DicFile Class Reference

Public class that represents a dictionary file, composed of blocks with tables. More...

#include <DicFile.h>

Inheritance diagram for DicFile:

Collaboration diagram for DicFile:

Public Member Functions
	DicFile (const eFileMode fileMode, const std::string &objFileName, const bool verbose=false, const Char::eCompareType caseSense=Char::eCASE_SENSITIVE, const unsigned int maxLineLength=STD_CIF_LINE_LENGTH, const std::string &nullValue=CifString::UnknownValue)
	DicFile (const bool verbose=false, const Char::eCompareType caseSense=Char::eCASE_SENSITIVE, const unsigned int maxLineLength=STD_CIF_LINE_LENGTH, const std::string &nullValue=CifString::UnknownValue)
	~DicFile ()
void	WriteItemAliases (const std::string &fileName)
ISTable *	GetFormatTable ()
int	WriteFormatted (const std::string &cifFileName, ISTable *formatP=NULL)
int	WriteFormatted (const std::string &cifFileName, TableFile *ddl, ISTable *formatP=NULL)
void	Compress (CifFile *ddl)
CifFile *	GetRefFile ()
void	Write (const std::string &cifFileName, const bool sortTables=false, const bool writeEmptyTables=false)
void	Write (const std::string &cifFileName, const std::vector< std::string > &tableOrder, const bool writeEmptyTables=false)
void	Write (std::ostream &outStream, const bool sortTables=false, const bool writeEmptyTables=false)
void	Write (std::ostream &cifo, const std::vector< std::string > &catOrder, const bool writeEmptyTables=false)
void	Write (std::ostream &cifo, std::vector< unsigned int > &tables, const bool writeEmptyTables=false)
Public Member Functions inherited from CifFile
	CifFile (const eFileMode fileMode, const std::string &fileName, const bool verbose=false, const Char::eCompareType caseSense=Char::eCASE_SENSITIVE, const unsigned int maxLineLength=STD_CIF_LINE_LENGTH, const std::string &nullValue=CifString::UnknownValue)
	CifFile (const bool verbose=false, const Char::eCompareType caseSense=Char::eCASE_SENSITIVE, const unsigned int maxLineLength=STD_CIF_LINE_LENGTH, const std::string &nullValue=CifString::UnknownValue)
	~CifFile ()
void	SetSrcFileName (const std::string &srcFileName)
const std::string &	GetSrcFileName ()
bool	GetVerbose ()
void	SetSmartPrint (bool smartPrint=true)
bool	IsSmartPrint ()
void	SetQuoting (eQuoting quoting)
unsigned int	GetQuoting ()
void	SetLooping (const std::string &catName, bool looping=false)
bool	GetLooping (const std::string &catName)
void	Write (const std::string &cifFileName, const bool sortTables=false, const bool writeEmptyTables=false)
void	Write (const std::string &cifFileName, const std::vector< std::string > &tableOrder, const bool writeEmptyTables=false)
void	Write (std::ostream &outStream, const bool sortTables=false, const bool writeEmptyTables=false)
void	WriteNmrStar (const std::string &nmrStarFileName, const std::string &globalBlockName, const bool sortTables=false, const bool writeEmptyTables=false)
int	DataChecking (CifFile &dicRef, const std::string &diagFileName, const bool extraDictChecks=false, const bool extraCifChecks=false)
int	DataChecking (Block &block, Block &refBlock, std::ostringstream &buf, const bool extraDictChecks=false, const bool extraCifChecks=false)
void	SetEnumCheck (bool caseSense=false)
bool	GetEnumCheck ()
const std::string &	GetParsingDiags ()
void	FindCifNullRows (std::vector< unsigned int > &nullRowsIndices, const ISTable &isTable)
void	GetAttributeValue (std::string &attribVal, const std::string &blockId, const std::string &category, const std::string &attribute)
void	GetAttributeValueIf (std::string &attribVal, const std::string &blockId, const std::string &category, const std::string &attributeA, const std::string &attributeB, const std::string &valB)
bool	IsAttributeValueDefined (const std::string &blockId, const std::string &category, const std::string &attribute)
void	SetAttributeValue (const std::string &blockId, const std::string &category, const std::string &attribute, const std::string &value, const bool create=false)
void	SetAttributeValueIf (const std::string &blockId, const std::string &category, const std::string &attributeA, const std::string &valA, const std::string &attributeB, const std::string &valB, const bool create=false)
void	SetAttributeValueIfNull (const std::string &blockId, const std::string &category, const std::string &attribute, const std::string &value)
void	GetAttributeValues (std::vector< std::string > &strings, const std::string &blockId, const std::string &category, const std::string &attribute)
void	GetAttributeValuesIf (std::vector< std::string > &strings, const std::string &blockId, const std::string &category, const std::string &attributeA, const std::string &attributeB, const std::string &valB)
void	SetAttributeValues (const std::string &blockId, const std::string &category, const std::string &attribute, const std::vector< std::string > &values)
int	CheckCategories (Block &block, Block &refBlock, std::ostringstream &log)
void	CheckCategoryKey (Block &block, std::ostringstream &log)
void	CheckItemsTable (Block &block, std::ostringstream &log)
int	CheckItems (Block &block, Block &refBlock, std::ostringstream &log)
Public Member Functions inherited from TableFile
	TableFile (const Char::eCompareType caseSense=Char::eCASE_SENSITIVE)
	TableFile (const eFileMode fileMode, const string &fileName, const Char::eCompareType caseSense=Char::eCASE_SENSITIVE)
virtual	~TableFile ()
string	GetFileName (void)
eFileMode	GetFileMode (void)
Char::eCompareType	GetCaseSensitivity (void)
unsigned int	GetStatusInd (void)
unsigned int	GetNumBlocks ()
void	GetBlockNames (vector< string > &blockNames)
string	GetFirstBlockName ()
bool	IsBlockPresent (const string &blockName)
string	AddBlock (const string &blockName)
Block &	GetBlock (const string &blockName)
string	RenameBlock (const string &oldBlockName, const string &newBlockName)
string	RenameFirstBlock (const string &newBlockName)
void	Flush ()
void	Serialize (const string &fileName)
void	Close ()

Protected Member Functions
int	WriteFormatted (std::ostream &cifo, ISTable *formatP)
int	WriteFormatted (std::ostream &cifo, TableFile *ddl, ISTable *formatP)
void	WriteItemAliases (std::ostream &cifo)
Protected Member Functions inherited from CifFile
int	_IsQuotableText (const std::string &itemValue)
eIdentType	_FindPrintType (const std::vector< std::string > &values)
void	_PrintItemIdent (std::ostream &cifo, unsigned int &linePos)
void	_PrintItemName (std::ostream &cifo, const std::string &category, const std::string &itemName, unsigned int &linePos)
void	_PrintPostItemSeparator (std::ostream &cifo, unsigned int &linePos, const bool ident=false, const unsigned int numSpaces=1)
int	_PrintItemValue (std::ostream &cifo, const std::string &itemValue, unsigned int &linePos, const eIdentType identType=eNONE, const unsigned int width=0)
int	_PrintItemNameInHeader (std::ostream &cifo, const std::string &itemValue, unsigned int &linePos, const eIdentType identType=eNONE, const unsigned int width=0)
void	_PrintHeaderedItems (std::ostream &cifo, const std::vector< std::string > &colNames, const std::vector< unsigned int > &colWidths, const std::vector< eIdentType > colPrintType)
void	Write (std::ostream &cifo, const std::vector< std::string > &catOrder, const bool writeEmptyTables=false)
void	Write (std::ostream &cifo, std::vector< unsigned int > &tables, const bool writeEmptyTables=false)
Protected Member Functions inherited from TableFile
void	_SetStatusInd (const string &blockName)
void	_AddBlock (const string &blockName, Serializer *serP)
void	_GetNumTablesInBlocks (vector< UInt32 > &numTablesInBlocks)
ISTable *	_GetTablePtr (const unsigned int blockIndex, const unsigned int tableIndex)
void	_GetAllTables ()
unsigned int	GetTotalNumTables ()
void	GetTableNames (vector< string > &tableNames)
void	GetTablesIndices (vector< unsigned int > &tablesIndices)
void	GetSortedTablesIndices (vector< unsigned int > &tablesIndices)
void	_ReadFileIndex ()
void	_ReadFileIndexVersion0 ()
void	_ReadFileIndexVersion1 ()
void	_WriteFileIndex (Serializer *serP, const vector< unsigned int > &tableLocs)

Protected Attributes
ISTable *	_formatP
Protected Attributes inherited from CifFile
std::string	_beginDataKeyword
std::string	_endDataKeyword
std::string	_beginLoopKeyword
std::string	_endLoopKeyword
unsigned int	_maxCifLineLength
std::string	_nullValue
bool	_verbose
bool	_smartPrint
std::string	_quotes
std::map< std::string, bool >	_looping
bool	_enumCaseSense
Protected Attributes inherited from TableFile
string	_fileName
eFileMode	_fileMode
Char::eCompareType	_caseSense
unsigned int	_statusInd
mapped_ptr_vector< Block, StringLess >	_blocks
Serializer *	_f

Additional Inherited Members
Public Types inherited from CifFile
enum	eQuoting { eSINGLE = 0, eDOUBLE }
Public Types inherited from TableFile
enum	eStatusInd { eCLEAR_STATUS = 0x0000, eDUPLICATE_BLOCKS = 0x0001, eUNNAMED_BLOCKS = 0x0002 }
Public Attributes inherited from CifFile
std::string	_parsingDiags
std::string	_checkingDiags
Static Public Attributes inherited from CifFile
static const unsigned int	STD_CIF_LINE_LENGTH = 80
Protected Types inherited from CifFile
enum	eIdentType { eNONE = 0, eLEFT, eRIGHT }
Static Protected Attributes inherited from CifFile
static const unsigned int	STD_PRINT_SPACING = 3
static const unsigned int	SMART_PRINT_SPACING = 1
static const unsigned int	HEADER_SPACING = 40

Detailed Description

Public class that represents a dictionary file, composed of blocks with tables.

This class represents a dictionary file. In addition to inherited methods from CifFile class, this class provides a method for writing the content of "item_aliases" table to a text file.

Constructor & Destructor Documentation

DicFile() [1/2]

DicFile::DicFile	(	const eFileMode	fileMode,
		const std::string &	objFileName,
		const bool	verbose = false,
		const Char::eCompareType	caseSense = Char::eCASE_SENSITIVE,
		const unsigned int	maxLineLength = STD_CIF_LINE_LENGTH,
		const std::string &	nullValue = CifString::UnknownValue
	)

Constructs a dictionary file.

Parameters

[in]	fileMode	- dictionary file mode. Possible values are read-only, create, update and virtual. Detailed description of file mode is given in TableFile documentation.
[in]	fileName	- relative or absolute name of the file where object persistency is maintained. If fileMode specifies virtual mode, this parameter is ignored.
[in]	verbose	- optional parameter that indicates whether logging should be turned on (if true) or off (if false). If verbose is not specified, logging is turned off.
[in]	caseSense	- optional parameter that indicates case sensitivity of table names. Possible values are case sensitive and case in-sensitive. If not specified, case sensitive table names are assumed.
[in]	maxLineLength	- optional parameter that indicates the maximum number of written characters in one line in the written text file. If not specified, STD_CIF_LINE_LENGTH is used.
[in]	nullValue	- optional parameter that indicates the character that is to be used to denote unknown value in the written CIF file. If not specified, CifString::UnknownValue is used.

Returns

Not applicable

Precondition

None

Postcondition

None

Exceptions

DicFile() [2/2]

DicFile::DicFile	(	const bool	verbose = false,
		const Char::eCompareType	caseSense = Char::eCASE_SENSITIVE,
		const unsigned int	maxLineLength = STD_CIF_LINE_LENGTH,
		const std::string &	nullValue = CifString::UnknownValue
	)

Constructs a dictionary file in virtual mode.

Parameters

[in]	verbose	- optional parameter that indicates whether logging should be turned on (if true) or off (if false). If verbose is not specified, logging is turned off.
[in]	caseSense	- optional parameter that indicates case sensitivity of table names. Possible values are case sensitive and case in-sensitive. If not specified, case sensitive table names are assumed.
[in]	maxLineLength	- optional parameter that indicates the maximum number of written characters in one line in the written text file. If not specified, STD_CIF_LINE_LENGTH is used.
[in]	nullValue	- optional parameter that indicates the character that is to be used to denote unknown value in the written CIF file. If not specified, CifString::UnknownValue is used.

Returns

Not applicable

Precondition

None

Postcondition

None

Exceptions

~DicFile()

DicFile::~DicFile

(

)

Destructs a dictionary file, by releasing all consumed resources.

Parameters

Not applicable

Returns

Not applicable

Precondition

None

Postcondition

None

Exceptions

Member Function Documentation

Compress()

void DicFile::Compress

(

CifFile *

ddl

)

Method, not currently part of users public API, and will soon be re-examined.

GetFormatTable()

ISTable* DicFile::GetFormatTable

(

)

Method, not currently part of users public API, and will soon be re-examined.

GetRefFile()

CifFile* DicFile::GetRefFile

(

)

Write() [1/5]

void CifFile::Write

Writes the data out to a text file.

Parameters

[in]	cifFileName	- relative or absolute name of the text file to which the data from CifFile object is to be written to.
[in]	sortTables	- optional parameter that indicates whether written tables should be sorted (if true) or not sorted (if false). If sortTables is not specified, tables are not sorted prior to writing them.
[in]	writeEmptyTables	- optional parameter that indicates whether empty tables (0 rows) are to be written (if true) or not written (if false). If writeEmptyTables is not specified, empty tables are not written.

Returns

None

Precondition

None

Postcondition

None

Exceptions

Write() [2/5]

void CifFile::Write

Writes the data out to a text file.

Parameters

[in]	cifFileName	- relative or absolute name of the text file to which the data from CifFile object is to be written to.
[in]	tableOrder	- vector of table names that indicates the order of written tables.
[in]	writeEmptyTables	- optional parameter that indicates whether empty tables (0 rows) are to be written (if true) or not written (if false). If writeEmptyTables is not specified, empty tables are not written.

Returns

None

Precondition

None

Postcondition

None

Exceptions

Write() [3/5]

void CifFile::Write

Write() [4/5]

void CifFile::Write

Write() [5/5]

void CifFile::Write

Writes the data out to an output stream.

Parameters

[in]	outStream	- a reference to the output stream
[in]	sortTables	- optional parameter that indicates whether written tables should be sorted (if true) or not sorted (if false). If sortTables is not specified, tables are not sorted prior to writing them.
[in]	writeEmptyTables	- optional parameter that indicates whether empty tables (0 rows) are to be written (if true) or not written (if false). If writeEmptyTables is not specified, empty tables are not written.

Returns

None

Precondition

None

Postcondition

None

Exceptions

WriteFormatted() [1/4]

int DicFile::WriteFormatted	(	const std::string &	cifFileName,
		ISTable *	formatP = NULL
	)

Method, not currently part of users public API, and will soon be re-examined.

WriteFormatted() [2/4]

int DicFile::WriteFormatted	(	const std::string &	cifFileName,
		TableFile *	ddl,
		ISTable *	formatP = NULL
	)

Method, not currently part of users public API, and will soon be re-examined.

WriteFormatted() [3/4]

int DicFile::WriteFormatted ( std::ostream &  cifo, ISTable *  formatP  )

protected

WriteFormatted() [4/4]

int DicFile::WriteFormatted ( std::ostream &  cifo, TableFile *  ddl, ISTable *  formatP  )

protected

WriteItemAliases() [1/2]

void DicFile::WriteItemAliases

(

const std::string &

fileName

)

Writes the content of "item_aliases" table to a text file.

Parameters

[in]

fileName

- relative or absolute name of the text file to which the content of "item_aliases" table is to be written to.

Returns

None

Precondition

None

Postcondition

None

Exceptions

WriteItemAliases() [2/2]

void DicFile::WriteItemAliases ( std::ostream &  cifo )

protected

Member Data Documentation

_formatP

ISTable* DicFile::_formatP

protected

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The documentation for this class was generated from the following file:

• rcsb/DicFile.h