org.sbml.jsbml.ext.render.director

Class SimpleLayoutAlgorithm

java.lang.Object

org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

All Implemented Interfaces:

LayoutAlgorithm

public abstract class SimpleLayoutAlgorithm
extends Object
implements LayoutAlgorithm

SimpleLayoutAlgorithm is a partial implementation of the LayoutAlgorithm interface which collects functions which are independent of the output format of the LayoutDirector.

Since:

1.4

Author:

Andreas Dräger

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SimpleLayoutAlgorithm.RelativePosition Enumeration types (enums) for relative positions.

Field Summary

Fields

Modifier and Type	Field and Description
protected Layout	layout The Layout object of the SBML Model.
protected int	level SBML level
protected Set<GraphicalObject>	setOfLayoutedGlyphs Set to hold all layouted glyphs
protected Set<GraphicalObject>	setOfUnlayoutedGlyphs Set to hold all unlayouted glyphs
protected int	version SBML version

Constructor Summary

Constructors

Constructor and Description
SimpleLayoutAlgorithm()

Method Summary

Modifier and Type	Method and Description
protected Point	calculateAverageCurvePosition(SpeciesReferenceRole specRefRole, List<SpeciesReferenceGlyph> specRefGlyphList) This method calculates the average position of a curve at the direction of the reaction glyph, if the role of a species reference glyph is PRODUCT, the start point of the curve is at the reaction glyph, else the start point is at the species and the end point at the reaction glyph.
protected Point	calculateAverageSpeciesPosition(SpeciesReferenceRole specRefRole, List<SpeciesReferenceGlyph> specRefGlyphList) method calculates the average position of the species glyphs belonging to the given list of species reference glyphs, the role of the species reference glyph must be of the given type
protected Point	calculateCenter(GraphicalObject graphicalObject) Compute the coordinates of the central point of a GraphicalObject.
static Point	calculateCenter(GraphicalObject graphicalObject, int level, int version)
protected Point	calculateOldSpeciesGlyphDockingPosition(Point middleOfSpecies, SimpleLayoutAlgorithm.RelativePosition relativeSpeciesGlyphPosition, SpeciesGlyph specGlyph) Deprecated.
protected Point	calculateReactionGlyphDockingPoint(ReactionGlyph reacGlyph, double rotationAngle, SpeciesReferenceGlyph specRef) c
double	calculateReactionGlyphRotationAngle(ReactionGlyph reactionGlyph) method to calculate the rotation angle of the lines from the reaction box, in degrees
static double	calculateRotationAngle(Point startPoint, Point endPoint) Calculate the rotation angle for a line determined by two Points.
protected Point	calculateSpeciesGlyphDockingPosition(Point centerOfSpecies, ReactionGlyph reactionGlyph, SpeciesReferenceRole speciesReferenceRole, SpeciesGlyph speciesGlyph) Compute the docking Point at the species for the curve defined by the ReactionGlyph and the SpeciesGlyph.
void	correctDimensions(GraphicalObject glyph) Correct the dimensions of a GraphicalObject by changing its BoundingBox.
protected double	correctRotationAngle(double rotationAngle) Normalize a given rotation angle, i.e., express the angle in the range from 0° to 90° (excluding 90°).
protected BoundingBox	createBoundingBoxWithLevelAndVersion() Creates a BoundingBox with the level and version of this layout.
Dimensions	createReactionGlyphDimension(ReactionGlyph reactionGlyph) method to create a Dimensions for a ReactionGlyph if it was missing in the layout model
protected Point	createReactionGlyphPosition(ReactionGlyph reactionGlyph)
protected Point	createReactionGlyphPositionNew(ReactionGlyph reactionGlyph)
protected Point	createSpeciesReferenceGlyphPosition(ReactionGlyph reactionGlyph, SpeciesReferenceGlyph specRefGlyph)
Layout	findLayout(GraphicalObject graphicalObject) Find the Layout to which the given GraphicalObject belongs.
protected SpeciesGlyph	findSpeciesGlyphByRole(List<SpeciesReferenceGlyph> speciesReferenceGlyphList, SpeciesReferenceRole speciesReferenceRole) Return the first SpeciesGlyph from a list of SpeciesReferenceGlyphs which has the given SpeciesReferenceRole.
Layout	getLayout()
protected static SimpleLayoutAlgorithm.RelativePosition	getRelativePosition(Point startGlyph, Point endGlyph) method calculates the relative position of the second bounding box with respect to the first bounding box ABOVE: middle of the second bounding box is directly above the middle of the first bounding box BELOW: middle of the second bounding box is directly below the middle of the first bounding box LEFT: middle of the second bounding box is directly left of the middle of the first bounding box RIGHT: middle of the second bounding box is directly right of the middle of the first bounding box
boolean	isSetLayout()
void	setLayout(Layout layout)

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm

addLayoutedEdge, addLayoutedGlyph, addUnlayoutedEdge, addUnlayoutedGlyph, completeGlyphs, createCompartmentGlyphDimension, createCompartmentGlyphPosition, createCurve, createGlyphBoundingBox, createLayoutDimension, createSpeciesGlyphDimension, createSpeciesReferenceGlyphDimension, createTextGlyphDimension

Field Detail

level

protected int level

SBML level

version

protected int version

SBML version

layout

protected Layout layout

The Layout object of the SBML Model.

setOfLayoutedGlyphs

protected Set<GraphicalObject> setOfLayoutedGlyphs

Set to hold all layouted glyphs

setOfUnlayoutedGlyphs

protected Set<GraphicalObject> setOfUnlayoutedGlyphs

Set to hold all unlayouted glyphs

Constructor Detail

SimpleLayoutAlgorithm

public SimpleLayoutAlgorithm()

Method Detail

getLayout

public Layout getLayout()

Specified by:

getLayout in interface LayoutAlgorithm

Returns:

the Layout set for this LayoutAlgorithm;

isSetLayout

public boolean isSetLayout()

Specified by:

isSetLayout in interface LayoutAlgorithm

Returns:

true if a Layout is set for this LayoutAlgorithm, else false

setLayout

public void setLayout(Layout layout)

Specified by:

setLayout in interface LayoutAlgorithm

Parameters:

layout - the Layout to be set for this LayoutAlgorithm

getRelativePosition

protected static SimpleLayoutAlgorithm.RelativePosition getRelativePosition(Point startGlyph,
                                                                            Point endGlyph)

method calculates the relative position of the second bounding box with respect to the first bounding box

• ABOVE: middle of the second bounding box is directly above the middle of the first bounding box
• BELOW: middle of the second bounding box is directly below the middle of the first bounding box
• LEFT: middle of the second bounding box is directly left of the middle of the first bounding box
• RIGHT: middle of the second bounding box is directly right of the middle of the first bounding box

Parameters:

startGlyphBB -

endGlyphBB -

Returns:

RelativePosition

calculateAverageCurvePosition

protected Point calculateAverageCurvePosition(SpeciesReferenceRole specRefRole,
                                              List<SpeciesReferenceGlyph> specRefGlyphList)

This method calculates the average position of a curve at the direction of the reaction glyph, if the role of a species reference glyph is PRODUCT, the start point of the curve is at the reaction glyph, else the start point is at the species and the end point at the reaction glyph.

Parameters:

specRefRole -

specRefGlyphList -

Returns:

a Position

calculateAverageSpeciesPosition

protected Point calculateAverageSpeciesPosition(SpeciesReferenceRole specRefRole,
                                                List<SpeciesReferenceGlyph> specRefGlyphList)

method calculates the average position of the species glyphs belonging to the given list of species reference glyphs, the role of the species reference glyph must be of the given type

Parameters:

specRefRole - the species reference glyphs of the given list must have

specRefGlyphList -

Returns:

a Position

calculateCenter

protected Point calculateCenter(GraphicalObject graphicalObject)

Compute the coordinates of the central point of a GraphicalObject.

Parameters:

graphicalObject - the GraphicalObject for which to calculate the center

Returns:

the center Point of the graphical object

calculateCenter

public static Point calculateCenter(GraphicalObject graphicalObject,
                                    int level,
                                    int version)

Parameters:

graphicalObject -

level -

version -

Returns:

calculateReactionGlyphDockingPoint

protected Point calculateReactionGlyphDockingPoint(ReactionGlyph reacGlyph,
                                                   double rotationAngle,
                                                   SpeciesReferenceGlyph specRef)

c

Parameters:

reacGlyph -

rotationAngle -

specRef -

Returns:

correctRotationAngle

protected double correctRotationAngle(double rotationAngle)

Normalize a given rotation angle, i.e., express the angle in the range from 0° to 90° (excluding 90°).

Parameters:

rotationAngle - in degrees

Returns:

the normalized rotation angle in degrees

createSpeciesReferenceGlyphPosition

protected Point createSpeciesReferenceGlyphPosition(ReactionGlyph reactionGlyph,
                                                    SpeciesReferenceGlyph specRefGlyph)

Parameters:

reactionGlyph -

specRefGlyph -

Returns:

createReactionGlyphPositionNew

protected Point createReactionGlyphPositionNew(ReactionGlyph reactionGlyph)

Parameters:

reactionGlyph -

Returns:

createReactionGlyphPosition

protected Point createReactionGlyphPosition(ReactionGlyph reactionGlyph)

createReactionGlyphDimension

public Dimensions createReactionGlyphDimension(ReactionGlyph reactionGlyph)

Description copied from interface: LayoutAlgorithm

method to create a Dimensions for a ReactionGlyph if it was missing in the layout model

Specified by:

createReactionGlyphDimension in interface LayoutAlgorithm

Parameters:

reactionGlyph - for which the Dimensions is missing

Returns:

a Dimensions

calculateReactionGlyphRotationAngle

public double calculateReactionGlyphRotationAngle(ReactionGlyph reactionGlyph)

Description copied from interface: LayoutAlgorithm

method to calculate the rotation angle of the lines from the reaction box, in degrees

Specified by:

calculateReactionGlyphRotationAngle in interface LayoutAlgorithm

Parameters:

reactionGlyph - for which the rotation angle shall be calculated

Returns:

the rotation angle in degrees

calculateRotationAngle

public static double calculateRotationAngle(Point startPoint,
                                            Point endPoint)

Calculate the rotation angle for a line determined by two Points.

Parameters:

startPoint - the first Point

endPoint - the second point Point

Returns:

the rotation angle in degrees of a line through the two points

calculateOldSpeciesGlyphDockingPosition

@Deprecated
protected Point calculateOldSpeciesGlyphDockingPosition(Point middleOfSpecies,
                                                                    SimpleLayoutAlgorithm.RelativePosition relativeSpeciesGlyphPosition,
                                                                    SpeciesGlyph specGlyph)

Deprecated.

Compute the docking Point at the species depending on the SimpleLayoutAlgorithm.RelativePosition of the SpeciesGlyph. This method is deprecated because we decided to allow docking at any point rather than restricting the docking to the four orientations left, right, above and below. Use calculateSpeciesGlyphDockingPosition(Point, ReactionGlyph, SpeciesReferenceRole, SpeciesGlyph) instead.

Parameters:

middleOfSpecies - center Point of the species

relativeSpeciesGlyphPosition - the SimpleLayoutAlgorithm.RelativePosition of the species

specGlyph - the SpeciesGlyph

Returns:

the docking Point

calculateSpeciesGlyphDockingPosition

protected Point calculateSpeciesGlyphDockingPosition(Point centerOfSpecies,
                                                     ReactionGlyph reactionGlyph,
                                                     SpeciesReferenceRole speciesReferenceRole,
                                                     SpeciesGlyph speciesGlyph)

Compute the docking Point at the species for the curve defined by the ReactionGlyph and the SpeciesGlyph.

Parameters:

centerOfSpecies - the center Point of the SpeciesGlyph

reactionGlyph - the ReactionGlyph of the arc

speciesReferenceRole - the SpeciesReferenceRole of the involved SpeciesReferenceGlyph

speciesGlyph - the SpeciesGlyph of the arc

Returns:

the docking Point

createBoundingBoxWithLevelAndVersion

protected BoundingBox createBoundingBoxWithLevelAndVersion()

Creates a BoundingBox with the level and version of this layout.

Returns:

a BoundingBox with the level and version of the layout

findLayout

public Layout findLayout(GraphicalObject graphicalObject)

Find the Layout to which the given GraphicalObject belongs.

Parameters:

graphicalObject - GraphicalObject for which to find the layout

Returns:

the layout which contains the GraphicalObject

findSpeciesGlyphByRole

protected SpeciesGlyph findSpeciesGlyphByRole(List<SpeciesReferenceGlyph> speciesReferenceGlyphList,
                                              SpeciesReferenceRole speciesReferenceRole)

Return the first SpeciesGlyph from a list of SpeciesReferenceGlyphs which has the given SpeciesReferenceRole. Return null if no such SpeciesGlyph is found.

Parameters:

speciesReferenceGlyphList - List containing the SpeciesReferenceGlyphs

speciesReferenceRole - the SpeciesReferenceRole for which to look

Returns:

the first SpeciesGlyph which has the given SpeciesReferenceRole

correctDimensions

public void correctDimensions(GraphicalObject glyph)

Correct the dimensions of a GraphicalObject by changing its BoundingBox. According to the SBGN specification, some objects have to be represented as a circle or square and not as an ellipse or rectangle. fit to the glyph. If not this method corrects the layout informations.

Parameters:

glyph - the GraphicalObject for which to correct the dimensions