2.17.2: 2011-06-17

net.sf.basedb.plugins
Class IntensityCalculatorPlugin

java.lang.Object
  extended by net.sf.basedb.core.plugin.AbstractPlugin
      extended by 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: 2010-11-08 14:49:35 +0100 (Mon, 08 Nov 2010) $

Nested Class Summary
 
Nested classes/interfaces inherited from interface net.sf.basedb.core.plugin.Plugin
Plugin.MainType
 
Field Summary
private static About about
          Plugin description
private  RequestInformation configureJob
           
private  PluginParameter<Experiment> experimentParameter
           
private  ItemParameterType<Experiment> experimentType
           
private  PluginParameter<Formula> formulaParameter
           
private  ItemParameterType<Formula> formulaType
           
private static Set<GuiContext> guiContexts
           
private static PluginParameter<String> nameParameter
           
private static StringParameterType nameType
           
private static 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
IntensityCalculatorPlugin()
          Constructor should be empty.
 
Method Summary
 void configure(GuiContext context, Request request, Response response)
          Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN, and Request.COMMAND_CONFIGURE_JOB.
 About getAbout()
          Get information about the plugin, such as name, version, authors, etc.
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
checkInterrupted, 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.Plugin
done, init
 

Field Detail

about

private static final About about
Plugin description


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 Detail

IntensityCalculatorPlugin

public IntensityCalculatorPlugin()
Constructor should be empty.

Method Detail

getAbout

public About getAbout()
Description copied from interface: Plugin
Get information about the plugin, such as name, version, authors, etc.

Specified by:
getAbout in interface Plugin
Returns:
An About object

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()

2.17.2: 2011-06-17