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A
- accept(File, String) - Method in class MAEPlugin.PluginFilenameFilter
- accept() - Filter method for accepting a file.
- actionPerformed(ActionEvent) - Method in class MAEPlugin.MenuPlugin
- actionPerformed() - actionListener
C
- CheckBoxMenuPlugin - class MAEPlugin.CheckBoxMenuPlugin.
- This class extends the MAEPlugin base class to implement a CheckBoxMenuPlugin base class.
- CheckBoxMenuPlugin(String) - Constructor for class MAEPlugin.CheckBoxMenuPlugin
- CheckBoxMenuPlugin() - constuctor with user supplied label
- CheckBoxMenuPlugin(String, String) - Constructor for class MAEPlugin.CheckBoxMenuPlugin
- CheckBoxMenuPlugin() - constuctor with user supplied label and plugin filename
- CheckBoxMenuPlugin() - Constructor for class MAEPlugin.CheckBoxMenuPlugin
- CheckBoxMenuPlugin() - constuctor to use default "CheckBoxPlugin" label name
- calcIntensityScaleExtrema(float, float, float, float, int) - Method in interface MAEPlugin.Normalization
- calcIntensityScaleExtrema() - compute scaled Intensity upper and lower limits of raw data for each sample.
- classNameReplacementChar - Variable in class MAEPlugin.JarClassLoader
- Utility Char
- classes - Variable in class MAEPlugin.JarClassLoader
- Contains the loaded classes
D
- DBUG_MAEP - Static variable in class MAEPlugin.MAEPlugin
- DuplicatePluginLoadException - exception MAEPlugin.DuplicatePluginLoadException.
- This exception is used to allow self registering of plugins for a max number of plugins.
- DuplicatePluginLoadException() - Constructor for class MAEPlugin.DuplicatePluginLoadException
- dir - Variable in class MAEPlugin.FileClassLoader
- String path
- disableNormalizationPlugin() - Method in interface MAEPlugin.MAEStub
- disableNormalizationPlugin() - clear activeNormalization state.
F
- FileClassLoader - class MAEPlugin.FileClassLoader.
- Class to dynamic classes from local disks.
- FileClassLoader(String) - Constructor for class MAEPlugin.FileClassLoader
- FileClassLoader() - Constructor to load path.
- FileClassLoader(File) - Constructor for class MAEPlugin.FileClassLoader
- FileClassLoader() - Constructor to load .classfile.
- findFileClass(String) - Method in class MAEPlugin.FileClassLoader
- findFileClass() - find file of class by name.
- finishPipeline(int) - Method in interface MAEPlugin.Normalization
- finishPipeline() - finish filter at end of normalization of all genes (if required).
- formatClassName(String) - Method in class MAEPlugin.JarClassLoader
- formatClassName() - generate a name with ".class" extension
G
- getFlag() - Method in class MAEPlugin.MAEPlugin
- getFlag() - get the menu status (CheckBox) menuFlag
- getFrame() - Method in interface MAEPlugin.MAEStub
- getFrame() - provides Frame for Dialogs and other AWT components that need frames.
- getInstance() - Method in class MAEPlugin.MAEPlugin
- getInstance() - returns Registry instance of this class or new if not loaded
- getJarResources() - Method in class MAEPlugin.JarClassLoader
- getMAEStub() - Method in class MAEPlugin.MAEPlugin
- getMAEStub() - get the menu stub for this instance of plugin
- getMenuHook() - Method in class MAEPlugin.MAEPlugin
- getMenuHook() - get menu Item hook to put our instance of plugin
- getMenuHook() - Method in interface MAEPlugin.MAEStub
- getMenuHook() - method to retrieve the root menu
- getMenuInsertionPointName() - Method in class MAEPlugin.MAEPlugin
- getMenuInsertionPointName() - get the name of menu insertion point If it is not defined, then it returns null that indicates the Plugins menu.
- getMenuItem() - Method in class MAEPlugin.MAEPlugin
- getMenuItem() - get menu item for this instance of the plugin
- getNormalizationState() - Method in interface MAEPlugin.MAEStub
- getNormalizationState() - alias to: EventMenu.getNormalizationState used by: NormalizationPlugin
- getNumberPlugins() - Static method in class MAEPlugin.MAEPlugin
- getNumberPlugins() - get the number of plugins (loaded).
- getPluginDescription() - Method in class MAEPlugin.MAEPlugin
- getPluginDescription() - returns a human readable description of the Plugin if any is defined by the plugin writer.
- getPluginDescription() - Method in interface MAEPlugin.PluginStub
- getPluginDescription() - returns a human readable description of the Plugin.
- getPluginFileName() - Method in class MAEPlugin.MAEPlugin
- getPluginFileName() - returns the plugin file name without the ".jar"
- getPluginFileName() - Method in interface MAEPlugin.PluginStub
- getPluginFileName() - returns the plugin file name without the ".jar"
- getPluginName() - Method in class MAEPlugin.MAEPlugin
- getPluginName() - This is the human readable name for use in menu labels
- getPluginName() - Method in interface MAEPlugin.PluginStub
- getPluginName() - returns the human readable name for use in labels.
- getPlugins() - Static method in class MAEPlugin.MAEPlugin
- getPlugins() - gets Registry list of MAEPlugins
- getResource(String) - Method in class MAEPlugin.FileClassLoader
- getResource() - Returns a URL containing the location of the named resource.
- getResource(String) - Method in class MAEPlugin.JarResources
- getResource() - Extracts a jar resource as a blob.
- getResourceAsStream(String) - Method in class MAEPlugin.FileClassLoader
- getResourceAsStream() - returns an input stream to the named source.
- getSample() - Method in interface MAEPlugin.Normalization
- getSample() - get the sample object
- getSampleTotHistStats(Object) - Method in interface MAEPlugin.MAEStub
- getSampleTotHistStats() - get Hashtable list of a sample's total histogram statistics.
- getState() - Method in class MAEPlugin.CheckBoxMenuPlugin
- getState() - utility to get the checkbox state
- getState() - Method in interface MAEPlugin.Normalization
- getState() - get the state of the checkbox
I
- insertPluginMenu(MenuItem) - Method in interface MAEPlugin.MAEStub
- insertPluginMenu() - method to insert plugin into menu
- isResource(String) - Method in class MAEPlugin.JarResources
- isResource() - checks to see if resource exists
- isZip - Variable in class MAEPlugin.FileClassLoader
- zip path flag
- itemStateChanged(ItemEvent) - Method in class MAEPlugin.CheckBoxMenuPlugin
- itemStateChanged() - implements ItemListener for checkbox change
J
- JarClassLoader - class MAEPlugin.JarClassLoader.
- JarClassLoader provides a minimalistic ClassLoader which shows how to instantiate a class which resides in a .jar file.
- JarClassLoader(String) - Constructor for class MAEPlugin.JarClassLoader
- JarClassLoader() - default constructor that loads jar from the jarPath.
- JarClassLoader(File) - Constructor for class MAEPlugin.JarClassLoader
- JarClassLoader() - constructor2 that loads jar from the path that is derived from the jarFile.
- JarResources - class MAEPlugin.JarResources.
- JarResources: JarResources maps all resources included in a Zip or Jar file.
- JarResources(String) - Constructor for class MAEPlugin.JarResources
- JarResources() - constructor for createing a JarResources.
- jarContents - Variable in class MAEPlugin.JarResources
- jarFileName - Variable in class MAEPlugin.JarResources
- jarResources - Variable in class MAEPlugin.JarClassLoader
- utility object that loads resources from a Jar
- jarResources - Variable in class MAEPlugin.MAEPlugin
- access to the jar file for loading support files
L
- loadClass(String, boolean) - Method in class MAEPlugin.FileClassLoader
- loadClass() - Implementation of ClassLoader.loadClass() From javadoc v.
- loadClass(String) - Method in class MAEPlugin.FileClassLoader
- loadClass() - Implementation of ClassLoader.loadClass() by name of class.
- loadClass(File) - Method in class MAEPlugin.FileClassLoader
- loadClass() - Implementation of ClassLoader.loadClass() by name of File pointer.
- loadClass(File, boolean) - Method in class MAEPlugin.FileClassLoader
- * loadClass() - Implementation of ClassLoader.loadClass() by name of File pointer and user option to resolve.
- loadClass(String) - Method in class MAEPlugin.JarClassLoader
- loadClass() - load specified class and let it resolve the class if necessary.
- loadClass(String, boolean) - Method in class MAEPlugin.JarClassLoader
- loadClass() - load specified class
- loadClassBytes(String) - Method in class MAEPlugin.JarClassLoader
- loadClassBytes() loads bytes for class files.
- loadClassFromZip(String, String) - Method in class MAEPlugin.FileClassLoader
- loadClassFromZip() - loads classes and resources of a zip or jar file and loads the one class that has the same name as the archive.
- loadJarContents() - Method in class MAEPlugin.JarResources
- loadJarContents() - initializes internal hash tables with jar file resources.
- loadPluginsStartup() - Method in interface MAEPlugin.MAEStub
- loadPluginsStartup() - method to load plugins from file via startup
- logZero(double) - Method in interface MAEPlugin.MAEStub
- logZero() - compute log10((x==0.0 ? 0.0 : x) - avoid log(0.0)! This defaults log10(0.0) to log(1.0).
M
- MAEPlugin - package MAEPlugin
- MAEPlugin - class MAEPlugin.MAEPlugin.
- This abstract class defines the base MAEPlugin base class.
- MAEPlugin() - Constructor for class MAEPlugin.MAEPlugin
- MAEPlugin() - This private constructor prevents non-labeled and registered plugins
- MAEPlugin(String) - Constructor for class MAEPlugin.MAEPlugin
- MAEPlugin() - Constructor registers the plugin and sets up menu item.
- MAEPlugin(String, String) - Constructor for class MAEPlugin.MAEPlugin
- MAEPlugin() - Constructor registers the plugin and sets up menu item.
- MAEStub - interface MAEPlugin.MAEStub.
- This interface Enforces MAE compliance with Plugin requirements.
- MaxNumberPluginsException - exception MAEPlugin.MaxNumberPluginsException.
- This exception is used to allow self registering of plugins for a max number of plugins.
- MaxNumberPluginsException() - Constructor for class MAEPlugin.MaxNumberPluginsException
- MenuPlugin - class MAEPlugin.MenuPlugin.
- This abstract class defines MenuPlugin class.
- MenuPlugin(String) - Constructor for class MAEPlugin.MenuPlugin
- MenuPlugin() - constructor for menu.
- MenuPlugin() - Constructor for class MAEPlugin.MenuPlugin
- MenuPlugin() - constructor to override to implement the plugin
- maestub - Variable in class MAEPlugin.MAEPlugin
- This interface must be implemented in the user's plugin code
- menuActivated() - Method in class MAEPlugin.MAEPlugin
- menuActivated() - this method calls the pluginMain() method in GUI contexts.
- menuActivated() - Method in interface MAEPlugin.PluginStub
- menuActivated() - method called when menu is clicked for menu driven plugins.
- menuFlag - Variable in class MAEPlugin.MAEPlugin
- Menu flag, activated from menuItem.
- menuHook - Variable in class MAEPlugin.MAEPlugin
- Provides a hook into the mae Menubar
- menuHook - Static variable in interface MAEPlugin.MAEStub
- menu where plugins should hook themselves.
- menuInsertionPointName - Variable in class MAEPlugin.MAEPlugin
- menu insertion point name if not null.If null, then put into PluginMenu hook
- menuItem - Variable in class MAEPlugin.MAEPlugin
- GUI Elements
N
- Normalization - interface MAEPlugin.Normalization.
P
- PLUGIN_VERSION - Static variable in interface MAEPlugin.PluginStub
- MAEPlugin version # for tracking
- PluginException - exception MAEPlugin.PluginException.
- This exception is used to allow self registering of plugins for a max number of plugins.
- PluginException() - Constructor for class MAEPlugin.PluginException
- PluginFilenameFilter - class MAEPlugin.PluginFilenameFilter.
- Class Filename filter for class files.
- PluginFilenameFilter() - Constructor for class MAEPlugin.PluginFilenameFilter
- PluginFilenameFilter() - Filter for class files, may be modified by regedit style wild cards.
- PluginStub - interface MAEPlugin.PluginStub.
- Enforces method implementations in suport of MAEPlugin.
- plugInFileName - Variable in class MAEPlugin.MAEPlugin
- File name of the plugin without the ".jar"
- plugInName - Variable in class MAEPlugin.MAEPlugin
- The human readable name for labels and such, the class names need to be unique to identify the plugins
- pluginHalt() - Method in class MAEPlugin.MAEPlugin
- pluginHalt() - Plugin halt method.
- pluginHalt() - Method in interface MAEPlugin.PluginStub
- pluginHalt() - Plugin halt method.
- pluginInit() - Method in class MAEPlugin.MAEPlugin
- pluginInit() - Plugin init method.
- pluginInit() - Method in interface MAEPlugin.PluginStub
- pluginInit() - Plugin init method.
- pluginMain() - Method in class MAEPlugin.CheckBoxMenuPlugin
- pluginMain() - abstract the method end-users implement to use the API
- pluginMain() - Method in class MAEPlugin.MAEPlugin
- pluginMain() - abstract method end-users must implement to use the API.
- pluginMain() - Method in class MAEPlugin.MenuPlugin
- pluginMain() - abstract the method end-users implement to use the API
- pluginMain() - Method in interface MAEPlugin.PluginStub
- pluginMain() - this is the method end-users implement to use the API.
- propertySupport - Variable in class MAEPlugin.MAEPlugin
- bean property for future use
R
- recalcNormalizationExtrema() - Method in interface MAEPlugin.Normalization
- recalcNormalizationExtrema() - set the extreama for all samples for this plugin
- recalcNorms(String, boolean) - Method in interface MAEPlugin.MAEStub
- recalcNorms() - alias to: mae.cdb.recalcNorms(String, boolean); used by: NormalizationPlugin
- refreshDataFilter() - Method in interface MAEPlugin.MAEStub
- refreshDataFilter() - refresh the datsa filter
- registry - Static variable in class MAEPlugin.MAEPlugin
- Instance registry for all sub classes of MAEPLugin Works with constructors() and dispose() to maintain a database of all plugins
- registryMaxSize - Static variable in class MAEPlugin.MAEPlugin
- Set the initial and max size for the number of resgistry entries
- removePlugin(MAEPlugin) - Static method in class MAEPlugin.MAEPlugin
- removePlugin () - unloads plugin and removes it from the MAexplorer menu.
- removePluginMenu(MenuItem) - Method in interface MAEPlugin.MAEStub
- remove plugin menu
- resetPipeline(int) - Method in interface MAEPlugin.Normalization
- resetPipeline() - reset filter at start of data Normalization.
S
- scaleIntensityData(float) - Method in interface MAEPlugin.Normalization
- scaleIntensityData() - scale raw intensity data as fct of normalization mode.
- scaleIntensityData(float, int, int, int) - Method in interface MAEPlugin.Normalization
- scaleIntensityData() - scale raw intensity data as fct of normalization mode.
- scaleIntensityData(float, float, int, int, int) - Method in interface MAEPlugin.Normalization
- scaleIntensityData() - the gene normalization operating on gene mid for sampleIdx where the data is ether extracted here or from the resetPipeline pre-analysis.
- setClassNameReplacementChar(char) - Method in class MAEPlugin.JarClassLoader
- setClassNameReplacementChar() - remap class name.
- setFlag(boolean) - Method in class MAEPlugin.MAEPlugin
- setFlag() - set the menu status (CheckBox) menuFlag
- setJarResources(JarResources) - Method in class MAEPlugin.MAEPlugin
- setJarResources() - sets the JarResources object to get to the contents of the Jar object.
- setMAEStub(MAEStub) - Method in class MAEPlugin.MAEPlugin
- setMAEStub() - get the menu stub for this instance of plugin
- setMenuHook(MenuItem) - Method in class MAEPlugin.MAEPlugin
- setMenuHook() - set menu Item hook to put our instance of plugin
- setMenuHook(Menu) - Method in interface MAEPlugin.MAEStub
- setMenuHook() - method to set access root menu
- setMenuInsertionPointName(String) - Method in class MAEPlugin.MAEPlugin
- setMenuInsertionPointName() - set the name of menu insertion point.
- setMenuItem(MenuItem) - Method in class MAEPlugin.MAEPlugin
- setMenuItem() - get menu item for this instance of the plugin
- setMenuLabel(String) - Method in class MAEPlugin.MAEPlugin
- setMenuLabel() - changes the label on the mennItem
- setNormalizationState(boolean) - Method in interface MAEPlugin.MAEStub
- setNormalizationState() - alias to: EventMenu.setNormalizationState used by: NormalizationPlugin
- setNormalizationStateFromPlugin(String) - Method in interface MAEPlugin.MAEStub
- setNormalizationStateFromPlugin() - used by: NormalizationPlugin
- setSample(Object) - Method in interface MAEPlugin.Normalization
- setSample() - set the sample object
- setState(boolean) - Method in class MAEPlugin.CheckBoxMenuPlugin
- setState() - utility to set the checkbox state
- setState(boolean) - Method in interface MAEPlugin.Normalization
- setState() - set the state of the checkbox
- showMsg(String) - Method in interface MAEPlugin.MAEStub
- showMsg() - alias to: Util.showMsg(String); used by: (all).
A C D F G I J L M N P R S
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