Uses of Class
org.rcsb.openmms.cifparse.CifParseException

Packages that use CifParseException

org.rcsb.openmms.apps.rdb	Provides classes that implement PDBase, an application which loads macromolecular structure data files into a relational database.
org.rcsb.openmms.apps.stats	Provides classes to collect statistics on mmCIF data files using the low-level cifparse package.
org.rcsb.openmms.apps.xconv
org.rcsb.openmms.apps.xmc	Provides classes to convert macromolecular structure data files stored in mmCIF format into an XML style format (XMC).
org.rcsb.openmms.cifparse	Provides classes to parse mmCIF files.
org.rcsb.openmms.entry	A collection of classes that provide concrete implementations of Entry objects in the Corba modules and submodules and manage the Entry level MMS cache.
org.rcsb.openmms.loader	Provides classes to load macromolecular structure data files stored in mmCIF format into the MMS Entry data structure.
org.rcsb.openmms.meta	Provides classes and interfaces that create and manipulate a macromolecular structure metamodel based on the mmCIF dictionary.
org.rcsb.openmms.util	Provides utility classes required by the MMS metamodel, category loaders and various data format expressions.

Uses of CifParseException in org.rcsb.openmms.apps.rdb

Methods in org.rcsb.openmms.apps.rdb that throw CifParseException

void	DBLoader.processSingleEntry(InsertEntryFinal edbl, java.lang.String ename)
EntryImpl	DBLoader.readSingleEntry(java.lang.String id)

Uses of CifParseException in org.rcsb.openmms.apps.stats

Methods in org.rcsb.openmms.apps.stats that throw CifParseException

void	StatBuilder.readDataBlock(java.lang.String id, CifTokenizer ct)
void	StatBuilder.beginCompound()
void	StatBuilder.endCompound()
void	StatBuilder.setSingleItem(DataItem di)
void	StatBuilder.insertSingleValue(DataItem d, java.lang.String val)
void	StatBuilder.beginLoop()
void	StatBuilder.endLoop()
void	StatBuilder.beginRow()
void	StatBuilder.endRow()
void	StatBuilder.setLoopItem(int column, DataItem di)
void	StatBuilder.insertLoopValue(int column, DataItem d, java.lang.String val)
void	CifStats.initParams(java.lang.String[] argv)

Uses of CifParseException in org.rcsb.openmms.apps.xconv

Methods in org.rcsb.openmms.apps.xconv that throw CifParseException

void	ConvertBuilder.beginCompound()
void	ConvertBuilder.endCompound()
void	ConvertBuilder.setSingleItem(DataItem di)
void	ConvertBuilder.insertSingleValue(DataItem di, java.lang.String val)
void	ConvertBuilder.beginLoop()
void	ConvertBuilder.endLoop()
void	ConvertBuilder.beginRow()
void	ConvertBuilder.endRow()
void	ConvertBuilder.setLoopItem(int column, DataItem di)
void	ConvertBuilder.insertLoopValue(int column, DataItem d, java.lang.String val)

Uses of CifParseException in org.rcsb.openmms.apps.xmc

Methods in org.rcsb.openmms.apps.xmc that throw CifParseException

void	XBuilder.beginCompound()
void	XBuilder.endCompound()
void	XBuilder.setSingleItem(DataItem di)
void	XBuilder.insertSingleValue(DataItem d, java.lang.String val)
void	XBuilder.beginLoop()
void	XBuilder.endLoop()
void	XBuilder.beginRow()
void	XBuilder.endRow()
void	XBuilder.setLoopItem(int column, DataItem di)
void	XBuilder.insertLoopValue(int column, DataItem d, java.lang.String val)
protected void	XBuilder.setValue(DataItem d, java.lang.String val)

Uses of CifParseException in org.rcsb.openmms.cifparse

Methods in org.rcsb.openmms.cifparse that throw CifParseException

java.lang.String	CifTokenizer.getToken()
void	CifParser.readDictionary(CifTokenizer ct, CifDictionary cd, boolean parseAll)
int	CifParser.startNewSaveBlock(CifTokenizer ct, java.lang.String saveName, CifDictionary cd, boolean parseAll)
void	CifParser.readDataBlock(CifTokenizer ct, DataItemList dil)
void	DictionaryItemList.checkAllItemsDefined()
void	DictionaryCategoryList.checkAllItemsDefined()
void	CifDictionary.checkAllItemsDefined()
void	CatLoader.beginCategory()
void	CatLoader.endCompound(java.lang.Object e)
void	CatLoader.defineSingleItem(java.lang.Object e, int fieldCode)
void	CatLoader.insertSingleValue(java.lang.Object e, int fieldCode, java.lang.String value)
void	CatLoader.defineLoopItem(java.lang.Object e, int fieldCode)
void	CatLoader.beginRow()
void	CatLoader.endRow()
void	CatLoader.insertLoopValue(int fieldCode, java.lang.String value)
void	CatLoader.endLoop(java.lang.Object e)
void	Builder.beginCompound()
void	Builder.endCompound()
void	Builder.setSingleItem(DataItem di)
void	Builder.insertSingleValue(DataItem d, java.lang.String val)
void	Builder.beginLoop()
void	Builder.endLoop()
void	Builder.beginRow()
void	Builder.endRow()
void	Builder.setLoopItem(int column, DataItem di)
void	Builder.insertLoopValue(int column, DataItem d, java.lang.String val)

Uses of CifParseException in org.rcsb.openmms.entry

Methods in org.rcsb.openmms.entry that throw CifParseException

void	RefBuilder.beginCompound()
void	RefBuilder.endCompound()
void	RefBuilder.setSingleItem(DataItem di)
void	RefBuilder.insertSingleValue(DataItem d, java.lang.String val)
void	RefBuilder.beginLoop()
void	RefBuilder.endLoop()
void	RefBuilder.beginRow()
void	RefBuilder.endRow()
void	RefBuilder.setLoopItem(int column, DataItem di)
void	RefBuilder.insertLoopValue(int column, DataItem d, java.lang.String val)

Uses of CifParseException in org.rcsb.openmms.loader

Methods in org.rcsb.openmms.loader that throw CifParseException

void	SymmetryEquivCatLoader.endCompound(java.lang.Object e)
void	StructSiteViewCatLoader.endCompound(java.lang.Object e)
void	StructSiteKeywordsCatLoader.endCompound(java.lang.Object e)
void	StructSiteGenCatLoader.endCompound(java.lang.Object e)
void	StructSiteCatLoader.endCompound(java.lang.Object e)
void	StructSheetTopologyCatLoader.endCompound(java.lang.Object e)
void	StructSheetRangeCatLoader.endCompound(java.lang.Object e)
void	StructSheetOrderCatLoader.endCompound(java.lang.Object e)
void	StructSheetHbondCatLoader.endCompound(java.lang.Object e)
void	StructSheetCatLoader.endCompound(java.lang.Object e)
void	StructRefSeqDifCatLoader.endCompound(java.lang.Object e)
void	StructRefSeqCatLoader.endCompound(java.lang.Object e)
void	StructRefCatLoader.endCompound(java.lang.Object e)
void	StructNcsOperCatLoader.endCompound(java.lang.Object e)
void	StructNcsEnsGenCatLoader.endCompound(java.lang.Object e)
void	StructNcsEnsCatLoader.endCompound(java.lang.Object e)
void	StructNcsDomLimCatLoader.endCompound(java.lang.Object e)
void	StructNcsDomCatLoader.endCompound(java.lang.Object e)
void	StructMonProtCisCatLoader.endCompound(java.lang.Object e)
void	StructMonProtCatLoader.endCompound(java.lang.Object e)
void	StructMonNuclCatLoader.endCompound(java.lang.Object e)
void	StructMonDetailsCatLoader.endCompound(java.lang.Object e)
void	StructKeywordsCatLoader.endCompound(java.lang.Object e)
void	StructConnTypeCatLoader.endCompound(java.lang.Object e)
void	StructConnCatLoader.endCompound(java.lang.Object e)
void	SymmetryCatLoader.endCompound(java.lang.Object e)
void	StructConfTypeCatLoader.endCompound(java.lang.Object e)
void	StructConfCatLoader.endCompound(java.lang.Object e)
void	StructCatLoader.endCompound(java.lang.Object e)
void	StructBiolViewCatLoader.endCompound(java.lang.Object e)
void	StructBiolKeywordsCatLoader.endCompound(java.lang.Object e)
void	StructBiolGenCatLoader.endCompound(java.lang.Object e)
void	StructBiolCatLoader.endCompound(java.lang.Object e)
void	StructAsymCatLoader.endCompound(java.lang.Object e)
void	SoftwareCatLoader.endCompound(java.lang.Object e)
void	ReflnsShellCatLoader.endCompound(java.lang.Object e)
void	ReflnsScaleCatLoader.endCompound(java.lang.Object e)
void	ReflnsCatLoader.endCompound(java.lang.Object e)
void	ReflnCatLoader.endCompound(java.lang.Object e)
void	RefineOccupancyCatLoader.endCompound(java.lang.Object e)
void	RefineLsShellCatLoader.endCompound(java.lang.Object e)
void	RefineLsRestrNcsCatLoader.endCompound(java.lang.Object e)
void	RefineLsRestrCatLoader.endCompound(java.lang.Object e)
void	RefineHistCatLoader.endCompound(java.lang.Object e)
void	RefineBIsoCatLoader.endCompound(java.lang.Object e)
void	RefineAnalyzeCatLoader.endCompound(java.lang.Object e)
void	PhasingSetReflnCatLoader.endCompound(java.lang.Object e)
void	PhasingMirShellCatLoader.endCompound(java.lang.Object e)
void	PhasingMirDerSiteCatLoader.endCompound(java.lang.Object e)
void	PhasingMirDerShellCatLoader.endCompound(java.lang.Object e)
void	PhasingMirDerReflnCatLoader.endCompound(java.lang.Object e)
void	PhasingMirDerCatLoader.endCompound(java.lang.Object e)
void	PhasingSetCatLoader.endCompound(java.lang.Object e)
void	PhasingMirCatLoader.endCompound(java.lang.Object e)
void	PhasingMadSetCatLoader.endCompound(java.lang.Object e)
void	PhasingMadRatioCatLoader.endCompound(java.lang.Object e)
void	PhasingMadExptCatLoader.endCompound(java.lang.Object e)
void	PhasingMadClustCatLoader.endCompound(java.lang.Object e)
void	PhasingMadCatLoader.endCompound(java.lang.Object e)
void	PhasingIsomorphousCatLoader.endCompound(java.lang.Object e)
void	PhasingAveragingCatLoader.endCompound(java.lang.Object e)
void	PdbxXplorFileCatLoader.endCompound(java.lang.Object e)
void	PdbxStructSheetHbondCatLoader.endCompound(java.lang.Object e)
void	RefineCatLoader.endCompound(java.lang.Object e)
void	PdbxRefineTlsGroupCatLoader.endCompound(java.lang.Object e)
void	PdbxRefineTlsCatLoader.endCompound(java.lang.Object e)
void	PdbxRefineAuxFileCatLoader.endCompound(java.lang.Object e)
void	PdbxPrereleaseSeqCatLoader.endCompound(java.lang.Object e)
void	PdbxPolySeqSchemeCatLoader.endCompound(java.lang.Object e)
void	PdbxNonpolySchemeCatLoader.endCompound(java.lang.Object e)
void	PdbxNmrSpectrometerCatLoader.endCompound(java.lang.Object e)
void	PdbxNmrSoftwareCatLoader.endCompound(java.lang.Object e)
void	PdbxNmrSampleDetailsCatLoader.endCompound(java.lang.Object e)
void	PdbxNmrRepresentativeCatLoader.endCompound(java.lang.Object e)
void	PdbxNmrRefineCatLoader.endCompound(java.lang.Object e)
void	PdbxNmrForceConstantsCatLoader.endCompound(java.lang.Object e)
void	PdbxNmrExptlSampleConditionsCatLoader.endCompound(java.lang.Object e)
void	PdbxNmrExptlSampleCatLoader.endCompound(java.lang.Object e)
void	PdbxNmrEnsembleRmsCatLoader.endCompound(java.lang.Object e)
void	PdbxNmrEnsembleCatLoader.endCompound(java.lang.Object e)
void	PhasingCatLoader.endCompound(java.lang.Object e)
void	PdbxNmrDetailsCatLoader.endCompound(java.lang.Object e)
void	PdbxNmrConstraintsCatLoader.endCompound(java.lang.Object e)
void	PdbxEntitySrcSynCatLoader.endCompound(java.lang.Object e)
void	PdbxEntityNameCatLoader.endCompound(java.lang.Object e)
void	PdbxEntityAssemblyCatLoader.endCompound(java.lang.Object e)
void	PdbxDatabaseStatusCatLoader.endCompound(java.lang.Object e)
void	PdbxDatabaseRemarkCatLoader.endCompound(java.lang.Object e)
void	PdbxDatabaseRelatedCatLoader.endCompound(java.lang.Object e)
void	PdbxRefineCatLoader.endCompound(java.lang.Object e)
void	PdbxNmrExptlCatLoader.endCompound(java.lang.Object e)
void	PdbxDatabaseProcCatLoader.endCompound(java.lang.Object e)
void	PdbxDatabasePdbObsSprCatLoader.endCompound(java.lang.Object e)
void	PdbxDatabaseMessageCatLoader.endCompound(java.lang.Object e)
void	GeomTorsionCatLoader.endCompound(java.lang.Object e)
void	GeomHbondCatLoader.endCompound(java.lang.Object e)
void	GeomContactCatLoader.endCompound(java.lang.Object e)
void	GeomCatLoader.endCompound(java.lang.Object e)
void	GeomAngleCatLoader.endCompound(java.lang.Object e)
void	ExptlCrystalGrowCompCatLoader.endCompound(java.lang.Object e)
void	ExptlCrystalGrowCatLoader.endCompound(java.lang.Object e)
void	ExptlCrystalFaceCatLoader.endCompound(java.lang.Object e)
void	ExptlCrystalCatLoader.endCompound(java.lang.Object e)
void	GeomBondCatLoader.endCompound(java.lang.Object e)
void	ExptlCatLoader.endCompound(java.lang.Object e)
void	EntryLinkCatLoader.endCompound(java.lang.Object e)
void	EntitySrcNatCatLoader.endCompound(java.lang.Object e)
void	EntitySrcGenCatLoader.endCompound(java.lang.Object e)
void	EntityPolySeqCatLoader.endCompound(java.lang.Object e)
void	EntityPolyCatLoader.endCompound(java.lang.Object e)
void	EntityNameSysCatLoader.endCompound(java.lang.Object e)
void	EntityNameComCatLoader.endCompound(java.lang.Object e)
void	EntityLinkCatLoader.endCompound(java.lang.Object e)
void	EntityKeywordsCatLoader.endCompound(java.lang.Object e)
void	EntityCatLoader.endCompound(java.lang.Object e)
void	DiffrnStandardsCatLoader.endCompound(java.lang.Object e)
void	DiffrnStandardReflnCatLoader.endCompound(java.lang.Object e)
void	DiffrnSourceCatLoader.endCompound(java.lang.Object e)
void	DiffrnScaleGroupCatLoader.endCompound(java.lang.Object e)
void	DiffrnReflnsCatLoader.endCompound(java.lang.Object e)
void	DiffrnReflnCatLoader.endCompound(java.lang.Object e)
void	DiffrnRadiationWavelengthCatLoader.endCompound(java.lang.Object e)
void	DiffrnRadiationCatLoader.endCompound(java.lang.Object e)
void	DiffrnOrientReflnCatLoader.endCompound(java.lang.Object e)
void	DiffrnOrientMatrixCatLoader.endCompound(java.lang.Object e)
void	DiffrnMeasurementCatLoader.endCompound(java.lang.Object e)
void	DiffrnDetectorCatLoader.endCompound(java.lang.Object e)
void	DiffrnAttenuatorCatLoader.endCompound(java.lang.Object e)
void	DatabasePdbTvectCatLoader.endCompound(java.lang.Object e)
void	DiffrnCatLoader.endCompound(java.lang.Object e)
void	DatabasePdbRevRecordCatLoader.endCompound(java.lang.Object e)
void	DatabasePdbRevCatLoader.endCompound(java.lang.Object e)
void	DatabasePdbRemarkCatLoader.endCompound(java.lang.Object e)
void	DatabasePdbMatrixCatLoader.endCompound(java.lang.Object e)
void	DatabasePdbCaveatCatLoader.endCompound(java.lang.Object e)
void	DatabaseCatLoader.endCompound(java.lang.Object e)
void	ComputingCatLoader.endCompound(java.lang.Object e)
void	CitationEditorCatLoader.endCompound(java.lang.Object e)
void	CitationCatLoader.endCompound(java.lang.Object e)
void	CitationAuthorCatLoader.endCompound(java.lang.Object e)
void	ChemLinkTorValueCatLoader.endCompound(java.lang.Object e)
void	ChemLinkTorCatLoader.endCompound(java.lang.Object e)
void	ChemLinkPlaneCatLoader.endCompound(java.lang.Object e)
void	ChemLinkPlaneAtomCatLoader.endCompound(java.lang.Object e)
void	ChemLinkChirCatLoader.endCompound(java.lang.Object e)
void	ChemLinkChirAtomCatLoader.endCompound(java.lang.Object e)
void	ChemLinkCatLoader.endCompound(java.lang.Object e)
void	ChemLinkBondCatLoader.endCompound(java.lang.Object e)
void	ChemLinkAngleCatLoader.endCompound(java.lang.Object e)
void	ChemCompTorValueCatLoader.endCompound(java.lang.Object e)
void	ChemCompTorCatLoader.endCompound(java.lang.Object e)
void	ChemCompPlaneCatLoader.endCompound(java.lang.Object e)
void	ChemCompPlaneAtomCatLoader.endCompound(java.lang.Object e)
void	ChemCompLinkCatLoader.endCompound(java.lang.Object e)
void	ChemCompChirCatLoader.endCompound(java.lang.Object e)
void	ChemCompChirAtomCatLoader.endCompound(java.lang.Object e)
void	ChemCompCatLoader.endCompound(java.lang.Object e)
void	ChemCompBondCatLoader.endCompound(java.lang.Object e)
void	ChemCompAtomCatLoader.endCompound(java.lang.Object e)
void	ChemCompAngleCatLoader.endCompound(java.lang.Object e)
void	CellMeasurementReflnCatLoader.endCompound(java.lang.Object e)
void	CellMeasurementCatLoader.endCompound(java.lang.Object e)
void	CellCatLoader.endCompound(java.lang.Object e)
void	AtomTypeCatLoader.endCompound(java.lang.Object e)
void	AtomSitesFootnoteCatLoader.endCompound(java.lang.Object e)
void	AtomSitesCatLoader.endCompound(java.lang.Object e)
void	AtomSitesAltGenCatLoader.endCompound(java.lang.Object e)
void	AtomSitesAltEnsCatLoader.endCompound(java.lang.Object e)
void	AtomSitesAltCatLoader.endCompound(java.lang.Object e)
void	AtomSiteCatLoader.endCompound(java.lang.Object e)
void	AtomSiteAnisotropCatLoader.endCompound(java.lang.Object e)

Uses of CifParseException in org.rcsb.openmms.meta

Methods in org.rcsb.openmms.meta that throw CifParseException

void	MMSExpr.init(java.lang.String[] argv)

Uses of CifParseException in org.rcsb.openmms.util

Methods in org.rcsb.openmms.util that throw CifParseException

void	CatUtil.setChildIndex(java.lang.Object xe, java.util.ArrayList a, StringToIndex sti)