ambit2.core.io
Class CompoundImageTools

java.lang.Object
  ambit2.core.io.CompoundImageTools

public class CompoundImageTools
extends java.lang.Object

Generates BufferedImage from smiles or compound.

Field Summary

protected java.awt.Color	background
protected java.awt.Color	borderColor
protected int	borderWidth
protected java.awt.image.BufferedImage	defaultImage
protected java.awt.Dimension	imageSize
protected org.openscience.cdk.smiles.SmilesParser	parser

Constructor Summary

CompoundImageTools()

CompoundImageTools(java.awt.Dimension cellSize)

Method Summary

static void	generate2D(org.openscience.cdk.interfaces.IAtomContainer molecule, boolean generateCoordinates, org.openscience.cdk.interfaces.IMoleculeSet molecules)
java.awt.image.BufferedImage	generateImage(java.lang.String smiles)
java.awt.Color	getBackground()
java.awt.Color	getBorderColor()
int	getBorderWidth()
java.awt.Image	getDefaultImage()
java.awt.image.BufferedImage	getImage(java.util.ArrayList<?> list)
java.awt.image.BufferedImage	getImage(org.openscience.cdk.interfaces.IAtomContainer molecule)
java.awt.image.BufferedImage	getImage(org.openscience.cdk.interfaces.IAtomContainer molecule, org.openscience.cdk.interfaces.IAtomContainer highlighted)
java.awt.image.BufferedImage	getImage(org.openscience.cdk.interfaces.IAtomContainer molecule, org.openscience.cdk.interfaces.IAtomContainer highlighted, boolean build2d)
java.awt.image.BufferedImage	getImage(java.lang.Object o)
java.awt.image.BufferedImage	getImage(java.lang.String smiles)
java.awt.Dimension	getImageSize()
void	paint(org.openscience.cdk.renderer.Renderer2D renderer, org.openscience.cdk.interfaces.IMoleculeSet molecules, boolean explicitH, java.awt.Graphics2D g, org.openscience.cdk.interfaces.IAtomContainer highlighted)
static void	paint(org.openscience.cdk.renderer.Renderer2D renderer, org.openscience.cdk.interfaces.IMoleculeSet molecules, boolean explicitH, java.awt.Graphics2D g, org.openscience.cdk.interfaces.IAtomContainer highlighted, java.awt.Dimension imageSize) TODO sort molecules, in order to display the largest part first
protected static void	printCoordinates(org.openscience.cdk.renderer.Renderer2DModel model)
void	setBackground(java.awt.Color background)
void	setBorderColor(java.awt.Color borderColor) Creates gradient border of this color.
void	setBorderWidth(int borderWidth)
void	setDefaultImage(java.awt.image.BufferedImage defaultImage)
void	setImageSize(java.awt.Dimension imageSize)

Methods inherited from class java.lang.Object

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

Field Detail

imageSize

protected java.awt.Dimension imageSize

background

protected java.awt.Color background

defaultImage

protected java.awt.image.BufferedImage defaultImage

borderColor

protected java.awt.Color borderColor

borderWidth

protected int borderWidth

parser

protected org.openscience.cdk.smiles.SmilesParser parser

Constructor Detail

CompoundImageTools

public CompoundImageTools()

CompoundImageTools

public CompoundImageTools(java.awt.Dimension cellSize)

Method Detail

getBorderWidth

public int getBorderWidth()

setBorderWidth

public void setBorderWidth(int borderWidth)

getBorderColor

public java.awt.Color getBorderColor()

setBorderColor

public void setBorderColor(java.awt.Color borderColor)

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

Parameters:

borderColor -

getImage

public java.awt.image.BufferedImage getImage(java.lang.Object o)

generateImage

public java.awt.image.BufferedImage generateImage(java.lang.String smiles)
                                           throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

getImage

public java.awt.image.BufferedImage getImage(java.lang.String smiles)

getImage

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

getImage

public java.awt.image.BufferedImage getImage(org.openscience.cdk.interfaces.IAtomContainer molecule,
                                             org.openscience.cdk.interfaces.IAtomContainer highlighted)

getImage

public java.awt.image.BufferedImage getImage(org.openscience.cdk.interfaces.IAtomContainer molecule,
                                             org.openscience.cdk.interfaces.IAtomContainer highlighted,
                                             boolean build2d)

generate2D

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

paint

public void paint(org.openscience.cdk.renderer.Renderer2D renderer,
                  org.openscience.cdk.interfaces.IMoleculeSet molecules,
                  boolean explicitH,
                  java.awt.Graphics2D g,
                  org.openscience.cdk.interfaces.IAtomContainer highlighted)

paint

public static void paint(org.openscience.cdk.renderer.Renderer2D renderer,
                         org.openscience.cdk.interfaces.IMoleculeSet molecules,
                         boolean explicitH,
                         java.awt.Graphics2D g,
                         org.openscience.cdk.interfaces.IAtomContainer highlighted,
                         java.awt.Dimension imageSize)

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

Parameters:

renderer -

molecules -

explicitH -

g -

highlighted -

imageSize -

printCoordinates

protected static void printCoordinates(org.openscience.cdk.renderer.Renderer2DModel model)

getImage

public java.awt.image.BufferedImage getImage(java.util.ArrayList<?> list)

getBackground

public java.awt.Color getBackground()

setBackground

public void setBackground(java.awt.Color background)

getImageSize

public java.awt.Dimension getImageSize()

setImageSize

public void setImageSize(java.awt.Dimension imageSize)

getDefaultImage

public java.awt.Image getDefaultImage()

setDefaultImage

public void setDefaultImage(java.awt.image.BufferedImage defaultImage)