Constant Field Values

ubic.gemma.*

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

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

ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalysisFilter

Modifier and Type	Constant Field	Value
public static final double	DEFAULT_MINIMUM_FRACTION_OF_UNIQUE_VALUES	0.3
public static final int	DEFAULT_MINIMUM_NUMBER_OF_CELLS_PER_GENE	3
public static final int	DEFAULT_MINIMUM_NUMBER_OF_CELLS_PER_SAMPLE	100
public static final int	DEFAULT_MINIMUM_NUMBER_OF_SAMPLES_TO_APPLY_REPETITIVE_VALUES_FILTER	4
public static final double	DEFAULT_MINIMUM_VARIANCE	0.01

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.DiffExAnalyzerUtils

Modifier and Type	Constant Field	Value
public static final String	BIO_MATERIAL_RNAME_PREFIX	"biomat_"
public static final String	FACTOR_RNAME_PREFIX	"fact."
public static final String	FACTOR_VALUE_BASELINE_SUFFIX	"_base"
public static final String	FACTOR_VALUE_RNAME_PREFIX	"fv_"

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.AgilentScanDateExtractor

Modifier and Type	Constant Field	Value
public static final String	AGILENT_DATE_PATTERN	"MM-dd-yyyy hh:mm:ss"

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.BatchInfoPopulationHelperServiceImpl

Modifier and Type	Constant Field	Value
public static final String	BATCH_FACTOR_NAME_PREFIX	"Batch_"

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"

ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilter

Modifier and Type	Constant Field	Value
public static final int	MINIMUM_DESIGN_ELEMENTS	50
public static final int	MINIMUM_SAMPLES	20

ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig

Modifier and Type	Constant Field	Value
public static final double	DEFAULT_DISTINCT_VALUE_FRACTION	0.5
public static final double	DEFAULT_HIGH_EXPRESSION_CUT	1.0
public static final double	DEFAULT_LOW_EXPRESSION_CUT	0.2
public static final double	DEFAULT_LOW_VARIANCE_CUT	0.01
public static final boolean	DEFAULT_MASK_OUTLIERS	true
public static final int	DEFAULT_MIN_PRESENT_COUNT	7
public static final double	DEFAULT_MIN_PRESENT_FRACTION	0.3

ubic.gemma.core.analysis.preprocess.filter.LowVarianceFilter

Modifier and Type	Constant Field	Value
public static final double	DEFAULT_LOW_VARIANCE_CUT	0.01

ubic.gemma.core.analysis.preprocess.filter.MinimumCellsFilter

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_MINIMUM_NUMBER_OF_CELLS_PER_GENE	3
public static final int	DEFAULT_MINIMUM_NUMBER_OF_CELLS_PER_SAMPLE	100

ubic.gemma.core.analysis.preprocess.filter.RepetitiveValuesFilter

Modifier and Type	Constant Field	Value
public static final double	DEFAULT_MINIMUM_FRACTION_OF_UNIQUE_VALUES	0.3
public static final int	DEFAULT_MINIMUM_NUMBER_OF_SAMPLES_TO_APPLY_FILTER	4

ubic.gemma.core.analysis.sequence.Blat

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

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.SequenceManipulation

Modifier and Type	Constant Field	Value
public static final String	COLLAPSED_NAME_SUFFIX	"_collapsed"

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_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.ExpressionDataFileUtils

Modifier and Type	Constant Field	Value
public static final String	CELL_BROWSER_SC_DATA_SUFFIX	".scdata.cellbrowser.tsv.gz"
public static final String	CELL_BROWSER_SC_METADATA_SUFFIX	".scmetadata.cellbrowser.tsv.gz"
public static final String	JSON_BULK_DATA_FILE_SUFFIX	".data.json.gz"
public static final String	MEX_SC_DATA_SUFFIX	".scdata.mex"
public static final String	TABULAR_BULK_DATA_FILE_SUFFIX	".data.txt.gz"
public static final String	TABULAR_SC_DATA_SUFFIX	".scdata.tsv.gz"

ubic.gemma.core.config.ConfigUtils

Modifier and Type	Constant Field	Value
public static final String	FILE_INDIRECTION_SUFFIX	"_FILE"

ubic.gemma.core.context.EnvironmentProfiles

Modifier and Type	Constant Field	Value
public static final String	CLI	"cli"
public static final String	DEV	"dev"
public static final String	METRICS	"metrics"
public static final String	PRODUCTION	"production"
public static final String	PROFILING	"profiling"
public static final String	SCHEDULER	"scheduler"
public static final String	TEST	"test"
public static final String	WEB	"web"

ubic.gemma.core.job.TaskCommand

Modifier and Type	Constant Field	Value
public static final long	MAX_QUEUING_MILLIS	120000L
public static final long	MAX_RUNTIME_MILLIS	60000L

ubic.gemma.core.loader.entrez.EntrezUtils

Modifier and Type	Constant Field	Value
public static final String	EFETCH	"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
public static final String	ELINK	"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi"
public static final String	ESEARCH	"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
public static final String	ESUMMARY	"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi"

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.geo.GeoSourceMetadataBuilder

Modifier and Type	Constant Field	Value
public static final int	SCHEMA_VERSION	1

ubic.gemma.core.loader.expression.geo.singleCell.ArchiveBasedSingleCellDetector

Modifier and Type	Constant Field	Value
public static final long	DEFAULT_MAX_ENTRY_SIZE_IN_ARCHIVE_TO_SKIP	25000000L
public static final long	DEFAULT_MAX_NUMBER_OF_ENTRIES_TO_SKIP	10L

ubic.gemma.core.loader.expression.geo.singleCell.GeoSingleCellDetector

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

ubic.gemma.core.loader.expression.geo.singleCell.MexDetector

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_BARCODE_METADATA_FILE_SUFFIX	"barcode_metadata.tsv"
public static final String	DEFAULT_BARCODES_FILE_SUFFIX	"barcodes.tsv"
public static final String	DEFAULT_FEATURES_FILE_SUFFIX	"features.tsv"
public static final String	DEFAULT_GENES_FILE_SUFFIX	"genes.tsv"
public static final String	DEFAULT_MATRIX_FILE_SUFFIX	"matrix.mtx"

ubic.gemma.core.loader.expression.singleCell.transform.PythonBasedSingleCellDataTransformation

Modifier and Type	Constant Field	Value
public static final String	REQUIREMENTS_FILE	"/ubic/gemma/core/loader/expression/singleCell/transform/requirements.txt"

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.logging.log4j.BuildInfoThreadContextPopulator

Modifier and Type	Constant Field	Value
public static final String	BUILD_INFO_CONTEXT_KEY	"ubic.gemma.core.logging.log4j.ThreadContextKeys.buildInfo"

ubic.gemma.core.logging.log4j.ThreadContextPopulator

Modifier and Type	Constant Field	Value
public static final String	KEY_PREFIX	"ubic.gemma.core.logging.log4j.ThreadContextKeys"

ubic.gemma.core.ontology.OntologyUtils

Modifier and Type	Constant Field	Value
public static final String	BASE_CELLOSAURUS_URI	"https://www.cellosaurus.org/"
public static final String	BASE_EFO_URI	"http://www.ebi.ac.uk/efo/"
public static final String	BASE_GEMMA_ONTOLOGY_URI	"http://gemma.msl.ubc.ca/ont/"
public static final String	BASE_PURL_URI	"http://purl.obolibrary.org/obo/"
public static final String	CONSIDER_URI	"http://www.geneontology.org/formats/oboInOwl#consider"
public static final String	DEFINITION_URI	"http://purl.obolibrary.org/obo/IAO_0000115"
public static final String	TERM_REPLACED_BY_URI	"http://purl.obolibrary.org/obo/IAO_0100001"

ubic.gemma.core.ontology.chembl.ChemblCodeResolverImpl

Modifier and Type	Constant Field	Value
public static final String	CACHE_NAME	"ChemblCodeResolver.compounds"

ubic.gemma.core.ontology.jena.TGFVO

Modifier and Type	Constant Field	Value
public static final String	NS	"http://gemma.msl.ubc.ca/ont/TGFVO#"

ubic.gemma.core.ontology.ols.OlsTermResolverImpl

Modifier and Type	Constant Field	Value
public static final String	CACHE_NAME	"OlsTermResolver.terms"

ubic.gemma.core.ontology.providers.CellosaurusOntologyService

Modifier and Type	Constant Field	Value
public static final String	URI_PREFIX	"https://www.cellosaurus.org/"

ubic.gemma.core.ontology.providers.MeshDiseaseSynonymOntologyService

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

ubic.gemma.core.ontology.providers.MgiStrainOntologyService

Modifier and Type	Constant Field	Value
public static final String	URI_PREFIX	"https://www.informatics.jax.org/strain/"

ubic.gemma.core.ontology.providers.OntologySlimExtractor

Modifier and Type	Constant Field	Value
public static final String	SLIM_VERSION_SUFFIX	"+gemma-slim"

ubic.gemma.core.ontology.providers.OntologySlimMeta

Modifier and Type	Constant Field	Value
public static final int	SCHEMA_VERSION	2
public static final String	SEED_POLICY_CORPUS	"corpus"

ubic.gemma.core.ontology.relation.CellosaurusRelationProducer

Modifier and Type	Constant Field	Value
public static final String	SOURCE	"CELLOSAURUS"

ubic.gemma.core.ontology.relation.ClInferredLocationProducer

Modifier and Type	Constant Field	Value
public static final String	SOURCE	"CL_INFERRED"

ubic.gemma.core.ontology.relation.MgiRelationProducer

Modifier and Type	Constant Field	Value
public static final String	SOURCE	"MGI"

ubic.gemma.core.ontology.search.OntologyQueries

Modifier and Type	Constant Field	Value
public static final double	DEFAULT_MIN_SHOULD_MATCH	0.67

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_NCBI_ID_SCORE	1.0
public static final double	MATCH_BY_SHORT_NAME_SCORE	1.0

ubic.gemma.core.security.AuthorityConstants

Modifier and Type	Constant Field	Value
public static final String	ADMIN_GROUP_AUTHORITY	"GROUP_ADMIN"
public static final String	ADMIN_GROUP_NAME	"Administrators"
public static final String	AGENT_GROUP_AUTHORITY	"GROUP_AGENT"
public static final String	AGENT_GROUP_NAME	"Agents"
public static final String	CURATOR_GROUP_AUTHORITY	"GROUP_CURATOR"
public static final String	CURATOR_GROUP_NAME	"Curators"
public static final String	ROLE_PREFIX	"GROUP_"
public static final String	RUN_AS_ADMIN_AUTHORITY	"GROUP_RUN_AS_ADMIN"
public static final String	RUN_AS_USER_AUTHORITY	"GROUP_RUN_AS_USER"
public static final String	USER_GROUP_AUTHORITY	"GROUP_USER"
public static final String	USER_GROUP_NAME	"Users"

ubic.gemma.core.security.acl.voter.AclEntryVoter

Modifier and Type	Constant Field	Value
public static final String	IGNORE_TRANSIENT_SUFFIX	"_IGNORE_TRANSIENT"

ubic.gemma.core.security.authentication.GemmaLegacyAwarePasswordEncoder

Modifier and Type	Constant Field	Value
public static final String	BCRYPT_PREFIX	"{bcrypt}"

ubic.gemma.core.security.authentication.LegacyAwareDaoAuthenticationProvider

Modifier and Type	Constant Field	Value
public static final String	SYSTEM_WIDE_SALT	"gooblyfoobly"

ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationQuietReadProvider

Modifier and Type	Constant Field	Value
public static final String	ATTRIBUTE	"AFTER_ACL_READ_QUIET"

ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationStreamFilteringProvider

Modifier and Type	Constant Field	Value
public static final String	ATTRIBUTE	"AFTER_ACL_STREAM_READ"

ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationValueObjectCollectionReadProvider

Modifier and Type	Constant Field	Value
public static final String	ATTRIBUTE	"AFTER_ACL_VALUE_OBJECT_COLLECTION_READ"

ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationValueObjectMapReadProvider

Modifier and Type	Constant Field	Value
public static final String	ATTRIBUTE	"AFTER_ACL_VALUE_OBJECT_MAP_READ"

ubic.gemma.core.security.authorization.acl.AclEntryAfterInvocationValueObjectReadProvider

Modifier and Type	Constant Field	Value
public static final String	ATTRIBUTE	"AFTER_ACL_VALUE_OBJECT_READ"

ubic.gemma.core.util.Constants

Modifier and Type	Constant Field	Value
public static final String	GEMMA_COPYRIGHT_NOTICE	"Copyright \u00a9 2007-2025 The University of British Columbia"
public static final String	GEMMA_LICENSE_NOTICE	"Gemma Data and Graphics by the Pavlidis Lab are licensed under CC BY-SA 4.0 https://creativecommons.org/licenses/by-sa/4.0/."

ubic.gemma.core.util.RoundingUtils

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

ubic.gemma.core.util.TsvUtils

Modifier and Type	Constant Field	Value
public static final char	COMMENT	'#'
public static final String	NA	""
public static final char	SUB_DELIMITER	'|'

ubic.gemma.core.util.graphics.ColorMap

Modifier and Type	Constant Field	Value
public static final int	m_defaultSuggestedNumberOfColors	32

ubic.gemma.core.util.graphics.MatrixDisplay<R,C>

Modifier and Type	Constant Field	Value
protected final int	m_defaultResolution	120
protected final int	m_maxFontSize	10

ubic.gemma.core.util.math.Constants

Modifier and Type	Constant Field	Value
public static final double	M_1_PI	0.3183098861837907
public static final double	M_1_SQRT_2	0.7071067811865476
public static final double	M_1_SQRT_2PI	0.3989422804014327
public static final double	M_LN_2	0.6931471805599453
public static final double	M_LN_SQRT_2PI	0.9189385332046728
public static final double	M_LN_SQRT_PI	0.5723649429247001
public static final double	M_LN_SQRT_PId2	0.22579135264472744
public static final double	M_LOG10_2	0.3010299956639812
public static final double	M_PI_2	1.5707963267948966
public static final double	M_PI_4	0.7853981633974483
public static final double	M_PI_half	1.5707963267948966
public static final double	M_SQRT_2	1.4142135623730951
public static final double	M_SQRT_2dPI	0.7978845608028654
public static final double	M_SQRT_PI	1.772453850905516
public static final double	SMALL	1.0E-10
public static final double	SMALLISH	1.0E-5
public static final double	TINY	1.0E-20

ubic.gemma.core.util.math.linearmodels.LinearModelSummary

Modifier and Type	Constant Field	Value
public static final String	INTERCEPT_COEFFICIENT_NAME	"(Intercept)"

ubic.gemma.core.util.matrix.AbstractMatrix<R,C,V>

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

ubic.gemma.core.util.matrix.MatrixWriter<R,C>

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_SEP	"\t"
public static final String	DEFAULT_TOP_LEFT	"ID"

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.auditAndSecurity.AuditEvent

Modifier and Type	Constant Field	Value
public static final int	MAX_DETAIL_LENGTH	65535
public static final int	MAX_NOTE_LENGTH	65535

ubic.gemma.model.common.description.ExternalDatabases

Modifier and Type	Constant Field	Value
public static final String	ARRAY_EXPRESS	"ArrayExpress"
public static final String	ARXIV	"arXiv"
public static final String	BIO_STUDIES	"BioStudies"
public static final String	BIORXIV	"bioRxiv"
public static final String	CELLOSAURUS	"Cellosaurus"
public static final String	CELLXGENE	"CELLxGENE"
public static final String	DOI	"DOI"
public static final String	GENBANK	"GenBank"
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	MGI	"MGI"
public static final String	MULTIFUNCTIONALITY	"multifunctionality"
public static final String	PUBMED	"PubMed"
public static final String	SRA	"SRA"
public static final String	SYNAPSE	"Synapse"
public static final String	UCSC_CELL_BROWSER	"UCSC Cell Browser"
public static final String	ZENODO	"Zenodo"

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.bioAssay.BioAssay

Modifier and Type	Constant Field	Value
public static final int	MAX_NAME_LENGTH	255

ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristics

Modifier and Type	Constant Field	Value
public static final int	UNKNOWN_CHARACTERISTIC	-1

ubic.gemma.model.expression.bioAssayData.CellTypeAssignment

Modifier and Type	Constant Field	Value
public static final int	UNKNOWN_CELL_TYPE	-1

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.biomaterial.BioMaterial

Modifier and Type	Constant Field	Value
public static final int	MAX_NAME_LENGTH	255

ubic.gemma.model.expression.experiment.ExperimentFactorUtils

Modifier and Type	Constant Field	Value
public static final String	BATCH_FACTOR_NAME	"batch"

ubic.gemma.model.expression.experiment.ExpressionExperiment

Modifier and Type	Constant Field	Value
public static final int	MAX_BATCH_CONFOUND_LENGTH	65535
public static final int	MAX_NAME_LENGTH	255

ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet

Modifier and Type	Constant Field	Value
public static final int	MAX_NAME_LENGTH	255
public static final String	NAME_DELIMITER	" - "

ubic.gemma.model.expression.experiment.FactorValueUtils

Modifier and Type	Constant Field	Value
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.model.genome.Gene

Modifier and Type	Constant Field	Value
public static final String	NCBI_URI_PREFIX	"http://purl.org/commons/record/ncbi_gene/"

ubic.gemma.persistence.persister.CommonPersister

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

ubic.gemma.persistence.persister.GenomePersister

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

ubic.gemma.persistence.service.AbstractVoEnabledDao<O,VO>

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

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

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

ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetService

Modifier and Type	Constant Field	Value
public static final String	PRE_COMMIT_SNAPSHOT_RUN_ID_PREFIX	"precommit-"

ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockService

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_TTL_MINUTES	30

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.designElement.CompositeSequenceDao

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

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.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.expression.experiment.SingleCellExpressionExperimentServiceImpl

Modifier and Type	Constant Field	Value
public static final int	MAX_SAFE_INMEMORY_SC_MATRIX_SAMPLES	5000
public static final long	SC_MATRIX_VECTOR_COUNT_LIMIT	1000000L

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.Cursor

Modifier and Type	Constant Field	Value
public static final int	CURRENT_VERSION	1

ubic.gemma.persistence.util.QueryUtils

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