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MAEPlugin.analysis
Class NormalizationPlugin
java.lang.ObjectMAEPlugin.MAEPlugin
- All Implemented Interfaces:
- java.util.EventListener, java.awt.event.ItemListener, MAEPlugin.Normalization, MAEPlugin.PluginStub
- public abstract class NormalizationPlugin
- extends AnalysisPlugin
- implements MAEPlugin.Normalization
- extends AnalysisPlugin
This class extends the analysis MAEPlugin base class to implement the Normalization base class. The "active normalization" is a static reference that all Normalization classes share. Whichever one is active will be the one used. Created on September 7, 2001, 5:46 PM
This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government. As a work of the United States Government there is no associated copyright. It is offered as open source software under the Mozilla Public License (version 1.1) subject to the limitations noted in the accompanying LEGAL file. This notice must be included with the code. The MAExplorer Mozilla and Legal files are available on http://maexplorer.sourceforge.net/.
- Version:
- $Date: 2003/03/03 16:22:10 $ / $Revision: 1.6 $
| Field Summary | |
protected static MAEPlugin.Normalization |
activeNormalization
Pointer to the current active Normalization object. |
protected java.lang.Object |
sample
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| Fields inherited from class MAEPlugin.MAEPlugin |
DBUG_MAEP, jarResources, registryMaxSize |
| Fields inherited from interface MAEPlugin.PluginStub |
PLUGIN_VERSION |
| Constructor Summary | |
NormalizationPlugin()
NormalizationPlugin() - Default Constructor puts default menu name in menu. |
|
NormalizationPlugin(java.lang.String menuLabel)
NormalizationPlugin() - Default Constructor puts menu name in menu. |
|
NormalizationPlugin(java.lang.String menuLabel,
java.lang.String pluginFileName)
NormalizationPlugin() - Default Constructor puts menu name in menu and file name. |
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| Method Summary | |
abstract float[] |
calcIntensityScaleExtrema(float maxRI,
float minRI,
float maxRaw,
float minRaw,
int sampleNbr)
calcIntensityScaleExtrema() - compute scaled Intensity upper and lower limits of raw data for each sample. |
abstract void |
close(boolean preserveDataStructuresFlag)
close() - close the plugin |
static void |
disableNormalizationPlugin()
disableNormalizationPlugin() - clear activeNormalization state. |
abstract boolean |
finishPipeline(int optArg)
finishPipeline() - finish filter at end of normalization of all genes (if required). |
static MAEPlugin.Normalization |
getActiveNormalization()
getActiveNormalization() - Bean-style method for getting the activeNormalization. |
static boolean |
getNormalizationState()
getNormalizationState() - Static method for using testing getActiveNormalization(). |
java.lang.Object |
getSample()
getSample() - used to Get the primary sample, to get the variables |
void |
pluginHalt()
pluginHalt() - stop the plugin |
void |
pluginMain()
pluginMain() is the method activated when end-users check a checkbox API. |
abstract void |
recalcNormalizationExtrema()
recalcNormalizationExtrema() - set the extreama for all samples for this plugin |
abstract boolean |
resetPipeline(int optArg)
resetPipeline() - reset filter at start of data Normalization. |
abstract float |
scaleIntensityData(float rawData)
scaleIntensityData() - scale raw intensity data as fct of normalization mode. |
abstract float |
scaleIntensityData(float rawIntensity,
float rawBkgrd,
int mid,
int gid,
int sampleIdx)
scaleIntensityData() - the gene normalization operating on gene mid for sampleIdx where the data is ether extracted here or from the resetPipeline pre-analysis. |
abstract float |
scaleIntensityData(float rawData,
int mid,
int gid,
int sampleNbr)
scaleIntensityData() - scale raw intensity data as fct of normalization mode. |
void |
setActiveNormalization(MAEPlugin.Normalization obj)
setActiveNormalization() - Bean-style method for setting the activeNormalization. |
void |
setSample(java.lang.Object obj)
setSample() - method used to set primary variables from the sample. |
abstract void |
updateCurGene(int mid)
updateCurGene() - abstract method end-users must implement to use the API. |
abstract void |
updateFilter()
updateFilter() - abstract method end-users must implement to use the API. |
abstract void |
updateLabels()
updateLabels() - abstract method end-users must implement to use the API. |
abstract void |
updateSlider()
updateSlider() - abstract method end-users must implement to use the API. |
| Methods inherited from class MAEPlugin.CheckBoxMenuPlugin |
getState, itemStateChanged, setState |
| Methods inherited from class MAEPlugin.MAEPlugin |
getFlag, getInstance, getMAEStub, getMenuHook, getMenuInsertionPointName, getMenuItem, getNumberPlugins, getPluginDescription, getPluginFileName, getPluginName, getPlugins, menuActivated, pluginInit, removePlugin, setFlag, setJarResources, setMAEStub, setMenuHook, setMenuInsertionPointName, setMenuItem, setMenuLabel |
| Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
| Methods inherited from interface MAEPlugin.Normalization |
getState, setState |
| Field Detail |
activeNormalization
protected static MAEPlugin.Normalization activeNormalization
- Pointer to the current active Normalization object. Reference to this
object allows normalization methods to find the active normalization.
This is static since only one normalization method may be active at a time.
If the value is null, then there is NO active NormalizationPlugin
even if several are loaded.
sample
protected java.lang.Object sample
| Constructor Detail |
NormalizationPlugin
public NormalizationPlugin()
- NormalizationPlugin() - Default Constructor puts default menu name in menu.
NormalizationPlugin
public NormalizationPlugin(java.lang.String menuLabel)
- NormalizationPlugin() - Default Constructor puts menu name in menu.
NormalizationPlugin
public NormalizationPlugin(java.lang.String menuLabel, java.lang.String pluginFileName)
- NormalizationPlugin() - Default Constructor puts menu name in menu and file name.
| Method Detail |
pluginMain
public final void pluginMain()
- pluginMain() is the method activated when end-users check a checkbox API.
This is unlike other plugins in that analysis will be done passively.
- Specified by:
pluginMainin interfaceMAEPlugin.PluginStub
disableNormalizationPlugin
public static final void disableNormalizationPlugin()
- disableNormalizationPlugin() - clear activeNormalization state.
If the state is null, then there are no active normalization plugins
even if one or more is loaded.
getNormalizationState
public static final boolean getNormalizationState()
- getNormalizationState() - Static method for using testing getActiveNormalization().
It is used in MaeJavaAPI.
If there is no active NormalizationPlugin instance, then this is false.
getActiveNormalization
public static final MAEPlugin.Normalization getActiveNormalization()
- getActiveNormalization() - Bean-style method for getting the activeNormalization.
If there is no active NormalizationPlugin instance, then this is null.
setActiveNormalization
public final void setActiveNormalization(MAEPlugin.Normalization obj)
- setActiveNormalization() - Bean-style method for setting the activeNormalization.
This method calls underlying methods in MAExplorer to treat the checkbox
as a radio button and make sure that it disables other Normalization
methods whether built-in or other normalization plugins.
pluginHalt
public void pluginHalt()
- pluginHalt() - stop the plugin
- Specified by:
pluginHaltin interfaceMAEPlugin.PluginStub
getSample
public final java.lang.Object getSample()
- getSample() - used to Get the primary sample, to get the variables
- Specified by:
getSamplein interfaceMAEPlugin.Normalization
setSample
public final void setSample(java.lang.Object obj)
- setSample() - method used to set primary variables from the sample.
- Specified by:
setSamplein interfaceMAEPlugin.Normalization
resetPipeline
public abstract boolean resetPipeline(int optArg)
- resetPipeline() - reset filter at start of data Normalization.
We will test for ALL GENES (if required) using the midOK[] boolean
created here to later determine if we actually perform the test.
This sets up the state that may be used during the pipeline operation.
- Specified by:
resetPipelinein interfaceMAEPlugin.Normalization
finishPipeline
public abstract boolean finishPipeline(int optArg)
- finishPipeline() - finish filter at end of normalization of all genes (if required).
This may be used to clean up the state after the pipeline operation.
- Specified by:
finishPipelinein interfaceMAEPlugin.Normalization
calcIntensityScaleExtrema
public abstract float[] calcIntensityScaleExtrema(float maxRI,
float minRI,
float maxRaw,
float minRaw,
int sampleNbr)
- calcIntensityScaleExtrema() - compute scaled Intensity upper
and lower limits of raw data for each sample. It is called
to get extrema for use in scaling displays and other computations
where the limits must be known.
- Specified by:
calcIntensityScaleExtremain interfaceMAEPlugin.Normalization
scaleIntensityData
public abstract float scaleIntensityData(float rawData)
- scaleIntensityData() - scale raw intensity data as fct of normalization
mode. This is called on a per-spot basis.
- Specified by:
scaleIntensityDatain interfaceMAEPlugin.Normalization
scaleIntensityData
public abstract float scaleIntensityData(float rawData,
int mid,
int gid,
int sampleNbr)
- scaleIntensityData() - scale raw intensity data as fct of normalization mode.
There is a (gid,sampleNbr) dependence on the normalization.
This is called on a per-spot basis.
- Specified by:
scaleIntensityDatain interfaceMAEPlugin.Normalization
scaleIntensityData
public abstract float scaleIntensityData(float rawIntensity,
float rawBkgrd,
int mid,
int gid,
int sampleIdx)
- scaleIntensityData() - the gene normalization operating on gene mid
for sampleIdx where the data is ether extracted here or from the resetPipeline
pre-analysis.
If the normalization is inoperative, then just return 0.0.
The mid must be >=0 since -1 indicates an illegal gene.
The midOK[mid] must be true, else it indicates an illegal gene.
[NOTE] The plugin writer should try to avoid doing special analyses here that
need to be computed DURING the processing and instead do the computations
during the resetPipeline() operation if possible. That may be able to
optimized and the data cached to avoid constant recomputation.
- Specified by:
scaleIntensityDatain interfaceMAEPlugin.Normalization
recalcNormalizationExtrema
public abstract void recalcNormalizationExtrema()
- recalcNormalizationExtrema() - set the extreama for all samples for this plugin
- Specified by:
recalcNormalizationExtremain interfaceMAEPlugin.Normalization
updateCurGene
public abstract void updateCurGene(int mid)
- updateCurGene() - abstract method end-users must implement to use
the API. It is called by the popup Registry for the user to update
any dependent data since the current gene has changed.
updateFilter
public abstract void updateFilter()
- updateFilter() - abstract method end-users must implement to use the API.
It is called by the popup Registry for the user to update
any dependent data since the data Filter has changed.
updateSlider
public abstract void updateSlider()
- updateSlider() - abstract method end-users must implement to use the API.
It is called by the popup Registry for the user to update
any dependent data since the threshold sliders have changed.
This is invoked from the PopupRegistry.
updateLabels
public abstract void updateLabels()
- updateLabels() - abstract method end-users must implement to use the API.
It is called by the popup Registry for the user to update
any dependent data since some global labels have changed.
close
public abstract void close(boolean preserveDataStructuresFlag)
- close() - close the plugin
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DETAIL: FIELD | CONSTR | METHOD | ||||||||