Package net.sf.basedb.plugins

Class LowessNormalization

java.lang.Object

net.sf.basedb.core.plugin.AbstractPlugin

net.sf.basedb.core.plugin.AbstractAnalysisPlugin

net.sf.basedb.plugins.LowessNormalization

All Implemented Interfaces:

InteractivePlugin, Plugin, SignalTarget

public class LowessNormalization
extends AbstractAnalysisPlugin
implements InteractivePlugin, SignalTarget

Version:

2.0

Author:

enell, Nicklas

Last modified

$Date: 2015-05-12 11:27:08 +0200 (ti, 12 maj 2015) $

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) static class	LowessNormalization.CallableWorker
private static class	LowessNormalization.SpotData

Nested classes/interfaces inherited from interface net.sf.basedb.core.plugin.Plugin

Plugin.MainType

Field Summary

Fields

Modifier and Type	Field	Description
private static final PluginParameter<Integer>	blockGroupParameter
private RequestInformation	configureJob
private static final PluginParameter<Float>	deltaParameter
private static final PluginParameter<Float>	fitFractionParameter
private static final PluginParameter<Integer>	iterParameter
protected static final PluginParameter<String>	lowessSection	Section for lowess options
private static final Set<Permissions>	permissions
private EnhancedThreadSignalHandler	signalHandler
private static double	ywRangeFactor

Fields inherited from class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

CHILD_DESCRIPTION, CHILD_NAME, CONTEXT_BIOASSAYS, CONTEXT_BIOASSAYSET, CONTEXT_DERIVEDBIOASSAY, defaultGuiContexts, nameType, optionalNameType, SOURCE_BIOASSAYS, SOURCE_BIOASSAYSET, SOURCE_DERIVEDBIOASSAY, TRANSFORMATION_NAME

Fields inherited from class net.sf.basedb.core.plugin.AbstractPlugin

annotationSection, configuration, COPY_ANNOTATIONS, job, OVERWRITE_ANNOTATIONS, sc

Constructor Summary

Constructors

Constructor	Description
LowessNormalization()

Method Summary

Modifier and Type	Method	Description
private static List<Double>	calculateWeights(List<LowessNormalization.SpotData> data, double A1, List<Double> wFit)
void	configure(GuiContext context, Request request, Response response)	Configure the plugin.
private RequestInformation	getConfigureJobParameters()
private PluginParameter<ReporterList>	getExcludeReportersParameters(DbControl dc)
Collection<Permissions>	getPermissions()	Request use access to Experiment:s and read access to Job:s.
RequestInformation	getRequestInformation(GuiContext context, String command)	This method will return the RequestInformation for a given command, i.e.
SignalHandler	getSignalHandler()	Get the signal handler that is handling signals on behalf of this object.
String	isInContext(GuiContext context, Object item)	Check that the item is a bioassayset/derived bioassay and that the logged in user has permission to use the current item.
private static List<Double>	lowess(List<LowessNormalization.SpotData> data, double f, int iter, double delta)
private static double	medianCorrection(List<LowessNormalization.SpotData> data, Double[] smoothCurve)
BioAssaySet	normalize(DbControl dc, BioAssaySet source, Job job, float fitFraction, float delta, int iterations, int blockGroupSize, ProgressReporter progress)	Normalise the source bioassay set using LOWESS normalization.
BioAssaySet	normalize(DbControl dc, BioAssaySet source, Job job, float fitFraction, float delta, int iterations, int blockGroupSize, ReporterList excludeReporters, ProgressReporter progress)	Normalise the source bioassay set using LOWESS normalization.
private List<LowessNormalization.SpotData>	readData(DbControl dc, DynamicSpotQuery query, BioAssay assay, MACalculator mac)
boolean	requiresConfiguration()	Returns FALSE, since that is how the plugins used to work before this method was introduced.
void	run(Request request, Response response, ProgressReporter progress)	Run the plugin.
boolean	supportsConfigurations()	Returns TRUE, since that is how the plugins used to work before this method was introduced.
private static double[]	weightedLeastSquaresRegression(List<LowessNormalization.SpotData> data, List<Double> w)

Methods inherited from class net.sf.basedb.core.plugin.AbstractAnalysisPlugin

getChildDescriptionParameter, getChildNameParameter, getCurrentBioAssaySet, getCurrentDerivedBioAssay, getCurrentExperiment, getGuiContexts, getMainType, getSourceBioAssays, getSourceBioAssaySet, getSourceBioAssaySetParameter, getSourceBioAssaysParameter, getSourceDerivedBioAssay, getSourceDerivedBioAssayParameter, getTransformationName, getTransformationNameParameter, restrictSource

Methods inherited from class net.sf.basedb.core.plugin.AbstractPlugin

cloneParameterWithDefaultValue, closeLogFile, createLogFile, done, getCopyAnnotationsParmeter, getCurrentConfiguration, getCurrentJob, getJobOrConfigurationValue, getOverwriteAnnotationsParameters, init, isLogging, log, log, storeValue, storeValue, storeValues, validateRequestParameters

Methods inherited from class java.lang.Object

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

Methods inherited from interface net.sf.basedb.core.plugin.InteractivePlugin

getGuiContexts

Methods inherited from interface net.sf.basedb.core.plugin.Plugin

done, getMainType, init

Field Details

permissions

private static final Set<Permissions> permissions

fitFractionParameter

private static final PluginParameter<Float> fitFractionParameter

deltaParameter

private static final PluginParameter<Float> deltaParameter

iterParameter

private static final PluginParameter<Integer> iterParameter

blockGroupParameter

private static final PluginParameter<Integer> blockGroupParameter

lowessSection

protected static final PluginParameter<String> lowessSection

Section for lowess options

ywRangeFactor

private static double ywRangeFactor

configureJob

private RequestInformation configureJob

signalHandler

private EnhancedThreadSignalHandler signalHandler

Constructor Details

LowessNormalization

public LowessNormalization()

Method Details

supportsConfigurations

public boolean supportsConfigurations()

Description copied from class: AbstractPlugin

Returns TRUE, since that is how the plugins used to work before this method was introduced.

Specified by:

supportsConfigurations in interface Plugin

Overrides:

supportsConfigurations in class AbstractPlugin

Returns:

TRUE or FALSE

requiresConfiguration

public boolean requiresConfiguration()

Description copied from class: AbstractPlugin

Returns FALSE, since that is how the plugins used to work before this method was introduced.

Specified by:

requiresConfiguration in interface Plugin

Overrides:

requiresConfiguration in class AbstractPlugin

Returns:

TRUE or FALSE

getPermissions

public Collection<Permissions> getPermissions()

Request use access to Experiment:s and read access to Job:s.

Specified by:

getPermissions in interface Plugin

Overrides:

getPermissions in class AbstractPlugin

Returns:

A collection of permissions or null to not use permissions

Since:

2.0.2

run

public void run(Request request,
 Response response,
 ProgressReporter progress)

Description copied from interface: Plugin

Run the plugin. If a progress reporter object is passed it is recommended that the plugin makes use of it.

Specified by:

run in interface Plugin

Parameters:

request - Request object with the command and parameters

response - Response object in for the plugin to response through

progress - A ProgressReporter where the plugin can report its progess, can be null

isInContext

public String isInContext(GuiContext context,
 Object item)

Description copied from class: AbstractAnalysisPlugin

Check that the item is a bioassayset/derived bioassay and that the logged in user has permission to use the current item.

Specified by:

isInContext in interface InteractivePlugin

Overrides:

isInContext in class AbstractAnalysisPlugin

Parameters:

context - Current guicontext

item - The item to check.

Returns:

null if the item is a valid item, an error message otherwise

getRequestInformation

public RequestInformation getRequestInformation(GuiContext context,
 String command)
                                         throws BaseException

Description copied from interface: InteractivePlugin

This method will return the RequestInformation for a given command, i.e. the list of parameters and some nice help text.

Specified by:

getRequestInformation in interface InteractivePlugin

Parameters:

context - The current context of the client application, it is one of the values found in set returned by InteractivePlugin.getGuiContexts()

command - The command

Returns:

The RequestInformation for the command

Throws:

BaseException - if there is an error

configure

public void configure(GuiContext context,
 Request request,
 Response response)

Description copied from interface: InteractivePlugin

Configure the plugin. Hopefully the client is supplying values for the parameters specified by InteractivePlugin.getRequestInformation(GuiContext, String).

Specified by:

configure in interface InteractivePlugin

Parameters:

context - The current context of the client application, it is one of the values found in set returned by InteractivePlugin.getGuiContexts()

request - Request object with the command and parameters

response - Response object in for the plugin to response through

getSignalHandler

public SignalHandler getSignalHandler()

Description copied from interface: SignalTarget

Get the signal handler that is handling signals on behalf of this object. Multiple invokations of this method may receive the same or different objects. Null may be returned if, for some reason, the current object instance doesn't want to receive signals. Returning null is the same as not implementing this interface.

Specified by:

getSignalHandler in interface SignalTarget

Returns:

A SignalHandler object, or null if the current instance doesn't support signals

normalize

public BioAssaySet normalize(DbControl dc,
 BioAssaySet source,
 Job job,
 float fitFraction,
 float delta,
 int iterations,
 int blockGroupSize,
 ProgressReporter progress)

Normalise the source bioassay set using LOWESS normalization. All reporters are included.

Since:

2.5

See Also:

• normalize(DbControl, BioAssaySet, Job, float, float, int, int, ReporterList, ProgressReporter)

normalize

public BioAssaySet normalize(DbControl dc,
 BioAssaySet source,
 Job job,
 float fitFraction,
 float delta,
 int iterations,
 int blockGroupSize,
 ReporterList excludeReporters,
 ProgressReporter progress)

Normalise the source bioassay set using LOWESS normalization.

Parameters:

dc - The DbControl to use for database access

source - The source bioassay set that is going to be normalized

job - The job that is doing the normalization, or null

blockGroupSize - The number of blocks to group and normalise at the same time, if <=0, all blocks on a bioassay are grouped to a single dataset

excludeReporters - A reporter list containing reporters that should not be used in when normalizing, or null to use all spots

progress - Progress reporter used by the caller to keep track of the progress. Null is allowed

Returns:

The normalized bioassayset

Since:

2.6

readData

private List<LowessNormalization.SpotData> readData(DbControl dc,
 DynamicSpotQuery query,
 BioAssay assay,
 MACalculator mac)
                                             throws SQLException

Throws:

SQLException

getConfigureJobParameters

private RequestInformation getConfigureJobParameters()

getExcludeReportersParameters

private PluginParameter<ReporterList> getExcludeReportersParameters(DbControl dc)

lowess

private static List<Double> lowess(List<LowessNormalization.SpotData> data,
 double f,
 int iter,
 double delta)

medianCorrection

private static double medianCorrection(List<LowessNormalization.SpotData> data,
 Double[] smoothCurve)

weightedLeastSquaresRegression

private static double[] weightedLeastSquaresRegression(List<LowessNormalization.SpotData> data,
 List<Double> w)

calculateWeights

private static List<Double> calculateWeights(List<LowessNormalization.SpotData> data,
 double A1,
 List<Double> wFit)