eu.isas.peptideshaker.gui.protein_sequence

Class ProteinSequencePanel

java.lang.Object

eu.isas.peptideshaker.gui.protein_sequence.ProteinSequencePanel

public class ProteinSequencePanel
extends Object

This class can be used to create a protein sequence plot.

Author:

Harald Barsnes, Marc Vaudel

Constructor Summary

Constructors

Constructor and Description
ProteinSequencePanel(Color backgroundColor) Creates a new ProteinSequencePanel object.

Method Summary

Modifier and Type	Method and Description
org.jfree.chart.ChartPanel	getChartPanel() Returns the chart panel.
org.jfree.chart.ChartPanel	getSequencePlot(ProteinSequencePanelParent aProteinSequencePanelParent, no.uib.jsparklines.data.JSparklinesDataset sparklineDataset, HashMap<Integer,ArrayList<ResidueAnnotation>> proteinAnnotations, boolean addReferenceLine, boolean allowZooming) Returns a sequence plot as a ChartPanel.
static ArrayList<no.uib.jsparklines.data.JSparklinesDataSeries>	getSparkLineDataSeriesCoverage(double[] aaHeight, int[] aaColorIndex, HashMap<Integer,Color> colors) Returns an array list with the coverage.
void	setBackground(Color backgroundColor) Set the background color.
void	setReferenceLine(double referenceLineWidth, Color referenceLineColor) Set the reference line properties.

Methods inherited from class java.lang.Object

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

Constructor Detail

ProteinSequencePanel

public ProteinSequencePanel(Color backgroundColor)

Creates a new ProteinSequencePanel object. Use getSequencePlot() to get the plot/chart.

Parameters:

backgroundColor - the plot/chart background color

Method Detail

setBackground

public void setBackground(Color backgroundColor)

Set the background color.

Parameters:

backgroundColor - the plot/chart background color

setReferenceLine

public void setReferenceLine(double referenceLineWidth,
                             Color referenceLineColor)

Set the reference line properties. Will not have any effect until getSequencePlot(..) is called again with 'addReferenceLine' set to true.

Parameters:

referenceLineWidth - reference line width

referenceLineColor - reference line color

getSequencePlot

public org.jfree.chart.ChartPanel getSequencePlot(ProteinSequencePanelParent aProteinSequencePanelParent,
                                                  no.uib.jsparklines.data.JSparklinesDataset sparklineDataset,
                                                  HashMap<Integer,ArrayList<ResidueAnnotation>> proteinAnnotations,
                                                  boolean addReferenceLine,
                                                  boolean allowZooming)

Returns a sequence plot as a ChartPanel.

Parameters:

aProteinSequencePanelParent - the protein sequence panel parent

sparklineDataset - the dataset

proteinAnnotations - the protein annotations

addReferenceLine - if true, a reference line is added

allowZooming - if true, the user can zoom in the created plot/chart

Returns:

a sequence plot

getChartPanel

public org.jfree.chart.ChartPanel getChartPanel()

Returns the chart panel.

Returns:

the chart panel

getSparkLineDataSeriesCoverage

public static ArrayList<no.uib.jsparklines.data.JSparklinesDataSeries> getSparkLineDataSeriesCoverage(double[] aaHeight,
                                                                                                      int[] aaColorIndex,
                                                                                                      HashMap<Integer,Color> colors)

Returns an array list with the coverage.

Parameters:

aaHeight - the heights

aaColorIndex - the color indexes

colors - the index to color map

Returns:

an array list with the coverage