org.knime.base.node.viz.enrichment
Class EnrichmentPlotterSettings

java.lang.Object
  org.knime.base.node.viz.enrichment.EnrichmentPlotterSettings

public class EnrichmentPlotterSettings
extends Object

This class holds the settings for the enrichment plotter node.

Author:

Thorsten Meinl, University of Konstanz

Nested Class Summary

static class	EnrichmentPlotterSettings.Curve A simple container that holds the necessary information for specifying a curve that should be plotted.
static class	EnrichmentPlotterSettings.PlotMode Enum for the three different plot modes.

Constructor Summary

EnrichmentPlotterSettings()

Method Summary

void	addCurve(String sortColumn, String activityColumn, boolean sortDescending) Adds a new curve to the settings.
EnrichmentPlotterSettings.Curve	getCurve(int index) Returns the curve settings for the given index.
int	getCurveCount() Returns the number of curves that should be plotted.
double	hitThreshold() Returns the threshold above and including which a data point is considered a hit.
void	hitThreshold(double thres) Sets the threshold above and including which a data point is considered a hit.
void	loadSettings(NodeSettingsRO settings) Loads the settings from the given node settings object.
void	loadSettingsForDialog(NodeSettingsRO settings) Loads the settings from the given node settings object.
int	minClusterMembers() Returns the minimum number of molecules from the same cluster that have to be found so that a cluster is declared to be found.
void	minClusterMembers(int min) Sets the minimum number of molecules from the same cluster that have to be found so that a cluster is declared to be found.
EnrichmentPlotterSettings.PlotMode	plotMode() Returns the desired plot mode.
void	plotMode(EnrichmentPlotterSettings.PlotMode mode) Sets the desired plot mode.
boolean	removeCurve(EnrichmentPlotterSettings.Curve curve) Removes the given curve from the settings.
void	saveSettings(NodeSettingsWO settings) Saves this object's settings to the given node settings.

Methods inherited from class java.lang.Object

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

Constructor Detail

EnrichmentPlotterSettings

public EnrichmentPlotterSettings()

Method Detail

addCurve

public void addCurve(String sortColumn,
                     String activityColumn,
                     boolean sortDescending)

Adds a new curve to the settings.

Parameters:

sortColumn - the column by which the table should be sorted

activityColumn - the column with the activity or cluster values

sortDescending - true if the sortColumn should be sorted descending, false if it should be sorted ascending

getCurve

public EnrichmentPlotterSettings.Curve getCurve(int index)

Returns the curve settings for the given index.

Parameters:

index - an index

Returns:

the curve settings at the index

getCurveCount

public int getCurveCount()

Returns the number of curves that should be plotted.

Returns:

the number of curves

removeCurve

public boolean removeCurve(EnrichmentPlotterSettings.Curve curve)

Removes the given curve from the settings.

Parameters:

curve - a curve

Returns:

true if the curve was removed, false otherwise (likely because the curve does not exist)

saveSettings

public void saveSettings(NodeSettingsWO settings)

Saves this object's settings to the given node settings.

Parameters:

settings - the node settings

loadSettings

public void loadSettings(NodeSettingsRO settings)
                  throws InvalidSettingsException

Loads the settings from the given node settings object.

Parameters:

settings - the node settings

Throws:

InvalidSettingsException - if the settings are invalid

loadSettingsForDialog

public void loadSettingsForDialog(NodeSettingsRO settings)

Loads the settings from the given node settings object.

Parameters:

settings - the node settings

plotMode

public EnrichmentPlotterSettings.PlotMode plotMode()

Returns the desired plot mode.

Returns:

the plot mode

plotMode

public void plotMode(EnrichmentPlotterSettings.PlotMode mode)

Sets the desired plot mode.

Parameters:

mode - the plot mode

hitThreshold

public double hitThreshold()

Returns the threshold above and including which a data point is considered a hit. This settings is only relevant if plotMode() is EnrichmentPlotterSettings.PlotMode.PlotHits.

Returns:

the hit threshold

hitThreshold

public void hitThreshold(double thres)

Sets the threshold above and including which a data point is considered a hit. This settings is only relevant if plotMode() is EnrichmentPlotterSettings.PlotMode.PlotHits.

Parameters:

thres - the hit threshold

minClusterMembers

public int minClusterMembers()

Returns the minimum number of molecules from the same cluster that have to be found so that a cluster is declared to be found.

Returns:

the minimum number of cluster members

minClusterMembers

public void minClusterMembers(int min)

Sets the minimum number of molecules from the same cluster that have to be found so that a cluster is declared to be found.

Parameters:

min - the minimum number of cluster members