ambit2.rendering

Class CompoundImageTools

java.lang.Object

ambit2.rendering.CompoundImageTools

All Implemented Interfaces:

IStructureDiagramDepiction<BufferedImage>, IStructureDiagramHighlights, ICompoundImageTools

Direct Known Subclasses:

DbCompoundImageTools

public class CompoundImageTools
extends Object
implements IStructureDiagramHighlights, ICompoundImageTools

Generates BufferedImage from smiles or compound.

Author:

Nina Jeliazkova nina@acad.bg Modified 2006-3-5

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CompoundImageTools.Mode2D

Field Summary

Fields

Modifier and Type	Field and Description
static String	ATOM_ANNOTATION
protected Color	background
protected Color	borderColor
protected int	borderWidth
protected String	comma
protected BufferedImage	defaultImage
protected StringBuilder	imageMap
protected Dimension	imageSize
protected static Logger	logger
protected org.openscience.cdk.smiles.SmilesParser	parser
static String	SELECTED_ATOM_COLOR
static String	SELECTED_ATOM_SIZE
static Color	whiteTransparent

Constructor Summary

Constructors

Constructor and Description
CompoundImageTools()
CompoundImageTools(Dimension cellSize)

Method Summary

Modifier and Type	Method and Description
protected BufferedImage	createBuffer()
BufferedImage	createDefaultImage()
BufferedImage	createDefaultImage(String msg)
void	generate2D(org.openscience.cdk.interfaces.IAtomContainer molecule, boolean generateCoordinates, org.openscience.cdk.interfaces.IAtomContainerSet molecules)
BufferedImage	generateImage(String value)
BufferedImage	generateImage(String value, IAtomContainerHighlights selector, boolean build2d, boolean atomNumbers)
BufferedImage	generateImage(String value, IAtomContainerHighlights selector, boolean build2d, boolean atomNumbers, CompoundImageTools.Mode2D mode2D)
Color	getBackground()
Color	getBorderColor()
int	getBorderWidth()
Image	getDefaultImage()
BufferedImage	getImage(ArrayList<?> list)
BufferedImage	getImage(org.openscience.cdk.interfaces.IAtomContainer molecule)
BufferedImage	getImage(org.openscience.cdk.interfaces.IAtomContainer molecule, IAtomContainerHighlights selector, boolean build2d, boolean atomNumbers)
BufferedImage	getImage(org.openscience.cdk.interfaces.IAtomContainer molecule, IAtomContainerHighlights selector, boolean build2d, boolean atomNumbers, boolean explicitH)
BufferedImage	getImage(org.openscience.cdk.interfaces.IAtomContainer molecule, IAtomContainerHighlights selector, boolean build2d, boolean atomNumbers, boolean explicitH, CompoundImageTools.Mode2D mode2d)
BufferedImage	getImage(org.openscience.cdk.interfaces.IAtomContainer mol, String smarts, int width, int height, boolean atomnumbers)
BufferedImage	getImage(Object o)
BufferedImage	getImage(String smiles)
StringBuilder	getImageMap()
Dimension	getImageSize()
BufferedImage	getLegend(int width, int height)
org.openscience.cdk.smiles.SmilesParser	getParser()
void	paint(org.openscience.cdk.renderer.IRenderer renderer, org.openscience.cdk.interfaces.IAtomContainerSet molecules, boolean explicitH, Graphics2D g, IAtomContainerHighlights selector, boolean atomNumbers)
void	paint(org.openscience.cdk.renderer.IRenderer renderer, org.openscience.cdk.interfaces.IAtomContainerSet molecules, boolean explicitH, Graphics2D g, IAtomContainerHighlights selector, Dimension imageSize, boolean atomNumbers) TODO sort molecules, in order to display the largest part first
void	setBackground(Color background)
void	setBorderColor(Color borderColor) Creates gradient border of this color.
void	setBorderWidth(int borderWidth)
void	setDefaultImage(BufferedImage defaultImage)
void	setImageMap(StringBuilder imageMap)
void	setImageSize(Dimension imageSize)
void	setParser(org.openscience.cdk.smiles.SmilesParser parser)

Methods inherited from class java.lang.Object

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

Field Detail

logger

protected static Logger logger

imageMap

protected StringBuilder imageMap

comma

protected String comma

SELECTED_ATOM_COLOR

public static final String SELECTED_ATOM_COLOR

See Also:

Constant Field Values

SELECTED_ATOM_SIZE

public static final String SELECTED_ATOM_SIZE

See Also:

Constant Field Values

ATOM_ANNOTATION

public static final String ATOM_ANNOTATION

See Also:

Constant Field Values

whiteTransparent

public static final Color whiteTransparent

imageSize

protected Dimension imageSize

background

protected Color background

defaultImage

protected BufferedImage defaultImage

borderColor

protected Color borderColor

borderWidth

protected int borderWidth

parser

protected org.openscience.cdk.smiles.SmilesParser parser

Constructor Detail

CompoundImageTools

public CompoundImageTools()

CompoundImageTools

public CompoundImageTools(Dimension cellSize)

Method Detail

getImageMap

public StringBuilder getImageMap()

setImageMap

public void setImageMap(StringBuilder imageMap)

getBorderWidth

public int getBorderWidth()

setBorderWidth

public void setBorderWidth(int borderWidth)

getBorderColor

public Color getBorderColor()

Specified by:

getBorderColor in interface ICompoundImageTools

setBorderColor

public void setBorderColor(Color borderColor)

Creates gradient border of this color. Set the same as background color if you don't want shadowing effect.

Specified by:

setBorderColor in interface ICompoundImageTools

Parameters:

borderColor -

getParser

public org.openscience.cdk.smiles.SmilesParser getParser()

setParser

public void setParser(org.openscience.cdk.smiles.SmilesParser parser)

getImage

public BufferedImage getImage(Object o)

Specified by:

getImage in interface ICompoundImageTools

generateImage

public BufferedImage generateImage(String value)
                            throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

generateImage

public BufferedImage generateImage(String value,
                                   IAtomContainerHighlights selector,
                                   boolean build2d,
                                   boolean atomNumbers)
                            throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

generateImage

public BufferedImage generateImage(String value,
                                   IAtomContainerHighlights selector,
                                   boolean build2d,
                                   boolean atomNumbers,
                                   CompoundImageTools.Mode2D mode2D)
                            throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

getImage

public BufferedImage getImage(String smiles)

getImage

public BufferedImage getImage(org.openscience.cdk.interfaces.IAtomContainer molecule)

Specified by:

getImage in interface IStructureDiagramDepiction<BufferedImage>

Specified by:

getImage in interface ICompoundImageTools

getImage

public BufferedImage getImage(org.openscience.cdk.interfaces.IAtomContainer molecule,
                              IAtomContainerHighlights selector,
                              boolean build2d,
                              boolean atomNumbers)

getImage

public BufferedImage getImage(org.openscience.cdk.interfaces.IAtomContainer molecule,
                              IAtomContainerHighlights selector,
                              boolean build2d,
                              boolean atomNumbers,
                              boolean explicitH)

getImage

public BufferedImage getImage(org.openscience.cdk.interfaces.IAtomContainer molecule,
                              IAtomContainerHighlights selector,
                              boolean build2d,
                              boolean atomNumbers,
                              boolean explicitH,
                              CompoundImageTools.Mode2D mode2d)

createBuffer

protected BufferedImage createBuffer()

generate2D

public void generate2D(org.openscience.cdk.interfaces.IAtomContainer molecule,
                       boolean generateCoordinates,
                       org.openscience.cdk.interfaces.IAtomContainerSet molecules)

paint

public void paint(org.openscience.cdk.renderer.IRenderer renderer,
                  org.openscience.cdk.interfaces.IAtomContainerSet molecules,
                  boolean explicitH,
                  Graphics2D g,
                  IAtomContainerHighlights selector,
                  boolean atomNumbers)

paint

public void paint(org.openscience.cdk.renderer.IRenderer renderer,
                  org.openscience.cdk.interfaces.IAtomContainerSet molecules,
                  boolean explicitH,
                  Graphics2D g,
                  IAtomContainerHighlights selector,
                  Dimension imageSize,
                  boolean atomNumbers)

TODO sort molecules, in order to display the largest part first

Parameters:

renderer -

molecules -

explicitH -

g -

highlighted -

imageSize -

getImage

public BufferedImage getImage(ArrayList<?> list)

getBackground

public Color getBackground()

Specified by:

getBackground in interface ICompoundImageTools

setBackground

public void setBackground(Color background)

Specified by:

setBackground in interface ICompoundImageTools

getImageSize

public Dimension getImageSize()

Specified by:

getImageSize in interface IStructureDiagramDepiction<BufferedImage>

Specified by:

getImageSize in interface ICompoundImageTools

setImageSize

public void setImageSize(Dimension imageSize)

Specified by:

setImageSize in interface IStructureDiagramDepiction<BufferedImage>

Specified by:

setImageSize in interface ICompoundImageTools

getDefaultImage

public Image getDefaultImage()

Specified by:

getDefaultImage in interface ICompoundImageTools

setDefaultImage

public void setDefaultImage(BufferedImage defaultImage)

createDefaultImage

public BufferedImage createDefaultImage()

createDefaultImage

public BufferedImage createDefaultImage(String msg)

getImage

public BufferedImage getImage(org.openscience.cdk.interfaces.IAtomContainer mol,
                              String smarts,
                              int width,
                              int height,
                              boolean atomnumbers)
                       throws net.idea.modbcum.i.exceptions.AmbitException

Specified by:

getImage in interface IStructureDiagramDepiction<BufferedImage>

Throws:

net.idea.modbcum.i.exceptions.AmbitException

getLegend

public BufferedImage getLegend(int width,
                               int height)
                        throws net.idea.modbcum.i.exceptions.AmbitException

Specified by:

getLegend in interface IStructureDiagramDepiction<BufferedImage>

Throws:

net.idea.modbcum.i.exceptions.AmbitException