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A
- AnalysisPlugin - class MAEPlugin.analysis.AnalysisPlugin.
- This class is the analysis MAEPlugin base class and is used to implement specialized base classes based on CheckBoxMenuPlugin.
- AnalysisPlugin() - Constructor for class MAEPlugin.analysis.AnalysisPlugin
- AnalysisPlugin() - Constructor for new AnalysisPlugin with default label "Analysis Plugin".
- AnalysisPlugin(String) - Constructor for class MAEPlugin.analysis.AnalysisPlugin
- AnalysisPlugin() - Constructor for new AnalysisPlugin with label.
- AnalysisPlugin(String, String) - Constructor for class MAEPlugin.analysis.AnalysisPlugin
- AnalysisPlugin() - Constructor for new AnalysisPlugin with label and file name.
- activeFilterPluginList - Static variable in class MAEPlugin.analysis.FilterPlugin
- pointer to the active FilterPlugin object.
- activeNormalization - Static variable in class MAEPlugin.analysis.NormalizationPlugin
- Pointer to the current active Normalization object.
C
- calcIntensityScaleExtrema(float, float, float, float, int) - Method in class MAEPlugin.analysis.NormalizationPlugin
- calcIntensityScaleExtrema() - compute scaled Intensity upper and lower limits of raw data for each sample.
- close(boolean) - Method in class MAEPlugin.analysis.NormalizationPlugin
- close() - close the plugin
D
- disableNormalizationPlugin() - Static method in class MAEPlugin.analysis.NormalizationPlugin
- disableNormalizationPlugin() - clear activeNormalization state.
F
- FilterPlugin - class MAEPlugin.analysis.FilterPlugin.
- This class is the filter MAEPlugin base class and is be used to implement a filter base class:
- FilterPlugin() - Constructor for class MAEPlugin.analysis.FilterPlugin
- FilterPlugin() - Constructor for new FilterPlugin called when load the plugin.
- FilterPlugin(String) - Constructor for class MAEPlugin.analysis.FilterPlugin
- FilterPlugin() - Constructor for new FilterPlugin
- finishPipeline(int) - Method in class MAEPlugin.analysis.FilterPlugin
- finishPipeline() - finish filter at end of test of all genes (if required).
- finishPipeline(int) - Method in class MAEPlugin.analysis.NormalizationPlugin
- finishPipeline() - finish filter at end of normalization of all genes (if required).
G
- geneOperation(int) - Method in class MAEPlugin.analysis.FilterPlugin
- geneOperation() - implemented by plugin writer.
- getActiveFilterPluginList() - Static method in class MAEPlugin.analysis.FilterPlugin
- getActiveFilterPluginList() - Bean-style method for getting activeFilterPluginList.
- getActiveNormalization() - Static method in class MAEPlugin.analysis.NormalizationPlugin
- getActiveNormalization() - Bean-style method for getting the activeNormalization.
- getFilterState() - Static method in class MAEPlugin.analysis.FilterPlugin
- getFilterState() - Static method for using getActiveFilter().
- getNormalizationState() - Static method in class MAEPlugin.analysis.NormalizationPlugin
- getNormalizationState() - Static method for using testing getActiveNormalization().
- getSample() - Method in class MAEPlugin.analysis.NormalizationPlugin
- getSample() - used to Get the primary sample, to get the variables
M
- MAEPlugin.analysis - package MAEPlugin.analysis
N
- NormalizationPlugin - class MAEPlugin.analysis.NormalizationPlugin.
- This class extends the analysis MAEPlugin base class to implement the Normalization base class.
- NormalizationPlugin() - Constructor for class MAEPlugin.analysis.NormalizationPlugin
- NormalizationPlugin() - Default Constructor puts default menu name in menu.
- NormalizationPlugin(String) - Constructor for class MAEPlugin.analysis.NormalizationPlugin
- NormalizationPlugin() - Default Constructor puts menu name in menu.
- NormalizationPlugin(String, String) - Constructor for class MAEPlugin.analysis.NormalizationPlugin
- NormalizationPlugin() - Default Constructor puts menu name in menu and file name.
P
- pluginHalt() - Method in class MAEPlugin.analysis.FilterPlugin
- pluginHalt() - stop the plugin
- pluginHalt() - Method in class MAEPlugin.analysis.NormalizationPlugin
- pluginHalt() - stop the plugin
- pluginInit() - Method in class MAEPlugin.analysis.FilterPlugin
- pluginInit() - Plugin init method.
- pluginMain() - Method in class MAEPlugin.analysis.FilterPlugin
- pluginMain() is the method activated when end-users check a checkbox API.
- pluginMain() - Method in class MAEPlugin.analysis.NormalizationPlugin
- pluginMain() is the method activated when end-users check a checkbox API.
R
- recalcNormalizationExtrema() - Method in class MAEPlugin.analysis.NormalizationPlugin
- recalcNormalizationExtrema() - set the extreama for all samples for this plugin
- removeActiveFilter(FilterPlugin) - Method in class MAEPlugin.analysis.FilterPlugin
- removeActiveFilter() - Bean-style method for removing from activeFilterPluginList.
- resetPipeline(int) - Method in class MAEPlugin.analysis.FilterPlugin
- resetPipeline() - reset filter at start of test of all genes (if required).
- resetPipeline(int) - Method in class MAEPlugin.analysis.NormalizationPlugin
- resetPipeline() - reset filter at start of data Normalization.
S
- sample - Variable in class MAEPlugin.analysis.NormalizationPlugin
- scaleIntensityData(float) - Method in class MAEPlugin.analysis.NormalizationPlugin
- scaleIntensityData() - scale raw intensity data as fct of normalization mode.
- scaleIntensityData(float, int, int, int) - Method in class MAEPlugin.analysis.NormalizationPlugin
- scaleIntensityData() - scale raw intensity data as fct of normalization mode.
- scaleIntensityData(float, float, int, int, int) - Method in class MAEPlugin.analysis.NormalizationPlugin
- scaleIntensityData() - the gene normalization operating on gene mid for sampleIdx where the data is ether extracted here or from the resetPipeline pre-analysis.
- setActiveFilter(FilterPlugin) - Method in class MAEPlugin.analysis.FilterPlugin
- setActiveFilter() - Bean-style method for setting the activeFilterPluginList.
- setActiveNormalization(Normalization) - Method in class MAEPlugin.analysis.NormalizationPlugin
- setActiveNormalization() - Bean-style method for setting the activeNormalization.
- setOperation(int[], int) - Method in class MAEPlugin.analysis.FilterPlugin
- setOperation() - used in Filter intersection chain to process additional MAEPlugin filter tests.
- setSample(Object) - Method in class MAEPlugin.analysis.NormalizationPlugin
- setSample() - method used to set primary variables from the sample.
U
- updateCurGene(int) - Method in class MAEPlugin.analysis.NormalizationPlugin
- updateCurGene() - abstract method end-users must implement to use the API.
- updateFilter() - Method in class MAEPlugin.analysis.NormalizationPlugin
- updateFilter() - abstract method end-users must implement to use the API.
- updateLabels() - Method in class MAEPlugin.analysis.NormalizationPlugin
- updateLabels() - abstract method end-users must implement to use the API.
- updateSlider() - Method in class MAEPlugin.analysis.NormalizationPlugin
- updateSlider() - abstract method end-users must implement to use the API.
A C D F G M N P R S U
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