adams.data.filter
Class FeatureGenerator

java.lang.Object
  adams.core.ConsoleObject
      adams.core.option.AbstractOptionHandler
          adams.data.filter.AbstractFilter<T>
              adams.data.filter.AbstractDatabaseConnectionFilter<Heatmap>
                  adams.data.filter.FeatureGenerator

Type Parameters:

T - the type of data to filter

All Implemented Interfaces:

CleanUpHandler, Debuggable, Destroyable, OptionHandler, ShallowCopySupporter<AbstractFilter>, SizeOfHandler, DatabaseConnectionHandler, DatabaseConnectionProvider, Serializable, Comparable

public class FeatureGenerator
extends AbstractDatabaseConnectionFilter<Heatmap>

A filter that modifies the quantitation reports of chromatograms being passed through. The supplied quantitation report filter updates/modifies the quantitation report.

Valid options are:

-D (property: debug)
         If set to true, scheme may output additional info to the console.
 

-debug-out <java.io.File> (property: debugOutputFilePrefix)
         If the file is not pointing to a directory, then the filtered data gets
         dumped to a file with a filename consisting of this prefix, the database
          ID and the extension 'chrom'.
         default: .
 

-filter <gcms.data.quantitation.AbstractFeatureGenerator [options]> (property: filter)
         The filter to use for updating/modifying the quantitation report.
         default: gcms.data.quantitation.PassThrough -debug-out .
 

Default options for gcms.data.quantitation.PassThrough (-filter/filter):

-D (property: debug)
         If set to true, scheme may output additional info to the console.
 

-debug-out <java.io.File> (property: debugOutputFilePrefix)
         If the file is not pointing to a directory, then the filtered data gets
         dumped to a file with a filename consisting of this prefix, the database
          ID and the extension 'chrom'.
         default: .
 

Version:

$Revision: 6027 $

Author:

fracpete (fracpete at waikato dot ac dot nz)

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class adams.data.filter.AbstractFilter

AbstractFilter.FilterJob<T extends DataContainer>

Field Summary

protected AbstractFeatureGenerator

m_Generator the report filter.

Fields inherited from class adams.data.filter.AbstractDatabaseConnectionFilter

m_DatabaseConnection

Fields inherited from class adams.core.option.AbstractOptionHandler

m_DebugLevel, m_OptionManager

Constructor Summary

FeatureGenerator()

Method Summary

void	defineOptions() Adds options to the internal list of options.
String	generatorTipText() Returns the tip text for this property.
protected AbstractDatabaseConnection	getDefaultDatabaseConnection() Returns the default database connection.
AbstractFeatureGenerator	getGenerator() Returns the current generator.
String	globalInfo() Returns a string describing the object.
protected Heatmap	processData(Heatmap data) Performs the actual filtering.
void	setGenerator(AbstractFeatureGenerator value) Sets the generator to use.
protected void	updateDatabaseConnection() Updates the database connection in the filter.

Methods inherited from class adams.data.filter.AbstractDatabaseConnectionFilter

getDatabaseConnection, initialize, setDatabaseConnection

Methods inherited from class adams.data.filter.AbstractFilter

checkData, cleanUp, compareTo, destroy, equals, filter, filter, filter, filter, filter, forCommandLine, forName, getFilters, reset, shallowCopy, shallowCopy

Methods inherited from class adams.core.option.AbstractOptionHandler

cleanUpOptions, debug, debug, debugLevelTipText, finishInit, getDebugLevel, getOptionManager, isDebugOn, newOptionManager, setDebugLevel, toCommandLine, toString

Methods inherited from class adams.core.ConsoleObject

getDebugging, getSystemErr, getSystemOut, sizeOf

Methods inherited from class java.lang.Object

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

Field Detail

m_Generator

protected AbstractFeatureGenerator m_Generator

the report filter.

Constructor Detail

FeatureGenerator

public FeatureGenerator()

Method Detail

globalInfo

public String globalInfo()

Returns a string describing the object.

Specified by:

globalInfo in class AbstractOptionHandler

Returns:

a description suitable for displaying in the gui

defineOptions

public void defineOptions()

Adds options to the internal list of options.

Specified by:

defineOptions in interface OptionHandler

Overrides:

defineOptions in class AbstractOptionHandler

getDefaultDatabaseConnection

protected AbstractDatabaseConnection getDefaultDatabaseConnection()

Returns the default database connection.

Specified by:

getDefaultDatabaseConnection in class AbstractDatabaseConnectionFilter<Heatmap>

Returns:

the default database connection

setGenerator

public void setGenerator(AbstractFeatureGenerator value)

Sets the generator to use.

Parameters:

value - the generator

getGenerator

public AbstractFeatureGenerator getGenerator()

Returns the current generator.

Returns:

the generator

generatorTipText

public String generatorTipText()

Returns the tip text for this property.

Returns:

tip text for this property suitable for displaying in the gui

updateDatabaseConnection

protected void updateDatabaseConnection()

Updates the database connection in the filter.

Overrides:

updateDatabaseConnection in class AbstractDatabaseConnectionFilter<Heatmap>

processData

protected Heatmap processData(Heatmap data)

Performs the actual filtering.

Specified by:

processData in class AbstractFilter<Heatmap>

Parameters:

data - the data to filter

Returns:

the filtered data