Package | Description |
---|---|
org.sbml.jsbml.ext.layout |
Provides classes for the Layout
package.
|
org.sbml.jsbml.ext.render |
Provides classes for the render package, see the specification at sbml.org.
|
org.sbml.jsbml.ext.render.director |
This package contains interfaces and classes to create an implementation
to create a graphical representation of the
Layout
of a SBML document. |
Modifier and Type | Class | Description |
---|---|---|
class |
AbstractReferenceGlyph |
Abstract super class for all kinds of glyphs that graphically represent an
instance of
NamedSBase . |
class |
CompartmentGlyph |
The
CompartmentGlyph class is derived from GraphicalObject
and inherits its attributes. |
class |
GeneralGlyph |
The
GeneralGlyph is used to facilitate the representation of elements
other than Compartment , Species
and Reaction and thus
can be used for the display of relationships of Rule
or
elements defined by other SBML packages. |
class |
ReactionGlyph |
Analogous to how a
Reaction object has to at least have one reactant
or product, the ReactionGlyph has to at least have one
SpeciesReferenceGlyph stored in the
ReactionGlyph.listOfSpeciesReferenceGlyphs . |
class |
ReferenceGlyph |
The
ReferenceGlyph element describes the graphical connection between
an arbitrary GraphicalObject (or derived element) and a
GeneralGlyph (which would be an arrow or some curve in most cases). |
class |
SpeciesGlyph |
The
SpeciesGlyph class has an optional species attribute, in
addition to to the attributes from GraphicalObject . |
class |
SpeciesReferenceGlyph |
The
SpeciesReferenceGlyph class describes the graphical connection
between a SpeciesGlyph and a ReactionGlyph (which would be
an arrow or some curve in most cases). |
class |
TextGlyph |
The
TextGlyph class describes the position and dimension of text labels. |
Modifier and Type | Method | Description |
---|---|---|
GraphicalObject |
GraphicalObject.clone() |
|
GraphicalObject |
GeneralGlyph.createGraphicalObject() |
Creates a new
GraphicalObject element and adds it to the ListOfSubGlyphs list. |
GraphicalObject |
GeneralGlyph.createGraphicalObject(java.lang.String id) |
Creates a new
GraphicalObject element and adds it to the ListOfSubGlyphs list. |
GraphicalObject |
Layout.getAdditionalGraphicalObject(int i) |
|
GraphicalObject |
TextGlyph.getGraphicalObjectInstance() |
Direct access to the
GraphicalObject linked to this
TextGlyph . |
Modifier and Type | Method | Description |
---|---|---|
ListOf<GraphicalObject> |
Layout.getListOfAdditionalGraphicalObjects() |
|
ListOf<GraphicalObject> |
GeneralGlyph.getListOfSubGlyphs() |
Returns the listOfSubGlyphs.
|
Modifier and Type | Method | Description |
---|---|---|
void |
Layout.addAdditionalGraphicalObject(GraphicalObject object) |
Adds an arbitrary additional
GraphicalObject . |
void |
Layout.addGraphicalObject(GraphicalObject object) |
Adds an arbitrary additional
GraphicalObject . |
boolean |
GeneralGlyph.addSubGlyph(GraphicalObject subGlyph) |
Adds a new
GraphicalObject to the listOfSubGlyphs. |
boolean |
GeneralGlyph.removeGeneralGlyph(GraphicalObject subGlyph) |
Removes an element from the listOfSubGlyphs.
|
boolean |
GeneralGlyph.removeSubGlyph(GraphicalObject subGlyph) |
Removes an element from the listOfSubGlyphs.
|
void |
TextGlyph.setGraphicalObject(GraphicalObject graphicalObject) |
Modifier and Type | Method | Description |
---|---|---|
void |
Layout.setAddGraphicalObjects(ListOf<GraphicalObject> addGraphicalObjects) |
This element is optional.
|
void |
Layout.setListOfAdditionalGraphicalObjects(ListOf<GraphicalObject> additionalGraphicalObjects) |
Sets the
Layout.listOfAdditionalGraphicalObjects . |
void |
GeneralGlyph.setListOfSubGlyphs(ListOf<GraphicalObject> listOfSubGlyphs) |
The listOfSubGlyphs is an optional list that can contain sub-glyphs of the
GeneralGlyph . |
Constructor | Description |
---|---|
GraphicalObject(GraphicalObject graphicalObject) |
Constructor | Description |
---|---|
RenderGraphicalObjectPlugin(GraphicalObject graphicalObject) |
Creates a new
RenderGraphicalObjectPlugin instance. |
Modifier and Type | Method | Description |
---|---|---|
java.util.Set<GraphicalObject> |
LayoutAlgorithm.completeGlyphs() |
Return the input set of unlayouted glyphs with completed layout
information.
|
Modifier and Type | Method | Description |
---|---|---|
void |
LayoutAlgorithm.addLayoutedGlyph(GraphicalObject glyph) |
Add a fully layouted glyph (i.e. glyph with boundingbox, dimensions and
position) to the input of the algorithm.
|
void |
LayoutAlgorithm.addUnlayoutedGlyph(GraphicalObject glyph) |
Add a glyph with missing layout information (i.e. no dimensions or no
position specified) to the input of the algorithm.
|
static Point |
SimpleLayoutAlgorithm.calculateCenter(GraphicalObject graphicalObject,
int level,
int version) |
|
void |
SimpleLayoutAlgorithm.correctDimensions(GraphicalObject glyph) |
Correct the dimensions of a
GraphicalObject by changing its
BoundingBox . |
BoundingBox |
LayoutAlgorithm.createGlyphBoundingBox(GraphicalObject glyph,
SpeciesReferenceGlyph specRefGlyph) |
method to create a
BoundingBox for every kind of GraphicalObject . |
Layout |
SimpleLayoutAlgorithm.findLayout(GraphicalObject graphicalObject) |
Find the
Layout to which the given GraphicalObject
belongs. |
static boolean |
LayoutDirector.glyphHasDimensions(GraphicalObject glyph) |
Check if a glyph has dimensions.
|
static boolean |
LayoutDirector.glyphHasPosition(GraphicalObject glyph) |
Check if a glyph has a position.
|
static boolean |
LayoutDirector.glyphIsLayouted(GraphicalObject glyph) |
Check if a glyph as complete layout information (i.e. if it as both
dimensions and position).
|
static void |
RenderProcessor.linkObjectRoleToStyle(java.util.Map<java.lang.String,LocalStyle> roles,
GraphicalObject go) |