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A
ABSMIDDLE
- Static variable in class fr.ens.transcriptome.doelan.gui.
MyImageView
APP_DESCRITPION
- Static variable in class fr.ens.transcriptome.doelan.
Defaults
Name of the application.
APP_NAME
- Static variable in class fr.ens.transcriptome.doelan.
Defaults
Name of the application.
ARRAY_PLOT_MARGIN
- Static variable in class fr.ens.transcriptome.doelan.
Defaults
Array plot margin.
ARRAY_PLOT_WIDTH
- Static variable in class fr.ens.transcriptome.doelan.
Defaults
Array plot width.
AUTHORS
- Static variable in class fr.ens.transcriptome.doelan.
Defaults
Authors
AboutWidget
- class fr.ens.transcriptome.doelan.gui.
AboutWidget
.
About widget
AboutWidget()
- Constructor for class fr.ens.transcriptome.doelan.gui.
AboutWidget
Public constructor.
AbsentSpotTest
- class fr.ens.transcriptome.doelan.tests.
AbsentSpotTest
.
This class implements the Empty spot test.
AbsentSpotTest()
- Constructor for class fr.ens.transcriptome.doelan.tests.
AbsentSpotTest
Public constructor.
App
- class fr.ens.transcriptome.doelan.
App
.
A Class to test the application with standalone application.
App()
- Constructor for class fr.ens.transcriptome.doelan.
App
about()
- Static method in class fr.ens.transcriptome.doelan.
DoelanRegistery
Get information about the project.
aboutModule()
- Method in class fr.ens.transcriptome.doelan.algorithms.
DoelanConfigure
Get the description of the module.
aboutModule()
- Method in class fr.ens.transcriptome.doelan.algorithms.
DoelanExecuteGlobalTests
Get the description of the module.
aboutModule()
- Method in class fr.ens.transcriptome.doelan.algorithms.
DoelanGenerateReport
Get the description of the module.
aboutModule()
- Method in class fr.ens.transcriptome.doelan.algorithms.
DoelanLoadGenepixData
Get the description of the module.
aboutModule()
- Method in class fr.ens.transcriptome.doelan.algorithms.
DoelanShowReport
Get the description of the module.
aboutModule()
- Method in class fr.ens.transcriptome.doelan.data.
QualityGlobalTestResultData
Get the description of the module.
aboutModule()
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResultData
Get the description of the module.
aboutModule()
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResultData
Get the description of the module.
aboutModule()
- Method in class fr.ens.transcriptome.doelan.tests.
AbsentSpotTest
Get the description of the module.
aboutModule()
- Method in class fr.ens.transcriptome.doelan.tests.
BadFeatureTest
Get the description of the module.
aboutModule()
- Method in class fr.ens.transcriptome.doelan.tests.
DiameterFeatureTest
Get the description of the module.
aboutModule()
- Method in class fr.ens.transcriptome.doelan.tests.
FeatureFlagTest
Get the description of the module.
aboutModule()
- Method in class fr.ens.transcriptome.doelan.tests.
GenericTest
Get the description of the module.
aboutModule()
- Method in class fr.ens.transcriptome.doelan.tests.
GlobalMaxBadFeatureRemoved
Get the description of the module.
aboutModule()
- Method in class fr.ens.transcriptome.doelan.tests.
GlobalMaxBadFeaturesTest
Get the description of the module.
aboutModule()
- Method in class fr.ens.transcriptome.doelan.tests.
HeterogeneousFeatureTest
Get the description of the module.
aboutModule()
- Method in class fr.ens.transcriptome.doelan.tests.
MaxDiameterFeatureTest
Get the description of the module.
aboutModule()
- Method in class fr.ens.transcriptome.doelan.tests.
MinDiameterFeatureTest
Get the description of the module.
aboutModule()
- Method in class fr.ens.transcriptome.doelan.tests.
MinimalIntensityTest
Get the description of the module.
aboutModule()
- Method in class fr.ens.transcriptome.doelan.tests.
NotFoundFeatureTest
Get the description of the module.
aboutModule()
- Method in class fr.ens.transcriptome.doelan.tests.
SaturatedPixelsTest
Get the description of the module.
addChipType(String)
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestSuiteList
Add a chip type to the list
addGlobalTest(QualityGlobalTest, Parameters)
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResult
Add a global test.
addGlobalTest(TestSuiteResult.GlobalTest)
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResult
Add a global test.
addTestId(String)
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResult
Add a test id for the test order in the report.
addTestSuite(String, QualityTestSuiteURL)
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestSuiteList
Add a testSuite to the list
algorithmStateChanged(AlgorithmEvent)
- Method in class fr.ens.transcriptome.doelan.gui.
QualityTestSuiteTableModel
Handle algorithm events
B
BOTTOM
- Static variable in class fr.ens.transcriptome.doelan.gui.
MyImageView
BadFeatureTest
- class fr.ens.transcriptome.doelan.tests.
BadFeatureTest
.
This class defines a test for not found spot flag.
BadFeatureTest()
- Constructor for class fr.ens.transcriptome.doelan.tests.
BadFeatureTest
Public constructor.
C
CENTER
- Static variable in class fr.ens.transcriptome.doelan.gui.
MyImageView
CHIP_TYPE_ANNOTATION_KEY
- Static variable in class fr.ens.transcriptome.doelan.
Defaults
Annaotation key of the type of the chip.
CONFIGURE_ALGORITHM
- Static variable in class fr.ens.transcriptome.doelan.
Core
Identifier of the show report algorithm.
CONFIGURE_TEST_EVENT
- Static variable in class fr.ens.transcriptome.doelan.algorithms.
QualityTest
Identifier for result event.
CONFIG_FILE
- Static variable in class fr.ens.transcriptome.doelan.
Defaults
Config file.
COPYRIGHT_DATE
- Static variable in class fr.ens.transcriptome.doelan.
Defaults
Copyrigth date.
CommonWindow
- class fr.ens.transcriptome.doelan.gui.
CommonWindow
.
Common GUI for applet and normal application.
CommonWindow(Applet, URL)
- Constructor for class fr.ens.transcriptome.doelan.gui.
CommonWindow
Public constructor for applet mode.
CommonWindow(JFrame, URL)
- Constructor for class fr.ens.transcriptome.doelan.gui.
CommonWindow
Public constructor for standalone mode.
Core
- class fr.ens.transcriptome.doelan.
Core
.
Manage the Workflows
calcColumnWidths(JTable)
- Static method in class fr.ens.transcriptome.doelan.gui.
TestSuitePanel
Calculate the number of column to display.
changedUpdate(DocumentEvent, Shape, ViewFactory)
- Method in class fr.ens.transcriptome.doelan.gui.
MyImageView
My attributes may have changed.
clear()
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestSuiteList
Clear the list.
clear()
- Method in class fr.ens.transcriptome.doelan.gui.
ReportTabWidget
clearResults()
- Method in class fr.ens.transcriptome.doelan.gui.
QualityTestSuiteTableModel
Clear results.
clearResults()
- Method in class fr.ens.transcriptome.doelan.gui.
TestSuitePanel
Clear the result column.
close()
- Method in class fr.ens.transcriptome.doelan.gui.
EditParametersWidget
Hide the widget.
close()
- Method in class fr.ens.transcriptome.doelan.gui.
NewWorkflowElementWidget
Hide the widget.
create(Element)
- Method in class fr.ens.transcriptome.doelan.gui.
DoelanEditorKit.HTMLFactoryX
Display an element.
createDemoWorkflow()
- Method in class fr.ens.transcriptome.doelan.
Core
Create and activate the demo test suite.
createEmptyWorkflow()
- Method in class fr.ens.transcriptome.doelan.
Core
Create and activate the empty test suite.
createQualityTestSuiteListIO(String)
- Method in class fr.ens.transcriptome.doelan.io.
QualityTestIOFactory
Create IO object for quality tests suites lists.
createQualityTestSuiteListIO(InputStream)
- Method in class fr.ens.transcriptome.doelan.io.
QualityTestIOFactory
Create IO object for quality tests suites lists.
createQualityTestSuiteListIO(OutputStream)
- Method in class fr.ens.transcriptome.doelan.io.
QualityTestIOFactory
Create IO object for quality tests suites lists.
D
DEBUG
- Static variable in class fr.ens.transcriptome.doelan.
Defaults
Debug mode.
DEFAULT_TEST_VERSION
- Static variable in class fr.ens.transcriptome.doelan.
Defaults
Default version of the tests.
DOELAN_CHART_HEIGHT
- Static variable in class fr.ens.transcriptome.doelan.
Defaults
Chart plot height.
DOELAN_WORKFLOW_TYPE
- Static variable in class fr.ens.transcriptome.doelan.
Defaults
Type of workflow for doelan test suite.
DOELAN_WORKFLOW_VERSION
- Static variable in class fr.ens.transcriptome.doelan.
Defaults
Version of the workflow for doelan test suite.
DOELAN_WORKFLOW_VERSION_ANNOTATION_KEY
- Static variable in class fr.ens.transcriptome.doelan.
Defaults
Annatation key for the version of the test suite workflow.
DOLEAN_CHART_WIDTH
- Static variable in class fr.ens.transcriptome.doelan.
Defaults
Chart plot width.
Defaults
- class fr.ens.transcriptome.doelan.
Defaults
.
Default values of the application.
Defaults()
- Constructor for class fr.ens.transcriptome.doelan.
Defaults
DescriptionWidget
- class fr.ens.transcriptome.doelan.gui.
DescriptionWidget
.
This class implements a file chooser.
DescriptionWidget(String, int, JPanel, int)
- Constructor for class fr.ens.transcriptome.doelan.gui.
DescriptionWidget
Public constructor.
DiameterFeatureTest
- class fr.ens.transcriptome.doelan.tests.
DiameterFeatureTest
.
This class defines a quality test based on spot diameter.
DiameterFeatureTest()
- Constructor for class fr.ens.transcriptome.doelan.tests.
DiameterFeatureTest
Public constructor.
DoelanChart
- class fr.ens.transcriptome.doelan.
DoelanChart
.
This class allow to generate a plot.
DoelanChart()
- Constructor for class fr.ens.transcriptome.doelan.
DoelanChart
DoelanConfigure
- class fr.ens.transcriptome.doelan.algorithms.
DoelanConfigure
.
Configure Defaults for the test suite.
DoelanConfigure()
- Constructor for class fr.ens.transcriptome.doelan.algorithms.
DoelanConfigure
Public constructor.
DoelanDataDefaults
- class fr.ens.transcriptome.doelan.data.
DoelanDataDefaults
.
This class defines constants for doelan data types.
DoelanDataDefaults()
- Constructor for class fr.ens.transcriptome.doelan.data.
DoelanDataDefaults
DoelanDataUtils
- class fr.ens.transcriptome.doelan.data.
DoelanDataUtils
.
This class defines some useful method for quality tests
DoelanEditorKit
- class fr.ens.transcriptome.doelan.gui.
DoelanEditorKit
.
HTML viewer which can display image.
DoelanEditorKit()
- Constructor for class fr.ens.transcriptome.doelan.gui.
DoelanEditorKit
DoelanEditorKit.HTMLFactoryX
- class fr.ens.transcriptome.doelan.gui.
DoelanEditorKit.HTMLFactoryX
.
This class implements a HTML factory which can display image.
DoelanException
- exception fr.ens.transcriptome.doelan.
DoelanException
.
A nestable quality exception.
DoelanException(String)
- Constructor for class fr.ens.transcriptome.doelan.
DoelanException
Create a new QualityException with a message.
DoelanException(Throwable)
- Constructor for class fr.ens.transcriptome.doelan.
DoelanException
Create a new QualityException with a cause.
DoelanException(Throwable, String)
- Constructor for class fr.ens.transcriptome.doelan.
DoelanException
Deprecated.
use new QualityException(message, ex) instead
DoelanException(String, Throwable)
- Constructor for class fr.ens.transcriptome.doelan.
DoelanException
Create a new QualityException with a cause and a message.
DoelanException()
- Constructor for class fr.ens.transcriptome.doelan.
DoelanException
Create a new QualityException.
DoelanExecuteGlobalTests
- class fr.ens.transcriptome.doelan.algorithms.
DoelanExecuteGlobalTests
.
This algorithm execute all the global tests and compute the ouput array list.
DoelanExecuteGlobalTests()
- Constructor for class fr.ens.transcriptome.doelan.algorithms.
DoelanExecuteGlobalTests
Public constructor.
DoelanGenerateReport
- class fr.ens.transcriptome.doelan.algorithms.
DoelanGenerateReport
.
This class define an algorithm to show test suite report.
DoelanGenerateReport()
- Constructor for class fr.ens.transcriptome.doelan.algorithms.
DoelanGenerateReport
Public constructor.
DoelanLoadGenepixData
- class fr.ens.transcriptome.doelan.algorithms.
DoelanLoadGenepixData
.
This class implements a module witch load GPR and GAL file.
DoelanLoadGenepixData()
- Constructor for class fr.ens.transcriptome.doelan.algorithms.
DoelanLoadGenepixData
Public constructor.
DoelanRegistery
- class fr.ens.transcriptome.doelan.
DoelanRegistery
.
Globals setting for the application
DoelanShowReport
- class fr.ens.transcriptome.doelan.algorithms.
DoelanShowReport
.
This algorithm show in doelan GUI the status and the report of the test suite.
DoelanShowReport()
- Constructor for class fr.ens.transcriptome.doelan.algorithms.
DoelanShowReport
Public constructor.
defineParameters()
- Method in class fr.ens.transcriptome.doelan.algorithms.
DoelanConfigure
Set the parameters of the element.
defineParameters()
- Method in class fr.ens.transcriptome.doelan.algorithms.
DoelanExecuteGlobalTests
Set the parameters of the element.
defineParameters()
- Method in class fr.ens.transcriptome.doelan.algorithms.
DoelanGenerateReport
Set the parameters of the element.
defineParameters()
- Method in class fr.ens.transcriptome.doelan.algorithms.
DoelanLoadGenepixData
Set the parameters of the element.
defineParameters()
- Method in class fr.ens.transcriptome.doelan.algorithms.
DoelanShowReport
Set the parameters of the element.
defineParameters()
- Method in class fr.ens.transcriptome.doelan.tests.
DiameterFeatureTest
Set the parameters of the element.
defineParameters()
- Method in class fr.ens.transcriptome.doelan.tests.
FeatureFlagTest
Set the parameters of the element.
defineParameters()
- Method in class fr.ens.transcriptome.doelan.tests.
GenericTest
Set the parameters of the element.
defineParameters()
- Method in class fr.ens.transcriptome.doelan.tests.
GlobalMaxBadFeatureRemoved
Set the parameters of the element.
defineParameters()
- Method in class fr.ens.transcriptome.doelan.tests.
GlobalMaxBadFeaturesTest
Set the parameters of the element.
defineParameters()
- Method in class fr.ens.transcriptome.doelan.tests.
HeterogeneousFeatureTest
Set the parameters of the element.
defineParameters()
- Method in class fr.ens.transcriptome.doelan.tests.
MaxDiameterFeatureTest
Set the parameters of the element.
defineParameters()
- Method in class fr.ens.transcriptome.doelan.tests.
MinDiameterFeatureTest
Set the parameters of the element.
defineParameters()
- Method in class fr.ens.transcriptome.doelan.tests.
MinimalIntensityTest
Define the parameters of the algorithm.
defineParameters()
- Method in class fr.ens.transcriptome.doelan.tests.
SaturatedPixelsTest
Set the parameters of the element.
doIt(Container, Parameters)
- Method in class fr.ens.transcriptome.doelan.algorithms.
DoelanConfigure
doIt(Container, Parameters)
- Method in class fr.ens.transcriptome.doelan.algorithms.
DoelanExecuteGlobalTests
This method contains all the code to manipulate the container
c
in this element.
doIt(Container, Parameters)
- Method in class fr.ens.transcriptome.doelan.algorithms.
DoelanGenerateReport
This method contains all the code to manipulate the container
c
in this element.
doIt(Container, Parameters)
- Method in class fr.ens.transcriptome.doelan.algorithms.
DoelanLoadGenepixData
This method contains all the code to manipulate the container
c
in this element.
doIt(Container, Parameters)
- Method in class fr.ens.transcriptome.doelan.algorithms.
DoelanShowReport
This method contains all the code to manipulate the container
c
in this element.
doIt(Container, Parameters)
- Method in class fr.ens.transcriptome.doelan.algorithms.
QualityGlobalTest
doIt(Container, Parameters)
- Method in class fr.ens.transcriptome.doelan.algorithms.
QualityUnitTest
doTest(Container, Parameters)
- Method in class fr.ens.transcriptome.doelan.algorithms.
QualityGlobalTest
This method is called once all the unit tests was executed.
E
EXECUTE_GLOBAL_TESTS_ALGORITHM
- Static variable in class fr.ens.transcriptome.doelan.
Core
Identifier of the algorithm for executing global test.
EclipseApp
- class fr.ens.transcriptome.doelan.
EclipseApp
.
This class allow to launch Doelan within Eclipse
EditParametersWidget
- class fr.ens.transcriptome.doelan.gui.
EditParametersWidget
.
This class describe a widhet used to edit parameters of an algorithm.
EditParametersWidget(Algorithm)
- Constructor for class fr.ens.transcriptome.doelan.gui.
EditParametersWidget
Public consructor.
edit()
- Method in class fr.ens.transcriptome.doelan.gui.
EditParametersWidget
Show the widget for editing parameters.
executeTest(Container)
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResult.GlobalTest
Excecute the test with its parameters
F
FeatureFlagTest
- class fr.ens.transcriptome.doelan.tests.
FeatureFlagTest
.
This class defines a test for not found spot flag.
FeatureFlagTest()
- Constructor for class fr.ens.transcriptome.doelan.tests.
FeatureFlagTest
Public constructor.
FileChooserWidget
- class fr.ens.transcriptome.doelan.gui.
FileChooserWidget
.
This class implements a file chooser.
FileChooserWidget(boolean, String, int, String, String, String, JPanel, int)
- Constructor for class fr.ens.transcriptome.doelan.gui.
FileChooserWidget
Public constructor.
filterModule(AboutModule, Algorithm, boolean)
- Method in class fr.ens.transcriptome.doelan.gui.
QualityTestSuiteTableModel
Test if an algorithm is a showable quality test.
filterWorkflowElement(WorkflowElement)
- Method in class fr.ens.transcriptome.doelan.gui.
QualityTestSuiteTableModel
Test if an element is a showable Workflow element.
fr.ens.transcriptome.doelan
- package fr.ens.transcriptome.doelan
fr.ens.transcriptome.doelan.algorithms
- package fr.ens.transcriptome.doelan.algorithms
fr.ens.transcriptome.doelan.data
- package fr.ens.transcriptome.doelan.data
doelan data package.
fr.ens.transcriptome.doelan.gui
- package fr.ens.transcriptome.doelan.gui
fr.ens.transcriptome.doelan.io
- package fr.ens.transcriptome.doelan.io
fr.ens.transcriptome.doelan.tests
- package fr.ens.transcriptome.doelan.tests
G
GENERATE_REPORT_ALGORITHM
- Static variable in class fr.ens.transcriptome.doelan.
Core
Identifier of the generate report algorithm.
GLOBAL_TEST_INIT_EVENT
- Static variable in class fr.ens.transcriptome.doelan.algorithms.
QualityTest
Identifier for result event.
GLOBAL_TEST_RESULT_TYPE
- Static variable in class fr.ens.transcriptome.doelan.data.
DoelanDataDefaults
Global test result type.
GenepixApplet
- class fr.ens.transcriptome.doelan.
GenepixApplet
.
Applet of the application.
GenepixApplet()
- Constructor for class fr.ens.transcriptome.doelan.
GenepixApplet
GenericTest
- class fr.ens.transcriptome.doelan.tests.
GenericTest
.
This class define a generic unit test
GenericTest()
- Constructor for class fr.ens.transcriptome.doelan.tests.
GenericTest
Public constructor.
GlobalMaxBadFeatureRemoved
- class fr.ens.transcriptome.doelan.tests.
GlobalMaxBadFeatureRemoved
.
This class define a Global test which count the number of bad removed spot.
GlobalMaxBadFeatureRemoved()
- Constructor for class fr.ens.transcriptome.doelan.tests.
GlobalMaxBadFeatureRemoved
Public constructor.
GlobalMaxBadFeaturesTest
- class fr.ens.transcriptome.doelan.tests.
GlobalMaxBadFeaturesTest
.
This class defines an algorithm to count the maximal bad spots in a test suite.
GlobalMaxBadFeaturesTest()
- Constructor for class fr.ens.transcriptome.doelan.tests.
GlobalMaxBadFeaturesTest
Public constructor.
getAlgorithm()
- Method in class fr.ens.transcriptome.doelan.gui.
EditParametersWidget
Get the algorithm.
getAlignment(int)
- Method in class fr.ens.transcriptome.doelan.gui.
MyImageView
Determines the desired alignment for this view along an axis.
getAlternativeBrowserPath()
- Static method in class fr.ens.transcriptome.doelan.
DoelanRegistery
Get the path of the alterantive web browser.
getAppCompileDate()
- Static method in class fr.ens.transcriptome.doelan.
DoelanRegistery
Get the date of the compilation.
getAppCopyright()
- Static method in class fr.ens.transcriptome.doelan.
DoelanRegistery
Get the copyright.
getAppDescription()
- Static method in class fr.ens.transcriptome.doelan.
DoelanRegistery
Get the description of the application.
getAppName()
- Static method in class fr.ens.transcriptome.doelan.
DoelanRegistery
Get the name of the application.
getAppURL()
- Static method in class fr.ens.transcriptome.doelan.
DoelanRegistery
Get the URL of the project.
getAppVersion()
- Static method in class fr.ens.transcriptome.doelan.
DoelanRegistery
Get the version of the application.
getApplet()
- Method in class fr.ens.transcriptome.doelan.
Core
Get the applet.
getApplet()
- Method in class fr.ens.transcriptome.doelan.algorithms.
DoelanLoadGenepixData
Get the applet.
getArrayList(Container)
- Static method in class fr.ens.transcriptome.doelan.data.
DoelanDataUtils
This methods return the first array list found in a Container
getArrayLists(Container)
- Static method in class fr.ens.transcriptome.doelan.data.
DoelanDataUtils
This methods return all the BioAssay found in a Container
getArrayPlot()
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResult
Get the arrayplot image.
getAttributes()
- Method in class fr.ens.transcriptome.doelan.gui.
MyImageView
Fetches the attributes to use when rendering.
getBins()
- Method in class fr.ens.transcriptome.doelan.
DoelanChart
Set the number of bins
getBioAssay(Container)
- Static method in class fr.ens.transcriptome.doelan.data.
DoelanDataUtils
This methods return the first BioAssay found in a Container
getBioAssay()
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestResult
Get the bioassay reference.
getBioAssays(Container)
- Static method in class fr.ens.transcriptome.doelan.data.
DoelanDataUtils
This methods return all the BioAssay found in a Container
getBrowserPath()
- Static method in class fr.ens.transcriptome.doelan.
DoelanRegistery
Get the browser path.
getButtonText()
- Method in class fr.ens.transcriptome.doelan.gui.
FileChooserWidget
Get the text of the button
getChannel()
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResult.SummaryResult
Get the channel.
getChipType(QualityTestSuiteURL)
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestSuiteList
Get the type of a test suite from this test suite url.
getChipTypeName()
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResult
Get the name of the type of the chip.
getChipTypes()
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestSuiteList
Get the type list of the TestSuites
getColumnClass(int)
- Method in class fr.ens.transcriptome.doelan.gui.
QualityTestSuiteTableModel
Get the class of a column.
getColumnCount()
- Method in class fr.ens.transcriptome.doelan.gui.
QualityTestSuiteTableModel
Get the number of column.
getColumnName(int)
- Method in class fr.ens.transcriptome.doelan.gui.
QualityTestSuiteTableModel
Get the name of a column.
getCopyrightDate()
- Static method in class fr.ens.transcriptome.doelan.
DoelanRegistery
Get the date of the copyright.
getCore()
- Static method in class fr.ens.transcriptome.doelan.
Core
Return the unique instance of the Core object
getCurrentChipTypeName()
- Method in class fr.ens.transcriptome.doelan.gui.
SuiteChooserWidget
getCurrentTestSuiteName()
- Method in class fr.ens.transcriptome.doelan.gui.
SuiteChooserWidget
getData()
- Method in class fr.ens.transcriptome.doelan.
DoelanChart
Get the data to plot
getDataClass()
- Method in class fr.ens.transcriptome.doelan.data.
QualityGlobalTestResultData
Get the class of the data.
getDataClass()
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResultData
Get the class of the data.
getDataClass()
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResultData
Get the class of the data.
getDefaultThreshold()
- Method in class fr.ens.transcriptome.doelan.tests.
AbsentSpotTest
getDefaultThreshold()
- Method in class fr.ens.transcriptome.doelan.tests.
BadFeatureTest
getDefaultThreshold()
- Method in class fr.ens.transcriptome.doelan.tests.
FeatureFlagTest
getDefaultThreshold()
- Method in class fr.ens.transcriptome.doelan.tests.
NotFoundFeatureTest
getDescription()
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResult
Get the data description
getDescription()
- Method in class fr.ens.transcriptome.doelan.gui.
DescriptionWidget
Get the text of the description.
getDoelanChartHeigth()
- Static method in class fr.ens.transcriptome.doelan.
DoelanRegistery
Get the height of the doelan charts.
getDoelanChartWidth()
- Static method in class fr.ens.transcriptome.doelan.
DoelanRegistery
Get the width of the doelan charts.
getDoelanDataDirectory()
- Static method in class fr.ens.transcriptome.doelan.
DoelanRegistery
Get the absolute path of the directory for plugins.
getDoelanReportDirectory()
- Static method in class fr.ens.transcriptome.doelan.
DoelanRegistery
Get the absolute path of the directory for plugins.
getEmptySpotIds()
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResult
Get the identifiers of the empty spots.
getFile()
- Method in class fr.ens.transcriptome.doelan.gui.
FileChooserWidget
Get the data file.
getFlagFilerType()
- Method in class fr.ens.transcriptome.doelan.tests.
AbsentSpotTest
getFlagFilerType()
- Method in class fr.ens.transcriptome.doelan.tests.
BadFeatureTest
getFlagFilerType()
- Method in class fr.ens.transcriptome.doelan.tests.
FeatureFlagTest
getFlagFilerType()
- Method in class fr.ens.transcriptome.doelan.tests.
NotFoundFeatureTest
getFlagFilterValue()
- Method in class fr.ens.transcriptome.doelan.tests.
AbsentSpotTest
getFlagFilterValue()
- Method in class fr.ens.transcriptome.doelan.tests.
BadFeatureTest
getFlagFilterValue()
- Method in class fr.ens.transcriptome.doelan.tests.
FeatureFlagTest
getFlagFilterValue()
- Method in class fr.ens.transcriptome.doelan.tests.
NotFoundFeatureTest
getFormat()
- Method in class fr.ens.transcriptome.doelan.data.
QualityGlobalTestResultData
Get the format of the data.
getFormat()
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResultData
Get the format of the data.
getFormat()
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResultData
Get the format of the data.
getGalData()
- Method in class fr.ens.transcriptome.doelan.gui.
ReportTabWidget
Get the new Gal data.
getGlobalTests()
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResult
Get the global tests
getHeight()
- Method in class fr.ens.transcriptome.doelan.
DoelanChart
Get the height of the image.
getHighlightColor()
- Method in class fr.ens.transcriptome.doelan.gui.
MyImageView
Returns the text editor's highlight color.
getHistCaption()
- Method in class fr.ens.transcriptome.doelan.
DoelanChart
Get the caption of the histogram
getHtmlReport()
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResult
Get the html report.
getId()
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestResult
Get identifier of the result.
getIdentifier()
- Method in class fr.ens.transcriptome.doelan.gui.
NewWorkflowElementWidget
Get the identifier of the new algorithm.
getImage()
- Method in class fr.ens.transcriptome.doelan.
DoelanChart
Get the image
getImage()
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestResult
Get the image.
getMainTab()
- Method in class fr.ens.transcriptome.doelan.
Core
Get the main tab widget.
getMainTabWidget()
- Method in class fr.ens.transcriptome.doelan.gui.
SuiteChooserWidget
Get the mainTabWidget.
getMapImages()
- Method in class fr.ens.transcriptome.doelan.gui.
DoelanEditorKit
Get the map of the images.
getMapImages()
- Method in class fr.ens.transcriptome.doelan.gui.
MyImageView
Get the map of the images.
getMessage()
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestResult
Get message of the test.
getMinimumSize()
- Method in class fr.ens.transcriptome.doelan.
App
Get the minimun size of the main window.
getMnemonicKey()
- Method in class fr.ens.transcriptome.doelan.gui.
DescriptionWidget
Get the mnemonic key.
getMnemonicKey()
- Method in class fr.ens.transcriptome.doelan.gui.
FileChooserWidget
Get the mnemonic key.
getModel()
- Method in class fr.ens.transcriptome.doelan.gui.
TestSuitePanel
Get the model of the table
getModuleLocationSelected()
- Method in class fr.ens.transcriptome.doelan.gui.
NewWorkflowElementWidget
Get the module location of the selected algorithm.
getName()
- Method in class fr.ens.transcriptome.doelan.data.
QualityGlobalTestResultData
Get the name of the data.
getName()
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestSuiteURL
Get the name of the TestSuiteURL
getName()
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResultData
Get the name of the data.
getName()
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResultData
Get the name of the data.
getNewArrayList()
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResult
Get the new array list.
getNewFlags()
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResult
Get the new flags of the bioAssay after the test.
getOrderedQualityTestResults(Container)
- Static method in class fr.ens.transcriptome.doelan.data.
DoelanDataUtils
This methods return all the test results found in a Container
getOrganizationName()
- Static method in class fr.ens.transcriptome.doelan.
DoelanRegistery
Get the name of the organization of the project.
getOrganizationURL()
- Static method in class fr.ens.transcriptome.doelan.
DoelanRegistery
Get the url of the organization
getPanel()
- Method in class fr.ens.transcriptome.doelan.gui.
StatusWidget
Get the panel.
getPanel()
- Method in class fr.ens.transcriptome.doelan.gui.
SuiteChooserWidget
Get the panel.
getParameters()
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestResult
Get the parameters
getParameters()
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResult.GlobalTest
Get the parameters.
getPreferredSize()
- Method in class fr.ens.transcriptome.doelan.
App
Get the minimun size of the main window.
getPreferredSpan(int)
- Method in class fr.ens.transcriptome.doelan.gui.
MyImageView
Determines the preferred span for this view along an axis.
getQualityGlobalTestResults(Container)
- Static method in class fr.ens.transcriptome.doelan.data.
DoelanDataUtils
This methods return all the global test results found in a Container
getQualityTestResults(Container)
- Static method in class fr.ens.transcriptome.doelan.data.
DoelanDataUtils
This methods return all the test results found in a Container
getQualityTestSuiteSelected()
- Method in class fr.ens.transcriptome.doelan.gui.
SuiteChooserWidget
Return the quality test suite url selected.
getQualityUnitTestResults(Container)
- Static method in class fr.ens.transcriptome.doelan.data.
DoelanDataUtils
This methods return all the unit test results found in a Container
getRealFeatures()
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResult
Get the count of the realFeatures (not abscent).
getReport()
- Method in class fr.ens.transcriptome.doelan.
Core
Get the report widget
getReport()
- Method in class fr.ens.transcriptome.doelan.algorithms.
DoelanShowReport
Get the report widget.
getResult()
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestResult
Get the result
getResult()
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResult
test is the test passed.
getResult()
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResult
Get the result of the test suite.
getResultAllChannels()
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResult
Get the result for all channel.
getResultChannel532()
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResult
Get the result for 532 channel.
getResultChannel635()
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResult
Get the result for 635 channel.
getSelectionState()
- Method in class fr.ens.transcriptome.doelan.gui.
MyImageView
Determines whether the image is selected, and if it's the only thing selected.
getSpotRejectedId()
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResult
Get the identifier of teh rejected spots.
getStatus()
- Method in class fr.ens.transcriptome.doelan.
Core
Get the status widget.
getStatus()
- Method in class fr.ens.transcriptome.doelan.algorithms.
DoelanShowReport
Get the status widget.
getStatus()
- Method in class fr.ens.transcriptome.doelan.gui.
StatusWidget
Get the status of the testsuite.
getStatusBar()
- Method in class fr.ens.transcriptome.doelan.
Core
Get the status bar object.
getStatusWidget()
- Static method in class fr.ens.transcriptome.doelan.gui.
StatusWidget
Get the status Widget.
getStyleSheet()
- Method in class fr.ens.transcriptome.doelan.gui.
MyImageView
getTable()
- Method in class fr.ens.transcriptome.doelan.
Core
Get the table.
getTable()
- Method in class fr.ens.transcriptome.doelan.gui.
TestSuiteTabWidget
Get the table widget.
getTest()
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResult.GlobalTest
Get the test.
getTestDescription()
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestResult
Get Test description.
getTestId()
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestResult
The identifier of the test.
getTestIdsOrder()
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResult
Get the order of the tests.
getTestSuiteList()
- Method in class fr.ens.transcriptome.doelan.gui.
SuiteChooserWidget
Get the test suite list.
getTestSuiteListFilename()
- Static method in class fr.ens.transcriptome.doelan.
DoelanRegistery
Get the absolute path of the test suite list file.
getTestSuiteListURL()
- Method in class fr.ens.transcriptome.doelan.
Core
Get the URL of the test suite list.
getTestSuiteName()
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResult
Get the test suite name.
getTestSuiteResult(Container)
- Static method in class fr.ens.transcriptome.doelan.data.
DoelanDataUtils
This methods return the first test suite result found in a Container
getTestSuiteTabWidget()
- Static method in class fr.ens.transcriptome.doelan.gui.
TestSuiteTabWidget
getTestSuiteURLs(String)
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestSuiteList
Return all the TestSuiteURL for a chip type
getTestType()
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestResult
Get the type of the test
getThreshold()
- Method in class fr.ens.transcriptome.doelan.
DoelanChart
Get the value of the threshold.
getThreshold()
- Method in class fr.ens.transcriptome.doelan.data.
QualityGlobalTestResult
Get the Threshold.
getThreshold()
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResult.SummaryResult
Get the Threshold.
getThresholdEqualityType()
- Method in class fr.ens.transcriptome.doelan.data.
QualityGlobalTestResult
Get the type of equality between the threshold and this value.
getThresholdEqualityType()
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResult.SummaryResult
Get the type of equality between the threshold and this value.
getTip(int)
- Method in class fr.ens.transcriptome.doelan.gui.
QualityTestSuiteTableModel
Get the tip
getTitle()
- Method in class fr.ens.transcriptome.doelan.
DoelanChart
Set the title of the plot.
getType()
- Method in class fr.ens.transcriptome.doelan.data.
QualityGlobalTestResultData
Get the type of the data.
getType()
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResultData
Get the type of the data.
getType()
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResultData
Get the type of the data.
getURL()
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestSuiteURL
Get the URL of the test TestSuiteURL
getUnit()
- Method in class fr.ens.transcriptome.doelan.data.
QualityGlobalTestResult
Get the unit of the value and the threshold.
getUnit()
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResult.SummaryResult
Get the unit of the value and the threshold.
getUrl()
- Method in class fr.ens.transcriptome.doelan.gui.
TestSuitePanel
Get the url of the test suite
getValue()
- Method in class fr.ens.transcriptome.doelan.data.
QualityGlobalTestResult
Get the value.
getValue()
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResult.SummaryResult
Get the value.
getValueAt(int, int)
- Method in class fr.ens.transcriptome.doelan.gui.
QualityTestSuiteTableModel
Get a value.
getViewFactory()
- Method in class fr.ens.transcriptome.doelan.gui.
DoelanEditorKit
Get the factor viewer.
getWidth()
- Method in class fr.ens.transcriptome.doelan.
DoelanChart
Get the width of the image.
getXAxisLegend()
- Method in class fr.ens.transcriptome.doelan.
DoelanChart
Get the x axis legend
getYAxisLegend()
- Method in class fr.ens.transcriptome.doelan.
DoelanChart
Get the y axis legend
getYPosition()
- Method in class fr.ens.transcriptome.doelan.gui.
StatusWidget
Get the y position of the panel.
getYPosition()
- Method in class fr.ens.transcriptome.doelan.gui.
SuiteChooserWidget
Get the y position of the panel.
H
HeterogeneousFeatureTest
- class fr.ens.transcriptome.doelan.tests.
HeterogeneousFeatureTest
.
This class defines a test for Test Heterogeneity of features.
HeterogeneousFeatureTest()
- Constructor for class fr.ens.transcriptome.doelan.tests.
HeterogeneousFeatureTest
Public constructor.
I
INTERNALS_MODULES
- Static variable in class fr.ens.transcriptome.doelan.
Defaults
Internals modules.
imageUpdate(Image, int, int, int, int, int)
- Method in class fr.ens.transcriptome.doelan.gui.
MyImageView
Update the image.
init()
- Static method in class fr.ens.transcriptome.doelan.
DoelanRegistery
Initialize default values.
init()
- Method in class fr.ens.transcriptome.doelan.
GenepixApplet
Applet init method.
init()
- Method in class fr.ens.transcriptome.doelan.gui.
CommonWindow
Initiatilze the application.
install(JEditorPane)
- Method in class fr.ens.transcriptome.doelan.gui.
DoelanEditorKit
Overide the install method of the EditorKit.
isATestSuite()
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestSuiteList
Test if a test suite is set.
isAddable()
- Method in class fr.ens.transcriptome.doelan.algorithms.
DoelanConfigure
Test if the test could be diplayed in the list of tests to add.
isAddable()
- Method in class fr.ens.transcriptome.doelan.algorithms.
QualityGlobalTest
Test if the test could be diplayed in the list of tests to add.
isAddable()
- Method in class fr.ens.transcriptome.doelan.algorithms.
QualityTest
Test if the test could be diplayed in the list of tests to add.
isAddable()
- Method in class fr.ens.transcriptome.doelan.algorithms.
QualityUnitTest
Test if the test could be diplayed in the list of tests to add.
isAppletMode()
- Method in class fr.ens.transcriptome.doelan.
Core
Test if the applet is enable.
isAppletMode()
- Static method in class fr.ens.transcriptome.doelan.
DoelanRegistery
Test if applet mode is set.
isCellEditable(int, int)
- Method in class fr.ens.transcriptome.doelan.gui.
QualityTestSuiteTableModel
Returns true if the cell at rowIndex and columnIndex is editable.
isChipTypeMode()
- Method in class fr.ens.transcriptome.doelan.gui.
RenameTestSuiteWidget
Test if is in chip type mode.
isDeletable()
- Method in class fr.ens.transcriptome.doelan.algorithms.
DoelanConfigure
Test if the test is deletable().
isDeletable()
- Method in class fr.ens.transcriptome.doelan.algorithms.
QualityGlobalTest
Test if the test is deletable().
isDeletable()
- Method in class fr.ens.transcriptome.doelan.algorithms.
QualityTest
Test if the test is deletable().
isDeletable()
- Method in class fr.ens.transcriptome.doelan.algorithms.
QualityUnitTest
Test if the test is deletable().
isEditable()
- Method in class fr.ens.transcriptome.doelan.gui.
MyImageView
isFilterFlags()
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResult
Test new flags must be filtered.
isGlobalResult()
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResult
Test if there is a result for each channel.
isModifiable()
- Method in class fr.ens.transcriptome.doelan.algorithms.
DoelanConfigure
Test if the test is modifiable.
isModifiable()
- Method in class fr.ens.transcriptome.doelan.algorithms.
QualityGlobalTest
Test if the test is modifiable.
isModifiable()
- Method in class fr.ens.transcriptome.doelan.algorithms.
QualityTest
Test if the test is modifiable.
isModifiable()
- Method in class fr.ens.transcriptome.doelan.algorithms.
QualityUnitTest
Test if the test is modifiable.
isOk()
- Method in class fr.ens.transcriptome.doelan.gui.
NewWorkflowElementWidget
Test if ok.
isPass()
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResult.SummaryResult
Test if the test pass.
isPercent()
- Method in class fr.ens.transcriptome.doelan.data.
QualityGlobalTestResult
Test if the value is a percentage.
isPercent()
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResult.SummaryResult
Test if the value is a percentage.
isShowable()
- Method in class fr.ens.transcriptome.doelan.algorithms.
DoelanConfigure
Test if the test could be showed.
isShowable()
- Method in class fr.ens.transcriptome.doelan.algorithms.
QualityGlobalTest
Test if the test could be showed.
isShowable()
- Method in class fr.ens.transcriptome.doelan.algorithms.
QualityTest
Test if the test could be showed.
isShowable()
- Method in class fr.ens.transcriptome.doelan.algorithms.
QualityUnitTest
Test if the test could be showed.
isSuite()
- Method in class fr.ens.transcriptome.doelan.
Core
Test if a suite is load in memory.
isThresholdCaptionRight()
- Method in class fr.ens.transcriptome.doelan.
DoelanChart
Test if the position of the caption for the threshold is on the right.
isUniqueInstance()
- Method in class fr.ens.transcriptome.doelan.algorithms.
DoelanConfigure
Test if only one instance of the test could be created.
isUniqueInstance()
- Method in class fr.ens.transcriptome.doelan.algorithms.
QualityGlobalTest
Test if only one instance of the test could be created.
isUniqueInstance()
- Method in class fr.ens.transcriptome.doelan.algorithms.
QualityTest
Test if only one instance of the test could be created.
isUniqueInstance()
- Method in class fr.ens.transcriptome.doelan.algorithms.
QualityUnitTest
Test if only one instance of the test could be created.
isYLogAxis()
- Method in class fr.ens.transcriptome.doelan.
DoelanChart
Test if the Y axis is in log scale
L
LICENCE
- Static variable in class fr.ens.transcriptome.doelan.
Defaults
Licence.
LOAD_ALGORITHM
- Static variable in class fr.ens.transcriptome.doelan.
Core
Identifier of the load algorithm.
licence()
- Static method in class fr.ens.transcriptome.doelan.
DoelanRegistery
Get information about the project.
loadNewWorkflow(QualityTestSuiteURL)
- Method in class fr.ens.transcriptome.doelan.
Core
Load an new workflow
M
MANUFACTURER
- Static variable in class fr.ens.transcriptome.doelan.
Defaults
Manufacturer.
MANUFACTURER_WEBSITE
- Static variable in class fr.ens.transcriptome.doelan.
Defaults
Web site.
MIDDLE
- Static variable in class fr.ens.transcriptome.doelan.gui.
MyImageView
MainTabWidget
- class fr.ens.transcriptome.doelan.gui.
MainTabWidget
.
Main Panel.
MainTabWidget()
- Constructor for class fr.ens.transcriptome.doelan.gui.
MainTabWidget
Public constructor.
MaxDiameterFeatureTest
- class fr.ens.transcriptome.doelan.tests.
MaxDiameterFeatureTest
.
This class defines a quality test based on spot diameter.
MaxDiameterFeatureTest()
- Constructor for class fr.ens.transcriptome.doelan.tests.
MaxDiameterFeatureTest
Public constructor.
MinDiameterFeatureTest
- class fr.ens.transcriptome.doelan.tests.
MinDiameterFeatureTest
.
This class defines a quality test based on the minimal spot diameter.
MinDiameterFeatureTest()
- Constructor for class fr.ens.transcriptome.doelan.tests.
MinDiameterFeatureTest
Public constructor.
MinimalIntensityTest
- class fr.ens.transcriptome.doelan.tests.
MinimalIntensityTest
.
Test there are real spots in "abscent" spot.
MinimalIntensityTest()
- Constructor for class fr.ens.transcriptome.doelan.tests.
MinimalIntensityTest
Public constructor.
MyImageView
- class fr.ens.transcriptome.doelan.gui.
MyImageView
.
Image viewer
MyImageView(Element, Map)
- Constructor for class fr.ens.transcriptome.doelan.gui.
MyImageView
Creates a new view that represents an IMG element.
main(String[])
- Static method in class fr.ens.transcriptome.doelan.
App
Main method.
main(InputStream)
- Static method in class fr.ens.transcriptome.doelan.
App
Main method.
main(Properties, String[])
- Static method in class fr.ens.transcriptome.doelan.
App
Main method.
main(String[])
- Static method in class fr.ens.transcriptome.doelan.
EclipseApp
Main method.
modelToView(int, Shape, Position.Bias)
- Method in class fr.ens.transcriptome.doelan.gui.
MyImageView
Provides a mapping from the document model coordinate space to the coordinate space of the view mapped to it.
mouseClicked(MouseEvent)
- Method in class fr.ens.transcriptome.doelan.gui.
MyImageView
On double-click, open image properties dialog.
mouseDragged(MouseEvent)
- Method in class fr.ens.transcriptome.doelan.gui.
MyImageView
Resize image if initial click was in grow-box:
mouseEntered(MouseEvent)
- Method in class fr.ens.transcriptome.doelan.gui.
MyImageView
Mouse event
mouseExited(MouseEvent)
- Method in class fr.ens.transcriptome.doelan.gui.
MyImageView
Mouse event
mouseMoved(MouseEvent)
- Method in class fr.ens.transcriptome.doelan.gui.
MyImageView
Mouse event
mousePressed(MouseEvent)
- Method in class fr.ens.transcriptome.doelan.gui.
MyImageView
Select or grow image when clicked.
mouseReleased(MouseEvent)
- Method in class fr.ens.transcriptome.doelan.gui.
MyImageView
Mouse event
N
NewTestSuiteWidget
- class fr.ens.transcriptome.doelan.gui.
NewTestSuiteWidget
.
Widget to create a new test suite list.
NewTestSuiteWidget(QualityTestSuiteList, String)
- Constructor for class fr.ens.transcriptome.doelan.gui.
NewTestSuiteWidget
This is the default constructor.
NewWorkflowElementWidget
- class fr.ens.transcriptome.doelan.gui.
NewWorkflowElementWidget
.
Widget for creating new WorkflowElement.
NewWorkflowElementWidget(ModuleLocation[])
- Constructor for class fr.ens.transcriptome.doelan.gui.
NewWorkflowElementWidget
This is the default constructor
NotFoundFeatureTest
- class fr.ens.transcriptome.doelan.tests.
NotFoundFeatureTest
.
This class define a test based on not found spot flags.
NotFoundFeatureTest()
- Constructor for class fr.ens.transcriptome.doelan.tests.
NotFoundFeatureTest
Public constructor.
P
paint(Graphics, Shape)
- Method in class fr.ens.transcriptome.doelan.gui.
MyImageView
Paints the image.
Q
QualityGlobalTest
- class fr.ens.transcriptome.doelan.algorithms.
QualityGlobalTest
.
This class define a abstract global test.
QualityGlobalTest()
- Constructor for class fr.ens.transcriptome.doelan.algorithms.
QualityGlobalTest
Public constructor.
QualityGlobalTestResult
- class fr.ens.transcriptome.doelan.data.
QualityGlobalTestResult
.
This class define a result from a QualityUnitTest
QualityGlobalTestResult(BioAssay, QualityGlobalTest)
- Constructor for class fr.ens.transcriptome.doelan.data.
QualityGlobalTestResult
Public constructor.
QualityGlobalTestResultData
- class fr.ens.transcriptome.doelan.data.
QualityGlobalTestResultData
.
Wrapper of QualityGlobalTestResult.
QualityGlobalTestResultData(QualityGlobalTestResult)
- Constructor for class fr.ens.transcriptome.doelan.data.
QualityGlobalTestResultData
Public constructor.
QualityTest
- class fr.ens.transcriptome.doelan.algorithms.
QualityTest
.
This class is the super class of QualityUnitTest and QualityGlobalTest.
QualityTest()
- Constructor for class fr.ens.transcriptome.doelan.algorithms.
QualityTest
Public constructor.
QualityTestIOFactory
- class fr.ens.transcriptome.doelan.io.
QualityTestIOFactory
.
A factory for testsuitelist io.
QualityTestIOFactory()
- Constructor for class fr.ens.transcriptome.doelan.io.
QualityTestIOFactory
QualityTestResult
- class fr.ens.transcriptome.doelan.data.
QualityTestResult
.
This clas is the abstract superclass of QualityUnitTest and QualityGlobalUnit
QualityTestResult()
- Constructor for class fr.ens.transcriptome.doelan.data.
QualityTestResult
QualityTestSuiteList
- class fr.ens.transcriptome.doelan.data.
QualityTestSuiteList
.
This class defines a container for testsuites.
QualityTestSuiteList()
- Constructor for class fr.ens.transcriptome.doelan.data.
QualityTestSuiteList
QualityTestSuiteListIO
- interface fr.ens.transcriptome.doelan.io.
QualityTestSuiteListIO
.
This interface defines generics methods to read and write test suites parameters.
QualityTestSuiteTableModel
- class fr.ens.transcriptome.doelan.gui.
QualityTestSuiteTableModel
.
Table model for QualityUnitTest
QualityTestSuiteTableModel()
- Constructor for class fr.ens.transcriptome.doelan.gui.
QualityTestSuiteTableModel
QualityTestSuiteURL
- class fr.ens.transcriptome.doelan.data.
QualityTestSuiteURL
.
This class define a location to a qualtity test suite.
QualityTestSuiteURL()
- Constructor for class fr.ens.transcriptome.doelan.data.
QualityTestSuiteURL
QualityUnitTest
- class fr.ens.transcriptome.doelan.algorithms.
QualityUnitTest
.
This class define a quality unit test.
QualityUnitTest()
- Constructor for class fr.ens.transcriptome.doelan.algorithms.
QualityUnitTest
Public constructor.
QualityUnitTestResult
- class fr.ens.transcriptome.doelan.data.
QualityUnitTestResult
.
This class define a result from a QualityUnitTest
QualityUnitTestResult(BioAssay, QualityUnitTest)
- Constructor for class fr.ens.transcriptome.doelan.data.
QualityUnitTestResult
Public constructor.
QualityUnitTestResult.SummaryResult
- class fr.ens.transcriptome.doelan.data.
QualityUnitTestResult.SummaryResult
.
This class define the result for a channel.
QualityUnitTestResultData
- class fr.ens.transcriptome.doelan.data.
QualityUnitTestResultData
.
Wrapper of QualityUnitTestResult.
QualityUnitTestResultData(QualityUnitTestResult)
- Constructor for class fr.ens.transcriptome.doelan.data.
QualityUnitTestResultData
Public constructor.
R
REJECTED_SPOT_IDENTIFIER
- Static variable in class fr.ens.transcriptome.doelan.
Defaults
The identifier of the rejected spots.
RESULT_EVENT
- Static variable in class fr.ens.transcriptome.doelan.algorithms.
QualityTest
Identifier for result event.
RenameTestSuiteWidget
- class fr.ens.transcriptome.doelan.gui.
RenameTestSuiteWidget
.
RenameTestSuiteWidget(QualityTestSuiteList, String, QualityTestSuiteURL)
- Constructor for class fr.ens.transcriptome.doelan.gui.
RenameTestSuiteWidget
This is the default constructor
ReportTabWidget
- class fr.ens.transcriptome.doelan.gui.
ReportTabWidget
.
Report widget.
ReportTabWidget(JLabel)
- Constructor for class fr.ens.transcriptome.doelan.gui.
ReportTabWidget
Public constructor.
read()
- Method in interface fr.ens.transcriptome.doelan.io.
QualityTestSuiteListIO
Read a test suite list.
removeChipType(String)
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestSuiteList
Remove a chip if it is empty.
removeTestSuite(QualityTestSuiteURL)
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestSuiteList
Remove a test suite
renameChipType(String, String)
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestSuiteList
Rename a chip type
renameTestSuite(String, String, String)
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestSuiteList
Rename a test suite
repaint(long)
- Method in class fr.ens.transcriptome.doelan.gui.
MyImageView
Request that this view be repainted.
requestFocus()
- Method in class fr.ens.transcriptome.doelan.gui.
RenameTestSuiteWidget
Set the focus on the textField
resize(int, int)
- Method in class fr.ens.transcriptome.doelan.gui.
MyImageView
Change the size of this image.
S
SHOW_REPORT_ALGORITHM
- Static variable in class fr.ens.transcriptome.doelan.
Core
Identifier of the show report algorithm.
STATUS_ERROR
- Static variable in class fr.ens.transcriptome.doelan.gui.
StatusWidget
Testsuite error.
STATUS_FAILLED
- Static variable in class fr.ens.transcriptome.doelan.gui.
StatusWidget
Testsuite failled.
STATUS_NOT_STARTED
- Static variable in class fr.ens.transcriptome.doelan.gui.
StatusWidget
Testsuite not started.
STATUS_NO_DATA_TO_TEST
- Static variable in class fr.ens.transcriptome.doelan.gui.
StatusWidget
Testsuite no data to test.
STATUS_PASS
- Static variable in class fr.ens.transcriptome.doelan.gui.
StatusWidget
Testsuite success.
STATUS_STARTED
- Static variable in class fr.ens.transcriptome.doelan.gui.
StatusWidget
Testsuite started.
SUBDIR_DATA
- Static variable in class fr.ens.transcriptome.doelan.
Defaults
sub directory for data.
SUBDIR_REPORT
- Static variable in class fr.ens.transcriptome.doelan.
Defaults
sub directory for the reports.
SaturatedPixelsTest
- class fr.ens.transcriptome.doelan.tests.
SaturatedPixelsTest
.
This class define a test for saturated pixel of features from a bioassay.
SaturatedPixelsTest()
- Constructor for class fr.ens.transcriptome.doelan.tests.
SaturatedPixelsTest
Public constructor.
StatusWidget
- class fr.ens.transcriptome.doelan.gui.
StatusWidget
.
Status widget.
StatusWidget(JPanel, int)
- Constructor for class fr.ens.transcriptome.doelan.gui.
StatusWidget
Public constructor.
SuiteChooserWidget
- class fr.ens.transcriptome.doelan.gui.
SuiteChooserWidget
.
Suite chooser widget.
SuiteChooserWidget(MainTabWidget, JPanel, int)
- Constructor for class fr.ens.transcriptome.doelan.gui.
SuiteChooserWidget
Public constructor.
saveWorkflow(QualityTestSuiteURL)
- Method in class fr.ens.transcriptome.doelan.
Core
Save a workflow.
setApplet(Applet)
- Method in class fr.ens.transcriptome.doelan.
Core
Set the applet.
setApplet(Applet)
- Method in class fr.ens.transcriptome.doelan.algorithms.
DoelanLoadGenepixData
Set the applet.
setAppletMode(boolean)
- Static method in class fr.ens.transcriptome.doelan.
DoelanRegistery
Set the applet mode.
setArrayPlot(Image)
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResult
Set the arrayplot image.
setBins(int)
- Method in class fr.ens.transcriptome.doelan.
DoelanChart
Set the number of bins
setBioAssay(String)
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestResult
Set the bioassay reference.
setBioAssay(BioAssay)
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestResult
Set the bioassay reference.
setButtonText(String)
- Method in class fr.ens.transcriptome.doelan.gui.
FileChooserWidget
Set the text of the button
setChipType(String)
- Method in class fr.ens.transcriptome.doelan.gui.
TestSuiteTabWidget
Set the chip type to display.
setChipTypeMode(boolean)
- Method in class fr.ens.transcriptome.doelan.gui.
RenameTestSuiteWidget
Set if the chip type mode is set.
setChipTypeName(String)
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResult
Set the name of the type of the chip.
setContainer(Container)
- Method in class fr.ens.transcriptome.doelan.gui.
CommonWindow
Set the Graphical Container.
setData(double[])
- Method in class fr.ens.transcriptome.doelan.
DoelanChart
set the data
setData(QualityGlobalTestResult)
- Method in class fr.ens.transcriptome.doelan.data.
QualityGlobalTestResultData
Set the Result.
setData(QualityUnitTestResult)
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResultData
Set the Result.
setData(TestSuiteResult)
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResultData
Set the Result.
setDescription(String)
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResult
Set the data description
setEmptySpotIds(String[])
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResult
Set the identifiers of the empty spots.
setFilterFlags(boolean)
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResult
Set if the new flags must be filtered.
setGalData(BioAssay)
- Method in class fr.ens.transcriptome.doelan.gui.
ReportTabWidget
Set the new Gal file.
setGlobalResultType(boolean)
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResult
Set if there is a result for each channel.
setHeight(int)
- Method in class fr.ens.transcriptome.doelan.
DoelanChart
Set the height of the image.
setHistCaption(String)
- Method in class fr.ens.transcriptome.doelan.
DoelanChart
Set the histogram caption
setHtmlReport(String)
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResult
Set the code of the html report.
setImage(Image)
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestResult
Set the image.
setImages(Map)
- Method in class fr.ens.transcriptome.doelan.gui.
ReportTabWidget
Set the image for the HTML render.
setLocation(int, int)
- Method in class fr.ens.transcriptome.doelan.gui.
EditParametersWidget
Set the location of the widget.
setMainTab(MainTabWidget)
- Method in class fr.ens.transcriptome.doelan.
Core
Set the main tab widget
setMainTabWidget(MainTabWidget)
- Method in class fr.ens.transcriptome.doelan.gui.
SuiteChooserWidget
Set the common window.
setMapImages(Map)
- Method in class fr.ens.transcriptome.doelan.gui.
DoelanEditorKit
Set the map of the images.
setMapImages(Map)
- Method in class fr.ens.transcriptome.doelan.gui.
MyImageView
Set the map of the images.
setMessage(String)
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestResult
Set the message of the test.
setMnemonicKey(int)
- Method in class fr.ens.transcriptome.doelan.gui.
DescriptionWidget
set the mnemonic key.
setMnemonicKey(int)
- Method in class fr.ens.transcriptome.doelan.gui.
FileChooserWidget
set the mnemonic key.
setName(String)
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestSuiteURL
Set the name of the TestSuiteURL
setNewArrayList(BioAssay)
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResult
Set the new array list.
setNewFlags(boolean[])
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResult
Set the new flags values after the test.
setPanel(JPanel)
- Method in class fr.ens.transcriptome.doelan.gui.
StatusWidget
Set the panel.
setPanel(JPanel)
- Method in class fr.ens.transcriptome.doelan.gui.
SuiteChooserWidget
Set the panel.
setParameters(Parameters)
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestResult
Set the parameters of the test.
setParameters(Parameters)
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResult.GlobalTest
Set the parameters
setParent(View)
- Method in class fr.ens.transcriptome.doelan.gui.
MyImageView
Establishes the parent view for this view.
setPass(boolean)
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResult.SummaryResult
Set if the test pass.
setPercent(boolean)
- Method in class fr.ens.transcriptome.doelan.data.
QualityGlobalTestResult
Set if the value is a percentage.
setPercent(boolean)
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResult.SummaryResult
Set if the value is a percentage.
setRealFeatures(int)
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResult
Set the count of the realFeatures (not abscent).
setReport(ReportTabWidget)
- Method in class fr.ens.transcriptome.doelan.
Core
Set the report widget.
setReport(ReportTabWidget)
- Method in class fr.ens.transcriptome.doelan.algorithms.
DoelanShowReport
Set the report widget.
setResult(boolean)
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestResult
Set the result
setResult(boolean)
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResult
Set the result of the test suite.
setSize(float, float)
- Method in class fr.ens.transcriptome.doelan.gui.
MyImageView
Set the size of the view.
setSpotRejectedId(String)
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResult
Set the identifier for the rejected spots.
setStartButtonEnable(boolean)
- Method in class fr.ens.transcriptome.doelan.gui.
TestSuitePanel
Enable the start button.
setStatus(StatusWidget)
- Method in class fr.ens.transcriptome.doelan.
Core
Set the status widget.
setStatus(StatusWidget)
- Method in class fr.ens.transcriptome.doelan.algorithms.
DoelanShowReport
Set the status widget.
setStatus(int)
- Method in class fr.ens.transcriptome.doelan.gui.
StatusWidget
Set the status of the testsuite.
setStatusBar(JLabel)
- Method in class fr.ens.transcriptome.doelan.
Core
Set the status bar object.
setTable(TestSuitePanel)
- Method in class fr.ens.transcriptome.doelan.
Core
Set the table.
setTest(QualityGlobalTest)
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResult.GlobalTest
Set the test.
setTestDescription(String)
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestResult
Set Test description.
setTestId(String)
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestResult
Set the identifier of the test.
setTestSuite(String)
- Method in class fr.ens.transcriptome.doelan.gui.
TestSuiteTabWidget
Set the test suite to display.
setTestSuiteList(QualityTestSuiteList)
- Method in class fr.ens.transcriptome.doelan.gui.
SuiteChooserWidget
Set the test suite list.
setTestSuiteListURL(URL)
- Method in class fr.ens.transcriptome.doelan.
Core
Set the URL of the test suite list.
setTestSuiteName(String)
- Method in class fr.ens.transcriptome.doelan.data.
TestSuiteResult
Set the test suite name.
setTestSuiteName(String)
- Method in class fr.ens.transcriptome.doelan.gui.
StatusWidget
Set the test suite name.
setTestSuiteRadioButton(JRadioButton)
- Method in class fr.ens.transcriptome.doelan.gui.
RenameTestSuiteWidget
setTestType(String)
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestResult
Set the type of the test.
setText(String)
- Method in class fr.ens.transcriptome.doelan.gui.
ReportTabWidget
Set the text of the report.
setThreshold(double)
- Method in class fr.ens.transcriptome.doelan.
DoelanChart
Set the threshold
setThreshold(double)
- Method in class fr.ens.transcriptome.doelan.data.
QualityGlobalTestResult
Set the threshold.
setThreshold(double)
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResult.SummaryResult
Set the threshold.
setThresholdCaptionRight(boolean)
- Method in class fr.ens.transcriptome.doelan.
DoelanChart
Set the position of the caption for the threshold.
setThresholdEqualityType(String)
- Method in class fr.ens.transcriptome.doelan.data.
QualityGlobalTestResult
Set the equality type between the the threshold and its value.
setThresholdEqualityType(String)
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResult.SummaryResult
Set the equality type between the the threshold and its value.
setTitle(String)
- Method in class fr.ens.transcriptome.doelan.
DoelanChart
Set the title of the plot.
setURL(URL)
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestSuiteURL
Set the url of the TestSuite
setUnit(String)
- Method in class fr.ens.transcriptome.doelan.data.
QualityGlobalTestResult
Set the unit of the value and the threshold.
setUnit(String)
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResult.SummaryResult
Set the unit of the value and the threshold.
setUrl(String)
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestSuiteURL
Set the url of the TestSuite
setUrl(QualityTestSuiteURL)
- Method in class fr.ens.transcriptome.doelan.gui.
TestSuitePanel
Set the url of the test suite
setValue(double)
- Method in class fr.ens.transcriptome.doelan.data.
QualityGlobalTestResult
Set the value.
setValue(double)
- Method in class fr.ens.transcriptome.doelan.data.
QualityUnitTestResult.SummaryResult
Set the value.
setValueAt(Object, int, int)
- Method in class fr.ens.transcriptome.doelan.gui.
QualityTestSuiteTableModel
Sets the value in the cell at columnIndex and rowIndex to aValue.
setWidth(int)
- Method in class fr.ens.transcriptome.doelan.
DoelanChart
Set the width of the image.
setWorking(boolean)
- Method in class fr.ens.transcriptome.doelan.gui.
MainTabWidget
Set the state of the application.
setXAxisLegend(String)
- Method in class fr.ens.transcriptome.doelan.
DoelanChart
Set the x axis legend
setYAxisLegend(String)
- Method in class fr.ens.transcriptome.doelan.
DoelanChart
Get the y axis legend
setYLogAxis(boolean)
- Method in class fr.ens.transcriptome.doelan.
DoelanChart
Set the log scale for the y axis
setYPosition(int)
- Method in class fr.ens.transcriptome.doelan.gui.
StatusWidget
Set the y position of the widget.
setYPosition(int)
- Method in class fr.ens.transcriptome.doelan.gui.
SuiteChooserWidget
Set the y position of the widget.
showMessage(String, boolean)
- Static method in class fr.ens.transcriptome.doelan.gui.
CommonWindow
Show a message to the user.
showStatusBarMessage(String)
- Static method in class fr.ens.transcriptome.doelan.gui.
CommonWindow
Set the message for the status bar.
size()
- Method in class fr.ens.transcriptome.doelan.data.
QualityTestSuiteList
Return the number of chip types.
start()
- Method in class fr.ens.transcriptome.doelan.gui.
MainTabWidget
Start analysis.
startWorkflow(String, String, String, String, String, Applet, WorkflowListener)
- Method in class fr.ens.transcriptome.doelan.
Core
Start the workflow.
stopWorkflow()
- Method in class fr.ens.transcriptome.doelan.
Core
Stop the workflow.
T
TESTSUITE_RESULT_TYPE
- Static variable in class fr.ens.transcriptome.doelan.data.
DoelanDataDefaults
Testsuite result type.
TEST_SUITE_LIST_FILE
- Static variable in class fr.ens.transcriptome.doelan.
Defaults
Default test suite list file.
TEST_SUITE_NAME_ANNOTATION_KEY
- Static variable in class fr.ens.transcriptome.doelan.
Defaults
Annatotation key of the test suite name.
TEXTTOP
- Static variable in class fr.ens.transcriptome.doelan.gui.
MyImageView
TOP
- Static variable in class fr.ens.transcriptome.doelan.gui.
MyImageView
TestSuitePanel
- class fr.ens.transcriptome.doelan.gui.
TestSuitePanel
.
TestSuitePanel()
- Constructor for class fr.ens.transcriptome.doelan.gui.
TestSuitePanel
Public constructor.
TestSuiteResult
- class fr.ens.transcriptome.doelan.data.
TestSuiteResult
.
This class contains the report information of a testsuite.
TestSuiteResult(String, String, String)
- Constructor for class fr.ens.transcriptome.doelan.data.
TestSuiteResult
Public Constructor.
TestSuiteResult.GlobalTest
- class fr.ens.transcriptome.doelan.data.
TestSuiteResult.GlobalTest
.
This class defines a object which contains a global test and its parameters
TestSuiteResult.GlobalTest(QualityGlobalTest, Parameters)
- Constructor for class fr.ens.transcriptome.doelan.data.
TestSuiteResult.GlobalTest
Public constructor.
TestSuiteResultData
- class fr.ens.transcriptome.doelan.data.
TestSuiteResultData
.
This class define a nividic data object for testsuite results.
TestSuiteResultData(TestSuiteResult)
- Constructor for class fr.ens.transcriptome.doelan.data.
TestSuiteResultData
Public constructor.
TestSuiteTabWidget
- class fr.ens.transcriptome.doelan.gui.
TestSuiteTabWidget
.
The testsuite panel
TestSuiteTabWidget()
- Constructor for class fr.ens.transcriptome.doelan.gui.
TestSuiteTabWidget
Public constructor
tableChanged(TableModelEvent)
- Method in class fr.ens.transcriptome.doelan.gui.
TestSuitePanel
This method is call when the table has been changed.
test(BioAssay, BioAssay, Parameters, QualityUnitTestResult[])
- Method in class fr.ens.transcriptome.doelan.algorithms.
QualityGlobalTest
Do the test.
test(BioAssay, BioAssay, Parameters)
- Method in class fr.ens.transcriptome.doelan.algorithms.
QualityUnitTest
Test the quality of the bioassay.
test(BioAssay, BioAssay, Parameters)
- Method in class fr.ens.transcriptome.doelan.tests.
DiameterFeatureTest
Test the quality of the bioassay.
test(BioAssay, BioAssay, Parameters)
- Method in class fr.ens.transcriptome.doelan.tests.
FeatureFlagTest
Test the quality of the bioassay.
test(BioAssay, BioAssay, Parameters)
- Method in class fr.ens.transcriptome.doelan.tests.
GenericTest
Test the quality of the bioassay.
test(BioAssay, BioAssay, Parameters, QualityUnitTestResult[])
- Method in class fr.ens.transcriptome.doelan.tests.
GlobalMaxBadFeatureRemoved
Do the test.
test(BioAssay, BioAssay, Parameters, QualityUnitTestResult[])
- Method in class fr.ens.transcriptome.doelan.tests.
GlobalMaxBadFeaturesTest
Do the test.
test(BioAssay, BioAssay, Parameters)
- Method in class fr.ens.transcriptome.doelan.tests.
HeterogeneousFeatureTest
Test the quality of the bioassay.
test(BioAssay, BioAssay, Parameters)
- Method in class fr.ens.transcriptome.doelan.tests.
MaxDiameterFeatureTest
Test the quality of the bioassay.
test(BioAssay, BioAssay, Parameters)
- Method in class fr.ens.transcriptome.doelan.tests.
MinDiameterFeatureTest
Test the quality of the bioassay.
test(BioAssay, BioAssay, Parameters)
- Method in class fr.ens.transcriptome.doelan.tests.
MinimalIntensityTest
Test the quality of the bioassay.
test(BioAssay, BioAssay, Parameters)
- Method in class fr.ens.transcriptome.doelan.tests.
SaturatedPixelsTest
Test the quality of the bioassay.
U
UNIT_TEST_RESULT_TYPE
- Static variable in class fr.ens.transcriptome.doelan.data.
DoelanDataDefaults
Unit test result type.
V
VERSION
- Static variable in class fr.ens.transcriptome.doelan.
Defaults
Version of the application.
viewToModel(float, float, Shape, Position.Bias[])
- Method in class fr.ens.transcriptome.doelan.gui.
MyImageView
Provides a mapping from the view coordinate space to the logical coordinate space of the model.
W
WEBSITE
- Static variable in class fr.ens.transcriptome.doelan.
Defaults
Web site.
WINDOW_HEIGHT
- Static variable in class fr.ens.transcriptome.doelan.
Defaults
Main window height.
WINDOW_WIDTH
- Static variable in class fr.ens.transcriptome.doelan.
Defaults
Main window width.
workflowNewException(PlatformException)
- Method in class fr.ens.transcriptome.doelan.
Core
Throws an execption to a listener.
workflowNewException(PlatformException)
- Method in class fr.ens.transcriptome.doelan.gui.
MainTabWidget
Throws an execption to a listener.
workflowNewException(PlatformException)
- Method in class fr.ens.transcriptome.doelan.gui.
QualityTestSuiteTableModel
Throws an execption to a listener.
workflowStateChanged(WorkflowEvent)
- Method in class fr.ens.transcriptome.doelan.
Core
Invoked when the target of the listener has changed its state.
workflowStateChanged(WorkflowEvent)
- Method in class fr.ens.transcriptome.doelan.gui.
MainTabWidget
Invoked when the target of the listener has changed its state.
write(QualityTestSuiteList)
- Method in interface fr.ens.transcriptome.doelan.io.
QualityTestSuiteListIO
Write a test suite
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