Layout (jsbml-layout 1.2 API)

java.lang.Object
- org.sbml.jsbml.AbstractTreeNode
- - org.sbml.jsbml.AbstractSBase
  - - org.sbml.jsbml.AbstractNamedSBase
    - - org.sbml.jsbml.ext.layout.Layout

All Implemented Interfaces:

Serializable, Cloneable, TreeNode, NamedSBase, SBase, UniqueNamedSBase, UniqueSId, TreeNodeWithChangeSupport
```
public class Layout
extends AbstractNamedSBase
implements UniqueNamedSBase
```
The Layout class stores layout information for some or all elements of the Model as well as additional objects that need not be connected to the Model. The Layout has two attributes: id and name. Additionally, a Dimensions element specifies the size of the Layout. The actual layout elements are contained in several lists, namely: a ListOfCompartmentGlyphs, a ListOfSpeciesGlyphs, a ListOfReactionGlyphs, a ListOfTextGlyphs, and a ListOfAdditionalGraphicalObjects. Each of these lists can only occur once, and, if present, are not allowed to be empty.

Since:

1.0

Author:

Nicolas Rodriguez, Sebastian Frölich, Andreas Dräger, Clemens Wrzodek

See Also:

Serialized Form

Field Summary
- Fields inherited from class org.sbml.jsbml.AbstractSBase
  ignoredExtensions, ignoredXMLElements, JSBML_WRONG_SBO_TERM, packageName
- Fields inherited from class org.sbml.jsbml.AbstractTreeNode
  listOfListeners, parent, resourceBundle

Constructor Summary

Constructors
Constructor and Description

Layout()

Layout(int level, int version)

Layout(Layout layout)

Layout(String id, int level, int version)

Constructors
Constructor and Description
`Layout()`
`Layout(int level, int version)`
`Layout(Layout layout)`
`Layout(String id, int level, int version)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addAdditionalGraphicalObject(GraphicalObject object)` Adds an arbitrary additional `GraphicalObject`.
`boolean`	`addCompartmentGlyph(CompartmentGlyph compartmentGlyph)` Adds a new `CompartmentGlyph` to the `listOfCompartmentGlyphs`.
`void`	`addGeneralGlyph(GeneralGlyph object)` Adds a `GeneralGlyph` object.
`void`	`addGraphicalObject(GraphicalObject object)` Adds an arbitrary additional `GraphicalObject`.
`void`	`addReactionGlyph(ReactionGlyph reactionGlyph)` Adds a `ReactionGlyph` to this layout
`void`	`addSpeciesGlyph(SpeciesGlyph speciesGlyph)`
`void`	`addTextGlyph(TextGlyph TextGlyph)`
`Layout`	`clone()`
`boolean`	`containsGlyph(Compartment compartment)`
`boolean`	`containsGlyph(Reaction reaction)`
`boolean`	`containsGlyph(Species species)`
`CompartmentGlyph`	`createCompartmentGlyph(String id)` Creates and adds a new `CompartmentGlyph`.
`CompartmentGlyph`	`createCompartmentGlyph(String id, String compartment)` Creates and adds a new `CompartmentGlyph`.
`Dimensions`	`createDimensions(double width, double height, double depth)` Creates, sets and returns `Dimensions` based on the given values.
`Dimensions`	`createDimensions(String id, double width, double height, double depth)` Creates, sets and returns `Dimensions` based on the given values.
`GeneralGlyph`	`createGeneralGlyph(String id)` Creates and adds a new `GeneralGlyph`.
`GeneralGlyph`	`createGeneralGlyph(String id, String reference)` Creates and adds a new `GeneralGlyph`.
`ReactionGlyph`	`createReactionGlyph(String id)` Creates and adds a new `ReactionGlyph`.
`ReactionGlyph`	`createReactionGlyph(String id, String reaction)` Creates and adds a new `ReactionGlyph`.
`SpeciesGlyph`	`createSpeciesGlyph(String id)` Creates and adds a new `SpeciesGlyph` with the given identifier.
`SpeciesGlyph`	`createSpeciesGlyph(String id, String species)` Creates and adds a new `SpeciesGlyph`.
`TextGlyph`	`createTextGlyph(String id)` Creates and adds a new `TextGlyph`.
`TextGlyph`	`createTextGlyph(String id, String text)` Creates and adds a new `TextGlyph`.
`boolean`	`equals(Object object)`
`List<CompartmentGlyph>`	`findCompartmentGlyphs(String compartmentID)` Searches all instances of `CompartmentGlyph` within this `Layout` that refer to the `Compartment` with the given id.
`List<ReactionGlyph>`	`findReactionGlyphs(String reactionID)` Searches all instances of `ReactionGlyph` within this `Layout` that refer to the `Reaction` with the given id.
`List<SpeciesGlyph>`	`findSpeciesGlyphs(String speciesID)` Searches all instances of `SpeciesGlyph` within this `Layout` that refer to the `Species` with the given id.
`List<TextGlyph>`	`findTextGlyphs(String id)` Searches within the `listOfTextGlyphs` for `TextGlyph`s whose `TextGlyph.getOriginOfText()` points to the given id.
`GraphicalObject`	`getAdditionalGraphicalObject(int i)`
`int`	`getAdditionalGraphicalObjectCount()`
`TreeNode`	`getChildAt(int index)`
`int`	`getChildCount()`
`CompartmentGlyph`	`getCompartmentGlyph(int i)` Gets an element from the listOfCompartmentGlyphs at the given index.
`CompartmentGlyph`	`getCompartmentGlyph(String id)` Gets an element from the listOfCompartmentGlyphs, with the given id.
`int`	`getCompartmentGlyphCount()` Returns the number of `CompartmentGlyph`s of this `Layout`.
`Dimensions`	`getDimensions()`
`ListOf<GraphicalObject>`	`getListOfAdditionalGraphicalObjects()`
`ListOf<CompartmentGlyph>`	`getListOfCompartmentGlyphs()`
`ListOf<ReactionGlyph>`	`getListOfReactionGlyphs()`
`ListOf<SpeciesGlyph>`	`getListOfSpeciesGlyphs()`
`ListOf<TextGlyph>`	`getListOfTextGlyphs()`
`int`	`getNumCompartmentGlyphs()` Returns the number of `CompartmentGlyph`s of this `Layout`.
`int`	`getNumReactionGlyphs()` Returns the number of `ReactionGlyph`s of this `Layout`.
`int`	`getNumSpeciesGlyphs()` Returns the number of `SpeciesGlyph`s of this `Layout`.
`int`	`getNumTextGlyphs()` Returns the number of `TextGlyph`s of this `Layout`.
`ReactionGlyph`	`getReactionGlyph(int i)`
`ReactionGlyph`	`getReactionGlyph(String id)`
`int`	`getReactionGlyphCount()` Returns the number of `ReactionGlyph`s of this `Layout`.
`SpeciesGlyph`	`getSpeciesGlyph(int i)`
`SpeciesGlyph`	`getSpeciesGlyph(String id)`
`int`	`getSpeciesGlyphCount()` Returns the number of `SpeciesGlyph`s of this `Layout`.
`TextGlyph`	`getTextGlyph(int i)`
`TextGlyph`	`getTextGlyph(String id)`
`int`	`getTextGlyphCount()` Returns the number of `TextGlyph`s of this `Layout`.
`int`	`hashCode()`
`boolean`	`isIdMandatory()`
`boolean`	`isSetAddGraphicalObjects()`
`boolean`	`isSetDimensions()`
`boolean`	`isSetListOfAdditionalGraphicalObjects()`
`boolean`	`isSetListOfCompartmentGlyphs()`
`boolean`	`isSetListOfReactionGlyphs()`
`boolean`	`isSetListOfSpeciesGlyphs()`
`boolean`	`isSetListOfTextGlyphs()`
`boolean`	`readAttribute(String attributeName, String prefix, String value)`
`boolean`	`removeCompartmentGlyph(CompartmentGlyph compartmentGlyph)` Removes an element from the listOfCompartmentGlyphs.
`CompartmentGlyph`	`removeCompartmentGlyph(int i)` Removes an element from the listOfCompartmentGlyphs at the given index.
`CompartmentGlyph`	`removeCompartmentGlyph(String compartmentGlyphId)` Removes an element from the listOfCompartmentGlyphs.
`GeneralGlyph`	`removeGeneralGlyph(GeneralGlyph toBeRemoved)`
`GeneralGlyph`	`removeGeneralGlyph(int i)` Removes an element from the `listOfAdditionalGraphicalObjects` at the given index.
`GeneralGlyph`	`removeGeneralGlyph(String id)`
`ReactionGlyph`	`removeReactionGlyph(int i)` Removes an element from the `listOfReactionGlyphs` at the given index.
`boolean`	`removeReactionGlyph(ReactionGlyph reactionGlyph)` Removes an element from the listOfReactionGlyphs.
`ReactionGlyph`	`removeReactionGlyph(String reactionGlyphId)` Removes an element from the listOfReactionGlyphs.
`boolean`	`removeSingletons()` Removes all singleton `SpeciesGlyph`s (no `SpeciesReferenceGlyph` in `ReactionGlyph`) and also removes their associated `TextGlyph`s
`SpeciesGlyph`	`removeSpeciesGlyph(int i)` Removes an element from the listOfSpeciesGlyphs at the given index.
`boolean`	`removeSpeciesGlyph(SpeciesGlyph speciesGlyph)` Removes an element from the listOfSpeciesGlyphs.
`SpeciesGlyph`	`removeSpeciesGlyph(String speciesGlyphId)` Removes an element from the listOfSpeciesGlyphs.
`TextGlyph`	`removeTextGlyph(int i)` Removes an element from the listOfTextGlyphs at the given index.
`TextGlyph`	`removeTextGlyph(String textGlyphId)` Removes an element from the listOfTextGlyphs.
`boolean`	`removeTextGlyph(TextGlyph textGlyph)` Removes an element from the listOfTextGlyphs.
`void`	`setAddGraphicalObjects(ListOf<GraphicalObject> addGraphicalObjects)` This element is optional.
`void`	`setDimensions(Dimensions dimensions)` The dimensions element of type `Dimensions` specifies the dimensions of this layout.
`void`	`setListOfAdditionalGraphicalObjects(ListOf<GraphicalObject> additionalGraphicalObjects)` Sets the `listOfAdditionalGraphicalObjects`.
`void`	`setListOfCompartmentGlyphs(ListOf<CompartmentGlyph> compartmentGlyphs)` This element is optional.
`void`	`setListOfReactionGlyphs(ListOf<ReactionGlyph> reactionGlyphs)` This element is optional.
`void`	`setListOfSpeciesGlyphs(ListOf<SpeciesGlyph> speciesGlyphs)` This element is optional.
`void`	`setListOfTextGlyphs(ListOf<TextGlyph> textGlyphs)` This element is optional.
`boolean`	`unsetListOfAdditionalGraphicalObjects()` Removes the `listOfAdditionalGraphicalObjects` from this `Model` and notifies all registered instances of `TreeNodeChangeListener`.
`boolean`	`unsetListOfCompartmentGlyphs()` Removes the `listOfCompartmentGlyphs` from this `Model` and notifies all registered instances of `TreeNodeChangeListener`.
`boolean`	`unsetListOfReactionGlyphs()` Removes the `listOfReactionGlyphs` from this `Model` and notifies all registered instances of `TreeNodeChangeListener`.
`boolean`	`unsetListOfSpeciesGlyphs()` Removes the `listOfSpeciesGlyphs` from this `Model` and notifies all registered instances of `TreeNodeChangeListener`.
`boolean`	`unsetListOfTextGlyphs()` Removes the `listOfTextGlyphs` from this `Model` and notifies all registered instances of `TreeNodeChangeListener`.
`Map<String,String>`	`writeXMLAttributes()`

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase
isValidId

Methods inherited from class org.sbml.jsbml.AbstractSBase
addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, checkAndSetPackageNamespaceAndVersion, checkAndSetPackageNamespaceAndVersion, checkAttribute, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllowsChildren, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getId, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageVersion, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, toString, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetId, unsetMetaId, unsetName, unsetNamespace, unsetNotes, unsetPlugin, unsetSBOTerm

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

Methods inherited from interface org.sbml.jsbml.NamedSBase
getId, getName, isSetId, isSetName, setId, setName, unsetId, unsetName

Methods inherited from interface org.sbml.jsbml.SBase
addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeTreeNodeChangeListener, setAnnotation, setAnnotation, setAnnotation, setHistory, setLevel, setMetaId, setNotes, setNotes, setPackageVersion, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, unsetNotes, unsetPlugin, unsetSBOTerm

Methods inherited from interface javax.swing.tree.TreeNode
children, getAllowsChildren, getIndex, getParent, isLeaf

- Constructor Detail
  - Layout
```
public Layout()
```
  - Layout
```
public Layout(int level,
              int version)
```
    Parameters:
    
    level -
    
    version -
  - Layout
```
public Layout(Layout layout)
```
    Parameters:
    
    layout -
  - Layout
```
public Layout(String id,
              int level,
              int version)
```
    Parameters:
    
    id -
    
    level -
    
    version -
- Method Detail
  - addAdditionalGraphicalObject
```
public void addAdditionalGraphicalObject(GraphicalObject object)
```
    Adds an arbitrary additional GraphicalObject.
    
    Parameters:
    
    object -
    
    Note: this method is kept here as it exist in libSBML.
    
    same as addGraphicalObject(GraphicalObject)
  - addCompartmentGlyph
```
public boolean addCompartmentGlyph(CompartmentGlyph compartmentGlyph)
```
    Adds a new CompartmentGlyph to the listOfCompartmentGlyphs.
    The listOfCompartmentGlyphs is initialized if necessary.
    
    Parameters:
    
    compartmentGlyph - the element to add to the list
    
    Returns:
    
    true (as specified by Collection.add(E))
  - addGeneralGlyph
```
public void addGeneralGlyph(GeneralGlyph object)
```
    Adds a GeneralGlyph object.
    
    Parameters:
    
    object -
  - addGraphicalObject
```
public void addGraphicalObject(GraphicalObject object)
```
    Adds an arbitrary additional GraphicalObject.
    
    Parameters:
    
    object -
  - addReactionGlyph
```
public void addReactionGlyph(ReactionGlyph reactionGlyph)
```
    Adds a ReactionGlyph to this layout
    
    Parameters:
    
    reactionGlyph -
  - addSpeciesGlyph
```
public void addSpeciesGlyph(SpeciesGlyph speciesGlyph)
```
    Parameters:
    
    speciesGlyph -
  - addTextGlyph
```
public void addTextGlyph(TextGlyph TextGlyph)
```
    Parameters:
    
    TextGlyph -
  - clone
```
public Layout clone()
```
    Specified by:
    
    clone in interface SBase
    
    Overrides:
    
    clone in class AbstractSBase
  - containsGlyph
```
public boolean containsGlyph(Compartment compartment)
```
    Parameters:
    
    compartment -
    
    Returns:
  - containsGlyph
```
public boolean containsGlyph(Reaction reaction)
```
    Parameters:
    
    reaction -
    
    Returns:
  - containsGlyph
```
public boolean containsGlyph(Species species)
```
    Parameters:
    
    species -
    
    Returns:
  - createCompartmentGlyph
```
public CompartmentGlyph createCompartmentGlyph(String id)
```
    Creates and adds a new CompartmentGlyph.
    
    Parameters:
    
    id - the identifier of the CompartmentGlyph to be created.
    
    Returns:
    
    a new CompartmentGlyph.
    
    See Also:
    
    createCompartmentGlyph(String, String)
  - createCompartmentGlyph
```
public CompartmentGlyph createCompartmentGlyph(String id,
                                               String compartment)
```
    Creates and adds a new CompartmentGlyph.
    
    Parameters:
    
    id - the identifier of the CompartmentGlyph to be created.
    
    compartment - Compartment ID.
    
    Returns:
    
    a new CompartmentGlyph.
  - createDimensions
```
public Dimensions createDimensions(double width,
                                   double height,
                                   double depth)
```
    Creates, sets and returns Dimensions based on the given values.
    
    Parameters:
    
    width -
    
    height -
    
    depth -
    
    Returns:
    
    a new Dimensions object.
    
    See Also:
    
    createDimensions(String, double, double, double)
  - createDimensions
```
public Dimensions createDimensions(String id,
                                   double width,
                                   double height,
                                   double depth)
```
    Creates, sets and returns Dimensions based on the given values.
    
    Parameters:
    
    id - the identifier of the Dimensions to be created.
    
    width -
    
    height -
    
    depth -
    
    Returns:
    
    a new Dimensions object.
  - createGeneralGlyph
```
public GeneralGlyph createGeneralGlyph(String id)
```
    Creates and adds a new GeneralGlyph.
    
    Parameters:
    
    id - the identifier of the GeneralGlyph to be created.
    
    Returns:
    
    a new GeneralGlyph.
    
    See Also:
    
    createGeneralGlyph(String, String)
  - createGeneralGlyph
```
public GeneralGlyph createGeneralGlyph(String id,
                                       String reference)
```
    Creates and adds a new GeneralGlyph.
    
    Parameters:
    
    id - the identifier of the GeneralGlyph to be created.
    
    reference - the identifier of an element in the model that this GeneralGlyph will represent.
    
    Returns:
    
    a new GeneralGlyph.
  - createReactionGlyph
```
public ReactionGlyph createReactionGlyph(String id)
```
    Creates and adds a new ReactionGlyph.
    
    Parameters:
    
    id - the identifier of the ReactionGlyph to be created.
    
    Returns:
    
    a new ReactionGlyph.
    
    See Also:
    
    createReactionGlyph(String, String)
  - createReactionGlyph
```
public ReactionGlyph createReactionGlyph(String id,
                                         String reaction)
```
    Creates and adds a new ReactionGlyph.
    
    Parameters:
    
    id - the identifier of the ReactionGlyph to be created.
    
    reaction - Reaction ID.
    
    Returns:
    
    a new ReactionGlyph.
  - createSpeciesGlyph
```
public SpeciesGlyph createSpeciesGlyph(String id)
```
    Creates and adds a new SpeciesGlyph with the given identifier.
    
    Parameters:
    
    id - the identifier for the SpeciesGlyph to be created.
    
    Returns:
    
    a new SpeciesGlyph.
    
    See Also:
    
    createSpeciesGlyph(String, String)
  - createSpeciesGlyph
```
public SpeciesGlyph createSpeciesGlyph(String id,
                                       String species)
```
    Creates and adds a new SpeciesGlyph.
    
    Parameters:
    
    id - the identifier for the SpeciesGlyph to be created.
    
    species - Species ID.
    
    Returns:
    
    a new SpeciesGlyph.
  - createTextGlyph
```
public TextGlyph createTextGlyph(String id)
```
    Creates and adds a new TextGlyph.
    
    Parameters:
    
    id - the identifier for the TextGlyph to be created.
    
    Returns:
    
    a new TextGlyph.
    
    See Also:
    
    createTextGlyph(String, String)
  - createTextGlyph
```
public TextGlyph createTextGlyph(String id,
                                 String text)
```
    Creates and adds a new TextGlyph.
    
    Parameters:
    
    id - the identifier for the TextGlyph to be created.
    
    text - the text for the new glyph
    
    Returns:
    
    a new TextGlyph.
  - equals
```
public boolean equals(Object object)
```
    Specified by:
    
    equals in interface SBase
    
    Overrides:
    
    equals in class AbstractSBase
  - findCompartmentGlyphs
```
public List<CompartmentGlyph> findCompartmentGlyphs(String compartmentID)
```
    Searches all instances of CompartmentGlyph within this Layout that refer to the Compartment with the given id.
    
    Parameters:
    
    compartmentID -
    
    Returns:
    
    a List containing all identified elements. It can be empty but not null.
  - findReactionGlyphs
```
public List<ReactionGlyph> findReactionGlyphs(String reactionID)
```
    Searches all instances of ReactionGlyph within this Layout that refer to the Reaction with the given id.
    
    Parameters:
    
    reactionID -
    
    Returns:
    
    a List containing all identified elements. It can be empty but not null.
  - findSpeciesGlyphs
```
public List<SpeciesGlyph> findSpeciesGlyphs(String speciesID)
```
    Searches all instances of SpeciesGlyph within this Layout that refer to the Species with the given id.
    
    Parameters:
    
    speciesID -
    
    Returns:
    
    a List containing all identified elements. It can be empty but not null.
  - findTextGlyphs
```
public List<TextGlyph> findTextGlyphs(String id)
```
    Searches within the listOfTextGlyphs for TextGlyphs whose TextGlyph.getOriginOfText() points to the given id.
    
    Parameters:
    
    id - the identifier of the element for which TextGlyphs are to be found.
    
    Returns:
    
    all TextGlyphs associated to an element with the given id.
  - getAdditionalGraphicalObject
```
public GraphicalObject getAdditionalGraphicalObject(int i)
```
    Parameters:
    
    i -
    
    Returns:
  - getAdditionalGraphicalObjectCount
```
public int getAdditionalGraphicalObjectCount()
```
    Returns:
  - getChildAt
```
public TreeNode getChildAt(int index)
```
    Specified by:
    
    getChildAt in interface TreeNode
    
    Overrides:
    
    getChildAt in class AbstractSBase
  - getChildCount
```
public int getChildCount()
```
    Specified by:
    
    getChildCount in interface TreeNode
    
    Overrides:
    
    getChildCount in class AbstractSBase
  - getCompartmentGlyph
```
public CompartmentGlyph getCompartmentGlyph(int i)
```
    Gets an element from the listOfCompartmentGlyphs at the given index.
    
    Parameters:
    
    i - the index of the CompartmentGlyph element to get.
    
    Returns:
    
    an element from the listOfCompartmentGlyphs at the given index.
    
    Throws:
    
    IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).
  - getCompartmentGlyph
```
public CompartmentGlyph getCompartmentGlyph(String id)
```
    Gets an element from the listOfCompartmentGlyphs, with the given id.
    
    Parameters:
    
    id - the id of the CompartmentGlyph element to get.
    
    Returns:
    
    an element from the listOfCompartmentGlyphs with the given id or null.
  - getCompartmentGlyphCount
```
public int getCompartmentGlyphCount()
```
    Returns the number of CompartmentGlyphs of this Layout.
    
    Returns:
    
    the number of CompartmentGlyphs of this Layout.
  - getDimensions
```
public Dimensions getDimensions()
```
    Returns:
  - getListOfAdditionalGraphicalObjects
```
public ListOf<GraphicalObject> getListOfAdditionalGraphicalObjects()
```
    Returns:
  - getListOfCompartmentGlyphs
```
public ListOf<CompartmentGlyph> getListOfCompartmentGlyphs()
```
    Returns:
  - getListOfReactionGlyphs
```
public ListOf<ReactionGlyph> getListOfReactionGlyphs()
```
    Returns:
  - getListOfSpeciesGlyphs
```
public ListOf<SpeciesGlyph> getListOfSpeciesGlyphs()
```
    Returns:
  - getListOfTextGlyphs
```
public ListOf<TextGlyph> getListOfTextGlyphs()
```
    Returns:
  - getNumCompartmentGlyphs
```
public int getNumCompartmentGlyphs()
```
    Returns the number of CompartmentGlyphs of this Layout.
    
    Returns:
    
    the number of CompartmentGlyphs of this Layout.
    
    Note: this method is kept here as it exist in libSBML.
    
    same as getCompartmentGlyphCount()
  - getNumReactionGlyphs
```
public int getNumReactionGlyphs()
```
    Returns the number of ReactionGlyphs of this Layout.
    
    Returns:
    
    the number of ReactionGlyphs of this Layout.
    
    Note: this method is kept here as it exist in libSBML.
    
    same as getReactionGlyphCount()
  - getNumSpeciesGlyphs
```
public int getNumSpeciesGlyphs()
```
    Returns the number of SpeciesGlyphs of this Layout.
    
    Returns:
    
    the number of SpeciesGlyphs of this Layout.
    
    Note: this method is kept here as it exist in libSBML.
    
    same as getSpeciesGlyphCount()
  - getNumTextGlyphs
```
public int getNumTextGlyphs()
```
    Returns the number of TextGlyphs of this Layout.
    
    Returns:
    
    the number of TextGlyphs of this Layout.
    
    Note: this method is kept here as it exist in libSBML.
    
    same as getTextGlyphCount()
  - getReactionGlyph
```
public ReactionGlyph getReactionGlyph(int i)
```
    Parameters:
    
    i -
    
    Returns:
  - getReactionGlyph
```
public ReactionGlyph getReactionGlyph(String id)
```
    Parameters:
    
    id -
    
    Returns:
  - getReactionGlyphCount
```
public int getReactionGlyphCount()
```
    Returns the number of ReactionGlyphs of this Layout.
    
    Returns:
    
    the number of ReactionGlyphs of this Layout.
  - getSpeciesGlyph
```
public SpeciesGlyph getSpeciesGlyph(int i)
```
    Parameters:
    
    i -
    
    Returns:
  - getSpeciesGlyph
```
public SpeciesGlyph getSpeciesGlyph(String id)
```
    Parameters:
    
    id -
    
    Returns:
  - getSpeciesGlyphCount
```
public int getSpeciesGlyphCount()
```
    Returns the number of SpeciesGlyphs of this Layout.
    
    Returns:
    
    the number of SpeciesGlyphs of this Layout.
  - getTextGlyph
```
public TextGlyph getTextGlyph(int i)
```
    Parameters:
    
    i -
    
    Returns:
  - getTextGlyph
```
public TextGlyph getTextGlyph(String id)
```
    Parameters:
    
    id -
    
    Returns:
  - getTextGlyphCount
```
public int getTextGlyphCount()
```
    Returns the number of TextGlyphs of this Layout.
    
    Returns:
    
    the number of TextGlyphs of this Layout.
  - hashCode
```
public int hashCode()
```
    Specified by:
    
    hashCode in interface SBase
    
    Overrides:
    
    hashCode in class AbstractSBase
  - isIdMandatory
```
public boolean isIdMandatory()
```
    Specified by:
    
    isIdMandatory in interface NamedSBase
    
    Specified by:
    
    isIdMandatory in interface SBase
    
    Overrides:
    
    isIdMandatory in class AbstractSBase
  - isSetAddGraphicalObjects
```
public boolean isSetAddGraphicalObjects()
```
    Returns:
  - isSetDimensions
```
public boolean isSetDimensions()
```
    Returns:
  - isSetListOfAdditionalGraphicalObjects
```
public boolean isSetListOfAdditionalGraphicalObjects()
```
    Returns:
  - isSetListOfCompartmentGlyphs
```
public boolean isSetListOfCompartmentGlyphs()
```
    Returns:
  - isSetListOfReactionGlyphs
```
public boolean isSetListOfReactionGlyphs()
```
    Returns:
  - isSetListOfSpeciesGlyphs
```
public boolean isSetListOfSpeciesGlyphs()
```
    Returns:
  - isSetListOfTextGlyphs
```
public boolean isSetListOfTextGlyphs()
```
    Returns:
  - readAttribute
```
public boolean readAttribute(String attributeName,
                             String prefix,
                             String value)
```
    Specified by:
    
    readAttribute in interface SBase
    
    Overrides:
    
    readAttribute in class AbstractSBase
    
    Parameters:
    
    attributeName -
    
    prefix -
    
    value -
    
    Returns:
  - removeCompartmentGlyph
```
public boolean removeCompartmentGlyph(CompartmentGlyph compartmentGlyph)
```
    Removes an element from the listOfCompartmentGlyphs.
    
    Parameters:
    
    compartmentGlyph - the element to be removed from the list.
    
    Returns:
    
    true if the list contained the specified element and it was removed.
    
    See Also:
    
    List.remove(Object)
  - removeCompartmentGlyph
```
public CompartmentGlyph removeCompartmentGlyph(int i)
```
    Removes an element from the listOfCompartmentGlyphs at the given index.
    
    Parameters:
    
    i - the index where to remove the CompartmentGlyph.
    
    Returns:
    
    the specified element, if it was successfully found and removed.
    
    Throws:
    
    IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).
  - removeCompartmentGlyph
```
public CompartmentGlyph removeCompartmentGlyph(String compartmentGlyphId)
```
    Removes an element from the listOfCompartmentGlyphs.
    
    Parameters:
    
    compartmentGlyphId - the id of the element to be removed from the list.
    
    Returns:
    
    the removed element, if it was successfully found and removed or null.
  - removeGeneralGlyph
```
public GeneralGlyph removeGeneralGlyph(GeneralGlyph toBeRemoved)
```
    Parameters:
    
    toBeRemoved -
    
    Returns:
    
    the given element in case of a successful operation, null otherwise.
  - removeGeneralGlyph
```
public GeneralGlyph removeGeneralGlyph(int i)
```
    Removes an element from the listOfAdditionalGraphicalObjects at the given index.
    
    Parameters:
    
    i - the index where to remove the GeneralGlyph.
    
    Returns:
    
    the removed object
    
    Throws:
    
    IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).
    
    ClassCastException - if the additional graphical object at the given index is not an instance of GeneralGlyph. Note that the element is still removed, but an exception will be thrown. The element will not be re-inserted.
  - removeGeneralGlyph
```
public GeneralGlyph removeGeneralGlyph(String id)
```
    Parameters:
    
    id -
    
    Returns:
    
    Throws:
    
    ClassCastException - if the additional graphical object with the given id is not an instance of GeneralGlyph. Note that the element is still removed, but an exception will be thrown. The element will not be re-inserted.
  - removeReactionGlyph
```
public ReactionGlyph removeReactionGlyph(int i)
```
    Removes an element from the listOfReactionGlyphs at the given index.
    
    Parameters:
    
    i - the index where to remove the ReactionGlyph.
    
    Returns:
    
    the specified element, if it was successfully found and removed.
    
    Throws:
    
    IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).
  - removeReactionGlyph
```
public boolean removeReactionGlyph(ReactionGlyph reactionGlyph)
```
    Removes an element from the listOfReactionGlyphs.
    
    Parameters:
    
    reactionGlyph - the element to be removed from the list.
    
    Returns:
    
    true if the list contained the specified element and it was removed.
    
    See Also:
    
    List.remove(Object)
  - removeReactionGlyph
```
public ReactionGlyph removeReactionGlyph(String reactionGlyphId)
```
    Removes an element from the listOfReactionGlyphs.
    
    Parameters:
    
    reactionGlyphId - the id of the element to be removed from the list.
    
    Returns:
    
    the removed element, if it was successfully found and removed or null.
  - removeSingletons
```
public boolean removeSingletons()
```
    Removes all singleton SpeciesGlyphs (no SpeciesReferenceGlyph in ReactionGlyph) and also removes their associated TextGlyphs
    
    Returns:
  - removeSpeciesGlyph
```
public SpeciesGlyph removeSpeciesGlyph(int i)
```
    Removes an element from the listOfSpeciesGlyphs at the given index.
    
    Parameters:
    
    i - the index where to remove the SpeciesGlyph.
    
    Returns:
    
    the specified element, if it was successfully found and removed.
    
    Throws:
    
    IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).
  - removeSpeciesGlyph
```
public boolean removeSpeciesGlyph(SpeciesGlyph speciesGlyph)
```
    Removes an element from the listOfSpeciesGlyphs.
    
    Parameters:
    
    speciesGlyph - the element to be removed from the list.
    
    Returns:
    
    true if the list contained the specified element and it was removed.
    
    See Also:
    
    List.remove(Object)
  - removeSpeciesGlyph
```
public SpeciesGlyph removeSpeciesGlyph(String speciesGlyphId)
```
    Removes an element from the listOfSpeciesGlyphs.
    
    Parameters:
    
    speciesGlyphId - the id of the element to be removed from the list.
    
    Returns:
    
    the removed element, if it was successfully found and removed or null.
  - removeTextGlyph
```
public TextGlyph removeTextGlyph(int i)
```
    Removes an element from the listOfTextGlyphs at the given index.
    
    Parameters:
    
    i - the index where to remove the TextGlyph.
    
    Returns:
    
    the specified element, if it was successfully found and removed.
    
    Throws:
    
    IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).
  - removeTextGlyph
```
public TextGlyph removeTextGlyph(String textGlyphId)
```
    Removes an element from the listOfTextGlyphs.
    
    Parameters:
    
    textGlyphId - the id of the element to be removed from the list.
    
    Returns:
    
    the removed element, if it was successfully found and removed or null.
  - removeTextGlyph
```
public boolean removeTextGlyph(TextGlyph textGlyph)
```
    Removes an element from the listOfTextGlyphs.
    
    Parameters:
    
    textGlyph - the element to be removed from the list.
    
    Returns:
    
    true if the list contained the specified element and it was removed.
    
    See Also:
    
    List.remove(Object)
  - setAddGraphicalObjects
```
public void setAddGraphicalObjects(ListOf<GraphicalObject> addGraphicalObjects)
```
    This element is optional. If set, this list cannot be empty.
    
    Parameters:
    
    addGraphicalObjects -
  - setDimensions
```
public void setDimensions(Dimensions dimensions)
```
    The dimensions element of type Dimensions specifies the dimensions of this layout. This element is required. It holds the dimensions of all layout elements (care should be taken when using CubicBeziers, that the described curve also lies within the given dimensions).
    
    Parameters:
    
    dimensions -
  - setListOfAdditionalGraphicalObjects
```
public void setListOfAdditionalGraphicalObjects(ListOf<GraphicalObject> additionalGraphicalObjects)
```
    Sets the listOfAdditionalGraphicalObjects.
    This element is optional. If set, this list cannot be empty. Most objects for which layout information is to be included in an SBML file have a corresponding object in Model. As there might be cases where the user wants to include object types in the layout that do fall in any of the other categories described below, we include a listOfAdditionalGraphicalObjects in each Layout object. This list holds an arbitrary number of GraphicalObject elements. The GraphicalObject only defines a bounding box in a specific place in the Layout without giving additional information about its contents.
    
    The listOfAdditionalGraphicalObjects, when present, must contain one or more of the following elements: GraphicalObject or GeneralGlyph. When using a GraphicalObject it is recommended that some form of meta-information is provided. For additional relationships such as SBML events or rules, the GeneralGlyph can be used.
    
    Parameters:
    
    additionalGraphicalObjects -
  - setListOfCompartmentGlyphs
```
public void setListOfCompartmentGlyphs(ListOf<CompartmentGlyph> compartmentGlyphs)
```
    This element is optional. If set, this list cannot be empty. Also, not all Compartments of a Model will need a corresponding CompartmentGlyph.
    
    Parameters:
    
    compartmentGlyphs -
  - setListOfReactionGlyphs
```
public void setListOfReactionGlyphs(ListOf<ReactionGlyph> reactionGlyphs)
```
    This element is optional. If set, this list cannot be empty. Also, not all Reactions of a Model need a corresponding ReactionGlyph.
    
    Parameters:
    
    reactionGlyphs -
  - setListOfSpeciesGlyphs
```
public void setListOfSpeciesGlyphs(ListOf<SpeciesGlyph> speciesGlyphs)
```
    This element is optional. If set, this list cannot be empty. Also, not all Species of a Model need a corresponding SpeciesGlyph.
    
    Parameters:
    
    speciesGlyphs -
  - setListOfTextGlyphs
```
public void setListOfTextGlyphs(ListOf<TextGlyph> textGlyphs)
```
    This element is optional. If set, this list cannot be empty.
    
    Parameters:
    
    textGlyphs -
  - unsetListOfAdditionalGraphicalObjects
```
public boolean unsetListOfAdditionalGraphicalObjects()
```
    Removes the listOfAdditionalGraphicalObjects from this Model and notifies all registered instances of TreeNodeChangeListener.
    
    Returns:
    
    true if calling this method lead to a change in this data structure.
  - unsetListOfCompartmentGlyphs
```
public boolean unsetListOfCompartmentGlyphs()
```
    Removes the listOfCompartmentGlyphs from this Model and notifies all registered instances of TreeNodeChangeListener.
    
    Returns:
    
    true if calling this method lead to a change in this data structure.
  - unsetListOfReactionGlyphs
```
public boolean unsetListOfReactionGlyphs()
```
    Removes the listOfReactionGlyphs from this Model and notifies all registered instances of TreeNodeChangeListener.
    
    Returns:
    
    true if calling this method lead to a change in this data structure.
  - unsetListOfSpeciesGlyphs
```
public boolean unsetListOfSpeciesGlyphs()
```
    Removes the listOfSpeciesGlyphs from this Model and notifies all registered instances of TreeNodeChangeListener.
    
    Returns:
    
    true if calling this method lead to a change in this data structure.
  - unsetListOfTextGlyphs
```
public boolean unsetListOfTextGlyphs()
```
    Removes the listOfTextGlyphs from this Model and notifies all registered instances of TreeNodeChangeListener.
    
    Returns:
    
    true if calling this method lead to a change in this data structure.
  - writeXMLAttributes
```
public Map<String,String> writeXMLAttributes()
```
    Specified by:
    
    writeXMLAttributes in interface SBase
    
    Overrides:
    
    writeXMLAttributes in class AbstractSBase

Class Layout

Field Summary

Fields inherited from class org.sbml.jsbml.AbstractSBase

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

Constructor Summary

Method Summary

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

Methods inherited from class org.sbml.jsbml.AbstractSBase

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

Methods inherited from class java.lang.Object

Methods inherited from interface org.sbml.jsbml.NamedSBase

Methods inherited from interface org.sbml.jsbml.SBase

Methods inherited from interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

Methods inherited from interface javax.swing.tree.TreeNode

Constructor Detail

Layout

Layout

Layout

Layout

Method Detail

addAdditionalGraphicalObject

addCompartmentGlyph

addGeneralGlyph

addGraphicalObject

addReactionGlyph

addSpeciesGlyph

addTextGlyph

clone

containsGlyph

containsGlyph

containsGlyph

createCompartmentGlyph

createCompartmentGlyph

createDimensions

createDimensions

createGeneralGlyph

createGeneralGlyph

createReactionGlyph

createReactionGlyph

createSpeciesGlyph

createSpeciesGlyph

createTextGlyph

createTextGlyph

equals

findCompartmentGlyphs

findReactionGlyphs

findSpeciesGlyphs

findTextGlyphs

getAdditionalGraphicalObject

getAdditionalGraphicalObjectCount

getChildAt

getChildCount

getCompartmentGlyph

getCompartmentGlyph

getCompartmentGlyphCount

getDimensions

getListOfAdditionalGraphicalObjects

getListOfCompartmentGlyphs

getListOfReactionGlyphs

getListOfSpeciesGlyphs

getListOfTextGlyphs

getNumCompartmentGlyphs

getNumReactionGlyphs

getNumSpeciesGlyphs

getNumTextGlyphs

getReactionGlyph

getReactionGlyph

getReactionGlyphCount

getSpeciesGlyph

getSpeciesGlyph

getSpeciesGlyphCount

getTextGlyph

getTextGlyph

getTextGlyphCount

hashCode

isIdMandatory

isSetAddGraphicalObjects

isSetDimensions

isSetListOfAdditionalGraphicalObjects

isSetListOfCompartmentGlyphs