librcsb-core-wrapper  1.000
Public Types | Public Member Functions | Public Attributes | Static Public Attributes | Protected Types | Protected Member Functions | Protected Attributes | Static Protected Attributes | List of all members
CifFile Class Reference

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

#include <CifFile.h>

Inheritance diagram for CifFile:
Inheritance graph
Collaboration diagram for CifFile:
Collaboration graph

Public Types

enum  eQuoting { eSINGLE = 0, eDOUBLE }
 
- Public Types inherited from TableFile
enum  eStatusInd { eCLEAR_STATUS = 0x0000, eDUPLICATE_BLOCKS = 0x0001, eUNNAMED_BLOCKS = 0x0002 }
 

Public Member Functions

 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 extraChecks=false)
 
int DataChecking (Block &block, Block &refBlock, std::ostringstream &buf, const bool extraChecks=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)
 
BlockGetBlock (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 ()
 

Public Attributes

std::string _parsingDiags
 
std::string _checkingDiags
 

Static Public Attributes

static const unsigned int STD_CIF_LINE_LENGTH = 80
 

Protected Types

enum  eIdentType { eNONE = 0, eLEFT, eRIGHT }
 

Protected Member Functions

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

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
 

Static Protected Attributes

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 CIF file, composed of blocks with tables.

This class represents a CIF file. In addition to inherited methods from TableFile class, this class provides methods for writing the data to a text file, along with methods for controlling how the data is written, and a method for verifying the CIF file against dictionary.

Member Enumeration Documentation

enum CifFile::eIdentType
protected
Enumerator
eNONE 
eLEFT 
eRIGHT 
Enumerator
eSINGLE 
eDOUBLE 

Constructor & Destructor Documentation

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 
)

Constructs a CIF file.

Parameters
[in]fileMode- CIF 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
None
CifFile::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 
)

Constructs a CIF 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
None
CifFile::~CifFile ( )

Destructs a CIF file, by releasing all consumed resources.

Parameters
Not applicable
Returns
Not applicable
Precondition
None
Postcondition
None
Exceptions
None

Member Function Documentation

eIdentType CifFile::_FindPrintType ( const std::vector< std::string > &  values)
protected
int CifFile::_IsQuotableText ( const std::string &  itemValue)
protected
void CifFile::_PrintHeaderedItems ( std::ostream &  cifo,
const std::vector< std::string > &  colNames,
const std::vector< unsigned int > &  colWidths,
const std::vector< eIdentType colPrintType 
)
protected
void CifFile::_PrintItemIdent ( std::ostream &  cifo,
unsigned int &  linePos 
)
protected
void CifFile::_PrintItemName ( std::ostream &  cifo,
const std::string &  category,
const std::string &  itemName,
unsigned int &  linePos 
)
protected
int CifFile::_PrintItemNameInHeader ( std::ostream &  cifo,
const std::string &  itemValue,
unsigned int &  linePos,
const eIdentType  identType = eNONE,
const unsigned int  width = 0 
)
protected
int CifFile::_PrintItemValue ( std::ostream &  cifo,
const std::string &  itemValue,
unsigned int &  linePos,
const eIdentType  identType = eNONE,
const unsigned int  width = 0 
)
protected
void CifFile::_PrintPostItemSeparator ( std::ostream &  cifo,
unsigned int &  linePos,
const bool  ident = false,
const unsigned int  numSpaces = 1 
)
protected
int CifFile::CheckCategories ( Block block,
Block refBlock,
std::ostringstream &  log 
)
void CifFile::CheckCategoryKey ( Block block,
std::ostringstream &  log 
)
int CifFile::CheckItems ( Block block,
Block refBlock,
std::ostringstream &  log 
)
void CifFile::CheckItemsTable ( Block block,
std::ostringstream &  log 
)
int CifFile::DataChecking ( CifFile dicRef,
const std::string &  diagFileName,
const bool  extraChecks = false 
)

Checks a CIF file (all blocks in it) against the dictionary.

Parameters
[in]dicRef- reference to a dictionary file. The check is done against the first block in the dictionary file.
[in]diagFileName- relative or absolute name of the file, where diagnostic information is stored.
[in]extraChecks- optional parameter that indicates whether to perform additional, non-standard, checks. If not specified, those checks are not performed.
Returns
0 - if all checks passed
different than 0 - if checks failed
Precondition
None
Postcondition
None
Exceptions
None
int CifFile::DataChecking ( Block block,
Block refBlock,
std::ostringstream &  buf,
const bool  extraChecks = false 
)

Checks a block of CIF file against the specified reference block.

Parameters
[in]block- reference to a block that is to be checked
[in]refBlock- reference to a reference block against which block is to be checked
[out]diagBuf- diagnostics buffer that holds checking results
[in]extraChecks- optional parameter that indicates whether to perform additional, non-standard, checks. If not specified, those checks are not performed.
Returns
0 - if all checks passed
different than 0 - if checks failed
Precondition
None
Postcondition
None
Exceptions
None
void CifFile::FindCifNullRows ( std::vector< unsigned int > &  nullRowsIndices,
const ISTable isTable 
)

Finds indices of rows that contain all CIF null values. A CIF null value is defined as a "?" or "".

Parameters
[out]nullRowsIndices- vector of null rows indices.
[in]isTable- table reference
Returns
None
Precondition
None
Postcondition
None
Exceptions
None
void CifFile::GetAttributeValue ( std::string &  attribVal,
const std::string &  blockId,
const std::string &  category,
const std::string &  attribute 
)
void CifFile::GetAttributeValueIf ( std::string &  attribVal,
const std::string &  blockId,
const std::string &  category,
const std::string &  attributeA,
const std::string &  attributeB,
const std::string &  valB 
)
void CifFile::GetAttributeValues ( std::vector< std::string > &  strings,
const std::string &  blockId,
const std::string &  category,
const std::string &  attribute 
)
void CifFile::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 
)
bool CifFile::GetEnumCheck ( )

Retrieves enumerations checking option for case-insensitive types.

Parameters
None
Returns
true - if case-sensitive enumeration check is enabled
false - if case-insensitive enumeration check is enabled
Precondition
None
Postcondition
None
Exceptions
None
bool CifFile::GetLooping ( const std::string &  catName)

Retrieves looping option of a category.

Parameters
catName- category name
Returns
- category looping option, as described in SetLooping() method.
Precondition
None
Postcondition
None
Exceptions
None
const std::string& CifFile::GetParsingDiags ( )

Gets parsing diagnostics.

Parameters
None
Returns
- reference to parsing diagnostics
Precondition
None
Postcondition
None
Exceptions
None
unsigned int CifFile::GetQuoting ( )

Retrieves quoting option.

Parameters
None
Returns
eSINGLE - if single quotes are used
eDOUBLE - if double quotes are used
Precondition
None
Postcondition
None
Exceptions
None
const std::string& CifFile::GetSrcFileName ( )

Retrieves source file name.

Parameters
None
Returns
- source file name
Precondition
None
Postcondition
None
Exceptions
None
bool CifFile::GetVerbose ( )
inline

Retrieves logging option.

Parameters
None
Returns
true - if logging is turned on
false - if logging is turned off
Precondition
None
Postcondition
None
Exceptions
None

References _verbose.

bool CifFile::IsAttributeValueDefined ( const std::string &  blockId,
const std::string &  category,
const std::string &  attribute 
)
bool CifFile::IsSmartPrint ( )
inline

Retrieves smart printing option.

Parameters
None
Returns
true - if smart printing is enabled
false - if smart printing is disabled
Precondition
None
Postcondition
None
Exceptions
None

References _smartPrint.

void CifFile::SetAttributeValue ( const std::string &  blockId,
const std::string &  category,
const std::string &  attribute,
const std::string &  value,
const bool  create = false 
)
void CifFile::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 CifFile::SetAttributeValueIfNull ( const std::string &  blockId,
const std::string &  category,
const std::string &  attribute,
const std::string &  value 
)
void CifFile::SetAttributeValues ( const std::string &  blockId,
const std::string &  category,
const std::string &  attribute,
const std::vector< std::string > &  values 
)
void CifFile::SetEnumCheck ( bool  caseSense = false)

Sets enumerations checking option for case-insensitive types.

Parameters
caseSense- case sensitivity of enumeration values check. If false, enumeration values of case-insensitive types will be checked as case-insensitive. If true, enumeration values of case-insensitive types will be checked as case-sensitive.
Returns
None
Precondition
None
Postcondition
None
Exceptions
None
void CifFile::SetLooping ( const std::string &  catName,
bool  looping = false 
)

This method is used in order to control how single row categories are written: in form of a "loop_" construct or as an item-value pair.

Parameters
catName- category name
looping- category looping option. If false and the category is a single row category, that category will not be written with "loop_" construct. Otherwise, if true, single row category will be written with "loop_" construct.
Returns
None
Precondition
None
Postcondition
None
Exceptions
None
void CifFile::SetQuoting ( eQuoting  quoting)

Sets quoting option. This option is used in order to select the type of quoting to be used in the written text file.

Parameters
quoting- type of quoting. If eSINGLE, single quotes are used. If eDOUBLE, double quotes are used.
Returns
None
Precondition
None
Postcondition
None
Exceptions
None
void CifFile::SetSmartPrint ( bool  smartPrint = true)
inline

Sets smart printing option. Smart printing is used to beautify the output of a written text file.

Parameters
smartPrint- smart printing. If false, smart printing is disabled. If true, smart printing is enabled. If not specified, smart printing is enabled.
Returns
None
Precondition
None
Postcondition
None
Exceptions
None

References _smartPrint.

void CifFile::SetSrcFileName ( const std::string &  srcFileName)

Sets file name of a file that was the source of the object data.

Parameters
srcFileName- The name of the source data file.
Returns
None
Precondition
None
Postcondition
None
Exceptions
None
void CifFile::Write ( const std::string &  cifFileName,
const bool  sortTables = false,
const bool  writeEmptyTables = false 
)

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
None
void CifFile::Write ( const std::string &  cifFileName,
const std::vector< std::string > &  tableOrder,
const bool  writeEmptyTables = false 
)

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
None
void CifFile::Write ( std::ostream &  outStream,
const bool  sortTables = false,
const bool  writeEmptyTables = false 
)

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
None
void CifFile::Write ( std::ostream &  cifo,
const std::vector< std::string > &  catOrder,
const bool  writeEmptyTables = false 
)
protected
void CifFile::Write ( std::ostream &  cifo,
std::vector< unsigned int > &  tables,
const bool  writeEmptyTables = false 
)
protected
void CifFile::WriteNmrStar ( const std::string &  nmrStarFileName,
const std::string &  globalBlockName,
const bool  sortTables = false,
const bool  writeEmptyTables = false 
)

Writes the data out to a text file in NMR-STAR format.

Parameters
[in]nmrStarFileName- relative or absolute name of the text file to which the data from CifFile object is to be written to.
[in]globalBlockName- the name of the global NMR-STAR block.
[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
None

Member Data Documentation

std::string CifFile::_beginDataKeyword
protected
std::string CifFile::_beginLoopKeyword
protected
std::string CifFile::_checkingDiags
std::string CifFile::_endDataKeyword
protected
std::string CifFile::_endLoopKeyword
protected
bool CifFile::_enumCaseSense
protected
std::map<std::string, bool> CifFile::_looping
protected
unsigned int CifFile::_maxCifLineLength
protected
std::string CifFile::_nullValue
protected
std::string CifFile::_parsingDiags
std::string CifFile::_quotes
protected
bool CifFile::_smartPrint
protected

Referenced by IsSmartPrint(), and SetSmartPrint().

bool CifFile::_verbose
protected

Referenced by GetVerbose().

const unsigned int CifFile::HEADER_SPACING = 40
staticprotected
const unsigned int CifFile::SMART_PRINT_SPACING = 1
staticprotected
const unsigned int CifFile::STD_CIF_LINE_LENGTH = 80
static
const unsigned int CifFile::STD_PRINT_SPACING = 3
staticprotected

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