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java.lang.Object | +--MaeJavaAPI
This class implements MAEPlugin.MAEStub and is the Open Java API. The Application Programming Interface (API) is used to access MAExplorer data structures in a uniform way. This hides the actual complexity of the internal data structures making it much easier for MAEPlugin writters to use. It is designed to be used with MAExplorer MAEPlugins.
The technique we use to expose MAExplorer data structures is called "gather-scatter". For each group of data requested by a user, a collection of this data is "gathered" from internal MAExplorer data stuctures and assembled into a portable object that is returned to the user. Conversely, when the user wishes to save a (known type of) complex object back into MAExplorer, it disassembles the user'sobject and "scatters" the data (remapped back to internal data structures if necessary) into the internal MAExplorer data structures.
Because of this independence between programming domains, the MAEPlugin-writer can code to the API rather than to the underlying MAExplorer data structures. The added advantage is that the internal data structures may then be changed and improved without affecting existing user plugins.
1. Design
Data is passed in the API using standard JDK data objects so the
plugin-writer does not need to understand the internal MAExplorer data
structures.
Data objects that the user sees - packed collections of data
The data types include (int, short, float, double, byte, char, String,
Hashtable) and arrays of these types. We use Hashtable as a (Name,Value)
collection packaging class. Each Hashtable entry holds triples (String
name; Object value; class-type). Each entry is saved as an Object,
so it can be interrogated to determine its class type (see Class and
Object class definitions) - although the types and names of the objects
put into the hash tables are listed in the method descriptions.
To access any array or complex object just cast it to the required type:
E.g. Hashtable ht = (some MJA method that returns a Hashtable)
float abc[][] = (float[][]) ht.get("abc");
String xyz = (String) ht.get("xyz");
To access a scalar object, the user needs to cast the hash table object
and then use a converter method:
E.g. Hashtable ht = (some MJA method that returns a Hashtable)
float a = ((Float)ht.get("a")).floatValue();
int b = ((Integer)ht.get("b")).intValue();
short c = ((Short)ht.get("c")).shortValue();
long d = ((Long)ht.get("d")).longValue();
boolean e = ((Boolean)ht.get("e")).booleanValue();
byte f = ((Byte)ht.get("f")).byteValue();
char g = ((Character)ht.get("g")).charValue();
The MAEPlugin writer may access many of the internal MAExplorer data structures using get_xxxx() and set_xxxx() access methods in the MJAxxxx classes.
2. List of categories of MJAxxxx classes
MJAxxxx Class Objects and method access ------------- ------------------------- MJAbase constants used by other MJA classes MJAcluster cluster data structures and support MJAcondition condition lists of samples and ordered lists of condition lists MJAeval MAExplorer command interpreter MJAexprProfile expression profiles data MJAfilter gene data filters MJAgene single gene data (genomic and quantitative) MJAgeneList lists of genes and get sets MJAgenomicDB genomic databases on the Internet MJAgeometry array geometry, spot to gene maps, etc. MJAhelp popup browser help methods MJAhistogram histogram plots and methods MJAmath built-in math functions MJAnormalziation normalization data and methods MJAplot scrollable 2D plot support [Future] MJAproperty get and put individual properties MJApropList get lists of properties MJAReval Execute R program .R scripts using MAExplorer data MJAsample get and put single sample top-level data MJAsampleList get lists of samples top-level data MJAscrollablePlot scrollable 2D plot support [Future] MJAsort built-in sort methods MJAstatistics built-in statistics methods MJAstate get and save state, get additional state info MJAutil built-in utility methods
3. [TODO] Adding a plugin to particular stub in the MAExplorer menu Plugins are added by adding the following triple to the Configuration file or .mae startup file (each entry is defined by a 4-tuple for '#' being (1, 2, etc.) PluginMenuName# New sample report PluginMenuStubName# ReportMenu:sample PluginClassFile# NewSampleReport.class PluginCallAtStartup# "TRUE" Plugins may also be added at run time and either inserted into the Plugin menu, or [TODO] using information in the Plugin itself may insert itself into the appropriate menu stub.
3.1 List of acceptable Menu stub names for: PluginMenuStubName (When enabled), you will be able to insert plugins into specified parts of the MAExplorer menu. If the menu stub is not found, it will install them in the generic "Plugin" pull-down menu.
4. List of public MJA access instances for Plugin-writers in this class
MJAbase majBase - access constants and methods used by other MJA classes
MJAcluster mjaCluster - access cluster data structures and methods
MJAexprProfile mjaExprProfile - access expression profile library MJA methods
MJAfilter mjaFilter - access data filter state and methods
MJAgene mjaGene - access single gene data methods
MJAgeneList mjaGeneList - access lists of genes and gene set operations
MJAgenomicDB mjaGenomicDB - access genomic Internet databases methods
MJAgeometry mjaGeometry - array geometry, spot to gene maps, etc. methods
MJAhelp mjaHelp - access popup browser help methods
MJAhistogram mjaHistogram - histogram plots methods
MJAmath majMAth - built-in math methods
MJAnormalization mjaNormalization - access normalization data and methods
MJApopupRegistry mjaPopupRegistry - access popup registry of active windows methods
MJAplot mjaPlot - 2D plot base class methods [Future]
MJAproperty mjaProperty - access individual properties methods
MJApropList mjaPropList - access lists of properties methods
MJAreport mjaReport - access report methods
MJAsample mjaSample - access single sample top-level data methods
MJAsampleList mjaSampleList - access lists of samples top-level data
MJAscrollablePlot mjaScrollablePlot - access scrollable 2D plot base class methods [Future]
MJAstate mjaState - access MAExplorer state saving, additional state info, methods
MJAstatistics mjaStatistics - access built-in statistics methods
MJAutil mjaUtil - access built-in general utility methods
4.1 List of public methods implemented for Plugin-writers in this class
[NOTE: this will be changed as we migrate some of these methods out of the top
level MaeJavaAPI into the MJAxxxx classes where appropriate.]
refreshDataFilter() - regenerate scrollers, refresh the data filter and repaint
insertPluginMenu() - insert plugin into menu using (menuName:menuSubtreeName)
removePluginMenu() - remove plugin from the menubar.
loadPluginsAtStartup() - load plugins from file via startup
getMenuHook() - insert plugin into menu
getFrame() - provide the dominate Frame for other AWT components
loadPluginsStartup() - load plugins from file via startup
setMenuHook() - set menu hook for the plugin
getMenuHook() - get the menu hook for the plugin
getFrame() - provide the dominate Frame for other AWT components
recalcNorms() - recalculate normalizations of all samples
getNormalizationState() - update the Normalization state based on normalization method
setNormalizationState() - update Normalization state based on normalization method
setNormalizationStateFromPlugin() - set normalization state from plugin.
getActiveNormalization() - get active normalization.
showMsg() - display string in text field 1 in main window.
getSampleTotHistStats() - get Hashtable list of a sample's total histogram statistics.
logZero() - compute log10((x==0.0 ? 0.0 : x) - avoid log(0.0)!
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/.
MJAbase,
MJAcluster,
MJAcondition,
MJAeval,
MJAexprProfile,
MJAfilter,
MJAgene,
MJAgeneList,
MJAgenomicDB,
MJAgeometry,
MJAhelp,
MJAhistogram,
MJAmath,
MJAnormalization,
MJAplot,
MJAscrollablePlot,
MJApopupRegistry,
MJAproperty,
MJApropList,
MJAmath,
MJAReval,
MJAreport,
MJAsample,
MJAsampleList,
MJAsort,
MJAstatistics,
MJAstate,
| Field Summary | |
static MJAbase |
mjaBase
constants and methods used by other MJA classes |
static MJAcluster |
mjaCluster
cluster data structures and methods |
MJAcondition |
mjaCondition
condition lists of samples, and ordered lists of condition lists |
MJAeval |
mjaEval
command interpreter |
MJAexprProfile |
mjaExprProfile
expression profile data and methods |
static MJAfilter |
mjaFilter
data filter flags and methods |
static MJAgene |
mjaGene
single gene data |
static MJAgeneList |
mjaGeneList
lists of genes and gene sets methods |
static MJAgenomicDB |
mjaGenomicDB
genomic databases on the Internet |
static MJAgeometry |
mjaGeometry
array geometry, spot to gene maps, etc. |
static MJAhelp |
mjaHelp
popup browser help methods |
static MJAhistogram |
mjaHistogram
histogram plots |
static MJAmath |
mjaMath
built-in math methods |
static MJAnormalization |
mjaNormalization
Access normalization data and methods |
static MJAplot |
mjaPlot
2D plot popup window base class [Future] |
static MJApopupRegistry |
mjaPopupRegistry
popup registry of active windows |
static MJAproperty |
mjaProperty
individual MAExplorer properties methods |
static MJApropList |
mjaPropList
lists of MAExplorer properties methods |
static MJAreport |
mjaReport
report methods |
static MJAReval |
mjaReval
Execute R program .R scripts using MAExplorer data |
static MJAsample |
mjaSample
single sample top-level data methods |
static MJAsampleList |
mjaSampleList
get lists of samples top-level data methods |
static MJAscrollablePlot |
mjaScrollablePlot
Scrollable 2D plot base class [Future] |
static MJAsort |
mjaSort
built-in sorting methods |
static MJAstate |
mjaState
MAExplorer state saving, additional state info, methods |
static MJAstatistics |
mjaStatistics
built-in statistics methods |
static MJAutil |
mjaUtil
built-in general utility methods |
| Fields inherited from interface MAEPlugin.MAEStub |
menuHook |
| Method Summary | |
void |
disableNormalizationPlugin()
disableNormalizationPlugin() - clear activeNormalization state. |
Normalization |
getActiveNormalization()
getActiveNormalization() - get active normalization. |
java.awt.Frame |
getFrame()
getFrame() - provide the dominate Frame for other AWT components |
java.awt.Menu |
getMenuHook()
getMenuHook() - get the menu hook for the plugin |
boolean |
getNormalizationState()
getNormalizationState() - update Normalization state based on normalization method selected in plugins. |
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() - insert plugin into menu using (menuName:menuSubtreeName) [TODO] |
void |
loadPluginsAtStartup()
loadPluginsAtStartup() - load plugins from file via startup. |
void |
loadPluginsStartup()
loadPluginsStartup() - 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() - recalculate normalizations of all samples |
void |
refreshDataFilter()
refreshDataFilter() - regenerate scrollers, refresh the data filter and repaint |
void |
removePluginMenu(java.awt.MenuItem mi)
removePluginMenu() - remove plugin from the menubar. |
void |
setMenuHook(java.awt.Menu menu)
setMenuHook() - set menu hook for the plugin |
void |
setNormalizationState(boolean flag)
setNormalizationState() - update Normalization state based on normalization method selected in non-plugin menus |
void |
setNormalizationStateFromPlugin(java.lang.String methodName)
setNormalizationStateFromPlugin() - set normalization state FROM the plugin. |
void |
showMsg(java.lang.String str)
showMsg() - display string in text field 1 in main window. |
| Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
| Field Detail |
public static MJAbase mjaBase
public static MJAcluster mjaCluster
public MJAcondition mjaCondition
public MJAeval mjaEval
public MJAexprProfile mjaExprProfile
public static MJAfilter mjaFilter
public static MJAgene mjaGene
public static MJAgeneList mjaGeneList
public static MJAgenomicDB mjaGenomicDB
public static MJAgeometry mjaGeometry
public static MJAhelp mjaHelp
public static MJAhistogram mjaHistogram
public static MJAmath mjaMath
public static MJAnormalization mjaNormalization
public static MJApopupRegistry mjaPopupRegistry
public static MJAplot mjaPlot
public static MJAproperty mjaProperty
public static MJApropList mjaPropList
public static MJAreport mjaReport
public static MJAReval mjaReval
public static MJAsample mjaSample
public static MJAsampleList mjaSampleList
public static MJAscrollablePlot mjaScrollablePlot
public static MJAsort mjaSort
public static MJAstate mjaState
public static MJAstatistics mjaStatistics
public static MJAutil mjaUtil
| Method Detail |
public final void refreshDataFilter()
refreshDataFilter in interface MAEStubpublic final void loadPluginsAtStartup()
public final void insertPluginMenu(java.awt.MenuItem mi)
insertPluginMenu in interface MAEStubmaeplugin - MAEPlugin.MAEPlugin to loadpublic final void removePluginMenu(java.awt.MenuItem mi)
removePluginMenu in interface MAEStubpublic final void loadPluginsStartup()
loadPluginsStartup in interface MAEStubpublic final void setMenuHook(java.awt.Menu menu)
setMenuHook in interface MAEStubmenu - menu to set as the menu hookpublic final java.awt.Menu getMenuHook()
getMenuHook in interface MAEStubpublic final java.awt.Frame getFrame()
getFrame in interface MAEStub
public final void recalcNorms(java.lang.String msg,
boolean flag)
recalcNorms in interface MAEStubmsg - title stringflag - flag passed to recalcNorms...public final void disableNormalizationPlugin()
disableNormalizationPlugin in interface MAEStubpublic final boolean getNormalizationState()
getNormalizationState in interface MAEStubpublic final void setNormalizationState(boolean flag)
setNormalizationState in interface MAEStubpublic final void setNormalizationStateFromPlugin(java.lang.String methodName)
setNormalizationStateFromPlugin in interface MAEStubmethodName - name of the methodpublic Normalization getActiveNormalization()
public final void showMsg(java.lang.String str)
showMsg in interface MAEStubMAEPlugin.MAEStubstr - message to draw in top text line of main window.public java.util.Hashtable getSampleTotHistStats(java.lang.Object o)
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
. . .
getSampleTotHistStats in interface MAEStubsampleNbr - sample number data to accessnull if not found or error.public double logZero(double x)
logZero in interface MAEStubx - argument for log
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