adams.data.instances
Class IntensityInstanceGenerator

java.lang.Object
  adams.core.ConsoleObject
      adams.core.option.AbstractOptionHandler
          adams.data.instances.AbstractInstanceGenerator<Heatmap>
              adams.data.instances.AbstractFieldInstanceGenerator
                  adams.data.instances.IntensityInstanceGenerator

All Implemented Interfaces:

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

public class IntensityInstanceGenerator
extends AbstractFieldInstanceGenerator

A generator for turning a heatmap's intensities and fields of its report into weka.core.Instance objects.

Valid options are:

-D <int> (property: debugLevel)
    The greater the number the more additional info the scheme may output to
    the console (0 = off).
    default: 0
    minimum: 0
 

-add-db-id (property: addDatabaseID)
    If set to true, then the database ID will be added to the output.
 

-add-herd-number (property: addHerdNumber)
    If set to true, then the herd number will be added to the output.
 

-add-cow-number (property: addCowNumber)
    If set to true, then the cow number will be added to the output.
 

-field <adams.data.report.Field> [-field ...] (property: fields)
    The fields to add to the output.
    default:
 

-min-intensity <double> (property: minIntensity)
    The minimum intensity to keep.
    default: -1.0
    minimum: -1.0
 

-max-intensity <double> (property: maxIntensity)
    The maximum intensity to keep.
    default: -1.0
    minimum: -1.0
 

Version:

$Revision: 6027 $

Author:

fracpete (fracpete at waikato dot ac dot nz)

See Also:

Serialized Form

Field Summary

protected double	m_MaxIntensity the maximum m/z ratio to keep.
protected double	m_MinIntensity the minimum m/z ratio to keep.

Fields inherited from class adams.data.instances.AbstractFieldInstanceGenerator

m_Fields

Fields inherited from class adams.data.instances.AbstractInstanceGenerator

LABEL_FALSE, LABEL_TRUE, m_AddDatabaseID, m_DatabaseConnection, m_OutputHeader, m_TolerateHeaderChanges

Fields inherited from class adams.core.option.AbstractOptionHandler

m_DebugLevel, m_OptionManager

Constructor Summary

IntensityInstanceGenerator()

Method Summary

protected void	checkHeader(Heatmap data) Checks whether the number of waves are the same.
void	defineOptions() Adds options to the internal list of options.
protected void	generateHeader(Heatmap data) Generates the header of the output data.
protected Instance	generateOutput(Heatmap data) Generates the actual data.
double	getMaxIntensity() Returns the maximum intensity to keep.
double	getMinIntensity() Returns the minimum intensity to keep.
String	globalInfo() Returns a string describing the object.
String	maxIntensityTipText() Returns the tip text for this property.
String	minIntensityTipText() Returns the tip text for this property.
void	setMaxIntensity(double value) Sets the maximum intensity to keep.
void	setMinIntensity(double value) Sets the minimum intensity to keep.

Methods inherited from class adams.data.instances.AbstractFieldInstanceGenerator

addFields, createAttribute, fieldsTipText, getDefaultDatabaseConnection, getFields, setFields

Methods inherited from class adams.data.instances.AbstractInstanceGenerator

addDatabaseIDTipText, checkInput, checkSetup, cleanUp, compareTo, destroy, equals, forCommandLine, forName, generate, getAddDatabaseID, getDatabaseConnection, getGenerators, getOutputHeader, getTolerateHeaderChanges, initialize, interpretePosition, postProcessHeader, postProcessOutput, reset, setAddDatabaseID, setDatabaseConnection, setTolerateHeaderChanges, shallowCopy, shallowCopy, tolerateHeaderChangesTipText

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_MinIntensity

protected double m_MinIntensity

the minimum m/z ratio to keep.

m_MaxIntensity

protected double m_MaxIntensity

the maximum m/z ratio to keep.

Constructor Detail

IntensityInstanceGenerator

public IntensityInstanceGenerator()

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 AbstractFieldInstanceGenerator

setMinIntensity

public void setMinIntensity(double value)

Sets the minimum intensity to keep.

Parameters:

value - the intensity

getMinIntensity

public double getMinIntensity()

Returns the minimum intensity to keep.

Returns:

the intensity

minIntensityTipText

public String minIntensityTipText()

Returns the tip text for this property.

Returns:

tip text for this property suitable for displaying in the gui

setMaxIntensity

public void setMaxIntensity(double value)

Sets the maximum intensity to keep.

Parameters:

value - the intensity

getMaxIntensity

public double getMaxIntensity()

Returns the maximum intensity to keep.

Returns:

the intensity

maxIntensityTipText

public String maxIntensityTipText()

Returns the tip text for this property.

Returns:

tip text for this property suitable for displaying in the gui

checkHeader

protected void checkHeader(Heatmap data)

Checks whether the number of waves are the same.

Overrides:

checkHeader in class AbstractFieldInstanceGenerator

Parameters:

data - the input data

generateHeader

protected void generateHeader(Heatmap data)

Generates the header of the output data.

Specified by:

generateHeader in class AbstractInstanceGenerator<Heatmap>

Parameters:

data - the input data

generateOutput

protected Instance generateOutput(Heatmap data)

Generates the actual data.

Specified by:

generateOutput in class AbstractInstanceGenerator<Heatmap>

Parameters:

data - the input data to transform

Returns:

the generated data