maltcms.commands.fragments.visualization
Class PairwiseAlignmentVisualizer

java.lang.Object
  cross.commands.fragments.AFragmentCommand
      maltcms.commands.fragments.visualization.PairwiseAlignmentVisualizer

All Implemented Interfaces:

cross.commands.fragments.IFragmentCommand, cross.commands.ICommand<cross.datastructures.tuple.TupleND<cross.datastructures.fragments.IFileFragment>,cross.datastructures.tuple.TupleND<cross.datastructures.fragments.IFileFragment>>, cross.datastructures.workflow.IWorkflowElement, cross.event.IEventSource<cross.datastructures.workflow.IWorkflowResult>, cross.IConfigurable, cross.io.xml.IXMLSerializable, Serializable

public class PairwiseAlignmentVisualizer
extends cross.commands.fragments.AFragmentCommand

Plots a pairwise alignment, by displaying both time series' tics, connected by lines depicting the path obtained from alignment.

Author:

Nils.Hoffmann@cebitec.uni-bielefeld.de

See Also:

Serialized Form

Constructor Summary

PairwiseAlignmentVisualizer()

Method Summary

cross.datastructures.tuple.TupleND<cross.datastructures.fragments.IFileFragment>	apply(cross.datastructures.tuple.TupleND<cross.datastructures.fragments.IFileFragment> t)
void	configure(org.apache.commons.configuration.Configuration cfg)
BufferedImage	createMapImage(List<cross.datastructures.tuple.Tuple2DI> l, int upper_width, int lower_width, int height)
BufferedImage	createSuperimposedImage(List<cross.datastructures.tuple.Tuple2DI> l, Array lhs, Array rhs, int height)
Collection<org.jfree.chart.annotations.XYAnnotation>	getAnnotations(cross.datastructures.fragments.IFileFragment iff, Array domain, Array yVals)
String	getDescription()
JPanel	getJPanel()
cross.datastructures.workflow.WorkflowSlot	getWorkflowSlot()
void	makeComparativeTICChart(AChart<org.jfree.chart.plot.XYPlot> tc1, AChart<org.jfree.chart.plot.XYPlot> tc2, cross.datastructures.fragments.IFileFragment ref, cross.datastructures.fragments.IFileFragment query, String x_label, String y_label, Collection<org.jfree.chart.annotations.XYAnnotation> c1, Collection<org.jfree.chart.annotations.XYAnnotation> c2, double minY, double maxY)
void	makeDifferentialTICChart(List<cross.datastructures.tuple.Tuple2DI> map1, cross.datastructures.fragments.IFileFragment ref, cross.datastructures.fragments.IFileFragment query, Array lhs, Array rhs, Array lhs_domain, String x_label, String y_label, Collection<org.jfree.chart.annotations.XYAnnotation> c1, Collection<org.jfree.chart.annotations.XYAnnotation> c2)
void	makeMapChart(AChart<org.jfree.chart.plot.XYPlot> tc1, AChart<org.jfree.chart.plot.XYPlot> tc2, cross.datastructures.fragments.IFileFragment alignment, Array tc1Domain, Array tc2Domain, String x_label, cross.datastructures.fragments.IFileFragment filea1, cross.datastructures.fragments.IFileFragment fileb1, Collection<org.jfree.chart.annotations.XYAnnotation> c1, Collection<org.jfree.chart.annotations.XYAnnotation> c2)
void	makeRatioTICChart(List<cross.datastructures.tuple.Tuple2DI> map1, cross.datastructures.fragments.IFileFragment ref, cross.datastructures.fragments.IFileFragment query, Array lhs, Array rhs, Array lhs_domain, String x_label, String y_label, Collection<org.jfree.chart.annotations.XYAnnotation> c1, Collection<org.jfree.chart.annotations.XYAnnotation> c2)
void	makeSuperimposedChart(List<cross.datastructures.tuple.Tuple2DI> map1, cross.datastructures.fragments.IFileFragment ref, cross.datastructures.fragments.IFileFragment query, Array lhs, Array rhs, Array lhs_domain, String x_label, String y_label, Collection<org.jfree.chart.annotations.XYAnnotation> c1, Collection<org.jfree.chart.annotations.XYAnnotation> c2)
void	setFragments(cross.datastructures.fragments.IFileFragment filea1, cross.datastructures.fragments.IFileFragment fileb1, cross.datastructures.fragments.IFileFragment alignment)
void	setImages(BufferedImage a1im, BufferedImage b1im, BufferedImage map1)
String	toString()

Methods inherited from class cross.commands.fragments.AFragmentCommand

addListener, addWorkflowResult, addWorkflowResult, addWorkflowResult, addWorkflowResult, addWorkflowResults, addWorkflowResults, appendXML, canEqual, createBlockingCompletionService, createCompletionService, createNonBlockingCompletionService, createWorkFragment, createWorkFragments, equals, fireEvent, getProgress, getWorkflow, hashCode, initProgress, initSubCommand, mapToInput, postProcess, removeListener, setProgress, setWorkflow

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

PairwiseAlignmentVisualizer

public PairwiseAlignmentVisualizer()

Method Detail

toString

public String toString()

Overrides:

toString in class cross.commands.fragments.AFragmentCommand

apply

public cross.datastructures.tuple.TupleND<cross.datastructures.fragments.IFileFragment> apply(cross.datastructures.tuple.TupleND<cross.datastructures.fragments.IFileFragment> t)

configure

public void configure(org.apache.commons.configuration.Configuration cfg)

Specified by:

configure in interface cross.IConfigurable

Overrides:

configure in class cross.commands.fragments.AFragmentCommand

createMapImage

public BufferedImage createMapImage(List<cross.datastructures.tuple.Tuple2DI> l,
                                    int upper_width,
                                    int lower_width,
                                    int height)

createSuperimposedImage

public BufferedImage createSuperimposedImage(List<cross.datastructures.tuple.Tuple2DI> l,
                                             Array lhs,
                                             Array rhs,
                                             int height)

getAnnotations

public Collection<org.jfree.chart.annotations.XYAnnotation> getAnnotations(cross.datastructures.fragments.IFileFragment iff,
                                                                           Array domain,
                                                                           Array yVals)

getDescription

public String getDescription()

Specified by:

getDescription in class cross.commands.fragments.AFragmentCommand

getJPanel

public JPanel getJPanel()

getWorkflowSlot

public cross.datastructures.workflow.WorkflowSlot getWorkflowSlot()

makeComparativeTICChart

public void makeComparativeTICChart(AChart<org.jfree.chart.plot.XYPlot> tc1,
                                    AChart<org.jfree.chart.plot.XYPlot> tc2,
                                    cross.datastructures.fragments.IFileFragment ref,
                                    cross.datastructures.fragments.IFileFragment query,
                                    String x_label,
                                    String y_label,
                                    Collection<org.jfree.chart.annotations.XYAnnotation> c1,
                                    Collection<org.jfree.chart.annotations.XYAnnotation> c2,
                                    double minY,
                                    double maxY)

makeDifferentialTICChart

public void makeDifferentialTICChart(List<cross.datastructures.tuple.Tuple2DI> map1,
                                     cross.datastructures.fragments.IFileFragment ref,
                                     cross.datastructures.fragments.IFileFragment query,
                                     Array lhs,
                                     Array rhs,
                                     Array lhs_domain,
                                     String x_label,
                                     String y_label,
                                     Collection<org.jfree.chart.annotations.XYAnnotation> c1,
                                     Collection<org.jfree.chart.annotations.XYAnnotation> c2)

makeMapChart

public void makeMapChart(AChart<org.jfree.chart.plot.XYPlot> tc1,
                         AChart<org.jfree.chart.plot.XYPlot> tc2,
                         cross.datastructures.fragments.IFileFragment alignment,
                         Array tc1Domain,
                         Array tc2Domain,
                         String x_label,
                         cross.datastructures.fragments.IFileFragment filea1,
                         cross.datastructures.fragments.IFileFragment fileb1,
                         Collection<org.jfree.chart.annotations.XYAnnotation> c1,
                         Collection<org.jfree.chart.annotations.XYAnnotation> c2)

makeRatioTICChart

public void makeRatioTICChart(List<cross.datastructures.tuple.Tuple2DI> map1,
                              cross.datastructures.fragments.IFileFragment ref,
                              cross.datastructures.fragments.IFileFragment query,
                              Array lhs,
                              Array rhs,
                              Array lhs_domain,
                              String x_label,
                              String y_label,
                              Collection<org.jfree.chart.annotations.XYAnnotation> c1,
                              Collection<org.jfree.chart.annotations.XYAnnotation> c2)

makeSuperimposedChart

public void makeSuperimposedChart(List<cross.datastructures.tuple.Tuple2DI> map1,
                                  cross.datastructures.fragments.IFileFragment ref,
                                  cross.datastructures.fragments.IFileFragment query,
                                  Array lhs,
                                  Array rhs,
                                  Array lhs_domain,
                                  String x_label,
                                  String y_label,
                                  Collection<org.jfree.chart.annotations.XYAnnotation> c1,
                                  Collection<org.jfree.chart.annotations.XYAnnotation> c2)

setFragments

public void setFragments(cross.datastructures.fragments.IFileFragment filea1,
                         cross.datastructures.fragments.IFileFragment fileb1,
                         cross.datastructures.fragments.IFileFragment alignment)

setImages

public void setImages(BufferedImage a1im,
                      BufferedImage b1im,
                      BufferedImage map1)