info.bioinfweb.libralign.alignmentarea.tokenpainter

Class NucleotideTokenPainter

java.lang.Object

info.bioinfweb.libralign.alignmentarea.tokenpainter.AbstractTokenPainter

info.bioinfweb.libralign.alignmentarea.tokenpainter.SingleColorTokenPainter

info.bioinfweb.libralign.alignmentarea.tokenpainter.AbstractBioPolymerTokenPainter

info.bioinfweb.libralign.alignmentarea.tokenpainter.NucleotideTokenPainter

All Implemented Interfaces:

TokenPainter

public class NucleotideTokenPainter
extends AbstractBioPolymerTokenPainter

Token painter that paints nucleotides.

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
NucleotideTokenPainter() Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
protected 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 boolean	isAmbiguity(java.lang.String tokenRepresentation) To be implemented by inherited classes to determine whether the specified token representation is an ambiguity code.
static void	putNucleotideColors(java.util.Map<java.lang.String,java.awt.Color> map)

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

doPaintToken

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

NucleotideTokenPainter

public NucleotideTokenPainter()

Creates a new instance of this class.

Method Detail

putNucleotideColors

public static void putNucleotideColors(java.util.Map<java.lang.String,java.awt.Color> map)

isAmbiguity

protected boolean isAmbiguity(java.lang.String tokenRepresentation)

Description copied from class: AbstractBioPolymerTokenPainter

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

Specified by:

isAmbiguity in class AbstractBioPolymerTokenPainter

Parameters:

tokenRepresentation - the token representation

Returns:

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

calculateConstituents

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

Description copied from class: AbstractBioPolymerTokenPainter

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

Specified by:

calculateConstituents in class AbstractBioPolymerTokenPainter

Parameters:

tokenRepresentation - the ambiguous token representation

Returns:

an array with according token representations