Package org.sbml.jsbml.ext.render.director

Class LayoutDirector<P>

java.lang.Object

org.sbml.jsbml.ext.render.director.LayoutDirector<P>

Type Parameters:

P - Type of the product.

All Implemented Interfaces:

java.lang.Runnable

public class LayoutDirector<P>
extends java.lang.Object
implements java.lang.Runnable

LayoutDirector produces a graphical representation of a layout of an SBMLDocument.

Since:

1.4

Author:

Mirjam Gutekunst

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	COMPARTMENT_LINK	Constant for use as the key for compartment links, also see LAYOUT_LINK.
static java.lang.String	KEY_FOR_FLUX_VALUES	Constant for use as the key for flux values.
static java.lang.String	LAYOUT_LINK	Constant for use as the key for layout links.
static java.lang.String	NO_WHISKERS
static java.lang.String	PN_RELATIVE_DOCKING_POINT	Constant for use as the key for relative docking points.
static java.lang.String	SPECIAL_ROTATION_NEEDED
static java.lang.String	SPECIES_RELATIVE_DOCKING_POINT	Constant for use as the key for relative docking points for a species, also see PN_RELATIVE_DOCKING_POINT.

Constructor Summary

Constructors

Constructor	Description
LayoutDirector(java.io.File inputFile, LayoutBuilder<P> builder, LayoutAlgorithm algorithm)
LayoutDirector(Layout layout, LayoutBuilder<P> builder, LayoutAlgorithm algorithm)
LayoutDirector(org.sbml.jsbml.SBMLDocument doc, LayoutBuilder<P> builder, LayoutAlgorithm algorithm)
LayoutDirector(org.sbml.jsbml.SBMLDocument doc, LayoutBuilder<P> builder, LayoutAlgorithm algorithm, int index)

Method Summary

Modifier and Type	Method	Description
static SpeciesReferenceRole	determineRole(SpeciesReferenceGlyph srg)
static boolean	edgeIsLayouted(ReactionGlyph reactionGlyph, SpeciesReferenceGlyph speciesReferenceGlyph)	Check if the incoming edge is layouted, i.e. if it has a curve.
java.lang.Boolean	getAddWhiskers()	Returns the value of addWhiskers
LayoutAlgorithm	getAlgorithm()
LayoutBuilder<P>	getBuilder()
int	getLayoutIndex()
P	getProduct()	Return the product of the building process.
static boolean	glyphHasDimensions(GraphicalObject glyph)	Check if a glyph has dimensions.
static boolean	glyphHasPosition(GraphicalObject glyph)	Check if a glyph has a position.
static boolean	glyphIsLayouted(GraphicalObject glyph)	Check if a glyph as complete layout information (i.e. if it as both dimensions and position).
static boolean	isModifier(SpeciesReferenceGlyph srg)	Check if a species reference glyph can be interpreted as an activator, inhibitor, or generic modifier.
static boolean	isProduct(SpeciesReferenceGlyph srg)	Check if a species reference glyph is a product.
java.lang.Boolean	isSetAddWhiskers()	Returns whether addWhiskers is set
static boolean	isSubstrate(SpeciesReferenceGlyph srg)	Check if a species reference glyph is a substrate.
void	run()
void	setAddWhiskers(java.lang.Boolean addWhiskers)	Sets the value of addWhiskers
void	setAlgorithm(LayoutAlgorithm algorithm)
void	setBuilder(LayoutBuilder<P> builder)
void	setLayoutIndex(int layoutIndex)
static boolean	textGlyphIsIndependent(TextGlyph textGlyph)	Check whether a text glyph represents an independent text (i.e. it is not associated with any other graphical object or species.
java.lang.String	toString()
boolean	unsetAddWhiskers()	Unsets the variable addWhiskers

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

SPECIAL_ROTATION_NEEDED

public static final java.lang.String SPECIAL_ROTATION_NEEDED

See Also:

Constant Field Values

NO_WHISKERS

public static final java.lang.String NO_WHISKERS

See Also:

Constant Field Values

KEY_FOR_FLUX_VALUES

public static final java.lang.String KEY_FOR_FLUX_VALUES

Constant for use as the key for flux values.

See Also:

Constant Field Values

LAYOUT_LINK

public static final java.lang.String LAYOUT_LINK

Constant for use as the key for layout links. A layout link connects a core object (e.g., a species) with a all of its glyphs in the given layout.

See Also:

Constant Field Values

COMPARTMENT_LINK

public static final java.lang.String COMPARTMENT_LINK

Constant for use as the key for compartment links, also see LAYOUT_LINK.

See Also:

Constant Field Values

PN_RELATIVE_DOCKING_POINT

public static final java.lang.String PN_RELATIVE_DOCKING_POINT

Constant for use as the key for relative docking points. A relative docking point is a property stored in the user objects of a ReactionGlyph to denote the relative docking position of the connecting arcs.

See Also:

Constant Field Values

SPECIES_RELATIVE_DOCKING_POINT

public static final java.lang.String SPECIES_RELATIVE_DOCKING_POINT

Constant for use as the key for relative docking points for a species, also see PN_RELATIVE_DOCKING_POINT.

See Also:

Constant Field Values

Constructor Detail

LayoutDirector

public LayoutDirector(java.io.File inputFile,
                      LayoutBuilder<P> builder,
                      LayoutAlgorithm algorithm)
               throws javax.xml.stream.XMLStreamException,
                      java.io.IOException

Parameters:

inputFile - file containing the SBML document

builder - LayoutBuilder instance for producing the output

algorithm - LayoutAlgorithm instance for layouting elements

Throws:

javax.xml.stream.XMLStreamException

java.io.IOException

LayoutDirector

public LayoutDirector(org.sbml.jsbml.SBMLDocument doc,
                      LayoutBuilder<P> builder,
                      LayoutAlgorithm algorithm)

Parameters:

doc - the SBMLdocument

builder - LayoutBuilder instance for producing the output

algorithm - LayoutAlgorithm instance for layouting elements

LayoutDirector

public LayoutDirector(org.sbml.jsbml.SBMLDocument doc,
                      LayoutBuilder<P> builder,
                      LayoutAlgorithm algorithm,
                      int index)

Parameters:

doc - the SBMLdocument

builder - LayoutBuilder instance for producing the output

algorithm - LayoutAlgorithm instance for layouting elements

index - the index of the layout for which to produce the ouput

LayoutDirector

public LayoutDirector(Layout layout,
                      LayoutBuilder<P> builder,
                      LayoutAlgorithm algorithm)

Parameters:

layout - the SBML layout for which to produce the output

builder - LayoutBuilder instance for producing the output

algorithm - LayoutAlgorithm instance for layouting elements

Method Detail

getAddWhiskers

public java.lang.Boolean getAddWhiskers()

Returns the value of addWhiskers

Returns:

the value of addWhiskers

isSetAddWhiskers

public java.lang.Boolean isSetAddWhiskers()

Returns whether addWhiskers is set

Returns:

whether addWhiskers is set

setAddWhiskers

public void setAddWhiskers(java.lang.Boolean addWhiskers)

Sets the value of addWhiskers

unsetAddWhiskers

public boolean unsetAddWhiskers()

Unsets the variable addWhiskers

Returns:

true, if addWhiskers was set before, otherwise false

getLayoutIndex

public int getLayoutIndex()

Returns:

the layoutIndex

setLayoutIndex

public void setLayoutIndex(int layoutIndex)

Parameters:

layoutIndex - the index of the layout to be set

edgeIsLayouted

public static boolean edgeIsLayouted(ReactionGlyph reactionGlyph,
                                     SpeciesReferenceGlyph speciesReferenceGlyph)

Check if the incoming edge is layouted, i.e. if it has a curve.

Parameters:

reactionGlyph - process node of the edge

speciesReferenceGlyph - species node of the edge

Returns:

whether the edge is layouted

glyphIsLayouted

public static boolean glyphIsLayouted(GraphicalObject glyph)

Check if a glyph as complete layout information (i.e. if it as both dimensions and position).

Parameters:

glyph -

Returns:

glyphHasDimensions

public static boolean glyphHasDimensions(GraphicalObject glyph)

Check if a glyph has dimensions.

Parameters:

glyph -

Returns:

glyphHasPosition

public static boolean glyphHasPosition(GraphicalObject glyph)

Check if a glyph has a position.

Parameters:

glyph -

Returns:

isSubstrate

public static boolean isSubstrate(SpeciesReferenceGlyph srg)

Check if a species reference glyph is a substrate. Both species reference roles (higher priority) and SBO terms are used.

Parameters:

srg - a SpeciesReferenceGlyph

Returns:

true if the given SpeciesReferenceGlyph can be associated with a consuming process or false otherwise.

isModifier

public static boolean isModifier(SpeciesReferenceGlyph srg)

Check if a species reference glyph can be interpreted as an activator, inhibitor, or generic modifier.

Parameters:

srg - a SpeciesReferenceGlyph

Returns:

true if the given SpeciesReferenceGlyph acts as an SpeciesReferenceRole.ACTIVATOR, SpeciesReferenceRole.INHIBITOR or SpeciesReferenceRole.MODIFIER.

determineRole

public static SpeciesReferenceRole determineRole(SpeciesReferenceGlyph srg)

Parameters:

srg -

Returns:

isProduct

public static boolean isProduct(SpeciesReferenceGlyph srg)

Check if a species reference glyph is a product. Both species reference roles (higher priority) and SBO terms are used.

Parameters:

srg -

Returns:

textGlyphIsIndependent

public static boolean textGlyphIsIndependent(TextGlyph textGlyph)

Check whether a text glyph represents an independent text (i.e. it is not associated with any other graphical object or species.

Parameters:

textGlyph -

Returns:

run

public void run()

Specified by:

run in interface java.lang.Runnable

setBuilder

public void setBuilder(LayoutBuilder<P> builder)

Parameters:

builder - the builder to be set

getBuilder

public LayoutBuilder<P> getBuilder()

Returns:

the builder

setAlgorithm

public void setAlgorithm(LayoutAlgorithm algorithm)

Parameters:

algorithm - the algorithm to be set

getAlgorithm

public LayoutAlgorithm getAlgorithm()

Returns:

the algorithm

getProduct

public P getProduct()

Return the product of the building process.

Returns:

the product

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object