edu.mssm.crover.domain2d
Class UniqueResidueModelFactory

java.lang.Object
  |
  +--edu.mssm.crover.domain2d.UniqueResidueModelFactory

All Implemented Interfaces:

ResidueGlyphRenderingAttributes, ResidueModelFactory

public class UniqueResidueModelFactory

extends java.lang.Object

implements ResidueModelFactory, ResidueGlyphRenderingAttributes

The simplest implantation of ResidueModelFactory. Simply creates a new instance of a ResidueModel each time createResidueModel() is invoked.

See Also:

SharedResidueModelFactory

Field Summary

ResidueColorScheme	colorscheme
protected boolean	outline
protected int	shape

Constructor Summary

UniqueResidueModelFactory()

Method Summary

ResidueModel	createResidueModel(java.lang.Object sequence, java.lang.Object ResidueNumber, char label) Create a residue model.
java.awt.Color	getBackgroundColor(char label, int position) Returns the background color for a given residue.
ResidueColorScheme	getColorScheme() Gets the current color scheme.
boolean	getDefaultResidueGlyphOutline() Get the suggested default outline attribute.
int	getDefaultResidueShape() Get the shape of residues that are not hyperlinked.
java.awt.Color	getForegroundColor(char label, int position) Returns the foreground color for a given residue.
int	getLinkedResidueShape() Get the shape of residues that are hyperlinked.
int	getModelCount() Returns the number of models this factory built.
java.util.Enumeration	getModels() Returns the model built by this factory.
java.lang.String	getNumbering(java.lang.Object numbering) Returns a string that represent the residue number as an integer.
void	parseAnnotations(BiologicalAnnotations annotations) Parse sequence annotations.
void	release(ResidueModel model) Release the model.
void	setColorScheme(ResidueColorScheme rcs) Sets the color scheme.
void	setDefaultResidueGlyphOutline(boolean outline) Sets the outline attribute for future instances of ResidueGlyph.
void	setDefaultResidueShape(int shape) Sets the shape of linked residues.
void	setLinkedResidueShape(int shape) Sets the shape of linked residues.

Methods inherited from class java.lang.Object

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

Field Detail

colorscheme

public ResidueColorScheme colorscheme

shape

protected int shape

outline

protected boolean outline

Constructor Detail

UniqueResidueModelFactory

public UniqueResidueModelFactory()

Method Detail

setColorScheme

public void setColorScheme(ResidueColorScheme rcs)

Sets the color scheme. The color scheme determines the association of the color with each residue of the sequence.

Specified by:

setColorScheme in interface ResidueModelFactory

See Also:

ResidueModelFactory.getForegroundColor(char, int), ResidueModelFactory.getBackgroundColor(char, int)

getColorScheme

public ResidueColorScheme getColorScheme()

Gets the current color scheme.

createResidueModel

public ResidueModel createResidueModel(java.lang.Object sequence,
                                       java.lang.Object ResidueNumber,
                                       char label)

Description copied from interface: ResidueModelFactory

Create a residue model. This method is overloaded by the implementation.

Specified by:

createResidueModel in interface ResidueModelFactory

getBackgroundColor

public java.awt.Color getBackgroundColor(char label,
                                         int position)

Description copied from interface: ResidueModelFactory

Returns the background color for a given residue. This operation is usually delegated to a ResidueColorScheme implementation.

Specified by:

getBackgroundColor in interface ResidueModelFactory

See Also:

ResidueColorScheme

getForegroundColor

public java.awt.Color getForegroundColor(char label,
                                         int position)

Description copied from interface: ResidueModelFactory

Returns the foreground color for a given residue. This operation is usually delegated to a ResidueColorScheme implementation.

Specified by:

getForegroundColor in interface ResidueModelFactory

See Also:

ResidueColorScheme

getModels

public java.util.Enumeration getModels()

Description copied from interface: ResidueModelFactory

Returns the model built by this factory.

Specified by:

getModels in interface ResidueModelFactory

getModelCount

public int getModelCount()

Description copied from interface: ResidueModelFactory

Returns the number of models this factory built.

Specified by:

getModelCount in interface ResidueModelFactory

setDefaultResidueGlyphOutline

public void setDefaultResidueGlyphOutline(boolean outline)

Description copied from interface: ResidueGlyphRenderingAttributes

Sets the outline attribute for future instances of ResidueGlyph.

Specified by:

setDefaultResidueGlyphOutline in interface ResidueGlyphRenderingAttributes

Parameters:

outline - an outline display is suggested when true.

See Also:

for usage.

getDefaultResidueGlyphOutline

public boolean getDefaultResidueGlyphOutline()

Description copied from interface: ResidueGlyphRenderingAttributes

Get the suggested default outline attribute.

Specified by:

getDefaultResidueGlyphOutline in interface ResidueGlyphRenderingAttributes

release

public void release(ResidueModel model)

Description copied from interface: ResidueModelFactory

Release the model. In order to be garbage collected, a model must be released from the factory that created it.

Specified by:

release in interface ResidueModelFactory

getNumbering

public java.lang.String getNumbering(java.lang.Object numbering)

Returns a string that represent the residue number as an integer. The number starts at 1 for the first residue of a sequence.

Specified by:

getNumbering in interface ResidueModelFactory

parseAnnotations

public void parseAnnotations(BiologicalAnnotations annotations)

Parse sequence annotations. Now, extracts residues which are hyperlinked and set the linked state in the corresponding model.

Specified by:

parseAnnotations in interface ResidueModelFactory

setLinkedResidueShape

public void setLinkedResidueShape(int shape)

Description copied from interface: ResidueGlyphRenderingAttributes

Sets the shape of linked residues. Hyperlinked residues will have this shape by default. * When not set, linked residues have the same shape that non linked residues. Invalid shapes are silently ignored. * @param Type of the shape, as defined in ResidueGlyph

Specified by:

setLinkedResidueShape in interface ResidueGlyphRenderingAttributes

See Also:

ResidueGlyph.CIRCLE_SHAPE, edu.mssm.crover.domain2d.ResidueGlyph#RECTANGULAR_SHAPE, *

setDefaultResidueShape

public void setDefaultResidueShape(int shape)

Description copied from interface: ResidueGlyphRenderingAttributes

Sets the shape of linked residues. Residues will have this shape by default, unless hyperlinked. When not set, the shape of residues defaults to circles. Invalid shapes are silently ignored.

Specified by:

setDefaultResidueShape in interface ResidueGlyphRenderingAttributes

See Also:

ResidueGlyph.CIRCLE_SHAPE, edu.mssm.crover.domain2d.ResidueGlyph#RECTANGULAR_SHAPE, ResidueGlyph.OCTAGONAL_SHAPE

getLinkedResidueShape

public int getLinkedResidueShape()

Description copied from interface: ResidueGlyphRenderingAttributes

Get the shape of residues that are hyperlinked.

Specified by:

getLinkedResidueShape in interface ResidueGlyphRenderingAttributes

Returns:

Shape of the residues.

See Also:

for shape definitions.

getDefaultResidueShape

public int getDefaultResidueShape()

Description copied from interface: ResidueGlyphRenderingAttributes

Get the shape of residues that are not hyperlinked.

Specified by:

getDefaultResidueShape in interface ResidueGlyphRenderingAttributes