org.openscience.cdk.renderer.generators

Class HighlightGenerator

java.lang.Object

org.openscience.cdk.renderer.generators.HighlightGenerator

All Implemented Interfaces:

IGenerator<IAtomContainer>

public final class HighlightGenerator
extends Object
implements IGenerator<IAtomContainer>

Generate an under/overlaid highlight in structure depictions. The highlight emphasises atoms and bonds. Each atom and bond is optionally assigned an integer identifier. Entities with identifiers are then highlighted using the HighlightGenerator.Palette to determine the color. The size of the highlight is specified with the HighlightGenerator.HighlightRadius parameter. Basic usage:

// create with the highlight generator
 AtomContainerRenderer renderer = ...;

 IAtomContainer            m   = ...; // input molecule
 Map<IChemObject, Integer> ids = new HashMap<>();

 // set atom/bond ids, atoms with no id will not be highlighted, numbering
 // starts at 0
 ids.put(m.getAtom(0), 0);
 ids.put(m.getAtom(1), 0);
 ids.put(m.getAtom(2), 0);
 ids.put(m.getAtom(5), 2);
 ids.put(m.getAtom(6), 1);

 ids.put(m.getBond(0), 0);
 ids.put(m.getBond(1), 0);
 ids.put(m.getBond(3), 1);
 ids.put(m.getBond(4), 2);

 // attach ids to the structure
 m.setProperty(HighlightGenerator.ID_MAP, ids);

 // draw
 renderer.paint(m, new AWTDrawVisitor(g2), bounds, true);
 

By default colours are automatically generated, to assign specific colors a custom HighlightGenerator.Palette must be used. Here are some examples of setting the palette parameter in the renderer.

 AtomContainerRenderer renderer = ...;

 // opaque colors
 renderer.getRenderer2DModel()
         .set(HighlightGenerator.HighlightPalette.class,
              HighlightGenerator.createPalette(Color.RED, Color.BLUE, Color.GREEN));

 // opaque colors (hex)
 renderer.getRenderer2DModel()
         .set(HighlightGenerator.HighlightPalette.class,
              HighlightGenerator.createPalette(new Color(0xff0000), Color.BLUE, Color.GREEN));

 // first color is transparent
 renderer.getRenderer2DModel()
         .set(HighlightGenerator.HighlightPalette.class,
              HighlightGenerator.createPalette(new Color(0x88ff0000, true), Color.BLUE, Color.GREEN));
 

Author:

John May

Source code:

master

Belongs to CDK module:

renderextra

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	HighlightGenerator.HighlightPalette Defines the color palette used to provide the highlight colors.
static class	HighlightGenerator.HighlightRadius Magic number with unknown units that defines the radius around an atom, e.g.
static interface	HighlightGenerator.Palette Defines a color palette, the palette should provide a color the specified identifier (id).

Field Summary

Fields

Modifier and Type	Field and Description
static String	ID_MAP Property key.

Constructor Summary

Constructors

Constructor and Description
HighlightGenerator()

Method Summary

Methods

Modifier and Type	Method and Description
static HighlightGenerator.Palette	createAutoGenPalette(boolean transparent) Create an auto generating palette which will generate colors using the provided parameters.
static HighlightGenerator.Palette	createAutoGenPalette(float saturation, float brightness, boolean transparent) Create an auto generating palette which will generate colors using the provided parameters.
static HighlightGenerator.Palette	createAutoPalette(float saturation, float brightness, int alpha) Create an auto generating palette which will generate colors using the provided parameters.
static HighlightGenerator.Palette	createPalette(Color[] colors) Create a palette which uses the provided colors.
static HighlightGenerator.Palette	createPalette(Color color, Color... colors) Create a palette which uses the provided colors.
IRenderingElement	generate(IAtomContainer container, RendererModel model) Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
List<IGeneratorParameter<?>>	getParameters() Returns the list of IGeneratorParameter for this particular generator.

Methods inherited from class java.lang.Object

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

Field Detail

ID_MAP

public static final String ID_MAP

Property key.

See Also:

Constant Field Values

Constructor Detail

HighlightGenerator

public HighlightGenerator()

Method Detail

generate

public IRenderingElement generate(IAtomContainer container,
                         RendererModel model)

Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.

Specified by:

generate in interface IGenerator<IAtomContainer>

Parameters:

container - the chemical entity to be depicted

model - the rendering parameters

Returns:

a drawable chemical depiction component

getParameters

public List<IGeneratorParameter<?>> getParameters()

Returns the list of IGeneratorParameter for this particular generator.

Specified by:

getParameters in interface IGenerator<IAtomContainer>

Returns:

a List of IGeneratorParameters

createPalette

public static HighlightGenerator.Palette createPalette(Color[] colors)

Create a palette which uses the provided colors.

Parameters:

colors - colors to use in the palette

Returns:

a palette to use in highlighting

createPalette

public static HighlightGenerator.Palette createPalette(Color color,
                                       Color... colors)

Create a palette which uses the provided colors.

Parameters:

colors - colors to use in the palette

Returns:

a palette to use in highlighting

createAutoPalette

public static HighlightGenerator.Palette createAutoPalette(float saturation,
                                           float brightness,
                                           int alpha)

Create an auto generating palette which will generate colors using the provided parameters.

Parameters:

saturation - color saturation, 0.0 < x < 1.0

brightness - color brightness, 0.0 < x < 1.0

alpha - color alpha (transparency), 0 < x < 255

Returns:

a palette to use in highlighting

createAutoGenPalette

public static HighlightGenerator.Palette createAutoGenPalette(float saturation,
                                              float brightness,
                                              boolean transparent)

Create an auto generating palette which will generate colors using the provided parameters.

Parameters:

saturation - color saturation, 0.0 < x < 1.0

brightness - color brightness, 0.0 < x < 1.0

transparent - generate transparent colors, 0 < x < 255

Returns:

a palette to use in highlighting

createAutoGenPalette

public static HighlightGenerator.Palette createAutoGenPalette(boolean transparent)

Create an auto generating palette which will generate colors using the provided parameters.

Parameters:

transparent - generate transparent colors

Returns:

a palette to use in highlighting