MAEPlugin
Interface MAEStub

All Known Implementing Classes:

MaeJavaAPI

public interface MAEStub

This interface Enforces MAE compliance with Plugin requirements. It provides hooks into scattered parts of MAE. Created on September 6, 2001, 8:28 AM

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 16:21:29 $ / $Revision: 1.6 $

Author:

Jai Evans (DECA/CIT), C. Santos (DECA/CIT), P. Lemkin (NCI-FCRDC)

See Also:

MAExplorer Home, MaeJavaAPI, MAEPlugin

Field Summary

static java.awt.Menu

menuHook menu where plugins should hook themselves.

Method Summary

void	disableNormalizationPlugin() disableNormalizationPlugin() - clear activeNormalization state.
java.awt.Frame	getFrame() getFrame() - provides Frame for Dialogs and other AWT components that need frames.
java.awt.Menu	getMenuHook() getMenuHook() - method to retrieve the root menu
boolean	getNormalizationState() getNormalizationState() - alias to: EventMenu.getNormalizationState used by: NormalizationPlugin
java.util.Hashtable	getSampleTotHistStats(java.lang.Object o) getSampleTotHistStats() - get Hashtable list of a sample's total histogram statistics.
void	insertPluginMenu(java.awt.MenuItem mi) insertPluginMenu() - method to insert plugin into menu
void	loadPluginsStartup() loadPluginsStartup() - method to load plugins from file via startup
double	logZero(double x) logZero() - compute log10((x==0.0 ? 0.0 : x) - avoid log(0.0)! This defaults log10(0.0) to log(1.0).
void	recalcNorms(java.lang.String msg, boolean flag) recalcNorms() - alias to: mae.cdb.recalcNorms(String, boolean); used by: NormalizationPlugin
void	refreshDataFilter() refreshDataFilter() - refresh the datsa filter
void	removePluginMenu(java.awt.MenuItem mi) remove plugin menu
void	setMenuHook(java.awt.Menu menu) setMenuHook() - method to set access root menu
void	setNormalizationState(boolean flag) setNormalizationState() - alias to: EventMenu.setNormalizationState used by: NormalizationPlugin
void	setNormalizationStateFromPlugin(java.lang.String methodNmae) setNormalizationStateFromPlugin() - used by: NormalizationPlugin
void	showMsg(java.lang.String str) showMsg() - alias to: Util.showMsg(String); used by: (all).

Field Detail

menuHook

public static final java.awt.Menu menuHook

menu where plugins should hook themselves. alias to: mbar.pluginsMenu used by: MAEPlugins and children

Method Detail

refreshDataFilter

public void refreshDataFilter()

refreshDataFilter() - refresh the datsa filter

getFrame

public java.awt.Frame getFrame()

getFrame() - provides Frame for Dialogs and other AWT components that need frames.

showMsg

public void showMsg(java.lang.String str)

showMsg() - alias to: Util.showMsg(String); used by: (all). Draws on top text line of main window.

Parameters:

str - message to draw in top text line of main window.

recalcNorms

public void recalcNorms(java.lang.String msg,
                        boolean flag)

recalcNorms() - alias to: mae.cdb.recalcNorms(String, boolean); used by: NormalizationPlugin

Parameters:

msg - name of plugin message

flag - -

disableNormalizationPlugin

public 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 boolean getNormalizationState()

getNormalizationState() - alias to: EventMenu.getNormalizationState used by: NormalizationPlugin

setNormalizationState

public void setNormalizationState(boolean flag)

setNormalizationState() - alias to: EventMenu.setNormalizationState used by: NormalizationPlugin

setNormalizationStateFromPlugin

public void setNormalizationStateFromPlugin(java.lang.String methodNmae)

setNormalizationStateFromPlugin() - used by: NormalizationPlugin

loadPluginsStartup

public void loadPluginsStartup()

loadPluginsStartup() - method to load plugins from file via startup

insertPluginMenu

public void insertPluginMenu(java.awt.MenuItem mi)

insertPluginMenu() - method to insert plugin into menu

removePluginMenu

public void removePluginMenu(java.awt.MenuItem mi)

remove plugin menu

setMenuHook

public void setMenuHook(java.awt.Menu menu)

setMenuHook() - method to set access root menu

getMenuHook

public java.awt.Menu getMenuHook()

getMenuHook() - method to retrieve the root menu

getSampleTotHistStats

public java.util.Hashtable getSampleTotHistStats(java.lang.Object o)

getSampleTotHistStats() - get Hashtable list of a sample's total histogram statistics. This data is currently computed on non-data Filtered (i.e. all genes) list of data.

 The Hashtable list returned is defined as:
 name          - Value
 "minHistData"     - float total array: min hist data value
 "maxHistData"     - float total array: max hist data value
 "mnHPri"          - float total array: rawIntens mean, all genes
                     in HP sample without background
 "sdHPri"          - float total array: rawIntens StdDev, all genes
                     in HP sample without background
 "madHPri"         - float total array: rawIntens meanAbsDev, all
                     genes in HP sample without background
 "mnHPri1"         - float total array: rawIntens f1 mean, all
                     genes in HP sample without background
 "sdHPri1"         - float total array: rawIntens f1 StdDev, all
                     genes in HP sample without background
 "mnHPri2"         - float total array: rawIntens f2 mean, all genes
                     in HP sample without background
 "sdHPri2"         - float total array: rawIntens f2 StdDev, all
                     genes in HP sample without background
 "scaleToMaxIV"    - float total array: maxFV/maxRI scale factor to
                     compute the maximum range
 "maxFV"           - float maximum and fractions of dynamic range
 "logMeanRI"       - float total array: std dev of log of means
 "logStdDevRI"     - float total array: std dev of log of means
 "logMeanAbsDevRI" - float total array: Filter hist: log of mean
                     absolute deviation raw intensity
 "logMaxRI"        - float total array: log of maxRI
 "logMinRI"        - float total array: log of minRI
  . . .
 

Parameters:

sampleNbr - sample number data to access

Returns:

Hashtable else null if not found or error.

logZero

public double logZero(double x)

logZero() - compute log10((x==0.0 ? 0.0 : x) - avoid log(0.0)! This defaults log10(0.0) to log(1.0).

Parameters:

x - argument for log

Returns:

log10((x==0.0 ? 0.0 : x) - avoid log(0.0)!