public class MedianRatioNormalization extends AbstractAnalysisPlugin implements InteractivePlugin, SignalTarget
Modifier and Type | Class and Description |
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private static class |
MedianRatioNormalization.SpotData |
Plugin.MainType
Modifier and Type | Field and Description |
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private static PluginParameter<java.lang.Integer> |
blockGroupParameter
Used with 2-channel data only
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private RequestInformation |
configureJob |
private static PluginParameter<java.lang.Float> |
highExcludeParameter |
private static PluginParameter<java.lang.Float> |
lowExcludeParameter |
protected static PluginParameter<java.lang.String> |
medianRatioSection
Section for normalization options
|
private PluginParameter<java.lang.Float> |
minIntensityParameter |
private static java.util.Set<Permissions> |
permissions |
private ThreadSignalHandler |
signalHandler |
CHILD_DESCRIPTION, CHILD_NAME, CONTEXT_BIOASSAYS, CONTEXT_BIOASSAYSET, CONTEXT_DERIVEDBIOASSAY, defaultGuiContexts, nameType, optionalNameType, SOURCE_BIOASSAYS, SOURCE_BIOASSAYSET, SOURCE_DERIVEDBIOASSAY, TRANSFORMATION_NAME
annotationSection, configuration, COPY_ANNOTATIONS, job, OVERWRITE_ANNOTATIONS, sc
Constructor and Description |
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MedianRatioNormalization() |
Modifier and Type | Method and Description |
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void |
configure(GuiContext context,
Request request,
Response response)
Configure the plugin.
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private RequestInformation |
getConfigureJobParameters() |
java.util.Collection<Permissions> |
getPermissions()
Request use access to Experiment:s and read access to Job:s.
|
RequestInformation |
getRequestInformation(GuiContext context,
java.lang.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.
|
java.lang.String |
isInContext(GuiContext context,
java.lang.Object item)
Check that the item is a bioassayset/derived bioassay and that the
logged in user has permission to use the current item.
|
private float |
median(float[] sortedArray,
int first,
int last) |
private double |
median(java.util.List<MedianRatioNormalization.SpotData> data) |
BioAssaySet |
normalize(DbControl dc,
BioAssaySet source,
Job job,
float minIntensity,
float lowExclude,
float highExclude,
int blockGroupSize,
ProgressReporter progress)
Normalise the source bioassay set using MEDIAN-RATIO normalization.
|
private BioAssaySet |
normalize1ch(DbControl dc,
BioAssaySet source,
Job job,
float minIntensity,
float lowExclude,
float highExclude,
ProgressReporter progress)
Normalise the source bioassay set using MEDIAN-RATIO normalization.
|
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.
|
getChildDescriptionParameter, getChildNameParameter, getCurrentBioAssaySet, getCurrentDerivedBioAssay, getCurrentExperiment, getGuiContexts, getMainType, getSourceBioAssays, getSourceBioAssaySet, getSourceBioAssaySetParameter, getSourceBioAssaysParameter, getSourceDerivedBioAssay, getSourceDerivedBioAssayParameter, getTransformationName, getTransformationNameParameter, restrictSource
cloneParameterWithDefaultValue, closeLogFile, createLogFile, done, getCopyAnnotationsParmeter, getCurrentConfiguration, getCurrentJob, getJobOrConfigurationValue, getOverwriteAnnotationsParameters, init, log, log, storeValue, storeValue, storeValues, validateRequestParameters
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getGuiContexts
done, getMainType, init
private static final java.util.Set<Permissions> permissions
private PluginParameter<java.lang.Float> minIntensityParameter
private static final PluginParameter<java.lang.Float> highExcludeParameter
private static final PluginParameter<java.lang.Float> lowExcludeParameter
private static final PluginParameter<java.lang.Integer> blockGroupParameter
protected static final PluginParameter<java.lang.String> medianRatioSection
private RequestInformation configureJob
private ThreadSignalHandler signalHandler
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 java.util.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 java.lang.String isInContext(GuiContext context, java.lang.Object item)
AbstractAnalysisPlugin
isInContext
in interface InteractivePlugin
isInContext
in class AbstractAnalysisPlugin
context
- Current guicontextitem
- The item to check.public RequestInformation getRequestInformation(GuiContext context, java.lang.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 commandRequestInformation
for the commandBaseException
- 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 BioAssaySet normalize1ch(DbControl dc, BioAssaySet source, Job job, float minIntensity, float lowExclude, float highExclude, ProgressReporter progress)
dc
- The DbControl to use for database accesssource
- The source bioassay set that is going to be normalizedjob
- The job in which the normalization is done.minIntensity
- All spots which have a lower intensity value
in either channel will be filtered outlowExclude
- A percentage of the spots with lowest ratio that
are excuded in the median calculationhighExclude
- A percentage of the spots with highest ratio
that are excluded in the median calculationprogress
- Progress reporter for the caller to keep track of
the plugin's progress. Null is allowed.public BioAssaySet normalize(DbControl dc, BioAssaySet source, Job job, float minIntensity, float lowExclude, float highExclude, int blockGroupSize, ProgressReporter progress)
dc
- The DbControl to use for database accesssource
- The source bioassay set that is going to be normalizedjob
- The job that is doing the normalization, or nullminIntensity
- All spots which have a lower intensity value in either channel
will be filtered outlowExclude
- A percentage of the spots with lowest ratio that are excuded in the
median calculationhighExclude
- A percentage of the spots with highest ratio that are excluded in the
median calculationblockGroupSize
- progress
- Progress reporter for the caller to keep track of the plugin's progress. Null is allowed.private RequestInformation getConfigureJobParameters()
private float median(float[] sortedArray, int first, int last)
private double median(java.util.List<MedianRatioNormalization.SpotData> data)