Package net.sf.basedb.plugins
Class IntensityCalculatorPlugin
- java.lang.Object
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- net.sf.basedb.core.plugin.AbstractPlugin
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- net.sf.basedb.plugins.IntensityCalculatorPlugin
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- 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) $
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Nested Class Summary
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Nested classes/interfaces inherited from interface net.sf.basedb.core.plugin.Plugin
Plugin.MainType
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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 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
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Fields inherited from class net.sf.basedb.core.plugin.AbstractPlugin
annotationSection, configuration, COPY_ANNOTATIONS, job, OVERWRITE_ANNOTATIONS, sc
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Constructor Summary
Constructors Constructor Description IntensityCalculatorPlugin()
Constructor should be empty.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
configure(GuiContext context, Request request, Response response)
Store configuration settings forRequest.COMMAND_CONFIGURE_PLUGIN
, andRequest.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)
TheRequest.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, log, log, storeValue, storeValue, storeValues, validateRequestParameters
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Field Detail
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guiContexts
private static final Set<GuiContext> guiContexts
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permissions
private static final Set<Permissions> permissions
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nameType
private static final StringParameterType nameType
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nameParameter
private static final PluginParameter<String> nameParameter
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experimentType
private ItemParameterType<Experiment> experimentType
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experimentParameter
private PluginParameter<Experiment> experimentParameter
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rawBioAssaysType
private ItemParameterType<RawBioAssay> rawBioAssaysType
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rawBioAssaysParameter
private PluginParameter<RawBioAssay> rawBioAssaysParameter
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formulaType
private ItemParameterType<Formula> formulaType
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formulaParameter
private PluginParameter<Formula> formulaParameter
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configureJob
private RequestInformation configureJob
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signalHandler
private ThreadSignalHandler signalHandler
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Method Detail
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getMainType
public Plugin.MainType getMainType()
Returns the main plugin type this plugin belongs to.- Specified by:
getMainType
in interfacePlugin
- Returns:
Plugin.MainType.INTENSITY
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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 interfacePlugin
- Overrides:
supportsConfigurations
in classAbstractPlugin
- Returns:
- TRUE or FALSE
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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 interfacePlugin
- Overrides:
requiresConfiguration
in classAbstractPlugin
- Returns:
- TRUE or FALSE
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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 interfacePlugin
- Overrides:
getPermissions
in classAbstractPlugin
- Returns:
- A collection of permissions or null to not use permissions
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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 interfacePlugin
- Parameters:
request
- Request object with the command and parametersresponse
- Response object in for the plugin to response throughprogress
- AProgressReporter
where the plugin can report its progess, can be null
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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 containingItem.REPORTER
. This information is used by client applications to put the plugin in the proper place in the user interface.- Specified by:
getGuiContexts
in interfaceInteractivePlugin
- Returns:
- A
Set
containingItem
:s, or null if the plugin is not concerned about items
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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 interfaceInteractivePlugin
- Parameters:
context
- The current context of the client application, it is one of the values found in set returned byInteractivePlugin.getGuiContexts()
item
- The currently active item, it's type should match theGuiContext.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
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getRequestInformation
public RequestInformation getRequestInformation(GuiContext context, String command) throws BaseException
TheRequest.COMMAND_CONFIGURE_PLUGIN
command will not ask for any parameters. TheRequest.COMMAND_CONFIGURE_JOB
command will ask for the parameters mentioned in the class documentation.- Specified by:
getRequestInformation
in interfaceInteractivePlugin
- Parameters:
context
- The current context of the client application, it is one of the values found in set returned byInteractivePlugin.getGuiContexts()
command
- The command- Returns:
- The
RequestInformation
for the command - Throws:
BaseException
- if there is an error
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configure
public void configure(GuiContext context, Request request, Response response)
Store configuration settings forRequest.COMMAND_CONFIGURE_PLUGIN
, andRequest.COMMAND_CONFIGURE_JOB
.- Specified by:
configure
in interfaceInteractivePlugin
- Parameters:
context
- The current context of the client application, it is one of the values found in set returned byInteractivePlugin.getGuiContexts()
request
- Request object with the command and parametersresponse
- Response object in for the plugin to response through
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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 interfaceSignalTarget
- Returns:
- A SignalHandler object, or null if the current instance doesn't support signals
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getConfigureJobParameters
private RequestInformation getConfigureJobParameters()
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