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java.lang.Objectnet.sf.basedb.core.plugin.AbstractPlugin
net.sf.basedb.core.plugin.AbstractAnalysisPlugin
net.sf.basedb.plugins.JepIntensityTransformer
public class JepIntensityTransformer
This plugin transform channel intensities using mathematical formulas entered by the user.
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 List<PluginParameter<String>> |
channelParameters
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private RequestInformation |
configureJob
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private static Set<GuiContext> |
guiContexts
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private static Set<Permissions> |
permissions
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private ThreadSignalHandler |
signalHandler
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Fields inherited from class net.sf.basedb.core.plugin.AbstractAnalysisPlugin |
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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 |
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annotationSection, configuration, COPY_ANNOTATIONS, job, OVERWRITE_ANNOTATIONS, sc |
Constructor Summary | |
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JepIntensityTransformer()
Constructor should be empty. |
Method Summary | |
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void |
configure(GuiContext context,
Request request,
Response response)
Configure the plugin. |
private RequestInformation |
getConfigureJobParameters(GuiContext context)
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Set<GuiContext> |
getGuiContexts()
Get a set containing all items that the plugin handles. |
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. |
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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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, getMainType, init |
Field Detail |
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private static final Set<Permissions> permissions
private static final Set<GuiContext> guiContexts
private ThreadSignalHandler signalHandler
private RequestInformation configureJob
private List<PluginParameter<String>> channelParameters
Constructor Detail |
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public JepIntensityTransformer()
Method Detail |
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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
getGuiContexts
in class AbstractAnalysisPlugin
Set
containing Item
:s, or null
if the plugin is not concerned about itemspublic String isInContext(GuiContext context, Object item)
AbstractAnalysisPlugin
isInContext
in interface InteractivePlugin
isInContext
in class AbstractAnalysisPlugin
context
- Current guicontextitem
- The item to check.
public RequestInformation getRequestInformation(GuiContext context, String command) throws BaseException
InteractivePlugin
RequestInformation
for a given command, i.e.
the list of parameters and some nice help text.
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)
InteractivePlugin
InteractivePlugin.getRequestInformation(GuiContext, String)
.
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(GuiContext context)
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3.0.2: 2012-01-25 | ||||||||
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