info.bioinfweb.libralign.alignmentarea.tokenpainter

Class AbstractBioPolymerTokenPainter

java.lang.Object

info.bioinfweb.libralign.alignmentarea.tokenpainter.AbstractTokenPainter

info.bioinfweb.libralign.alignmentarea.tokenpainter.SingleColorTokenPainter

info.bioinfweb.libralign.alignmentarea.tokenpainter.AbstractBioPolymerTokenPainter

All Implemented Interfaces:

TokenPainter

Direct Known Subclasses:

AminoAcidTokenPainter, NucleotideTokenPainter

public abstract class AbstractBioPolymerTokenPainter
extends SingleColorTokenPainter

Implements shared functionality for painting nucleotide and amino acid tokens including their ambiguity codes.

Since:

0.4.0

Author:

Ben Stöver

Field Summary

Fields inherited from class info.bioinfweb.libralign.alignmentarea.tokenpainter.SingleColorTokenPainter

DEFAULT_HEIGHT, DEFAULT_WIDTH, FONT_SIZE_FACTOR, MIN_FONT_SIZE

Constructor Summary

Constructors

Constructor and Description
AbstractBioPolymerTokenPainter()

Method Summary

Modifier and Type	Method and Description
protected abstract char[]	calculateConstituents(java.lang.String tokenRepresentation) To be implemented by inherited classes to determine the non-ambiguous tokens that could be represented by the specified ambiguity code.
protected void	doPaintToken(AlignmentArea alignmentArea, java.lang.String sequenceID, int columnIndex, java.lang.Object token, java.lang.String tokenRepresentation, java.awt.Graphics2D g, java.awt.geom.Rectangle2D paintArea, java.awt.Color selectionColor) Method to be implemented by inherited classes performing the actual paint operation.
protected abstract boolean	isAmbiguity(java.lang.String tokenRepresentation) To be implemented by inherited classes to determine whether the specified token representation is an ambiguity code.

Methods inherited from class info.bioinfweb.libralign.alignmentarea.tokenpainter.SingleColorTokenPainter

backgroundColorByRepresentation, calculateFont, calculatePreferredWidth, equals, getBackgroundColorMap, getColor, getDefaultBackgroundColor, getFontColor, getFontName, getFontStyle, getPreferredHeight, getPreferredWidth, hashCode, paintText, setDefaultBackgroundColor, setFontColor, setFontName, setFontStyle

Methods inherited from class info.bioinfweb.libralign.alignmentarea.tokenpainter.AbstractTokenPainter

paintToken

Methods inherited from class java.lang.Object

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

Methods inherited from interface info.bioinfweb.libralign.alignmentarea.tokenpainter.TokenPainter

paintToken

Constructor Detail

AbstractBioPolymerTokenPainter

public AbstractBioPolymerTokenPainter()

Method Detail

isAmbiguity

protected abstract boolean isAmbiguity(java.lang.String tokenRepresentation)

To be implemented by inherited classes to determine whether the specified token representation is an ambiguity code.

Parameters:

tokenRepresentation - the token representation

Returns:

true if the token is ambiguous and shall have a background with multiple colors, false otherwise

calculateConstituents

protected abstract char[] calculateConstituents(java.lang.String tokenRepresentation)

To be implemented by inherited classes to determine the non-ambiguous tokens that could be represented by the specified ambiguity code.

Parameters:

tokenRepresentation - the ambiguous token representation

Returns:

an array with according token representations

doPaintToken

protected void doPaintToken(AlignmentArea alignmentArea,
                            java.lang.String sequenceID,
                            int columnIndex,
                            java.lang.Object token,
                            java.lang.String tokenRepresentation,
                            java.awt.Graphics2D g,
                            java.awt.geom.Rectangle2D paintArea,
                            java.awt.Color selectionColor)

Description copied from class: AbstractTokenPainter

Method to be implemented by inherited classes performing the actual paint operation. It extends the paint method specified in TokenPainter by an additional parameter providing the string representation of the token. - * @param alignmentArea the alignment area displaying the token to be painted

Overrides:

doPaintToken in class SingleColorTokenPainter

sequenceID - the ID of the sequence containing the token to be painted

columnIndex - the index of the alignment column containing the token to be painted

token - the token to be painted

tokenRepresentation - the string representation of token determined from the token set of alignmentModel

g - the graphics context to paint to

paintArea - the rectangle to be filled with the representation of the token

selectionColor - this color must be mixed by half with the painted output if it is not null