Package | Description |
---|---|
org.sbml.jsbml.ext.layout |
Provides classes for the Layout
package.
|
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 | Method | Description |
---|---|---|
SpeciesReferenceGlyph |
SpeciesReferenceGlyph.clone() |
|
SpeciesReferenceGlyph |
GeneralGlyph.createSpeciesReferenceGlyph() |
Creates a new
SpeciesReferenceGlyph element and adds it to the ListOfSubGlyphs list. |
SpeciesReferenceGlyph |
GeneralGlyph.createSpeciesReferenceGlyph(java.lang.String id) |
Creates a new
SpeciesReferenceGlyph element and adds it to the ListOfSubGlyphs list. |
SpeciesReferenceGlyph |
ReactionGlyph.createSpeciesReferenceGlyph(java.lang.String id) |
Creates and adds a new
SpeciesReferenceGlyph |
SpeciesReferenceGlyph |
ReactionGlyph.createSpeciesReferenceGlyph(java.lang.String id,
java.lang.String speciesGlyph) |
Creates and adds a new
SpeciesReferenceGlyph |
SpeciesReferenceGlyph |
ReactionGlyph.getSpeciesReferenceGlyph(int i) |
|
SpeciesReferenceGlyph |
ReactionGlyph.getSpeciesReferenceGlyph(java.lang.String srGlyphId) |
Modifier and Type | Method | Description |
---|---|---|
ListOf<SpeciesReferenceGlyph> |
ReactionGlyph.getListOfSpeciesReferenceGlyphs() |
Returns the list of
SpeciesReferenceGlyph s. |
Modifier and Type | Method | Description |
---|---|---|
boolean |
ReactionGlyph.addSpeciesReferenceGlyph(SpeciesReferenceGlyph glyph) |
Appends the specified element to the end of the
ReactionGlyph.listOfSpeciesReferenceGlyphs . |
Modifier and Type | Method | Description |
---|---|---|
void |
ReactionGlyph.setListOfSpeciesReferenceGlyphs(ListOf<SpeciesReferenceGlyph> listOfSpeciesReferencesGlyph) |
Sets the list of
SpeciesReferenceGlyph s. |
void |
ReactionGlyph.setListOfSpeciesReferencesGlyph(ListOf<SpeciesReferenceGlyph> listOfSpeciesReferencesGlyph) |
Deprecated.
|
Constructor | Description |
---|---|
SpeciesReferenceGlyph(SpeciesReferenceGlyph speciesReferenceGlyph) |
Modifier and Type | Method | Description |
---|---|---|
void |
LayoutAlgorithm.addLayoutedEdge(SpeciesReferenceGlyph srg,
ReactionGlyph rg) |
Add a layouted edge to the input of the algorithm.
|
void |
LayoutAlgorithm.addUnlayoutedEdge(SpeciesReferenceGlyph srg,
ReactionGlyph rg) |
Add an unlayouted edge to the input of the algorithm.
|
void |
LayoutBuilder.buildConnectingArc(SpeciesReferenceGlyph srg,
ReactionGlyph rg,
double curveWidth) |
method for the drawing of a connecting arc or line with the size and
position specified by the given SpeciesReferenceGlyph
|
SBGNArc<ArcT> |
AbstractLayoutBuilder.createArc(SpeciesReferenceGlyph srg,
ReactionGlyph reactionGlyph) |
|
Curve |
LayoutAlgorithm.createCurve(ReactionGlyph reactionGlyph,
SpeciesReferenceGlyph speciesReferenceGlyph) |
method to create the
Curve of a SpeciesReferenceGlyph ,
starting or ending at the given ReactionGlyph |
BoundingBox |
LayoutAlgorithm.createGlyphBoundingBox(GraphicalObject glyph,
SpeciesReferenceGlyph specRefGlyph) |
method to create a
BoundingBox for every kind of GraphicalObject . |
Dimensions |
LayoutAlgorithm.createSpeciesReferenceGlyphDimension(ReactionGlyph reactionGlyph,
SpeciesReferenceGlyph speciesReferenceGlyph) |
method to create a
Dimensions for a SpeciesReferenceGlyph
if it was missing in the layout model |
static SpeciesReferenceRole |
LayoutDirector.determineRole(SpeciesReferenceGlyph srg) |
|
static boolean |
LayoutDirector.edgeIsLayouted(ReactionGlyph reactionGlyph,
SpeciesReferenceGlyph speciesReferenceGlyph) |
Check if the incoming edge is layouted, i.e. if it has a curve.
|
static boolean |
LayoutDirector.isModifier(SpeciesReferenceGlyph srg) |
Check if a species reference glyph can be interpreted as an activator,
inhibitor, or generic modifier.
|
static boolean |
LayoutDirector.isProduct(SpeciesReferenceGlyph srg) |
Check if a species reference glyph is a product.
|
static boolean |
LayoutDirector.isSubstrate(SpeciesReferenceGlyph srg) |
Check if a species reference glyph is a substrate.
|