Constant Field Values

Contents

• ubic.gemma.*

ubic.gemma.*

ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis

Modifier and Type	Constant Field	Value
public static final int	HARD_LIMIT_MIN_NUM_USED	8

ubic.gemma.core.analysis.expression.coexpression.links.MatrixRowPairAnalysis

Modifier and Type	Constant Field	Value
public static final int	NUM_BINS	2048

ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisConfig

Modifier and Type	Constant Field	Value
public static final boolean	DEFAULT_EBAYES	true

ubic.gemma.core.analysis.expression.diff.DifferentialExpressionFileUtils

Modifier and Type	Constant Field	Value
public static final String	PVALUE_DIST_SUFFIX	".dist.txt"

ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionService

Modifier and Type	Constant Field	Value
public static final double	PVALUE_CLIP_THRESHOLD	1.0E-8

ubic.gemma.core.analysis.preprocess.TwoChannelMissingValues

Modifier and Type	Constant Field	Value
public static final double	DEFAULT_SIGNAL_TO_NOISE_THRESHOLD	1.5

ubic.gemma.core.analysis.preprocess.batcheffects.BaseScanDateExtractor

Modifier and Type	Constant Field	Value
protected static final String	GENEPIX_DATETIME_HEADER_REGEXP	"\"?DateTime=.*"

ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchCorrectionServiceImpl

Modifier and Type	Constant Field	Value
public static final String	COLLECTION_OF_MATERIAL_URI	"http://www.ebi.ac.uk/efo/EFO_0005066"
public static final String	DE_EXCLUDE_URI	"http://gemma.msl.ubc.ca/ont/TGEMO_00014"
public static final String	DE_INCLUDE_URI	"http://gemma.msl.ubc.ca/ont/TGEMO_00013"

ubic.gemma.core.analysis.preprocess.filter.FilterConfig

Modifier and Type	Constant Field	Value
public static final double	DEFAULT_DISTINCTVALUE_FRACTION	0.5
public static final double	DEFAULT_HIGHEXPRESSION_CUT	0.0
public static final double	DEFAULT_LOWEXPRESSIONCUT	0.2
public static final double	DEFAULT_LOWVARIANCECUT	0.05
public static final double	DEFAULT_MINPRESENT_FRACTION	0.3
public static final double	DEFAULT_TOOSMALLTOKEEP	0.5
public static final int	MINIMUM_ROWS_TO_BOTHER	50
public static final int	MINIMUM_SAMPLE	20

ubic.gemma.core.analysis.report.DatabaseViewGenerator

Modifier and Type	Constant Field	Value
public static final String	VIEW_FILE_SUFFIX	".view.txt.gz"

ubic.gemma.core.analysis.sequence.Blat

Modifier and Type	Constant Field	Value
public static final double	DEFAULT_BLAT_SCORE_THRESHOLD	0.7
public static final double	STEPSIZE	7.0

ubic.gemma.core.analysis.sequence.CompositeSequenceMapSummary

Modifier and Type	Constant Field	Value
public static final String	HEADER	"CompSeq\tBioSeq\t#BlatRes\tGeneProds\tGenes"

ubic.gemma.core.analysis.sequence.ProbeMapperConfig

Modifier and Type	Constant Field	Value
public static final boolean	DEFAULT_ALLOW_PARS	false
public static final boolean	DEFAULT_ALLOW_PREDICTED	false
public static final double	DEFAULT_IDENTITY_THRESHOLD	0.8
public static final double	DEFAULT_MINIMUM_EXON_OVERLAP_FRACTION	0.05
public static final double	DEFAULT_SCORE_THRESHOLD	0.75
public static final boolean	DEFAULT_TRIM_NONCANONICAL_CHROMOSOMES	true
public static final int	MAX_WARNINGS	100
public static final int	NON_REPEAT_NON_SPECIFIC_SITE_THRESHOLD	10
public static final int	NON_SPECIFIC_SITE_THRESHOLD	3
public static final double	REPEAT_FRACTION_MAXIMUM	0.3

ubic.gemma.core.analysis.sequence.SequenceWriter

Modifier and Type	Constant Field	Value
public static final String	SPACE_REPLACEMENT	"_____"

ubic.gemma.core.analysis.service.ArrayDesignAnnotationService

Modifier and Type	Constant Field	Value
public static final String	ANNOTATION_FILE_DIRECTORY_NAME	"microAnnots"
public static final String	ANNOTATION_FILE_SUFFIX	".an.txt.gz"
public static final String	BIO_PROCESS_FILE_SUFFIX	"_bioProcess"
public static final String	NO_PARENTS_FILE_SUFFIX	"_noParents"
public static final String	STANDARD_FILE_SUFFIX	""

ubic.gemma.core.analysis.service.ExpressionDataFileService

Modifier and Type	Constant Field	Value
public static final String	DATA_ARCHIVE_FILE_SUFFIX	".zip"
public static final String	DATA_FILE_SUFFIX	".data.txt"
public static final String	DATA_FILE_SUFFIX_COMPRESSED	".data.txt.gz"
public static final String	DISCLAIMER	"# If you use this file for your research, please cite: \n# Lim et al. (2021) Curation of over 10 000 transcriptomic studies to enable data reuse. \n# Database, baab006 (doi:10.1093/database/baab006). \n"
public static final String	JSON_FILE_SUFFIX	".data.json.gz"

ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants

Modifier and Type	Constant Field	Value
public static final String	DATASET_FOLDER_NAME	"AnnotationsByDataset"
public static final String	DISEASE_ONTOLOGY_ROOT	"MONDO_0000001"
public static final String	ERMINEJ_FOLDER_NAME	"ErmineJ"
public static final String	FILE_ALL_PHENOCARTA_ANNOTATIONS	"AllPhenocartaAnnotations.tsv"
public static final String	FILE_MANUAL_CURATION	"ManualCuration.tsv"
public static final String	LATEST_EVIDENCE_EXPORT	"LatestEvidenceExport"
public static final String	MANUAL_CURATION	"Manual Curation"
public static final String	PHENOCARTA_EXPORT	"PhenocartaExport"
public static final String	PHENOCARTA_NAME	"phenocarta"
public static final String	PHENOTYPE	"Phenotype"
public static final String	PHENOTYPE_CATEGORY_URI	"http://www.ebi.ac.uk/efo/EFO_0000651"
public static final String	TAXON_HUMAN	"human"
public static final String	TAXON_MOUSE	"mouse"
public static final String	TAXON_RAT	"rat"

ubic.gemma.core.context.EnvironmentProfiles

Modifier and Type	Constant Field	Value
public static final String	DEV	"dev"
public static final String	PRODUCTION	"production"
public static final String	TEST	"test"

ubic.gemma.core.datastructure.matrix.ExpressionDataWriterUtils

Modifier and Type	Constant Field	Value
public static final String	DELIMITER_BETWEEN_BIOMATERIAL_AND_BIOASSAYS	"___"

ubic.gemma.core.job.TaskCommand

Modifier and Type	Constant Field	Value
public static final int	MAX_QUEUING_MINUTES	120
public static final int	MAX_RUNTIME_MINUTES	60

ubic.gemma.core.loader.expression.AffyPowerToolsProbesetSummarize

Modifier and Type	Constant Field	Value
protected static final String	GEO_CEL_FILE_NAME_REGEX	"^(GSM[0-9]+).*\\.(?i)CEL(\\.gz)?"

ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl

Modifier and Type	Constant Field	Value
public static final String	DUPLICATE_PROBE_NAME_MUNGE_SEPARATOR	"___"

ubic.gemma.core.loader.expression.simple.ExperimentalDesignImporterImpl

Modifier and Type	Constant Field	Value
public static final String	EXPERIMENTAL_FACTOR_DESCRIPTION_LINE_INDICATOR	"#$"

ubic.gemma.core.loader.genome.SimpleFastaCmd

Modifier and Type	Constant Field	Value
public static final String	FASTA_CMD_ENV_VAR	"fastaCmd.exe"

ubic.gemma.core.loader.util.biomart.BiomartEnsemblNcbiFetcher

Modifier and Type	Constant Field	Value
public static final String	BIOMARTPATH	"protein.biomart.remotepath"

ubic.gemma.core.loader.util.fetcher.AbstractFetcher

Modifier and Type	Constant Field	Value
protected static final int	INFO_UPDATE_INTERVAL	10000

ubic.gemma.core.loader.util.parser.BasicLineMapParser<K,T>

Modifier and Type	Constant Field	Value
protected static final String	COMMENT_MARK	"#"

ubic.gemma.core.loader.util.parser.LineParser<T>

Modifier and Type	Constant Field	Value
public static final int	MIN_PARSED_LINES_FOR_UPDATE	100
public static final int	PARSE_ALERT_TIME_FREQUENCY_MS	2000

ubic.gemma.core.loader.util.parser.Parser<T>

Modifier and Type	Constant Field	Value
public static final int	PARSE_ALERT_FREQUENCY	10000

ubic.gemma.core.ontology.providers.GeneOntologyService

Modifier and Type	Constant Field	Value
public static final String	BASE_GO_URI	"http://purl.obolibrary.org/obo/"

ubic.gemma.core.search.source.DatabaseSearchSource

Modifier and Type	Constant Field	Value
public static final double	MATCH_BY_ACCESSION_SCORE	1.0
public static final double	MATCH_BY_ID_SCORE	1.0
public static final double	MATCH_BY_NAME_SCORE	0.95
public static final double	MATCH_BY_SHORT_NAME_SCORE	1.0
public static final String	NCBI_GENE_ID_URI_PREFIX	"http://purl.org/commons/record/ncbi_gene/"

ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject

Modifier and Type	Constant Field	Value
public static final double	DEFAULT_THRESHOLD	0.05

ubic.gemma.model.common.description.ExternalDatabases

Modifier and Type	Constant Field	Value
public static final String	GENE	"gene"
public static final String	GENE2CS	"gene2cs"
public static final String	GEO	"GEO"
public static final String	GO	"go"
public static final String	MULTIFUNCTIONALITY	"multifunctionality"

ubic.gemma.model.common.search.SearchSettings

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_MAX_RESULTS_PER_RESULT_TYPE	5000

ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject

Modifier and Type	Constant Field	Value
public static final String	OPT_AVG	"average"
public static final String	OPT_PICK_MAX	"pickmax"
public static final String	OPT_PICK_VAR	"pickvar"

ubic.gemma.model.expression.experiment.ExperimentalDesignUtils

Modifier and Type	Constant Field	Value
public static final String	BATCH_FACTOR_CATEGORY_NAME	"block"
public static final String	BATCH_FACTOR_CATEGORY_URI	"http://www.ebi.ac.uk/efo/EFO_0005067"
public static final String	BATCH_FACTOR_NAME	"batch"
public static final String	BATCH_FACTOR_NAME_PREFIX	"Batch_"
public static final String	FACTOR_VALUE_RNAME_PREFIX	"fv_"

ubic.gemma.model.genome.gene.phenotype.valueObject.PhenotypeAssPubValueObject

Modifier and Type	Constant Field	Value
public static final String	PRIMARY	"Primary"
public static final String	RELEVANT	"Relevant"

ubic.gemma.persistence.persister.AbstractPersister

Modifier and Type	Constant Field	Value
protected static final int	REPORT_BATCH_SIZE	100

ubic.gemma.persistence.service.AbstractVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>>

Modifier and Type	Constant Field	Value
protected static final int	REPORT_SLOW_QUERY_AFTER_MS	1000

ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_PA_LIMIT	10000

ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao<C extends Curatable,VO extends AbstractCuratableValueObject<C>>

Modifier and Type	Constant Field	Value
protected static final String	CURATION_DETAILS_ALIAS	"s"

ubic.gemma.persistence.service.common.description.CharacteristicDao

Modifier and Type	Constant Field	Value
public static final String	OBJECT_ALIAS	"ch"

ubic.gemma.persistence.service.common.description.DatabaseEntryDao

Modifier and Type	Constant Field	Value
public static final String	OBJECT_ALIAS	"accession"

ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao

Modifier and Type	Constant Field	Value
public static final String	OBJECT_ALIAS	"ad"

ubic.gemma.persistence.service.expression.bioAssay.BioAssayDao

Modifier and Type	Constant Field	Value
public static final String	OBJECT_ALIAS	"ba"

ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao

Modifier and Type	Constant Field	Value
public static final String	OBJECT_ALIAS	"probe"

ubic.gemma.persistence.service.expression.experiment.ExperimentalFactorService

Modifier and Type	Constant Field	Value
public static final String	BATCH_FACTOR_CATEGORY_NAME	"block"
public static final String	BATCH_FACTOR_CATEGORY_URI	"http://www.ebi.ac.uk/efo/EFO_0005067"
public static final String	BATCH_FACTOR_NAME	"batch"
public static final String	BATCH_FACTOR_NAME_PREFIX	"Batch_"
public static final String	FACTOR_VALUE_RNAME_PREFIX	"fv_"

ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao

Modifier and Type	Constant Field	Value
public static final String	OBJECT_ALIAS	"ee"

ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService

Modifier and Type	Constant Field	Value
public static final String	AUTOMATICALLY_GENERATED_EXPERIMENT_GROUP_DESCRIPTION	"Automatically generated for %s EEs"

ubic.gemma.persistence.service.expression.experiment.GeeqServiceImpl

Modifier and Type	Constant Field	Value
public static final double	BATCH_CONF_HAS	-1.0
public static final double	BATCH_CONF_NO_HAS	1.0
public static final double	BATCH_EFF_NONE	1.0
public static final double	BATCH_EFF_STRONG	-1.0
public static final double	BATCH_EFF_WEAK	0.0

ubic.gemma.persistence.service.genome.GeneDao

Modifier and Type	Constant Field	Value
public static final String	OBJECT_ALIAS	"gene"

ubic.gemma.persistence.service.genome.taxon.TaxonDao

Modifier and Type	Constant Field	Value
public static final String	OBJECT_ALIAS	"taxon"

ubic.gemma.persistence.service.maintenance.TableMaintenanceUtil

Modifier and Type	Constant Field	Value
public static final String	EE2AD_QUERY_SPACE	"EXPRESSION_EXPERIMENT2_ARRAY_DESIGN"
public static final String	EE2C_QUERY_SPACE	"EXPRESSION_EXPERIMENT2CHARACTERISTIC"
public static final int	GENE2CS_BATCH_SIZE	2048
public static final String	GENE2CS_QUERY_SPACE	"GENE2CS"

ubic.gemma.persistence.util.AclQueryUtils

Modifier and Type	Constant Field	Value
public static final String	AOI_ALIAS	"aoi"
public static final String	SID_ALIAS	"sid"

ubic.gemma.persistence.util.QueryUtils

Modifier and Type	Constant Field	Value
public static final int	MAX_PARAMETER_LIST_SIZE	2048