Uses of Interface
org.opencb.cellbase.core.serializer.CellBaseSerializer

Packages that use CellBaseSerializer

Package	Description
org.opencb.cellbase.core.serializer
org.opencb.cellbase.lib.builders
org.opencb.cellbase.lib.builders.clinical.variant

Uses of CellBaseSerializer in org.opencb.cellbase.core.serializer

Subinterfaces of CellBaseSerializer in org.opencb.cellbase.core.serializer

Modifier and Type	Interface and Description
interface	CellBaseFileSerializer Created by parce on 9/02/15.

Classes in org.opencb.cellbase.core.serializer that implement CellBaseSerializer

Modifier and Type	Class and Description
class	CellBaseJsonFileSerializer Created by parce on 2/6/15.

Uses of CellBaseSerializer in org.opencb.cellbase.lib.builders

Fields in org.opencb.cellbase.lib.builders declared as CellBaseSerializer

Modifier and Type	Field and Description
protected CellBaseSerializer	CellBaseParser.serializer

Constructors in org.opencb.cellbase.lib.builders with parameters of type CellBaseSerializer

Constructor and Description
CaddAllAnnotationParser(Path caddFilePath, String chrName, CellBaseSerializer serializer)
CaddScoreParser(Path caddFilePath, CellBaseSerializer serializer)
CellBaseParser(CellBaseSerializer serializer)
DgvParser(Path file, CellBaseSerializer serializer)
DisgenetParser(Path disgenetFilePath, CellBaseSerializer serializer) Deprecated.
DrugParser(Path drugbankPath, CellBaseSerializer serializer) Deprecated.
GeneExpressionAtlasParser(Path geneAtlasDirectoryPath, CellBaseSerializer serializer)
GeneParser(Path gtfFile, Path geneDescriptionFile, Path xrefsFile, Path uniprotIdMappingFile, Path tfbsFile, Path geneExpressionFile, Path geneDrugFile, Path hpoFile, Path disgenetFile, Path gnomadFile, Path genomeSequenceFilePath, SpeciesConfiguration speciesConfiguration, boolean flexibleGTFParsing, CellBaseSerializer serializer)
GeneParser(Path geneDirectoryPath, Path genomeSequenceFastaFile, SpeciesConfiguration speciesConfiguration, boolean flexibleGTFParsing, CellBaseSerializer serializer)
GeneParser(Path geneDirectoryPath, Path genomeSequenceFastaFile, SpeciesConfiguration speciesConfiguration, CellBaseSerializer serializer)
GenomeSequenceFastaParser(Path genomeReferenceFastaFile, CellBaseSerializer serializer)
InteractionParser(Path psimiTabFile, String species, CellBaseSerializer serializer)
ProteinParser(Path uniprotFilesDir, Path interproFilePath, String species, CellBaseSerializer serializer)
ProteinParser(Path uniprotFilesDir, String species, CellBaseSerializer serializer)
RegulatoryRegionParser(Path regulatoryRegionFilesDir, CellBaseSerializer serializer)
VariationPhenotypeAnnotationParser(Path ensemblVariationDir, CellBaseSerializer serializer)

Uses of CellBaseSerializer in org.opencb.cellbase.lib.builders.clinical.variant

Constructors in org.opencb.cellbase.lib.builders.clinical.variant with parameters of type CellBaseSerializer

Constructor and Description
ClinicalVariantParser(Path clinicalVariantFolder, boolean normalize, Path genomeSequenceFilePath, String assembly, CellBaseSerializer serializer)
ClinicalVariantParser(Path clinvarXMLFile, Path clinvarSummaryFile, Path clinvarVariationAlleleFile, Path clinvarEFOFile, Path cosmicFile, Path gwasFile, Path dbsnpFile, Path iarctp53GermlineFile, Path iarctp53GermlineReferencesFile, Path iarctp53SomaticFile, Path iarctp53SomaticReferencesFile, Path docmFile, boolean normalize, Path genomeSequenceFilePath, String assembly, CellBaseSerializer serializer)
ClinVarParser(Path clinvarXmlFile, Path clinvarSummaryFile, Path efosFile, String assembly, CellBaseSerializer serializer) Deprecated.
CosmicParser(Path cosmicFilePath, CellBaseSerializer serializer, String assembly) Deprecated.
GwasParser(Path gwasFile, Path dbSnpTabixFilePath, CellBaseSerializer serializer) Deprecated.