Constant Field Values

Contents

• ubic.erminej.*

ubic.erminej.*

ubic.erminej.ResultsPrinter

Modifier and Type	Constant Field	Value
protected static final String	END_OF_SETTINGS_SEPARATOR	"#!----"
protected static final String	RUN_INDICATOR	"!#======"
protected static final String	RUN_NAME_FIELD_PATTERN	"!# runName="

ubic.erminej.Settings

Modifier and Type	Constant Field	Value
protected static final String	HEADER	"Configuration file for ermineJ.Do not delete this file if you want your ermineJ settings to stay across sessions.\nFor more information see http://www.chibi.ubc.ca/ermineJ/"
protected static final String	USERGUI_DEFAULT_PROPERTIES	"ermineJdefault.properties"
protected static final String	USERGUI_PROPERTIES	"ermineJ.properties"

ubic.erminej.SettingsHolder

Modifier and Type	Constant Field	Value
protected static final String	ALWAYS_USE_EMPIRICAL	"alwaysUseEmpirical"
protected static final String	ANNOT_FILE	"annotFile"
protected static final String	ANNOT_FORMAT	"annotFormat"
protected static final String	BIG_IS_BETTER	"bigIsBetter"
protected static final String	CLASS_FILE	"classFile"
protected static final String	CLASS_SCORE_METHOD	"classScoreMethod"
protected static final String	CUSTOM_GENE_SET_DIRECTORY_PROPERTY	"classFolder"
protected static final String	CUSTOM_GENESET_FILES	"customGeneSetFiles"
protected static final String	DATA_COL	"dataCol"
protected static final String	DATA_DIRECTORY	"dataDirectory"
protected static final String	DEFAULT_CUSTOM_GENE_SET_DIR_NAME	"genesets"
protected static final String	DEFAULT_USER_DATA_DIR_NAME	"ermineJ.data"
protected static final String	DO_LOG	"doLog"
protected static final String	FILTER_NONSPECIFIC	"filterNonSpecific"
public static final String	GEMMA_URL_BASE	"http://gemma.chibi.ubc.ca/"
protected static final String	GENE_REP_TREATMENT	"geneRepTreatment"
protected static final String	GENE_SCORE_THRESHOLD_KEY	"scoreThreshold"
protected static final String	GENE_SCORE_THRESHOLD_LEGACY_KEY	"pValThreshold"
protected static final String	GENE_SET_RESAMPLING_SCORE_METHOD	"rawScoreMethod"
public static final String	GENE_URL_BASE	"gene.url.base"
protected static final String	GOLD_STANDARD_FILE	"goldStandardFile"
protected static final String	IS_TESTER	"isTester"
protected static final String	ITERATIONS	"iterations"
protected static final String	MAX_CLASS_SIZE	"maxClassSize"
protected static final String	MIN_CLASS_SIZE	"minClassSize"
protected static final String	MTC_CONFIG_NAME	"mtc"
protected static final String	OUTPUT_FILE	"outputFile"
protected static final String	PREFERENCES_FILE_NAME	"preferencesFileName"
protected static final String	QUANTILE_CONFIG_NAME	"quantile"
protected static final String	RAW_FILE_CONFIG_NAME	"rawFile"
protected static final String	SAVE_ALL_GENES_IN_OUTPUT	"saveAllGenesInOutput"
protected static final String	SCORE_COL	"scoreCol"
protected static final String	SCORE_FILE	"scoreFile"
protected static final String	SELECTED_CUSTOM_GENESETS	"selectedCustomGeneSets"
protected static final String	USE_BIOL_PROC	"useGOBiologicalProcess"
protected static final String	USE_CELL_COMP	"useGOCellularComponent"
protected static final String	USE_MOL_FUNC	"useGOMolecularFunction"
protected static final String	USE_MULTIFUNCTIONALITY_CORRECTION	"multifuncCorr"
protected static final String	USE_USER_DEFINED_GROUPS	"useUserDefinedGroups"

ubic.erminej.analysis.AbstractGeneSetPvalGenerator

Modifier and Type	Constant Field	Value
protected static final int	ALERT_UPDATE_FREQUENCY	300

ubic.erminej.analysis.AbstractResamplingGeneSetScore

Modifier and Type	Constant Field	Value
protected static final int	NORMAL_APPROX_SAMPLE_FREQUENCY	200
protected static final double	SPEDUPSIZEEXTRASTEP	0.1
protected static final int	SPEEDUPSIZECUT	20
protected static final double	TOLERANCE	1.0E-4

ubic.erminej.data.GeneAnnotations

Modifier and Type	Constant Field	Value
public static final boolean	DEFAULT_FILTER_NONSPECIFIC	false

ubic.erminej.data.GeneSetTerms

Modifier and Type	Constant Field	Value
public static final String	NO_ASPECT_AVAILABLE	"[No aspect available]"
public static final String	USER_DEFINED	"User-defined"

ubic.erminej.gui.MainFrame

Modifier and Type	Constant Field	Value
public static final String	RESOURCE_LOCATION	"/ubic/erminej/"

ubic.erminej.gui.geneset.GeneSetPanel

Modifier and Type	Constant Field	Value
public static final String	DELETED	"DELETED"
public static final double	FDR_THRESHOLD_FOR_FILTER	0.1
public static final int	MAX_DEFINITION_LENGTH	300
public static final String	NOACTION	"NOACTION"
public static final String	RESOURCE_LOCATION	"/ubic/erminej/"
public static final String	RESTORED	"RESTORED"

ubic.erminej.gui.geneset.details.GeneSetDetailsFrame

Modifier and Type	Constant Field	Value
protected static final String	GEMMA_GENE_SEARCH_URL_BASE	"http://www.chibi.ubc.ca/Gemma/searcher.html?scope=G&query="
public static final int	MAX_GENES_FOR_DETAIL_VIEWING	1000

ubic.erminej.gui.geneset.details.GeneSetDetailsTableModel

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_GENE_URL_BASE	"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=search&term=@@"

ubic.erminej.gui.geneset.table.GeneSetTableModel

Modifier and Type	Constant Field	Value
public static final int	INIT_COLUMNS	4

ubic.erminej.gui.geneset.table.GeneSetTablePanel

Modifier and Type	Constant Field	Value
public static final int	GENE_COUNT_COLUMN_INDEX	2
public static final int	MULTIFUNC_COLUMN_INDEX	3

ubic.erminej.gui.table.JBarGraphCellRenderer

Modifier and Type	Constant Field	Value
protected static final int	LINE_WIDTH	2