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java.lang.Object net.sf.basedb.core.plugin.AbstractPlugin net.sf.basedb.core.plugin.AbstractAnalysisPlugin net.sf.basedb.plugins.LowessNormalization
public class LowessNormalization
Nested Class Summary | |
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(package private) static class |
LowessNormalization.CallableWorker
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private static class |
LowessNormalization.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
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private RequestInformation |
configureJob
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private static PluginParameter<Float> |
deltaParameter
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private static PluginParameter<Float> |
fitFractionParameter
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private static PluginParameter<Integer> |
iterParameter
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protected static PluginParameter<String> |
lowessSection
Section for lowess options |
private static Set<Permissions> |
permissions
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private EnhancedThreadSignalHandler |
signalHandler
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private static double |
ywRangeFactor
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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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LowessNormalization()
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Method Summary | |
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private static List<Double> |
calculateWeights(List<LowessNormalization.SpotData> data,
double A1,
List<Double> wFit)
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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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private PluginParameter<ReporterList> |
getExcludeReportersParameters(DbControl dc)
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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 static List<Double> |
lowess(List<LowessNormalization.SpotData> data,
double f,
int iter,
double delta)
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private static double |
medianCorrection(List<LowessNormalization.SpotData> data,
Double[] smoothCurve)
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BioAssaySet |
normalize(DbControl dc,
BioAssaySet source,
Job job,
float fitFraction,
float delta,
int iterations,
int blockGroupSize,
ProgressReporter progress)
Normalise the source bioassay set using LOWESS normalization. |
BioAssaySet |
normalize(DbControl dc,
BioAssaySet source,
Job job,
float fitFraction,
float delta,
int iterations,
int blockGroupSize,
ReporterList excludeReporters,
ProgressReporter progress)
Normalise the source bioassay set using LOWESS normalization. |
private List<LowessNormalization.SpotData> |
readData(DbControl dc,
DynamicSpotQuery query,
BioAssay assay)
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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. |
private static double[] |
weightedLeastSquaresRegression(List<LowessNormalization.SpotData> data,
List<Double> w)
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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 static final PluginParameter<Float> fitFractionParameter
private static final PluginParameter<Float> deltaParameter
private static final PluginParameter<Integer> iterParameter
private static final PluginParameter<Integer> blockGroupParameter
protected static final PluginParameter<String> lowessSection
private static double ywRangeFactor
private RequestInformation configureJob
private EnhancedThreadSignalHandler signalHandler
Constructor Detail |
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public LowessNormalization()
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
public BioAssaySet normalize(DbControl dc, BioAssaySet source, Job job, float fitFraction, float delta, int iterations, int blockGroupSize, ProgressReporter progress)
normalize(DbControl, BioAssaySet, Job, float, float, int, int, ReporterList, ProgressReporter)
public BioAssaySet normalize(DbControl dc, BioAssaySet source, Job job, float fitFraction, float delta, int iterations, int blockGroupSize, ReporterList excludeReporters, 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 nullfitFraction
- delta
- iterations
- blockGroupSize
- The number of blocks to group and normalise at the same time,
if <=0, all blocks on a bioassay are grouped to a single datasetexcludeReporters
- A reporter list containing reporters that should not be
used in when normalizing, or null to use all spotsprogress
- Progress reporter used by the caller to keep track of the progress. Null is allowed
private List<LowessNormalization.SpotData> readData(DbControl dc, DynamicSpotQuery query, BioAssay assay) throws SQLException
SQLException
private RequestInformation getConfigureJobParameters()
private PluginParameter<ReporterList> getExcludeReportersParameters(DbControl dc)
private static List<Double> lowess(List<LowessNormalization.SpotData> data, double f, int iter, double delta)
private static double medianCorrection(List<LowessNormalization.SpotData> data, Double[] smoothCurve)
private static double[] weightedLeastSquaresRegression(List<LowessNormalization.SpotData> data, List<Double> w)
private static List<Double> calculateWeights(List<LowessNormalization.SpotData> data, double A1, List<Double> wFit)
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2.17.2: 2011-06-17 | ||||||||
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