Uses of Class
ubic.erminej.Settings

Packages that use Settings

Package	Description
ubic.erminej
ubic.erminej.data
ubic.erminej.gui
ubic.erminej.gui.analysis
ubic.erminej.gui.file
ubic.erminej.gui.geneset
ubic.erminej.gui.geneset.table
ubic.erminej.gui.geneset.tree

Uses of Settings in ubic.erminej

Fields in ubic.erminej declared as Settings

Modifier and Type	Field and Description
protected Settings	classScoreCMD.settings

Constructors in ubic.erminej with parameters of type Settings

Constructor and Description
ErmineJGui(Settings settings)

Uses of Settings in ubic.erminej.data

Methods in ubic.erminej.data that return Settings

Modifier and Type	Method and Description
Settings	GeneSetDetails.getSettings()

Methods in ubic.erminej.data with parameters of type Settings

Modifier and Type	Method and Description
GeneAnnotations	GeneAnnotationParser.read(String fileName, GeneAnnotationParser.Format format, Settings settings)

Constructors in ubic.erminej.data with parameters of type Settings

Constructor and Description
GeneScores(Collection<String> identifiers, Settings settings, StatusViewer m, GeneAnnotations geneAnnotations, String outputFileName) Constructor for the case when we are just taking in a hit list.
GeneSetDetails(GeneSetTerm classID, GeneSetResult result, GeneAnnotations geneData, Settings settings, GeneScores geneScores, StatusViewer statusViewer) The data matrix will be read in based on the settings, or can be changed later.
GeneSetTerms(String fileName, Settings settings)

Uses of Settings in ubic.erminej.gui

Methods in ubic.erminej.gui that return Settings

Modifier and Type	Method and Description
Settings	MainFrame.getSettings()

Constructors in ubic.erminej.gui with parameters of type Settings

Constructor and Description
MainFrame(Settings settings)
SaveAnalysisDialog(MainFrame owner, Settings settings, int initialSelection)
StartupPanel(Settings settings, StatusViewer statusMessenger)

Uses of Settings in ubic.erminej.gui.analysis

Constructors in ubic.erminej.gui.analysis with parameters of type Settings

Constructor and Description
AnalysisWizardStep1(AnalysisWizard wiz, Settings settings)
AnalysisWizardStep2(AnalysisWizard wiz, Settings settings)
AnalysisWizardStep3(AnalysisWizard wizard, Settings settings)
AnalysisWizardStep4(AnalysisWizard wiz, Settings settings)
AnalysisWizardStep5(AnalysisWizard wiz, Settings settings)

Uses of Settings in ubic.erminej.gui.file

Constructors in ubic.erminej.gui.file with parameters of type Settings

Constructor and Description
DataDirectoryDialog(Settings settings)

Uses of Settings in ubic.erminej.gui.geneset

Fields in ubic.erminej.gui.geneset declared as Settings

Modifier and Type	Field and Description
protected Settings	GeneSetPanel.settings

Constructors in ubic.erminej.gui.geneset with parameters of type Settings

Constructor and Description
GeneSetPanel(Settings settings, MainFrame callingFrame)

Uses of Settings in ubic.erminej.gui.geneset.table

Constructors in ubic.erminej.gui.geneset.table with parameters of type Settings

Constructor and Description
GeneSetTablePanel(MainFrame callingFrame, Settings settings)

Uses of Settings in ubic.erminej.gui.geneset.tree

Constructors in ubic.erminej.gui.geneset.tree with parameters of type Settings

Constructor and Description
GeneSetTreePanel(MainFrame callingFrame, Settings settings)