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
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 |
PairwiseAlignmentVisualizer
public PairwiseAlignmentVisualizer()
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)
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