Package net.sf.basedb.plugins

Class IntensityCalculatorPlugin

java.lang.Object

net.sf.basedb.core.plugin.AbstractPlugin

net.sf.basedb.plugins.IntensityCalculatorPlugin

All Implemented Interfaces:

InteractivePlugin, Plugin, SignalTarget

public class IntensityCalculatorPlugin
extends AbstractPlugin
implements InteractivePlugin, SignalTarget

This plugin provides methods to calculate the intensity for a root bioassayset using different formulas. It needs the following parameters:

   String              : name; The name of the new bioassayset
   Experiment          : experiment; The experiment we are working on
   List>RawBioAssay<   : rawBioAssays; The raw bioassays to create bioassays for
     (must be part of the experiment)
   Formula             : formula; The formula to use to for calculating intesities
   

Version:

2.0

Author:

Gregory, Nicklas

Last modified

$Date: 2019-02-26 11:10:15 +0100 (tis, 26 feb. 2019) $

Nested Class Summary

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

Plugin.MainType

Field Summary

Fields

Modifier and Type	Field	Description
private RequestInformation	configureJob
private PluginParameter<Experiment>	experimentParameter
private ItemParameterType<Experiment>	experimentType
private PluginParameter<Formula>	formulaParameter
private ItemParameterType<Formula>	formulaType
private static final Set<GuiContext>	guiContexts
private static final PluginParameter<String>	nameParameter
private static final StringParameterType	nameType
private static final Set<Permissions>	permissions
private PluginParameter<RawBioAssay>	rawBioAssaysParameter
private ItemParameterType<RawBioAssay>	rawBioAssaysType
private ThreadSignalHandler	signalHandler

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

annotationSection, configuration, COPY_ANNOTATIONS, job, OVERWRITE_ANNOTATIONS, sc

Constructor Summary

Constructors

Constructor	Description
IntensityCalculatorPlugin()	Constructor should be empty.

Method Summary

Modifier and Type	Method	Description
void	configure(GuiContext context, Request request, Response response)	Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN, and Request.COMMAND_CONFIGURE_JOB.
private RequestInformation	getConfigureJobParameters()
Set<GuiContext>	getGuiContexts()	Get a set containing all items that the plugin handles.
Plugin.MainType	getMainType()	Returns the main plugin type this plugin belongs to.
Collection<Permissions>	getPermissions()	Request use access to Experiment:s and read access to RawBioAssay:s, ArrayDesign:s, Formulas:s, Job:s and and Reporter:s.
RequestInformation	getRequestInformation(GuiContext context, String command)	The Request.COMMAND_CONFIGURE_PLUGIN command will not ask for any parameters.
SignalHandler	getSignalHandler()	Get the signal handler that is handling signals on behalf of this object.
String	isInContext(GuiContext context, Object item)	Check that the current experiment stores it's raw data in the database.
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.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.Plugin

done, init

Field Details

guiContexts

private static final Set<GuiContext> guiContexts

permissions

private static final Set<Permissions> permissions

nameType

private static final StringParameterType nameType

nameParameter

private static final PluginParameter<String> nameParameter

experimentType

private ItemParameterType<Experiment> experimentType

experimentParameter

private PluginParameter<Experiment> experimentParameter

rawBioAssaysType

private ItemParameterType<RawBioAssay> rawBioAssaysType

rawBioAssaysParameter

private PluginParameter<RawBioAssay> rawBioAssaysParameter

formulaType

private ItemParameterType<Formula> formulaType

formulaParameter

private PluginParameter<Formula> formulaParameter

configureJob

private RequestInformation configureJob

signalHandler

private ThreadSignalHandler signalHandler

Constructor Details

IntensityCalculatorPlugin

public IntensityCalculatorPlugin()

Constructor should be empty.

Method Details

getMainType

public Plugin.MainType getMainType()

Returns the main plugin type this plugin belongs to.

Specified by:

getMainType in interface Plugin

Returns:

Plugin.MainType.INTENSITY.

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 RawBioAssay:s, ArrayDesign:s, Formulas:s, Job:s and and Reporter:s.

Specified by:

getPermissions in interface Plugin

Overrides:

getPermissions in class AbstractPlugin

Returns:

A collection of permissions or null to not use permissions

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

getGuiContexts

public Set<GuiContext> getGuiContexts()

Description copied from interface: InteractivePlugin

Get a set containing all items that the plugin handles. Ie. if the plugin imports reporters, return a set containing Item.REPORTER. This information is used by client applications to put the plugin in the proper place in the user interface.

Specified by:

getGuiContexts in interface InteractivePlugin

Returns:

A Set containing Item:s, or null if the plugin is not concerned about items

isInContext

public String isInContext(GuiContext context,
 Object item)

Check that the current experiment stores it's raw data in the database.

Specified by:

isInContext 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()

item - The currently active item, it's type should match the GuiContext.getItem() type, or null if the context is a list context

Returns:

Null if the plugin can use that item, or a warning-level message explaining why the plugin can't be used

getRequestInformation

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

The Request.COMMAND_CONFIGURE_PLUGIN command will not ask for any parameters. The Request.COMMAND_CONFIGURE_JOB command will ask for the parameters mentioned in the class documentation.

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)

Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN, and Request.COMMAND_CONFIGURE_JOB.

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

getConfigureJobParameters

private RequestInformation getConfigureJobParameters()