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java.lang.Object net.sf.basedb.core.plugin.AbstractPlugin net.sf.basedb.plugins.IntensityCalculatorPlugin
public class IntensityCalculatorPlugin
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
Nested Class Summary |
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Nested classes/interfaces inherited from interface net.sf.basedb.core.plugin.Plugin |
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Plugin.MainType |
Field Summary | |
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private static About |
about
Plugin description |
private RequestInformation |
configureJob
|
private PluginParameter<Experiment> |
experimentParameter
|
private ItemParameterType<Experiment> |
experimentType
|
private PluginParameter<Formula> |
formulaParameter
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private ItemParameterType<Formula> |
formulaType
|
private static Set<GuiContext> |
guiContexts
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private static PluginParameter<String> |
nameParameter
|
private static StringParameterType |
nameType
|
private static Set<Permissions> |
permissions
|
private PluginParameter<RawBioAssay> |
rawBioAssaysParameter
|
private ItemParameterType<RawBioAssay> |
rawBioAssaysType
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private ThreadSignalHandler |
signalHandler
|
Fields inherited from class net.sf.basedb.core.plugin.AbstractPlugin |
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annotationSection, configuration, COPY_ANNOTATIONS, job, OVERWRITE_ANNOTATIONS, sc |
Constructor Summary | |
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IntensityCalculatorPlugin()
Constructor should be empty. |
Method Summary | |
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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 |
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checkInterrupted, cloneParameterWithDefaultValue, closeLogFile, createLogFile, done, getCopyAnnotationsParmeter, getCurrentConfiguration, getCurrentJob, getJobOrConfigurationValue, getOverwriteAnnotationsParameters, init, log, log, storeValue, storeValue, storeValues, validateRequestParameters |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface net.sf.basedb.core.plugin.Plugin |
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done, init |
Field Detail |
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private static final About about
private static final Set<GuiContext> guiContexts
private static final Set<Permissions> permissions
private static final StringParameterType nameType
private static final PluginParameter<String> nameParameter
private ItemParameterType<Experiment> experimentType
private PluginParameter<Experiment> experimentParameter
private ItemParameterType<RawBioAssay> rawBioAssaysType
private PluginParameter<RawBioAssay> rawBioAssaysParameter
private ItemParameterType<Formula> formulaType
private PluginParameter<Formula> formulaParameter
private RequestInformation configureJob
private ThreadSignalHandler signalHandler
Constructor Detail |
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public IntensityCalculatorPlugin()
Method Detail |
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public About getAbout()
Plugin
getAbout
in interface Plugin
About
objectpublic Plugin.MainType getMainType()
getMainType
in interface Plugin
Plugin.MainType.INTENSITY
.public boolean supportsConfigurations()
AbstractPlugin
supportsConfigurations
in interface Plugin
supportsConfigurations
in class AbstractPlugin
public boolean requiresConfiguration()
AbstractPlugin
requiresConfiguration
in interface Plugin
requiresConfiguration
in class AbstractPlugin
public Collection<Permissions> getPermissions()
getPermissions
in interface Plugin
getPermissions
in class AbstractPlugin
public void run(Request request, Response response, ProgressReporter progress)
Plugin
run
in interface Plugin
request
- Request object with the command and parametersresponse
- Response object in for the plugin to response
throughprogress
- A ProgressReporter
where the plugin can report
its progess, can be nullpublic Set<GuiContext> getGuiContexts()
InteractivePlugin
Item.REPORTER
.
This information is used by client applications to put the plugin
in the proper place in the user interface.
getGuiContexts
in interface InteractivePlugin
Set
containing Item
:s, or null
if the plugin is not concerned about itemspublic String isInContext(GuiContext context, Object item)
isInContext
in interface InteractivePlugin
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
Null
if the plugin can use that item, or
a warning-level message explaining why the plugin can't be usedpublic RequestInformation getRequestInformation(GuiContext context, String command) throws BaseException
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.
getRequestInformation
in interface InteractivePlugin
context
- The current context of the client application,
it is one of the values found in set returned by InteractivePlugin.getGuiContexts()
command
- The command
RequestInformation
for the command
BaseException
- if there is an errorpublic void configure(GuiContext context, Request request, Response response)
Request.COMMAND_CONFIGURE_PLUGIN
,
and Request.COMMAND_CONFIGURE_JOB
.
configure
in interface InteractivePlugin
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 parametersresponse
- Response object in for the plugin to response
throughpublic SignalHandler getSignalHandler()
SignalTarget
getSignalHandler
in interface SignalTarget
private RequestInformation getConfigureJobParameters()
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2.17.2: 2011-06-17 | ||||||||
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