Constant Field Values

Contents

• org.molgenis.*

org.molgenis.*

org.molgenis.data.annotation.core.RepositoryAnnotator

Modifier and Type	Constant Field	Value
public static final String	ANNOTATOR_PREFIX	"mgs_ann_"

org.molgenis.data.annotation.core.effects.EffectsMetaData

Modifier and Type	Constant Field	Value
public static final String	ALT	"Alt_Allele"
public static final String	ANNOTATION	"Annotation"
public static final String	C_DNA_POSITION	"cDNA_position"
public static final String	CDS_POSITION	"CDS_position"
public static final String	DISTANCE_TO_FEATURE	"Distance_to_feature"
public static final String	ERRORS	"Errors"
public static final String	FEATURE_ID	"Feature_ID"
public static final String	FEATURE_TYPE	"Feature_type"
public static final String	GENE_ID	"Gene_ID"
public static final String	GENE_NAME	"Gene_Name"
public static final String	HGVS_C	"HGVS_c"
public static final String	HGVS_P	"HGVS_p"
public static final String	ID	"id"
public static final String	PROTEIN_POSITION	"Protein_position"
public static final String	PUTATIVE_IMPACT	"Putative_impact"
public static final String	RANK_TOTAL	"Rank_total"
public static final String	TRANSCRIPT_BIOTYPE	"Transcript_biotype"
public static final String	VARIANT	"VARIANT"

org.molgenis.data.annotation.core.entity.impl.CaddAnnotator

Modifier and Type	Constant Field	Value
public static final String	CADD_ABS	"CADD"
public static final String	CADD_ABS_LABEL	"CADDABS"
public static final String	CADD_SCALED	"CADD_SCALED"
public static final String	CADD_SCALED_LABEL	"CADDSCALED"
public static final String	CADD_TABIX_RESOURCE	"CADDTabixResource"
public static final String	NAME	"cadd"

org.molgenis.data.annotation.core.entity.impl.CGDAnnotator

Modifier and Type	Constant Field	Value
public static final String	AGE_GROUP_LABEL	"CGDAGE"
public static final String	CONDITION_LABEL	"CGDCOND"
public static final String	GENERALIZED_INHERITANCE_LABEL	"CGDGIN"
public static final String	INHERITANCE_LABEL	"CGDINH"
public static final String	NAME	"CGD"

org.molgenis.data.annotation.core.entity.impl.ClinvarAnnotator

Modifier and Type	Constant Field	Value
public static final String	CLINVAR_CLINALL_ResourceAttributeName	"CLNALLE"
public static final String	CLINVAR_CLNALLE	"CLINVAR_CLNALLE"
public static final String	CLINVAR_CLNALLE_LABEL	"ClinVar clinical significant allele"
public static final String	CLINVAR_CLNSIG	"CLINVAR_CLNSIG"
public static final String	CLINVAR_CLNSIG_LABEL	"ClinVar clinical significance"
public static final String	CLINVAR_CLNSIG_ResourceAttributeName	"CLNSIG"
public static final String	CLINVAR_TABIX_RESOURCE	"clinVarTabixResource"
public static final String	NAME	"clinvar"

org.molgenis.data.annotation.core.entity.impl.DannAnnotator

Modifier and Type	Constant Field	Value
public static final String	DANN_SCORE	"DANN_SCORE"
public static final String	DANN_SCORE_LABEL	"DANNSCORE"
public static final String	DANN_TABIX_RESOURCE	"DANNTabixResource"
public static final String	NAME	"dann"

org.molgenis.data.annotation.core.entity.impl.ExacAnnotator

Modifier and Type	Constant Field	Value
public static final String	EXAC_AC_HET	"EXAC_AC_HET"
public static final String	EXAC_AC_HET_LABEL	"ExAC heterozygous genotype count"
public static final String	EXAC_AC_HET_ResourceAttributeName	"AC_Het"
public static final String	EXAC_AC_HOM	"EXAC_AC_HOM"
public static final String	EXAC_AC_HOM_LABEL	"ExAC homozygous alternative genotype count"
public static final String	EXAC_AC_HOM_ResourceAttributeName	"AC_Hom"
public static final String	EXAC_AF	"EXAC_AF"
public static final String	EXAC_AF_LABEL	"ExAC allele frequency"
public static final String	EXAC_AF_ResourceAttributeName	"AF"
public static final String	EXAC_TABIX_RESOURCE	"EXACTabixResource"
public static final String	NAME	"exac"

org.molgenis.data.annotation.core.entity.impl.FitConAnnotator

Modifier and Type	Constant Field	Value
public static final String	FITCON_SCORE	"FITCON_SCORE"
public static final String	FITCON_SCORE_LABEL	"FITCON_SCORE"
public static final String	FITCON_TABIX_RESOURCE	"FitConTabixResource"
public static final String	NAME	"fitcon"

org.molgenis.data.annotation.core.entity.impl.GoNLAnnotator

Modifier and Type	Constant Field	Value
public static final String	GONL_AF_LABEL	"Genome of the netherlands allele frequency"
public static final String	GONL_GENOME_AF	"GoNL_AF"
public static final String	GONL_GENOME_GTC	"GoNL_GTC"
public static final String	GONL_GTC_LABEL	"Genome of the netherlands Genotype counts frequency"
public static final String	GONL_MULTI_FILE_RESOURCE	"gonlresources"
public static final String	INFO_AC	"AC"
public static final String	INFO_AN	"AN"
public static final String	INFO_GTC	"GTC"
public static final String	NAME	"gonl"

org.molgenis.data.annotation.core.entity.impl.ThousandGenomesAnnotator

Modifier and Type	Constant Field	Value
public static final String	NAME	"thousandgenomes"
public static final String	THOUSAND_GENOME_AF	"Thousand_Genomes_AF"
public static final String	THOUSAND_GENOME_AF_LABEL	"Thousand genome allele frequency"
public static final String	THOUSAND_GENOME_AF_RESOURCE_ATTRIBUTE_NAME	"AF"
public static final String	THOUSAND_GENOME_MULTI_FILE_RESOURCE	"thousandGenomesSources"

org.molgenis.data.annotation.core.entity.impl.gavin.GavinAlgorithm

Modifier and Type	Constant Field	Value
public static final int	EXTRA_SENSITIVITY_FACTOR	5
public static final int	GENOMEWIDE_CADD_THRESHOLD	15
public static final double	GENOMEWIDE_MAF_THRESHOLD	0.003456145
public static final String	NAME	"GavinAnnotator"

org.molgenis.data.annotation.core.entity.impl.gavin.GavinAnnotator

Modifier and Type	Constant Field	Value
public static final String	CLASSIFICATION	"Classification"
public static final String	CONFIDENCE	"Confidence"
public static final String	NAME	"Gavin"
public static final String	REASON	"Reason"
public static final String	RESOURCE	"gavin"
public static final String	RESOURCE_ENTITY_NAME	"base_gavin"

org.molgenis.data.annotation.core.entity.impl.gavin.GavinThresholds

Modifier and Type	Constant Field	Value
public static final String	MEAN_PATHOGENIC_CADD_SCORE	"MeanPathogenicCADDScore"
public static final String	MEAN_POPULATION_CADD_SCORE	"MeanPopulationCADDScore"
public static final String	PATHO_MAF_THRESHOLD	"PathoMAFThreshold"
public static final String	SENS_95TH_PER_CADD_THRESHOLD	"Sens95thPerCADDThreshold"
public static final String	SPEC_95TH_PER_CADD_THRESHOLD	"Spec95thPerCADDThreshold"

org.molgenis.data.annotation.core.entity.impl.hpo.HPOAnnotator

Modifier and Type	Constant Field	Value
public static final String	HPO_IDS	"HPOIDS"
public static final String	HPO_TERMS	"HPOTERMS"
public static final String	NAME	"hpo"

org.molgenis.data.annotation.core.entity.impl.hpo.HPORepository

Modifier and Type	Constant Field	Value
public static final String	HPO_DISEASE_ID_COL_NAME	"diseaseId"
public static final String	HPO_GENE_SYMBOL_COL_NAME	"gene-symbol"
public static final String	HPO_ID_COL_NAME	"HPO-ID"
public static final String	HPO_TERM_COL_NAME	"HPO-term-name"

org.molgenis.data.annotation.core.entity.impl.omim.OmimAnnotator

Modifier and Type	Constant Field	Value
public static final String	NAME	"OMIM"
public static final String	OMIM_CAUSAL_IDENTIFIER	"OMIM_MIM_Numbers"
public static final String	OMIM_CYTO_LOCATIONS	"OMIM_Cyto_Locations"
public static final String	OMIM_DISORDER	"OMIM_Disorders"
public static final String	OMIM_ENTRY	"OMIM_Entry"
public static final String	OMIM_RESOURCE	"OMIMResource"
public static final String	OMIM_TYPE	"OMIM_Type"
public static final char	SEPARATOR	9

org.molgenis.data.annotation.core.entity.impl.omim.OmimRepository

Modifier and Type	Constant Field	Value
public static final String	OMIM_AUTO_ID_COL_NAME	"ID"
public static final String	OMIM_CYTO_LOCATION_COL_NAME	"CytoLocation"
public static final String	OMIM_ENTRY_COL_NAME	"OmimEntry"
public static final String	OMIM_GENE_SYMBOLS_COL_NAME	"Gene_Name"
public static final String	OMIM_MIM_NUMBER_COL_NAME	"MIMNumber"
public static final String	OMIM_PHENOTYPE_COL_NAME	"Phenotype"
public static final String	OMIM_TYPE_COL_NAME	"OmimType"

org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffAnnotator

Modifier and Type	Constant Field	Value
public static final String	NAME	"snpEff"

org.molgenis.data.annotation.core.entity.impl.snpeff.SnpEffRunner

Modifier and Type	Constant Field	Value
public static final String	ANN	"ANN"
public static final String	ENTITY_NAME_SUFFIX	"EFFECTS"
public static final String	NAME	"snpEff"

org.molgenis.data.annotation.core.resources.impl.MultiResourceConfigImpl

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_CHROMOSOMES	"1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,Y,X"
public static final String	DEFAULT_PATTERN	"chr%s.vcf"

org.molgenis.data.annotation.web.meta.AnnotationJobExecutionMetaData

Modifier and Type	Constant Field	Value
public static final String	ANNOTATION_JOB_EXECUTION	"sys_job_AnnotationJobExecution"
public static final String	ANNOTATORS	"annotators"
public static final String	TARGET_NAME	"targetName"

org.molgenis.data.annotation.web.settings.CaddAnnotatorSettings.Meta

Modifier and Type	Constant Field	Value
public static final String	CADD_LOCATION	"caddLocation"

org.molgenis.data.annotation.web.settings.CGDAnnotatorSettings.Meta

Modifier and Type	Constant Field	Value
public static final String	CGD_LOCATION	"cgdLocation"

org.molgenis.data.annotation.web.settings.ClinvarAnnotatorSettings

Modifier and Type	Constant Field	Value
public static final String	ID	"clinvar"

org.molgenis.data.annotation.web.settings.ClinvarAnnotatorSettings.Meta

Modifier and Type	Constant Field	Value
public static final String	CLINVAR_LOCATION	"clinvarLocation"

org.molgenis.data.annotation.web.settings.DannAnnotatorSettings

Modifier and Type	Constant Field	Value
public static final String	ID	"dann"

org.molgenis.data.annotation.web.settings.DannAnnotatorSettings.Meta

Modifier and Type	Constant Field	Value
public static final String	DANN_LOCATION	"dannLocation"

org.molgenis.data.annotation.web.settings.ExacAnnotatorSettings.Meta

Modifier and Type	Constant Field	Value
public static final String	EXAC_LOCATION	"exacLocation"

org.molgenis.data.annotation.web.settings.FitConAnnotatorSettings

Modifier and Type	Constant Field	Value
public static final String	ID	"fitcon"

org.molgenis.data.annotation.web.settings.FitConAnnotatorSettings.Meta

Modifier and Type	Constant Field	Value
public static final String	FITCON_LOCATION	"fitconLocation"

org.molgenis.data.annotation.web.settings.GavinAnnotatorSettings.Meta

Modifier and Type	Constant Field	Value
public static final String	VARIANT_FILE_LOCATION	"variantFileLocation"

org.molgenis.data.annotation.web.settings.GoNLAnnotatorSettings.Meta

Modifier and Type	Constant Field	Value
public static final String	CHROMOSOMES	"chromosomes"
public static final String	FILEPATTERN	"filepattern"
public static final String	OVERRIDE_CHROMOSOME_FILES	"overrideChromosomeFiles"
public static final String	ROOT_DIRECTORY	"rootDirectory"

org.molgenis.data.annotation.web.settings.HPOAnnotatorSettings.Meta

Modifier and Type	Constant Field	Value
public static final String	HPO_LOCATION	"hpoLocation"

org.molgenis.data.annotation.web.settings.OmimAnnotatorSettings.Meta

Modifier and Type	Constant Field	Value
public static final String	OMIM_LOCATION	"omimLocation"

org.molgenis.data.annotation.web.settings.SnpEffAnnotatorSettings

Modifier and Type	Constant Field	Value
public static final String	ID	"snpEff"

org.molgenis.data.annotation.web.settings.SnpEffAnnotatorSettings.Meta

Modifier and Type	Constant Field	Value
public static final String	SNPEFF_JAR_LOCATION	"snpEffJarLocation"

org.molgenis.data.annotation.web.settings.ThousendGenomesAnnotatorSettings.Meta

Modifier and Type	Constant Field	Value
public static final String	CHROMOSOMES	"chromosomes"
public static final String	FILEPATTERN	"filepattern"
public static final String	OVERRIDE_CHROMOSOME_FILES	"overrideChromosomeFile"
public static final String	ROOT_DIRECTORY	"rootDirectory"