Package org.rcsb.cif.model

Class BaseCategory

java.lang.Object

org.rcsb.cif.model.BaseCategory

All Implemented Interfaces:

Category

Direct Known Subclasses:

AtomSite, AtomSiteAnisotrop, AtomSites, AtomSitesAlt, AtomSitesAltEns, AtomSitesAltGen, AtomSitesFootnote, AtomType, Audit, AuditAuthor, AuditConform, AuditContactAuthor, AuditLink, Cell, CellMeasurement, CellMeasurementRefln, ChemComp, ChemCompAngle, ChemCompAtom, ChemCompBond, ChemCompChir, ChemCompChirAtom, ChemCompLink, ChemCompPlane, ChemCompPlaneAtom, ChemCompTor, ChemCompTorValue, Chemical, ChemicalConnAtom, ChemicalConnBond, ChemicalFormula, ChemLink, ChemLinkAngle, ChemLinkBond, ChemLinkChir, ChemLinkChirAtom, ChemLinkPlane, ChemLinkPlaneAtom, ChemLinkTor, ChemLinkTorValue, Citation, CitationAuthor, CitationEditor, Computing, Database, Database2, DatabasePDBCaveat, DatabasePDBMatrix, DatabasePDBRemark, DatabasePDBRev, DatabasePDBRevRecord, DatabasePDBTvect, Diffrn, DiffrnAttenuator, DiffrnDetector, DiffrnMeasurement, DiffrnOrientMatrix, DiffrnOrientRefln, DiffrnRadiation, DiffrnRadiationWavelength, DiffrnRefln, DiffrnReflns, DiffrnReflnsClass, DiffrnScaleGroup, DiffrnSource, DiffrnStandardRefln, DiffrnStandards, Em2dCrystalEntity, Em2dProjectionSelection, Em3dCrystalEntity, Em3dFitting, Em3dFittingList, Em3dReconstruction, EmAdmin, EmAssembly, EmAuthorList, EmBuffer, EmBufferComponent, EmCrystalFormation, EmCtfCorrection, EmDbReference, EmDbReferenceAuxiliary, EmDepositorInfo, EmDepui, EmDetector, EmDiffraction, EmDiffractionShell, EmDiffractionStats, EmEmbedding, EmEntityAssembly, EmEntityAssemblyMolwt, EmEntityAssemblyNaturalsource, EmEntityAssemblyRecombinant, EmEulerAngleAssignment, EmExperiment, EmFiducialMarkers, EmFigureDepositorInfo, EmFinalClassification, EmFocusedIonBeam, EmFscCurve, EmGridPretreatment, EmHelicalEntity, EmHighPressureFreezing, EmImageProcessing, EmImageRecording, EmImageScans, EmImaging, EmImagingOptics, EmInterpretFigure, EmLayerLines, EmLayerLinesDepositorInfo, EmMap, EmMapDepositorInfo, EmMaskDepositorInfo, EmObsolete, EmParticleSelection, EmSamplePreparation, EmSampleSupport, EmShadowing, EmSingleParticleEntity, EmSoftware, EmSpecimen, EmStaining, EmStartModel, EmStructureFactors, EmStructureFactorsDepositorInfo, EmSupersede, EmSupportFilm, EmTomography, EmTomographySpecimen, EmUltramicrotomy, EmVirusEntity, EmVirusNaturalHost, EmVirusShell, EmVitrification, EmVolumeSelection, Entity, EntityKeywords, EntityLink, EntityNameCom, EntityNameSys, EntityPoly, EntityPolySeq, EntitySrcGen, EntitySrcNat, Entry, EntryLink, Exptl, ExptlCrystal, ExptlCrystalFace, ExptlCrystalGrow, ExptlCrystalGrowComp, Geom, GeomAngle, GeomBond, GeomContact, GeomHbond, GeomTorsion, Ihm2demClassAverageFitting, Ihm2demClassAverageRestraint, Ihm3demRestraint, IhmCrossLinkList, IhmCrossLinkRestraint, IhmCrossLinkResult, IhmCrossLinkResultParameters, IhmDatasetExternalReference, IhmDatasetGroup, IhmDatasetList, IhmDatasetRelatedDbReference, IhmDerivedDistanceRestraint, IhmEnsembleInfo, IhmExternalFiles, IhmExternalReferenceInfo, IhmFeatureList, IhmGaussianObjEnsemble, IhmGaussianObjSite, IhmGeometricObjectAxis, IhmGeometricObjectCenter, IhmGeometricObjectDistanceRestraint, IhmGeometricObjectHalfTorus, IhmGeometricObjectList, IhmGeometricObjectPlane, IhmGeometricObjectSphere, IhmGeometricObjectTorus, IhmGeometricObjectTransformation, IhmHydroxylRadicalFpRestraint, IhmInterfaceResidueFeature, IhmLocalizationDensityFiles, IhmModelingPostProcess, IhmModelingProtocol, IhmModelList, IhmModelRepresentation, IhmModelRepresentative, IhmMultiStateModeling, IhmNonPolyFeature, IhmOrderedEnsemble, IhmPolyAtomFeature, IhmPolyResidueFeature, IhmPredictedContactRestraint, IhmPseudoSiteFeature, IhmRelatedDatasets, IhmResiduesNotModeled, IhmSasRestraint, IhmSphereObjSite, IhmStartingComparativeModels, IhmStartingComputationalModels, IhmStartingModelCoord, IhmStartingModelDetails, IhmStartingModelSeqDif, IhmStructAssembly, IhmStructAssemblyClass, IhmStructAssemblyClassList, IhmStructAssemblyDetails, Journal, JournalIndex, NdbOriginalNdbCoordinates, NdbStructConfNa, NdbStructFeatureNa, NdbStructNaBasePair, NdbStructNaBasePairStep, PdbxAtlas, PdbxAtomSiteAnisoTls, PdbxAudit, PdbxAuditAuthor, PdbxAuditConformExtension, PdbxAuditRevisionCategory, PdbxAuditRevisionDetails, PdbxAuditRevisionGroup, PdbxAuditRevisionHistory, PdbxAuditRevisionItem, PdbxAuditSupport, PdbxBondDistanceLimits, PdbxBranchScheme, PdbxBuffer, PdbxBufferComponents, PdbxChemCompAtomEdit, PdbxChemCompAtomFeature, PdbxChemCompAtomRelated, PdbxChemCompAudit, PdbxChemCompBondEdit, PdbxChemCompDepositorInfo, PdbxChemCompDescriptor, PdbxChemCompFeature, PdbxChemCompIdentifier, PdbxChemCompImport, PdbxChemCompInstanceDepositorInfo, PdbxChemCompModel, PdbxChemCompModelAtom, PdbxChemCompModelAudit, PdbxChemCompModelBond, PdbxChemCompModelDescriptor, PdbxChemCompModelFeature, PdbxChemCompModelReference, PdbxChemCompNonstandard, PdbxChemCompRelated, PdbxChemCompSubcomponentEntityList, PdbxChemCompSubcomponentStructConn, PdbxChemCompSynonyms, PdbxChemCompUploadDepositorInfo, PdbxColumninfo, PdbxConnect, PdbxConnectAtom, PdbxConnectModification, PdbxConnectType, PdbxConstruct, PdbxConstructFeature, PdbxContactAuthor, PdbxCoord, PdbxCoordinateModel, PdbxCrystalAlignment, PdbxDatabaseMessage, PdbxDatabasePDBMaster, PdbxDatabasePDBObsSpr, PdbxDatabasePdbOmit, PdbxDatabaseProc, PdbxDatabaseRelated, PdbxDatabaseRemark, PdbxDatabaseStatus, PdbxDatabaseStatusHistory, PdbxDataProcessingCell, PdbxDataProcessingDetector, PdbxDataProcessingReflns, PdbxDataProcessingStatus, PdbxDbref, PdbxDccDensity, PdbxDccDensityCorr, PdbxDccGeometry, PdbxDccMap, PdbxDccMapman, PdbxDccRsccMapman, PdbxDccRsccMapmanOverall, PdbxDepositGroup, PdbxDepositGroupIndex, PdbxDepositionMessageFileReference, PdbxDepositionMessageInfo, PdbxDepuiEntityFeatures, PdbxDepuiEntityStatusFlags, PdbxDepuiEntryDetails, PdbxDepuiStatusFlags, PdbxDepuiUpload, PdbxDepuiValidationStatusFlags, PdbxDiffrnReflnsShell, PdbxDistantSolventAtoms, PdbxDomain, PdbxDomainRange, PdbxDrugInfo, PdbxEntityAssembly, PdbxEntityBranch, PdbxEntityBranchLink, PdbxEntityBranchList, PdbxEntityDescriptor, PdbxEntityFuncBindMode, PdbxEntityFuncEnzyme, PdbxEntityFuncOther, PdbxEntityFuncRegulatory, PdbxEntityFuncStructural, PdbxEntityInstanceFeature, PdbxEntityName, PdbxEntityNameInstance, PdbxEntityNameTaxonomy, PdbxEntityNameTaxonomyTree, PdbxEntityNonpoly, PdbxEntityPolyCompLinkList, PdbxEntityPolyDomain, PdbxEntityPolyNaNonstandard, PdbxEntityPolyNaType, PdbxEntityPolyProteinClass, PdbxEntityProdProtocol, PdbxEntitySrcGenCharacter, PdbxEntitySrcGenChrom, PdbxEntitySrcGenClone, PdbxEntitySrcGenCloneLigation, PdbxEntitySrcGenCloneRecombination, PdbxEntitySrcGenDepositorInfo, PdbxEntitySrcGenExpress, PdbxEntitySrcGenExpressTimepoint, PdbxEntitySrcGenFract, PdbxEntitySrcGenLysis, PdbxEntitySrcGenProdDigest, PdbxEntitySrcGenProdOther, PdbxEntitySrcGenProdOtherParameter, PdbxEntitySrcGenProdPcr, PdbxEntitySrcGenProteolysis, PdbxEntitySrcGenPure, PdbxEntitySrcGenRefold, PdbxEntitySrcSyn, PdbxEntryDetails, PdbxExptlCrystalCryoTreatment, PdbxExptlCrystalGrowComp, PdbxExptlCrystalGrowSol, PdbxExptlPd, PdbxFamilyGroupIndex, PdbxFamilyPrdAudit, PdbxFeatureAssembly, PdbxFeatureDomain, PdbxFeatureEntry, PdbxFeatureMonomer, PdbxFeatureSequenceRange, PdbxHelicalSymmetry, PdbxHelicalSymmetryDepositorInfo, PdbxHybrid, PdbxInhibitorInfo, PdbxIonInfo, PdbxLinkedEntity, PdbxLinkedEntityInstanceList, PdbxLinkedEntityLinkList, PdbxLinkedEntityList, PdbxMissingAtomNonpoly, PdbxMissingAtomPoly, PdbxMissingResidueList, PdbxMolecule, PdbxMoleculeFeatures, PdbxMoleculeFeaturesDepositorInfo, PdbxNaStrandInfo, PdbxNaStructKeywds, PdbxNmrAssignedChemShiftList, PdbxNmrChemShiftExperiment, PdbxNmrChemShiftRef, PdbxNmrChemShiftReference, PdbxNmrChemShiftSoftware, PdbxNmrComputing, PdbxNmrConstraintFile, PdbxNmrConstraints, PdbxNmrDetails, PdbxNmrEnsemble, PdbxNmrEnsembleRms, PdbxNmrExptl, PdbxNmrExptlSample, PdbxNmrExptlSampleConditions, PdbxNmrForceConstants, PdbxNmrRefine, PdbxNmrRepresentative, PdbxNmrSampleDetails, PdbxNmrSoftware, PdbxNmrSoftwareTask, PdbxNmrSpectralDim, PdbxNmrSpectralPeakList, PdbxNmrSpectralPeakSoftware, PdbxNmrSpectrometer, PdbxNmrSystematicChemShiftOffset, PdbxNmrUpload, PdbxNonpolyScheme, PdbxNonstandardList, PdbxPdbCompnd, PdbxPdbSource, PdbxPhasingDm, PdbxPhasingDmShell, PdbxPhasingMADSet, PdbxPhasingMADSetShell, PdbxPhasingMADSetSite, PdbxPhasingMADShell, PdbxPhasingMR, PdbxPointSymmetry, PdbxPointSymmetryDepositorInfo, PdbxPolySeqScheme, PdbxPostProcessDetails, PdbxPostProcessStatus, PdbxPrdAudit, PdbxPrereleaseSeq, PdbxProteinInfo, PdbxReferenceEntityLink, PdbxReferenceEntityList, PdbxReferenceEntityNonpoly, PdbxReferenceEntityPoly, PdbxReferenceEntityPolyLink, PdbxReferenceEntityPolySeq, PdbxReferenceEntitySequence, PdbxReferenceEntitySrcNat, PdbxReferenceEntitySubcomponents, PdbxReferenceLinkedEntity, PdbxReferenceLinkedEntityCompLink, PdbxReferenceLinkedEntityCompList, PdbxReferenceLinkedEntityLink, PdbxReferenceMolecule, PdbxReferenceMoleculeAnnotation, PdbxReferenceMoleculeDetails, PdbxReferenceMoleculeFamily, PdbxReferenceMoleculeFeatures, PdbxReferenceMoleculeList, PdbxReferenceMoleculeRelatedStructures, PdbxReferenceMoleculeSynonyms, PdbxReferencePublicationList, PdbxRefine, PdbxRefineAuxFile, PdbxRefineComponent, PdbxRefineLsRestrNcs, PdbxRefineTls, PdbxRefineTlsGroup, PdbxReflnsTwin, PdbxRelatedExpDataSet, PdbxRemediationAtomSiteMapping, PdbxReRefinement, PdbxRmchOutlier, PdbxRmsDevsCovalent, PdbxRmsDevsCovByMonomer, PdbxRobotSystem, PdbxSeqMapDepositorInfo, PdbxSequenceAnnotation, PdbxSequencePattern, PdbxSequenceRange, PdbxSerialCrystallographyDataReduction, PdbxSerialCrystallographyMeasurement, PdbxSerialCrystallographySampleDelivery, PdbxSerialCrystallographySampleDeliveryFixedTarget, PdbxSerialCrystallographySampleDeliveryInjection, PdbxSGProject, PdbxSolnScatter, PdbxSolnScatterModel, PdbxSolventAtomSiteMapping, PdbxSolventInfo, PdbxSource, PdbxStereochemistry, PdbxStructAssembly, PdbxStructAssemblyAuthClassification, PdbxStructAssemblyAuthEvidence, PdbxStructAssemblyAuthEvidenceDepositorInfo, PdbxStructAssemblyDepositorInfo, PdbxStructAssemblyGen, PdbxStructAssemblyGenDepositorInfo, PdbxStructAssemblyProp, PdbxStructAssemblyPropDepositorInfo, PdbxStructAsymGen, PdbxStructBiolFunc, PdbxStructChemCompDiagnostics, PdbxStructChemCompFeature, PdbxStructConnAngle, PdbxStructEntityInst, PdbxStructGroupComponentRange, PdbxStructGroupComponents, PdbxStructGroupList, PdbxStructInfo, PdbxStructLegacyOperList, PdbxStructLink, PdbxStructModResidue, PdbxStructMsymGen, PdbxStructNcsVirusGen, PdbxStructOperList, PdbxStructOperListDepositorInfo, PdbxStructPackGen, PdbxStructRefSeqDeletion, PdbxStructRefSeqDepositorInfo, PdbxStructRefSeqDifDepositorInfo, PdbxStructRefSeqFeature, PdbxStructRefSeqFeatureProp, PdbxStructRefSeqInsertion, PdbxStructSheetHbond, PdbxStructSpecialSymmetry, PdbxSugarPhosphateGeometry, PdbxSummaryFlags, PdbxSupportingExpDataSet, PdbxTableinfo, PdbxTrnaInfo, PdbxUnobsOrZeroOccAtoms, PdbxUnobsOrZeroOccResidues, PdbxUnpair, PdbxValAngle, PdbxValBond, PdbxValChiral, PdbxValContact, PdbxValidateChiral, PdbxValidateCloseContact, PdbxValidateMainChainPlane, PdbxValidatePeptideOmega, PdbxValidatePlanes, PdbxValidatePlanesAtom, PdbxValidatePolymerLinkage, PdbxValidateRmsdAngle, PdbxValidateRmsdBond, PdbxValidateSymmContact, PdbxValidateTorsion, PdbxValSymContact, PdbxVersion, PdbxViewCategory, PdbxViewCategoryGroup, PdbxViewItem, PdbxVirtualAngle, PdbxVirtualBond, PdbxVirtualTorsion, PdbxXplorFile, Phasing, PhasingAveraging, PhasingIsomorphous, PhasingMAD, PhasingMADClust, PhasingMADExpt, PhasingMADRatio, PhasingMADSet, PhasingMIR, PhasingMIRDer, PhasingMIRDerRefln, PhasingMIRDerShell, PhasingMIRDerSite, PhasingMIRShell, PhasingSet, PhasingSetRefln, Publ, PublAuthor, PublBody, PublManuscriptIncl, Refine, RefineAnalyze, RefineBIso, RefineFunctMinimized, RefineHist, RefineLsClass, RefineLsRestr, RefineLsRestrNcs, RefineLsRestrType, RefineLsShell, RefineOccupancy, Refln, Reflns, ReflnsClass, ReflnsScale, ReflnsShell, ReflnSysAbs, Software, SpaceGroup, SpaceGroupSymop, Struct, StructAsym, StructBiol, StructBiolGen, StructBiolKeywords, StructBiolView, StructConf, StructConfType, StructConn, StructConnType, StructKeywords, StructMonDetails, StructMonNucl, StructMonProt, StructMonProtCis, StructNcsDom, StructNcsDomLim, StructNcsEns, StructNcsEnsGen, StructNcsOper, StructRef, StructRefSeq, StructRefSeqDif, StructSheet, StructSheetHbond, StructSheetOrder, StructSheetRange, StructSheetTopology, StructSite, StructSiteGen, StructSiteKeywords, StructSiteView, Symmetry, SymmetryEquiv, ValenceParam, ValenceRef

public class BaseCategory
extends Object
implements Category

Field Summary

Fields

Modifier and Type	Field	Description
protected boolean	isText
protected Map<String,Column>	textFields

Constructor Summary

Constructors

Constructor	Description
BaseCategory(String name)
BaseCategory(String name, int rowCount, Object[] encodedColumns)
BaseCategory(String name, Map<String,Column> textColumns)

Method Summary

Modifier and Type	Method	Description
protected Column	getBinaryColumn(String name)
String	getCategoryName()	The name of this Category.
Column	getColumn(String name)	Retrieve a specific Column by name.
List<String>	getColumnNames()	Names of all present columns.
int	getRowCount()	The number of rows in this Category.
boolean	isDefined()	States whether this Category is defined.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.rcsb.cif.model.Category

columnNames, columns, get

Field Detail

isText

protected final boolean isText

textFields

protected final Map<String,Column> textFields

Constructor Detail

BaseCategory

public BaseCategory(String name)

BaseCategory

public BaseCategory(String name,
                    Map<String,Column> textColumns)

BaseCategory

public BaseCategory(String name,
                    int rowCount,
                    Object[] encodedColumns)

Method Detail

getCategoryName

public String getCategoryName()

Description copied from interface: Category

The name of this Category.

Specified by:

getCategoryName in interface Category

Returns:

String of the name

getRowCount

public int getRowCount()

Description copied from interface: Category

The number of rows in this Category. 0 for undefined categories.

Specified by:

getRowCount in interface Category

Returns:

the number of rows

getColumn

public Column getColumn(String name)

Description copied from interface: Category

Retrieve a specific Column by name.

Specified by:

getColumn in interface Category

Parameters:

name - the column name

Returns:

the Column, empty BaseColumn if no column of that name exists

getBinaryColumn

protected Column getBinaryColumn(String name)

getColumnNames

public List<String> getColumnNames()

Description copied from interface: Category

Names of all present columns.

Specified by:

getColumnNames in interface Category

Returns:

a collection of Column names

isDefined

public boolean isDefined()

Description copied from interface: Category

States whether this Category is defined.

Specified by:

isDefined in interface Category

Returns:

true if this Category contains data