReferenceGlyph(LayoutPkgNamespaces layoutns)
                      throws SBMLConstructorException
```
    Ctor.
    
    Throws:
    
    SBMLConstructorException
  - SpeciesReferenceGlyph
```
public SpeciesReferenceGlyph(LayoutPkgNamespaces layoutns,
                     java.lang.String sid,
                     java.lang.String speciesGlyphId,
                     java.lang.String speciesReferenceId,
                     int role)
                      throws SBMLConstructorException
```
    Creates a new SpeciesReferenceGlyph. The id is given as the first argument, the id of the associated species glyph is given as the second argument. The third argument is the id of the associated species reference and the fourth argument is the role.
    
    Throws:
    
    SBMLConstructorException
  - SpeciesReferenceGlyph
```
public SpeciesReferenceGlyph(long level)
                      throws SBMLConstructorException
```
    Creates a new SpeciesReferenceGlyph with the given SBML level, version and package version. The id if the associated species reference and the id of the associated species glyph are set to the empty string. The role is set to SPECIES_ROLE_UNDEFINED.
    
    Throws:
    
    SBMLConstructorException
  - SpeciesReferenceGlyph
```
public SpeciesReferenceGlyph(long level,
                     long version)
                      throws SBMLConstructorException
```
    Creates a new SpeciesReferenceGlyph with the given SBML level, version and package version. The id if the associated species reference and the id of the associated species glyph are set to the empty string. The role is set to SPECIES_ROLE_UNDEFINED.
    
    Throws:
    
    SBMLConstructorException
  - SpeciesReferenceGlyph
```
public SpeciesReferenceGlyph(long level,
                     long version,
                     long pkgVersion)
                      throws SBMLConstructorException
```
    Creates a new SpeciesReferenceGlyph with the given SBML level, version and package version. The id if the associated species reference and the id of the associated species glyph are set to the empty string. The role is set to SPECIES_ROLE_UNDEFINED.
    
    Throws:
    
    SBMLConstructorException
  - SpeciesReferenceGlyph
```
public SpeciesReferenceGlyph(SpeciesReferenceGlyph source)
                      throws SBMLConstructorException
```
    Copy constructor.
    
    Throws:
    
    SBMLConstructorException
  - SpeciesReferenceGlyph
```
public SpeciesReferenceGlyph(XMLNode node)
                      throws SBMLConstructorException
```
    Creates a new SpeciesReferenceGlyph from the given XMLNode
    
    Throws:
    
    SBMLConstructorException
  - SpeciesReferenceGlyph
```
public SpeciesReferenceGlyph(XMLNode node,
                     long l2version)
                      throws SBMLConstructorException
```
    Creates a new SpeciesReferenceGlyph from the given XMLNode
    
    Throws:
    
    SBMLConstructorException
- Method Detail
  - cloneObject
```
public SpeciesReferenceGlyph cloneObject()
```
    Creates and returns a deep copy of this SpeciesReferenceGlyph.
    
    Overrides:
    
    cloneObject in class GraphicalObject
    
    Returns:
    a (deep) copy of this SpeciesReferenceGlyph.
  - createCubicBezier
```
public CubicBezier createCubicBezier()
```
    Creates a new CubicBezier object, adds it to the end of the list of curve segment objects of the curve and returns a reference to the newly created object.
  - createLineSegment
```
public LineSegment createLineSegment()
```
    Creates a new LineSegment object, adds it to the end of the list of curve segment objects of the curve and returns a reference to the newly created object.
  - 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 SpeciesReferenceGlyph.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 SpeciesReferenceGlyph.delete() themselves.
    
    Overrides:
    
    delete in class GraphicalObject
  - getCurve
```
public Curve getCurve()
```
    Returns the curve object for the species reference glyph
  - getCurveExplicitlySet
```
public boolean getCurveExplicitlySet()
```
  - getElementName
```
public java.lang.String getElementName()
```
    Returns the XML element name of this SBML object.
    
    Overrides:
    
    getElementName in class GraphicalObject
  - getRole
```
public int getRole()
```
    Returns the role.
  - getRoleString
```
public java.lang.String getRoleString()
```
    Returns a string representation of the role.
  - getSpeciesGlyphId
```
public java.lang.String getSpeciesGlyphId()
```
    Returns the id of the associated SpeciesGlyph.
  - getSpeciesReferenceId
```
public java.lang.String getSpeciesReferenceId()
```
    Returns the id of the associated species reference.
  - getTypeCode
```
public int getTypeCode()
```
    Returns the libSBML type code of this object instance.
    
    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 &ldquoSBML_&rdquo. 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:
    
    getTypeCode in class GraphicalObject
    
    Returns:
    the SBML type code for this object: SBML_LAYOUT_SPECIESREFERENCEGLYPH
    
    See Also:
    SpeciesReferenceGlyph.getElementName(), SBase.getPackageName()
    "Warning:"
    
    The specific integer values of the possible type codes may be reused by different Level 3 package plug-ins. Thus, to identifiy the correct code, it is necessary to invoke both getTypeCode() and getPackageName().
  - initDefaults
```
public void initDefaults()
```
    Calls initDefaults on GraphicalObject and sets role to SPECIES_ROLE_UNDEFINED.
    
    Overrides:
    
    initDefaults in class GraphicalObject
  - isSetCurve
```
public boolean isSetCurve()
```
    Returns true if the curve consists of one or more segments.
  - isSetRole
```
public boolean isSetRole()
```
    Returns true of role is different from SPECIES_ROLE_UNDEFINED.
  - isSetSpeciesGlyphId
```
public boolean isSetSpeciesGlyphId()
```
    Returns true if the id of the associated species glyph is not the empty string.
  - isSetSpeciesReferenceId
```
public boolean isSetSpeciesReferenceId()
```
    Returns true if the id of the associated species reference is not the empty string.
  - renameSIdRefs
```
public void renameSIdRefs(java.lang.String oldid,
                 java.lang.String newid)
```
    Renames all the SIdRef attributes on this element, including any found in MathML content (if such exists).
    This method works by looking at all attributes and (if appropriate) mathematical formulas, comparing the identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.
    
    Overrides:
    
    renameSIdRefs in class SBase
    
    Parameters:
    oldid - the old identifier
    newid - the new identifier
  - setCurve
```
public void setCurve(Curve curve)
```
    Sets the curve object for the species reference glyph.
  - setRole
```
public void setRole(int role)
```
    Sets the role.
  - setRole
```
public void setRole(java.lang.String role)
```
    Sets the role based on a string. The String can be one of: SUBSTRATE PRODUCT SIDESUBSTRATE SIDEPRODUCT MODIFIER ACTIVATOR INHIBITOR
  - setSpeciesGlyphId
```
public void setSpeciesGlyphId(java.lang.String speciesGlyphId)
```
    Sets the id of the associated species glyph.
  - setSpeciesReferenceId
```
public void setSpeciesReferenceId(java.lang.String id)
```
    Sets the id of the associated species reference.
  - toXML
```
public XMLNode toXML()
```
    Creates an XMLNode object from this.
    
    Overrides:
    
    toXML in class GraphicalObject

Class SpeciesReferenceGlyph

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.GraphicalObject

Methods inherited from class org.sbml.libsbml.SBase

Methods inherited from class java.lang.Object

Constructor Detail

SpeciesReferenceGlyph

SpeciesReferenceGlyph

SpeciesReferenceGlyph

SpeciesReferenceGlyph

SpeciesReferenceGlyph

SpeciesReferenceGlyph

SpeciesReferenceGlyph

SpeciesReferenceGlyph

SpeciesReferenceGlyph

Method Detail

cloneObject

createCubicBezier

createLineSegment

delete

getCurve

getCurveExplicitlySet

getElementName

getRole

getRoleString

getSpeciesGlyphId

getSpeciesReferenceId

getTypeCode

initDefaults

isSetCurve

isSetRole

isSetSpeciesGlyphId

isSetSpeciesReferenceId

renameSIdRefs

setCurve

setRole

setRole

setSpeciesGlyphId

setSpeciesReferenceId

toXML