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java.lang.Object net.sf.basedb.core.plugin.AbstractPlugin net.sf.basedb.core.plugin.AbstractAnalysisPlugin net.sf.basedb.plugins.MedianRatioNormalization
public class MedianRatioNormalization
Nested Class Summary | |
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private static class |
MedianRatioNormalization.SpotData
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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 static PluginParameter<Integer> |
blockGroupParameter
Used with 2-channel data only |
private RequestInformation |
configureJob
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private static PluginParameter<Float> |
highExcludeParameter
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private static PluginParameter<Float> |
lowExcludeParameter
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protected static PluginParameter<String> |
medianRatioSection
Section for normalization options |
private static PluginParameter<String> |
methodParameter
List of median normalization methods. |
private PluginParameter<Float> |
minIntensityParameter
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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, defaultGuiContexts, nameType, optionalNameType, SOURCE_BIOASSAYS, SOURCE_BIOASSAYSET, 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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MedianRatioNormalization()
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Method Summary | |
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void |
configure(GuiContext context,
Request request,
Response response)
Configure the plugin. |
About |
getAbout()
Get information about the plugin, such as name, version, authors, etc. |
private RequestInformation |
getConfigureJobParameters()
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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 and that the logged in user has permission to use the current experiment. |
private float |
median(float[] sortedArray,
int first,
int last)
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private double |
median(List<MedianRatioNormalization.SpotData> data)
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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,
boolean scale,
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. |
Methods inherited from class net.sf.basedb.core.plugin.AbstractAnalysisPlugin |
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getChildDescriptionParameter, getChildNameParameter, getCurrentBioAssaySet, getCurrentExperiment, getGuiContexts, getMainType, getSourceBioAssays, getSourceBioAssaySet, getSourceBioAssaySetParameter, getSourceBioAssaysParameter, getTransformationName, getTransformationNameParameter, restrictSource |
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.InteractivePlugin |
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getGuiContexts |
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 About about
private static final Set<Permissions> permissions
private PluginParameter<Float> minIntensityParameter
private static final PluginParameter<Float> highExcludeParameter
private static final PluginParameter<Float> lowExcludeParameter
private static final PluginParameter<String> methodParameter
private static final PluginParameter<Integer> blockGroupParameter
protected static final PluginParameter<String> medianRatioSection
private RequestInformation configureJob
private ThreadSignalHandler signalHandler
Constructor Detail |
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public MedianRatioNormalization()
Method Detail |
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public About getAbout()
Plugin
getAbout
in interface Plugin
About
objectpublic 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 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 BioAssaySet normalize1ch(DbControl dc, BioAssaySet source, Job job, float minIntensity, float lowExclude, float highExclude, boolean scale, 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 calculationscale
- If true, scale intensities with median intensity,
otherwise subtract median intensityprogress
- 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(List<MedianRatioNormalization.SpotData> data)
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2.17.2: 2011-06-17 | ||||||||
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