Module omix.api

Package omix.plugin.model.writable

Interface Pathway

All Superinterfaces:

AbstractModelComponent, AbstractModelComponent, AbstractVisibleComponent, AbstractVisibleComponent, Pathway, ReadOnlyInterface, WritableInterface

public interface Pathway
extends AbstractVisibleComponent, Pathway

Method Summary

Modifier and Type	Method	Description
void	addPublicIdentifier(PublicIdentifier publicIdentifier)	Adds a public identifier to the item.
default void	addSynonym(String synonym)	Adds a synonym to the item.
void	addSynonym(String synonym, String htmlSynonym)	Adds a synonym to the item.
void	exchangeSynonyms(int index1, int index2)	Exchanges the position of two synonyms.
List<? extends PathwayItem>	getDiagramItems()
List<? extends PathwayItem>	getDiagramItems(Diagram diagram)
Reaction	getReaction(String name)
List<? extends Reaction>	reactions()
void	removePublicIdentifier(PublicIdentifier publicIdentifier)	Removes the public identifier from the item.
void	removeSynonym(int synonymIndex)	Removes the synonym from the item.
void	removeSynonym(String synonym)	Removes the synonym from the item.
void	setBrush(Brush brush)	Sets the fill brush of the item's shape.
void	setBrushDefault()	Sets the fill brush of the item's shape to default.
void	setFont(Font font)	Changes the font of the text label of the item.
void	setFontDefault()	Changes the font of the text label of the item to default.
void	setFormattedLabel(String html)	Set items visible label in html.
void	setHidden(boolean hidden)	Changes the visibility of the item in the diagram.
void	setIdentifier(String identifier)	Changes identifier of the item.
void	setPublicIdentifiers(Collection<? extends PublicIdentifier> publicIdentifiers)	Set the public identifiers of the item.
void	setReactionFont(Font font)	Changes the default font for reactions' text labels.
void	setReactionFontDefault()	Changes the default font for reactions' text labels to default.
void	setReactionPaint(Paint paint)	Changes the default value for the reactions' paint.
void	setReactionPaintDefault()	Changes the default value for the reactions' paint to default.
void	setReactionPaintDefaultToPathwayBrush()	Changes the default value for the reactions' paint to default (to pathway brush).
void	setReactionPaintDefaultToStylesheet()	Changes the default value for the reactions' paint to default (to style sheet).
void	setReactionShadow(Shadow shadow)	Changes the default value for the reactions' shadow.
void	setReactionShadowDefault()	Changes the default value for the reactions' shadow to default.
void	setReactionShape(Shape shape)	Changes the default value for the reactions' shape.
void	setReactionShapeDefault()	Changes the default value for the reactions' shape to default.
void	setReactionStrokeColor(Color strokeColor)	Changes the default value for the reactions' stroke color.
void	setReactionStrokeColorDefault()	Changes the default value for the reactions' stroke color to default.
void	setReactionStrokeStyle(StrokeStyle strokeStyle)	Changes the default value for the reactions' stroke style.
void	setReactionStrokeStyleDefault()	Changes the default value for the reactions' stroke style to default.
void	setReactionStrokeWidth(double strokeWidth)	Changes the default value for the reactions' stroke width.
void	setReactionStrokeWidthDefault()	Changes the default value for the reactions' stroke width to default.
void	setReactionTextBrush(Brush textBrush)	Changes the default value for the reactions' text paint brush.
void	setReactionTextBrushDefault()	Changes the default value for the reactions' text paint brush to default.
void	setReactionTextStrokeColor(Color textStrokeColor)	Changes the default value for the reactions' text stroke color.
void	setReactionTextStrokeColorDefault()	Changes the default value for the reactions' text stroke color to default.
void	setReactionTextStrokeWidth(double textStrokeWidth)	Changes the default value for the reactions' text stroke width.
void	setReactionTextStrokeWidthDefault()	Changes the default value for the reactions' text stroke width to default.
void	setStrength(double strength)	Changes the strength of the contour the pathway paints around its reactions and edges.
void	setStrengthDefault()	Changes the strength of the contour the pathway paints around its reactions and edges to default.
void	setStrokeColor(Color strokeColor)	Changes the color for the stroke of the item's shape.
void	setStrokeColorDefault()	Changes the color for the stroke of the item's shape to default.
void	setStrokeStyle(StrokeStyle strokeStyle)	Changes the paint style for the stroke of the item's shape.
void	setStrokeStyleDefault()	Changes the paint style for the stroke of the item's shape to default.
void	setStrokeWidth(double strokeWidth)	Changes the stroke width of the item's shape.
void	setStrokeWidthDefault()	Changes the stroke width of the item's shape to default.
default void	setSynonym(int index, String synonymPlain)	Sets the synonym at the given position.
void	setSynonym(int index, String synonymPlain, String synonymRichText)	Sets the synonym at the given position.
void	setTextBrush(Brush textBrush)	Changes the fill brush of the item's text label.
void	setTextBrushDefault()	Changes the fill brush of the item's text label to default.
void	setTextStrokeColor(Color textStrokeColor)	Changes the color for the stroke of the item's text label.
void	setTextStrokeColorDefault()	Changes the color for the stroke of the item's text label to default.
void	setTextStrokeWidth(double textStrokeWidth)	Changes the stroke width of the item's text label.
void	setTextStrokeWidthDefault()	Changes the stroke width of the item's text label to default.
void	setTransparency(double transparency)	Changes the transparency of the item's shape.
void	setTransparencyDefault()	Changes the transparency of the item's shape to default.
Pathway	toReadOnly()

Methods inherited from interface omix.plugin.model.AbstractModelComponent

addChangeListener, addPropertyChangeListener, fieldExists, getIdentifier, removeChangeListener, removePropertyChangeListener

Methods inherited from interface omix.plugin.model.writable.AbstractModelComponent

getField, getField, isChangeable, model

Methods inherited from interface omix.plugin.model.AbstractVisibleComponent

accessoryExists, getAccessory, getAccessory, hasDiagramItems, hasDiagramItems

Methods inherited from interface omix.plugin.model.writable.AbstractVisibleComponent

getAccessories, getAccessories, getAccessory, getAccessory, getAllAccessories, getCustomProperty, getMethod, getMethod, getMethod, setCustomProperty, setTmpCustomProperty

Methods inherited from interface omix.plugin.model.Pathway

blur, brush, font, getCustomProperty, getPublicIdentifiers, hidden, name, reactionBlur, reactionCollapsed, reactionFillLevel, reactionFillLevelIndication, reactionFont, reactionPaint, reactionScale, reactionShadow, reactionShape, reactionStrokeColor, reactionStrokeStyle, reactionStrokeWidth, reactionTextBrush, reactionTextStrokeColor, reactionTextStrokeWidth, reactionTransparency, setCustomProperty, setTmpCustomProperty, strength, strokeColor, strokeStyle, strokeWidth, synonyms, textBlur, textBrush, textShadow, textStrokeColor, textStrokeWidth, textTransparency, transparency

Method Details

setIdentifier

void setIdentifier(String identifier) throws ComponentExistsException, IllegalChangeException

Changes identifier of the item.

Parameters:

identifier - the new name of the item. CAUTION, the name must be unique in the network.

Throws:

ComponentExistsException

IllegalChangeException

setFormattedLabel

void setFormattedLabel(String html) throws IllegalChangeException

Set items visible label in html.

Parameters:

html - item's label in HTML

Throws:

IllegalChangeException

addSynonym

default void addSynonym(String synonym) throws IllegalChangeException

Adds a synonym to the item.

Parameters:

synonym -

Throws:

IllegalChangeException

addSynonym

void addSynonym(String synonym, String htmlSynonym) throws IllegalChangeException

Adds a synonym to the item.

Parameters:

synonym -

html -

Throws:

IllegalChangeException

removeSynonym

void removeSynonym(String synonym) throws IllegalChangeException

Removes the synonym from the item.

Parameters:

synonym -

Throws:

IllegalChangeException

removeSynonym

void removeSynonym(int synonymIndex) throws IllegalChangeException

Removes the synonym from the item.

Parameters:

synonym - index

Throws:

IllegalChangeException

exchangeSynonyms

void exchangeSynonyms(int index1, int index2) throws IllegalChangeException

Exchanges the position of two synonyms.

Parameters:

index1 -

index2 -

Throws:

IllegalChangeException

setSynonym

default void setSynonym(int index, String synonymPlain) throws IllegalChangeException

Sets the synonym at the given position.

Parameters:

index -

synonymPlain - plain text

Throws:

IllegalChangeException

setSynonym

void setSynonym(int index, String synonymPlain, String synonymRichText) throws IllegalChangeException

Sets the synonym at the given position.

Parameters:

index -

synonymPlain - plain text

synonymRichText - rich text

Throws:

IllegalChangeException

addPublicIdentifier

void addPublicIdentifier(PublicIdentifier publicIdentifier) throws IllegalChangeException

Adds a public identifier to the item.

Parameters:

publicIdentifier -

Throws:

IllegalChangeException

setPublicIdentifiers

void setPublicIdentifiers(Collection<? extends PublicIdentifier> publicIdentifiers) throws IllegalChangeException

Set the public identifiers of the item.

Parameters:

publicIdentifiers -

Throws:

IllegalChangeException

removePublicIdentifier

void removePublicIdentifier(PublicIdentifier publicIdentifier) throws IllegalChangeException

Removes the public identifier from the item.

Parameters:

publicIdentifier -

Throws:

IllegalChangeException

setHidden

void setHidden(boolean hidden) throws IllegalChangeException

Changes the visibility of the item in the diagram.

Parameters:

node - the item

hidden -

Throws:

IllegalChangeException

setBrush

void setBrush(@NonNull Brush brush) throws IllegalChangeException

Sets the fill brush of the item's shape.

Parameters:

brush - the new brush

Throws:

IllegalChangeException

See Also:

Pathway.brush()

setTextStrokeWidth

void setTextStrokeWidth(double textStrokeWidth) throws IllegalChangeException

Changes the stroke width of the item's text label. The text stroke width of graphics nodes does not accept null.

Parameters:

textStrokeWidth -

Throws:

IllegalChangeException

See Also:

Pathway.textStrokeWidth()

setStrokeWidth

void setStrokeWidth(double strokeWidth) throws IllegalChangeException

Changes the stroke width of the item's shape. The stroke width of graphics nodes does not accept null.

Parameters:

strokeWidth -

Throws:

IllegalChangeException

See Also:

Pathway.strokeWidth()

setTextBrush

void setTextBrush(@NonNull Brush textBrush) throws IllegalChangeException

Changes the fill brush of the item's text label.

Parameters:

textBrush -

Throws:

IllegalChangeException

See Also:

Pathway.textBrush()

setFont

void setFont(@NonNull Font font) throws IllegalChangeException

Changes the font of the text label of the item.

Parameters:

font -

Throws:

IllegalChangeException

See Also:

Pathway.font()

setStrokeStyle

void setStrokeStyle(@NonNull StrokeStyle strokeStyle) throws IllegalChangeException

Changes the paint style for the stroke of the item's shape.

Parameters:

strokeStyle -

Throws:

IllegalChangeException

See Also:

Pathway.strokeStyle()

setTextStrokeColor

void setTextStrokeColor(@NonNull Color textStrokeColor) throws IllegalChangeException

Changes the color for the stroke of the item's text label.

Parameters:

textStrokeColor -

Throws:

IllegalChangeException

See Also:

Pathway.textStrokeColor()

setStrokeColor

void setStrokeColor(@NonNull Color strokeColor) throws IllegalChangeException

Changes the color for the stroke of the item's shape.

Parameters:

strokeColor -

Throws:

IllegalChangeException

See Also:

Pathway.strokeColor()

setStrength

void setStrength(double strength) throws IllegalChangeException

Changes the strength of the contour the pathway paints around its reactions and edges.

Parameters:

strength - pathway strength

Throws:

IllegalChangeException

See Also:

Pathway.strength()

setTransparency

void setTransparency(double transparency) throws IllegalChangeException

Changes the transparency of the item's shape.

Parameters:

transparency -

Throws:

IllegalChangeException

See Also:

Pathway.transparency()

setReactionFont

void setReactionFont(@NonNull Font font) throws IllegalChangeException

Changes the default font for reactions' text labels.

Parameters:

font -

Throws:

IllegalChangeException

See Also:

BioNode.font()

setReactionStrokeColor

void setReactionStrokeColor(@NonNull Color strokeColor) throws IllegalChangeException

Changes the default value for the reactions' stroke color.

Parameters:

strokeColor -

Throws:

IllegalChangeException

See Also:

BioNode.strokeColor()

setReactionTextStrokeColor

void setReactionTextStrokeColor(@NonNull Color textStrokeColor) throws IllegalChangeException

Changes the default value for the reactions' text stroke color.

Parameters:

textStrokeColor -

Throws:

IllegalChangeException

See Also:

BioNode.textStrokeColor()

setReactionTextBrush

void setReactionTextBrush(@NonNull Brush textBrush) throws IllegalChangeException

Changes the default value for the reactions' text paint brush.

Parameters:

textBrush -

Throws:

IllegalChangeException

See Also:

BioNode.textBrush()

setReactionTextStrokeWidth

void setReactionTextStrokeWidth(double textStrokeWidth) throws IllegalChangeException

Changes the default value for the reactions' text stroke width.

Parameters:

textStrokeWidth -

Throws:

IllegalChangeException

See Also:

BioNode.textStrokeWidth()

setReactionStrokeWidth

void setReactionStrokeWidth(double strokeWidth) throws IllegalChangeException

Changes the default value for the reactions' stroke width.

Parameters:

strokeWidth -

Throws:

IllegalChangeException

See Also:

BioNode.strokeWidth()

setReactionStrokeStyle

void setReactionStrokeStyle(@NonNull StrokeStyle strokeStyle) throws IllegalChangeException

Changes the default value for the reactions' stroke style.

Parameters:

strokeStyle -

Throws:

IllegalChangeException

See Also:

BioNode.strokeStyle()

setReactionShape

void setReactionShape(@NonNull Shape shape) throws IllegalChangeException

Changes the default value for the reactions' shape.

Parameters:

shape -

Throws:

IllegalChangeException

See Also:

BioNode.shape()

setReactionShadow

void setReactionShadow(@NonNull Shadow shadow) throws IllegalChangeException

Changes the default value for the reactions' shadow.

Parameters:

shadow -

Throws:

IllegalChangeException

See Also:

BioNode.shadow()

setReactionPaint

void setReactionPaint(@NonNull Paint paint) throws IllegalChangeException

Changes the default value for the reactions' paint.

Parameters:

paint -

Throws:

IllegalChangeException

See Also:

BioNode.paint()

setBrushDefault

void setBrushDefault() throws IllegalChangeException

Sets the fill brush of the item's shape to default.

Parameters:

brush - the new brush

Throws:

IllegalChangeException

See Also:

Pathway.brush()

setTextStrokeWidthDefault

void setTextStrokeWidthDefault() throws IllegalChangeException

Changes the stroke width of the item's text label to default.

Throws:

IllegalChangeException

See Also:

Pathway.textStrokeWidth()

setStrokeWidthDefault

void setStrokeWidthDefault() throws IllegalChangeException

Changes the stroke width of the item's shape to default.

Throws:

IllegalChangeException

See Also:

Pathway.strokeWidth()

setTextBrushDefault

void setTextBrushDefault() throws IllegalChangeException

Changes the fill brush of the item's text label to default.

Throws:

IllegalChangeException

See Also:

Pathway.textBrush()

setFontDefault

void setFontDefault() throws IllegalChangeException

Changes the font of the text label of the item to default.

Throws:

IllegalChangeException

See Also:

Pathway.font()

setStrokeStyleDefault

void setStrokeStyleDefault() throws IllegalChangeException

Changes the paint style for the stroke of the item's shape to default.

Throws:

IllegalChangeException

See Also:

Pathway.strokeStyle()

setTextStrokeColorDefault

void setTextStrokeColorDefault() throws IllegalChangeException

Changes the color for the stroke of the item's text label to default.

Throws:

IllegalChangeException

See Also:

Pathway.textStrokeColor()

setStrokeColorDefault

void setStrokeColorDefault() throws IllegalChangeException

Changes the color for the stroke of the item's shape to default.

Throws:

IllegalChangeException

See Also:

Pathway.strokeColor()

setStrengthDefault

void setStrengthDefault() throws IllegalChangeException

Changes the strength of the contour the pathway paints around its reactions and edges to default.

Throws:

IllegalChangeException

See Also:

Pathway.strength()

setTransparencyDefault

void setTransparencyDefault() throws IllegalChangeException

Changes the transparency of the item's shape to default.

Throws:

IllegalChangeException

See Also:

Pathway.transparency()

setReactionFontDefault

void setReactionFontDefault() throws IllegalChangeException

Changes the default font for reactions' text labels to default.

Throws:

IllegalChangeException

See Also:

BioNode.font()

setReactionStrokeColorDefault

void setReactionStrokeColorDefault() throws IllegalChangeException

Changes the default value for the reactions' stroke color to default.

Throws:

IllegalChangeException

See Also:

BioNode.strokeColor()

setReactionTextStrokeColorDefault

void setReactionTextStrokeColorDefault() throws IllegalChangeException

Changes the default value for the reactions' text stroke color to default.

Throws:

IllegalChangeException

See Also:

BioNode.textStrokeColor()

setReactionTextBrushDefault

void setReactionTextBrushDefault() throws IllegalChangeException

Changes the default value for the reactions' text paint brush to default.

Throws:

IllegalChangeException

See Also:

BioNode.textBrush()

setReactionTextStrokeWidthDefault

void setReactionTextStrokeWidthDefault() throws IllegalChangeException

Changes the default value for the reactions' text stroke width to default.

Throws:

IllegalChangeException

See Also:

BioNode.textStrokeWidth()

setReactionStrokeWidthDefault

void setReactionStrokeWidthDefault() throws IllegalChangeException

Changes the default value for the reactions' stroke width to default.

Throws:

IllegalChangeException

See Also:

BioNode.strokeWidth()

setReactionStrokeStyleDefault

void setReactionStrokeStyleDefault() throws IllegalChangeException

Changes the default value for the reactions' stroke style to default.

Throws:

IllegalChangeException

See Also:

BioNode.strokeStyle()

setReactionShapeDefault

void setReactionShapeDefault() throws IllegalChangeException

Changes the default value for the reactions' shape to default.

Throws:

IllegalChangeException

See Also:

BioNode.shape()

setReactionShadowDefault

void setReactionShadowDefault() throws IllegalChangeException

Changes the default value for the reactions' shadow to default.

Throws:

IllegalChangeException

See Also:

BioNode.shadow()

setReactionPaintDefaultToPathwayBrush

void setReactionPaintDefaultToPathwayBrush() throws IllegalChangeException

Changes the default value for the reactions' paint to default (to pathway brush).

Throws:

IllegalChangeException

See Also:

BioNode.paint()

setReactionPaintDefaultToStylesheet

void setReactionPaintDefaultToStylesheet() throws IllegalChangeException

Changes the default value for the reactions' paint to default (to style sheet).

Throws:

IllegalChangeException

See Also:

BioNode.paint()

setReactionPaintDefault

void setReactionPaintDefault() throws IllegalChangeException

Changes the default value for the reactions' paint to default.

Throws:

IllegalChangeException

See Also:

BioNode.paint()

getDiagramItems

List<? extends PathwayItem> getDiagramItems()

Specified by:

getDiagramItems in interface AbstractVisibleComponent

Specified by:

getDiagramItems in interface AbstractVisibleComponent

Specified by:

getDiagramItems in interface Pathway

getDiagramItems

List<? extends PathwayItem> getDiagramItems(Diagram diagram)

Specified by:

getDiagramItems in interface AbstractVisibleComponent

Specified by:

getDiagramItems in interface AbstractVisibleComponent

Specified by:

getDiagramItems in interface Pathway

reactions

List<? extends Reaction> reactions()

Specified by:

reactions in interface Pathway

getReaction

Reaction getReaction(String name)

Specified by:

getReaction in interface Pathway

toReadOnly

Pathway toReadOnly()

Specified by:

toReadOnly in interface AbstractModelComponent

Specified by:

toReadOnly in interface AbstractVisibleComponent

Specified by:

toReadOnly in interface WritableInterface