de.jstacs.utils

Class SeqLogoPlotter.SeqLogoPlotGenerator

java.lang.Object

de.jstacs.utils.SeqLogoPlotter.SeqLogoPlotGenerator

All Implemented Interfaces:

PlotGeneratorResult.PlotGenerator, Storable

Enclosing class:

SeqLogoPlotter

public static class SeqLogoPlotter.SeqLogoPlotGenerator
extends Object
implements PlotGeneratorResult.PlotGenerator

PlotGeneratorResult.PlotGenerator for plotting sequence logos.

Author:

Jan Grau

Constructor Summary

Constructors

Constructor and Description
SeqLogoPlotter.SeqLogoPlotGenerator(double[][] pwm, int height) Creates a new SeqLogoPlotter.SeqLogoPlotGenerator for the given PWM using the specified height of the plot.
SeqLogoPlotter.SeqLogoPlotGenerator(StringBuffer xml) Creates a SeqLogoPlotter.SeqLogoPlotGenerator from its XML representation.

Method Summary

Methods

Modifier and Type	Method and Description
void	generatePlot(GraphicsAdaptor ga) Generates the plot using the Graphics2D device of the supplied GraphicsAdaptor.
StringBuffer	toXML() This method returns an XML representation as StringBuffer of an instance of the implementing class.

Methods inherited from class java.lang.Object

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

Constructor Detail

SeqLogoPlotter.SeqLogoPlotGenerator

public SeqLogoPlotter.SeqLogoPlotGenerator(double[][] pwm,
                                   int height)

Creates a new SeqLogoPlotter.SeqLogoPlotGenerator for the given PWM using the specified height of the plot. The corresponding width is computed automatically using the SeqLogoPlotter.getWidth(int, double[][]) method.

Parameters:

pwm - the PWM

height - the height of the plot

SeqLogoPlotter.SeqLogoPlotGenerator

public SeqLogoPlotter.SeqLogoPlotGenerator(StringBuffer xml)
                                    throws NonParsableException

Creates a SeqLogoPlotter.SeqLogoPlotGenerator from its XML representation.

Parameters:

xml - the XML representation

Throws:

NonParsableException - if XML could not be parsed

Method Detail

toXML

public StringBuffer toXML()

Description copied from interface: Storable

This method returns an XML representation as StringBuffer of an instance of the implementing class.

Specified by:

toXML in interface Storable

Returns:

the XML representation

generatePlot

public void generatePlot(GraphicsAdaptor ga)
                  throws Exception

Description copied from interface: PlotGeneratorResult.PlotGenerator

Generates the plot using the Graphics2D device of the supplied GraphicsAdaptor.

Specified by:

generatePlot in interface PlotGeneratorResult.PlotGenerator

Parameters:

ga - the graphics adaptor

Throws:

Exception - if the plot could not be generated