org.jscience.chemistry.gui.extended.molecule
Class Renderer

java.lang.Object
  org.jscience.chemistry.gui.extended.molecule.Renderer

All Implemented Interfaces:

IRenderer

public class Renderer
extends java.lang.Object
implements IRenderer

An implementation of a JViewer's renderer interface for drawing and manipulating a Molecule.

See Also:

IRenderer

Field Summary

protected float	AB_DEV Aromatic bond separation
static int	ALL_ATOMS_ONE_COLOR DOCUMENT ME!
protected java.awt.Color	atombg Color of default atom background
protected java.awt.Font	atomFont Font to display atom labels
protected java.awt.Color	bondColor Default color to display bonds
static int	COLOR_BY_ATOM_TYPE Coloring scheme constants
protected int	colorScheme draw atom color according to which coloring scheme
protected float	DB_DEV Double bond separation
protected float	findRadius Upper bound of the distance (in pixel) between an atom (or bond) and the pick-location if the atom (or bond) is considered picked
protected java.awt.Color	highlightColor Color to display highlighted atoms
protected int	hTreatment Flag indicating how to handle the display of hydrogens
protected Molecule	mol molecule to be drawn
static int	PICK_ATOM_FIRST Indicate the atom is preferred picked object when an atom and a bond both lie close enough to a single-picking location
static int	PICK_ATOM_ONLY Indicate only atoms are pickable, bond picking is not interested
static int	PICK_BOND_FIRST Indicate the bond is preferred picked object when an atom and a bond both lie close enough to a single-picking location
static int	PICK_BOND_ONLY Indicate only bonds are pickable, atom picking is not interested
protected boolean	pickHiddenAtom Indicate whether hidden atoms are pickable
protected boolean	pickHiddenBond Indicate whether hidden atoms are pickable
int	pickPreference Indicate the picking preference is on atom, bond or distance
protected java.awt.Color	selectColor Color to display selected atoms
static int	SHORTEST_WIN Indicate distance is used to break the tie when an atom and a bond both lie close enough to a single-picking locaition
static int	SHOW_ALL_H Display all hydrogens
static int	SHOW_NO_H Don't display any hydrogens
static int	SHOW_NON_C_H Display hydrogens not attached to carbons
protected boolean	showAtomLabels Indicates whether atom labels should be displayed
protected float	TB_DEV Triple bond separation
protected float	WB_DEV Wedge bond separation

Constructor Summary

Renderer()
Default constructor

Renderer(Molecule mol)
Constructor

Renderer(Renderer r)
Copy constructor

Method Summary

java.lang.Object	copy() DOCUMENT ME!
void	draw(java.awt.Graphics g) Draw the Molecule.
protected void	drawAnyBond(java.awt.Graphics g, java.awt.Color c1, java.awt.Color c2, float x1, float y1, float x2, float y2) Draws an any bond
protected void	drawAromaticBond(java.awt.Graphics g, java.awt.Color c1, java.awt.Color c2, float x1, float y1, float x2, float y2) Draws an aromatic bond
void	drawAtom(java.awt.Graphics g, Atom a) Draws an atom.
void	drawBond(java.awt.Graphics g, Bond b) Draws a bond
protected void	drawDashBond(java.awt.Graphics g, float x1, float y1, float x2, float y2) Draws a dashed wedge bond (assumes black & white)
protected void	drawSingleBond(java.awt.Graphics g, java.awt.Color c1, java.awt.Color c2, float x1, float y1, float x2, float y2) Draws a single bond
protected void	drawWedgeBond(java.awt.Graphics g, float x1, float y1, float x2, float y2) Draws a wedge bond
Atom	findAtom(float tx, float ty)
void	findAtoms(java.awt.Polygon pickPolygon, java.util.Vector resultVector) Find a list of atoms within the given polygon
Bond	findBond(float tx, float ty)
void	findBonds(java.awt.Polygon pickPolygon, java.util.Vector resultVector) Find a list of bonds within the given polygon
java.lang.Object	findObject(float tx, float ty) Find an object given location
java.util.Vector	findObjects(java.awt.Polygon pickPolygon) Return a list of objects that are within the given polygon
float	getAB_DEV() Return aromatic bond separation
java.awt.Color	getAtombg() Return atom background color
java.awt.Font	getAtomFont() Return atom font
float[]	getBBox() Return the bounding box of the Molecule.
java.awt.Color	getBondColor() Return bond color
boolean	getColorByAtomType() Return flag that indicates whether to paint the atom according to its type
int	getColorScheme() Return color scheme
float	getDB_DEV() Return double bond separation
java.awt.Color	getHighlightColor() Return color to paint hightlighted atoms
int	getHTreatment() Return hydrogen treatment
Molecule	getMol() Return the molecule.
boolean	getPickHiddenAtom()
boolean	getPickHiddenBond()
java.awt.Color	getSelectColor() Return color to paint selected atoms
boolean	getShowAtomLabels() Return flag that indicates whether atom labels should display
float	getTB_DEV() Return triple bond separation
float	getWB_DEV() Return wedge bond separation
boolean	isHidden(Atom atom)
void	matMult(Matrix3D rhs) Multiply the Molecule's transformation matrix by the matrix specified.
void	matScale(float xf, float yf, float zf) Apply the specified scale to the Molecule's transformation matrix.
void	matTransform() Apply the Molecule's transformation matrix to its atoms.
void	matTranslate(float xt, float yt, float zt) Apply the specified translation to the Molecule's transformation matrix.
void	matUnit() Reset the Molecule's transformation matrix to the identity matrix.
void	setAB_DEV(float abDev) Set aromatic bond separation
void	setAtombg(java.awt.Color color) Set atom background color
void	setAtomFont(java.awt.Font font) Set atom font
void	setBondColor(java.awt.Color color) Set bond color
void	setColorByAtomType(boolean bool) Set flag to indicate whether to paint the atom according to its type As data member colorByAtomType, this method is redundent, but is kept to be compatible with pre-existing code
void	setColorScheme(int colorScheme) Set color scheme
void	setDB_DEV(float dbDev) Set double bond separation
void	setFindRadius(float findRadius) Set the findRadius
void	setHighlightColor(java.awt.Color color) Set color to paint hightlighted atoms
void	setHTreatment(int hTreatment) Set hydrogen treatment
void	setMol(Molecule mol) Set the molecule
void	setPickHiddenAtom(boolean pickHiddenAtom) Set the policy whether hidden atoms are pickable
void	setPickHiddenBond(boolean pickHiddenBond) Set the policy whether hidden bonds are pickable
void	setPickPreference(int pickPreference) Set the pickPreference policy
void	setSelectColor(java.awt.Color color) Set color to paint selected atoms
void	setShowAtomLabels(boolean bool) Set flag to indicate whether atom labels should display or not
void	setTB_DEV(float tbDev) Set triple bond separation
void	setWB_DEV(float wbDev) Set wedge bond separation

Methods inherited from class java.lang.Object

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

Field Detail

SHOW_ALL_H

public static final int SHOW_ALL_H

Display all hydrogens

See Also:

Constant Field Values

SHOW_NO_H

public static final int SHOW_NO_H

Don't display any hydrogens

See Also:

Constant Field Values

SHOW_NON_C_H

public static final int SHOW_NON_C_H

Display hydrogens not attached to carbons

See Also:

Constant Field Values

COLOR_BY_ATOM_TYPE

public static final int COLOR_BY_ATOM_TYPE

Coloring scheme constants

See Also:

Constant Field Values

ALL_ATOMS_ONE_COLOR

public static final int ALL_ATOMS_ONE_COLOR

DOCUMENT ME!

See Also:

Constant Field Values

PICK_ATOM_FIRST

public static final int PICK_ATOM_FIRST

Indicate the atom is preferred picked object when an atom and a bond both lie close enough to a single-picking location

See Also:

Constant Field Values

PICK_BOND_FIRST

public static final int PICK_BOND_FIRST

Indicate the bond is preferred picked object when an atom and a bond both lie close enough to a single-picking location

See Also:

Constant Field Values

SHORTEST_WIN

public static final int SHORTEST_WIN

Indicate distance is used to break the tie when an atom and a bond both lie close enough to a single-picking locaition

See Also:

Constant Field Values

PICK_ATOM_ONLY

public static final int PICK_ATOM_ONLY

Indicate only atoms are pickable, bond picking is not interested

See Also:

Constant Field Values

PICK_BOND_ONLY

public static final int PICK_BOND_ONLY

Indicate only bonds are pickable, atom picking is not interested

See Also:

Constant Field Values

mol

protected Molecule mol

molecule to be drawn

hTreatment

protected int hTreatment

Flag indicating how to handle the display of hydrogens

DB_DEV

protected float DB_DEV

Double bond separation

TB_DEV

protected float TB_DEV

Triple bond separation

AB_DEV

protected float AB_DEV

Aromatic bond separation

WB_DEV

protected float WB_DEV

Wedge bond separation

atomFont

protected java.awt.Font atomFont

Font to display atom labels

bondColor

protected java.awt.Color bondColor

Default color to display bonds

showAtomLabels

protected boolean showAtomLabels

Indicates whether atom labels should be displayed

colorScheme

protected int colorScheme

draw atom color according to which coloring scheme

selectColor

protected java.awt.Color selectColor

Color to display selected atoms

highlightColor

protected java.awt.Color highlightColor

Color to display highlighted atoms

atombg

protected java.awt.Color atombg

Color of default atom background

findRadius

protected float findRadius

Upper bound of the distance (in pixel) between an atom (or bond) and the pick-location if the atom (or bond) is considered picked

pickHiddenAtom

protected boolean pickHiddenAtom

Indicate whether hidden atoms are pickable

pickHiddenBond

protected boolean pickHiddenBond

Indicate whether hidden atoms are pickable

pickPreference

public int pickPreference

Indicate the picking preference is on atom, bond or distance

Constructor Detail

Renderer

public Renderer()

Default constructor

Renderer

public Renderer(Molecule mol)

Constructor

Parameters:

mol - the Molecule drawn and manipulated by this renderer.

Renderer

public Renderer(Renderer r)

Copy constructor

Parameters:

r - Renderer

Method Detail

getMol

public Molecule getMol()

Return the molecule.

setMol

public void setMol(Molecule mol)

Set the molecule

Parameters:

mol - Molecule

getBBox

public float[] getBBox()

Return the bounding box of the Molecule.

Specified by:

getBBox in interface IRenderer

Returns:

Array of 6 floats in order of xmin, xmax, ymin, ymax, zmin, zmax

matUnit

public void matUnit()

Reset the Molecule's transformation matrix to the identity matrix.

Specified by:

matUnit in interface IRenderer

matTranslate

public void matTranslate(float xt,
                         float yt,
                         float zt)

Apply the specified translation to the Molecule's transformation matrix.

Specified by:

matTranslate in interface IRenderer

Parameters:

xt - x component of translation

yt - y component of translation

zt - z component of translation

matScale

public void matScale(float xf,
                     float yf,
                     float zf)

Apply the specified scale to the Molecule's transformation matrix.

Specified by:

matScale in interface IRenderer

Parameters:

xf - x scale factor

yf - y scale factor

zf - z scale factor

matMult

public void matMult(Matrix3D rhs)

Multiply the Molecule's transformation matrix by the matrix specified.

Specified by:

matMult in interface IRenderer

Parameters:

rhs - matrix to be multiplied to Molecule's matrix: M = M * rhs

matTransform

public void matTransform()

Apply the Molecule's transformation matrix to its atoms.

Specified by:

matTransform in interface IRenderer

drawAtom

public void drawAtom(java.awt.Graphics g,
                     Atom a)

Draws an atom. Draws a filled circle, the atom name, then atom charge.

Parameters:

a - atom

g - graphics context

See Also:

draw(java.awt.Graphics)

drawBond

public void drawBond(java.awt.Graphics g,
                     Bond b)

Draws a bond

Parameters:

b - bond

g - graphics context

See Also:

draw(java.awt.Graphics), drawSingleBond(java.awt.Graphics, java.awt.Color, java.awt.Color, float, float, float, float), drawAromaticBond(java.awt.Graphics, java.awt.Color, java.awt.Color, float, float, float, float), drawWedgeBond(java.awt.Graphics, float, float, float, float), drawDashBond(java.awt.Graphics, float, float, float, float), drawAnyBond(java.awt.Graphics, java.awt.Color, java.awt.Color, float, float, float, float)

drawSingleBond

protected void drawSingleBond(java.awt.Graphics g,
                              java.awt.Color c1,
                              java.awt.Color c2,
                              float x1,
                              float y1,
                              float x2,
                              float y2)

Draws a single bond

Parameters:

g - graphics context

c1 - color of the first half of the bond

c2 - color of the second half of the bond

x1 - x coord of from atom

y1 - y coord of from atom

x2 - x coord of to atom

y2 - y coord of to atom

See Also:

drawBond(java.awt.Graphics, org.jscience.chemistry.gui.extended.molecule.Bond)

drawAromaticBond

protected void drawAromaticBond(java.awt.Graphics g,
                                java.awt.Color c1,
                                java.awt.Color c2,
                                float x1,
                                float y1,
                                float x2,
                                float y2)

Draws an aromatic bond

Parameters:

g - graphics context

c1 - color of the first half of the bond

c2 - color of the second half of the bond

x1 - x coord of from atom

y1 - y coord of from atom

x2 - x coord of to atom

y2 - y coord of to atom

See Also:

drawBond(java.awt.Graphics, org.jscience.chemistry.gui.extended.molecule.Bond)

drawWedgeBond

protected void drawWedgeBond(java.awt.Graphics g,
                             float x1,
                             float y1,
                             float x2,
                             float y2)

Draws a wedge bond

See Also:

drawBond(java.awt.Graphics, org.jscience.chemistry.gui.extended.molecule.Bond)

drawDashBond

protected void drawDashBond(java.awt.Graphics g,
                            float x1,
                            float y1,
                            float x2,
                            float y2)

Draws a dashed wedge bond (assumes black & white)

See Also:

drawBond(java.awt.Graphics, org.jscience.chemistry.gui.extended.molecule.Bond)

drawAnyBond

protected void drawAnyBond(java.awt.Graphics g,
                           java.awt.Color c1,
                           java.awt.Color c2,
                           float x1,
                           float y1,
                           float x2,
                           float y2)

Draws an any bond

Parameters:

g - graphics context

c1 - color of the first half of the bond

c2 - color of the second half of the bond

x1 - x coord of from atom

y1 - y coord of from atom

x2 - x coord of to atom

y2 - y coord of to atom

See Also:

drawBond(java.awt.Graphics, org.jscience.chemistry.gui.extended.molecule.Bond)

draw

public void draw(java.awt.Graphics g)

Draw the Molecule.

Specified by:

draw in interface IRenderer

Parameters:

g - the graphics context.

findObject

public java.lang.Object findObject(float tx,
                                   float ty)

Description copied from interface: IRenderer

Find an object given location

Specified by:

findObject in interface IRenderer

Parameters:

tx - transformed x coordinate

ty - transformed y coordinate

Returns:

an rendered object closest to the input transformed (tx, ty) coordinate within this renderer, with consideration to pickPreference.

See Also:

pickPreference

findAtom

public Atom findAtom(float tx,
                     float ty)

Parameters:

tx - transformed x coordinate

ty - transformed y coordinate

Returns:

a rendered atom closest to the input transformed (tx, ty) coordinate

findBond

public Bond findBond(float tx,
                     float ty)

Parameters:

tx - transformed x coordinate

ty - transformed y coordinate

Returns:

a rendered bond closest to the input transformed (tx, ty) coordinate

findObjects

public java.util.Vector findObjects(java.awt.Polygon pickPolygon)

Return a list of objects that are within the given polygon

Specified by:

findObjects in interface IRenderer

Parameters:

pickPolygon - the polygon within which objects are considered picked

Returns:

DOCUMENT ME!

findAtoms

public void findAtoms(java.awt.Polygon pickPolygon,
                      java.util.Vector resultVector)

Find a list of atoms within the given polygon

Parameters:

pickPolygon - the polygon with which atoms are considerred picked

resultVector - vector into which the found atoms are put

findBonds

public void findBonds(java.awt.Polygon pickPolygon,
                      java.util.Vector resultVector)

Find a list of bonds within the given polygon

Parameters:

pickPolygon - the polygon with which bonds are considerred picked

resultVector - vector into which the found bonds are put

isHidden

public boolean isHidden(Atom atom)

Parameters:

atom - the atom to be check whether it is hidden

Returns:

true iff an atom is hidden

getHTreatment

public int getHTreatment()

Return hydrogen treatment

getDB_DEV

public float getDB_DEV()

Return double bond separation

getTB_DEV

public float getTB_DEV()

Return triple bond separation

getAB_DEV

public float getAB_DEV()

Return aromatic bond separation

getWB_DEV

public float getWB_DEV()

Return wedge bond separation

getAtomFont

public java.awt.Font getAtomFont()

Return atom font

getBondColor

public java.awt.Color getBondColor()

Return bond color

getShowAtomLabels

public boolean getShowAtomLabels()

Return flag that indicates whether atom labels should display

getColorByAtomType

public boolean getColorByAtomType()

Return flag that indicates whether to paint the atom according to its type

getColorScheme

public int getColorScheme()

Return color scheme

getSelectColor

public java.awt.Color getSelectColor()

Return color to paint selected atoms

getHighlightColor

public java.awt.Color getHighlightColor()

Return color to paint hightlighted atoms

getAtombg

public java.awt.Color getAtombg()

Return atom background color

getPickHiddenAtom

public boolean getPickHiddenAtom()

Returns:

the policy (in boolean) whether hidden atoms are pickable

getPickHiddenBond

public boolean getPickHiddenBond()

Returns:

the policy (in boolean) whether hidden bonds are pickable

setHTreatment

public void setHTreatment(int hTreatment)

Set hydrogen treatment

Parameters:

hTreatment - int one of ( SHOW_ALL_H, SHOW_NO_H, SHOW_NON_C_H )

setDB_DEV

public void setDB_DEV(float dbDev)

Set double bond separation

Parameters:

dbDev - float

setTB_DEV

public void setTB_DEV(float tbDev)

Set triple bond separation

Parameters:

tbDev - float

setAB_DEV

public void setAB_DEV(float abDev)

Set aromatic bond separation

Parameters:

abDev - float

setWB_DEV

public void setWB_DEV(float wbDev)

Set wedge bond separation

Parameters:

wbDev - float

setAtomFont

public void setAtomFont(java.awt.Font font)

Set atom font

Parameters:

font - Font to paint atom label

setBondColor

public void setBondColor(java.awt.Color color)

Set bond color

Parameters:

color - Color to draw bond

setShowAtomLabels

public void setShowAtomLabels(boolean bool)

Set flag to indicate whether atom labels should display or not

Parameters:

bool - boolean

setColorByAtomType

public void setColorByAtomType(boolean bool)

Set flag to indicate whether to paint the atom according to its type As data member colorByAtomType, this method is redundent, but is kept to be compatible with pre-existing code

Parameters:

bool - boolean

setColorScheme

public void setColorScheme(int colorScheme)

Set color scheme

Parameters:

colorScheme - int

setSelectColor

public void setSelectColor(java.awt.Color color)

Set color to paint selected atoms

Parameters:

color - Color

setHighlightColor

public void setHighlightColor(java.awt.Color color)

Set color to paint hightlighted atoms

Parameters:

color - Color

setAtombg

public void setAtombg(java.awt.Color color)

Set atom background color

Parameters:

color - Color

setPickHiddenAtom

public void setPickHiddenAtom(boolean pickHiddenAtom)

Set the policy whether hidden atoms are pickable

Parameters:

pickHiddenAtom - the policy whether hidden atoms are pickable

setPickHiddenBond

public void setPickHiddenBond(boolean pickHiddenBond)

Set the policy whether hidden bonds are pickable

Parameters:

pickHiddenBond - the policy whether hidden bonds are pickable

setFindRadius

public void setFindRadius(float findRadius)

Set the findRadius

Parameters:

findRadius - the upper bound of distance between a mouse click location and the atom (or bond) when the atom (or bond) is a candidate of the picked object.

setPickPreference

public void setPickPreference(int pickPreference)

Set the pickPreference policy

Parameters:

pickPreference - one of the picking policies among ATOM_FIRST, BOND_FIRST, SHORTEST_WIN, ATOM_ONLY and BOND_ONLY

copy

public java.lang.Object copy()

DOCUMENT ME!

Specified by:

copy in interface IRenderer

Returns:

DOCUMENT ME!