net.sf.basedb.plugins
Class MedianRatioNormalization

java.lang.Object
  net.sf.basedb.core.plugin.AbstractPlugin
      net.sf.basedb.core.plugin.AbstractAnalysisPlugin
          net.sf.basedb.plugins.MedianRatioNormalization

All Implemented Interfaces:

InteractivePlugin, Plugin, SignalTarget

public class MedianRatioNormalization
extends AbstractAnalysisPlugin
implements InteractivePlugin, SignalTarget

Version:

2.0

Author:

enell, Nicklas

Last modified

$Date: 2011-08-11 11:09:06 +0200 (Thu, 11 Aug 2011) $

Nested Class Summary

private static class

MedianRatioNormalization.SpotData

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

Plugin.MainType

Field Summary

private static PluginParameter<Integer>	blockGroupParameter Used with 2-channel data only
private RequestInformation	configureJob
private static PluginParameter<Float>	highExcludeParameter
private static PluginParameter<Float>	lowExcludeParameter
protected static PluginParameter<String>	medianRatioSection Section for normalization options
private static PluginParameter<String>	methodParameter List of median normalization methods.
private PluginParameter<Float>	minIntensityParameter
private static Set<Permissions>	permissions
private ThreadSignalHandler	signalHandler

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

MedianRatioNormalization()

Method Summary

void	configure(GuiContext context, Request request, Response response) Configure the plugin.
private RequestInformation	getConfigureJobParameters()
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 float	median(float[] sortedArray, int first, int last)
private double	median(List<MedianRatioNormalization.SpotData> data)
BioAssaySet	normalize(DbControl dc, BioAssaySet source, Job job, float minIntensity, float lowExclude, float highExclude, int blockGroupSize, ProgressReporter progress) Normalise the source bioassay set using MEDIAN-RATIO normalization.
private BioAssaySet	normalize1ch(DbControl dc, BioAssaySet source, Job job, float minIntensity, float lowExclude, float highExclude, boolean scale, ProgressReporter progress) Normalise the source bioassay set using MEDIAN-RATIO normalization.
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.

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, 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 Detail

permissions

private static final Set<Permissions> permissions

minIntensityParameter

private PluginParameter<Float> minIntensityParameter

highExcludeParameter

private static final PluginParameter<Float> highExcludeParameter

lowExcludeParameter

private static final PluginParameter<Float> lowExcludeParameter

methodParameter

private static final PluginParameter<String> methodParameter

List of median normalization methods. The method to use depends whether data is log values or not. Absolute intensities should be scaled with the median whereas log intensities should be subtracted with the median intensity. Inew = Iold/Imedian for absolute intensities. log(Inew) = log(Iold) - log(Imedian) for log intensities. Used with 1-channel data only

blockGroupParameter

private static final PluginParameter<Integer> blockGroupParameter

Used with 2-channel data only

medianRatioSection

protected static final PluginParameter<String> medianRatioSection

Section for normalization options

configureJob

private RequestInformation configureJob

signalHandler

private ThreadSignalHandler signalHandler

Constructor Detail

MedianRatioNormalization

public MedianRatioNormalization()

Method Detail

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

normalize1ch

private BioAssaySet normalize1ch(DbControl dc,
                                 BioAssaySet source,
                                 Job job,
                                 float minIntensity,
                                 float lowExclude,
                                 float highExclude,
                                 boolean scale,
                                 ProgressReporter progress)

Normalise the source bioassay set using MEDIAN-RATIO normalization.

Parameters:

dc - The DbControl to use for database access

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

job - The job in which the normalization is done.

minIntensity - All spots which have a lower intensity value in either channel will be filtered out

lowExclude - A percentage of the spots with lowest ratio that are excuded in the median calculation

highExclude - A percentage of the spots with highest ratio that are excluded in the median calculation

scale - If true, scale intensities with median intensity, otherwise subtract median intensity

progress - Progress reporter for the caller to keep track of the plugin's progress. Null is allowed.

Returns:

The normalized bioassayset

Since:

2.7

normalize

public BioAssaySet normalize(DbControl dc,
                             BioAssaySet source,
                             Job job,
                             float minIntensity,
                             float lowExclude,
                             float highExclude,
                             int blockGroupSize,
                             ProgressReporter progress)

Normalise the source bioassay set using MEDIAN-RATIO normalization. NOTE! This normalization method only works with 2-channel data.

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

minIntensity - All spots which have a lower intensity value in either channel will be filtered out

lowExclude - A percentage of the spots with lowest ratio that are excuded in the median calculation

highExclude - A percentage of the spots with highest ratio that are excluded in the median calculation

blockGroupSize -

progress - Progress reporter for the caller to keep track of the plugin's progress. Null is allowed.

Returns:

The normalized bioassayset

Since:

2.5; This method was removed in 2.7.0 by accident, added in 2.7.2 again

getConfigureJobParameters

private RequestInformation getConfigureJobParameters()

median

private float median(float[] sortedArray,
                     int first,
                     int last)

median

private double median(List<MedianRatioNormalization.SpotData> data)