XMLConversion Class Reference

A subclass for conversion of XML formats. More...

#include <openbabel/xml.h>

Inheritance diagram for XMLConversion:

List of all members.

Option handling

enum Option_type { INOPTIONS, OUTOPTIONS, GENOPTIONS, ALL }

const char * IsOption (const char *opt, Option_type opttyp=OUTOPTIONS)

const std::map< std::string,
std::string > * GetOptions (Option_type opttyp)

void AddOption (const char *opt, Option_type opttyp=OUTOPTIONS, const char *txt=NULL)

bool RemoveOption (const char *opt, Option_type optype)

void SetOptions (const char *options, Option_type opttyp)

static void RegisterOptionParam (std::string name, OBFormat *pFormat, int numberParams=0, Option_type typ=OUTOPTIONS)

static int GetOptionParams (std::string name, Option_type typ)

Convenience functions

bool Write (OBBase *pOb, std::ostream *pout=NULL)

std::string WriteString (OBBase *pOb, bool trimWhitespace=false)

bool WriteFile (OBBase *pOb, std::string filePath)

void CloseOutFile ()

bool Read (OBBase *pOb, std::istream *pin=NULL)

bool ReadString (OBBase *pOb, std::string input)

bool ReadFile (OBBase *pOb, std::string filePath)

bool OpenInAndOutFiles (std::string infilepath, std::string outfilepath)

void ReportNumberConverted (int count, OBFormat *pFormat=NULL)

static OBFormat * GetDefaultFormat ()

static std::string BatchFileName (std::string &BaseName, std::string &InFile)

static std::string IncrementedFileName (std::string &BaseName, const int Count)

static bool CheckForUnintendedBatch (const std::string &infile, const std::string &outfile)

void InstallStreamFilter ()

Public Types

typedef std::map< std::string,
XMLBaseFormat * > NsMapType

Public Member Functions

XMLConversion (OBConversion *pConv)

~XMLConversion ()

bool SetupReader ()

bool SetupWriter ()

bool ReadXML (XMLBaseFormat *pFormat, OBBase *pOb)

int SkipXML (const char *ctag)

bool IsLast ()

int GetOutputIndex ()

xmlTextReaderPtr GetReader () const

xmlTextWriterPtr GetWriter () const

void OutputToStream ()

void LookForNamespace ()

std::string GetAttribute (const char *attrname)

std::string GetContent ()

bool GetContentInt (int &value)

bool GetContentDouble (double &value)

void CopyOptions (OBConversion *pSourceConv, Option_type typ=ALL)

Parameter get and set

std::istream * GetInStream () const

std::ostream * GetOutStream () const

void SetInStream (std::istream *pIn)

void SetOutStream (std::ostream *pOut)

bool SetInAndOutFormats (const char *inID, const char *outID)

bool SetInAndOutFormats (OBFormat *pIn, OBFormat *pOut)

bool SetInFormat (const char *inID)

bool SetInFormat (OBFormat *pIn)

bool SetOutFormat (const char *outID)

bool SetOutFormat (OBFormat *pOut)

OBFormat * GetInFormat () const

OBFormat * GetOutFormat () const

std::string GetInFilename () const

std::streampos GetInPos () const

size_t GetInLen () const

const char * GetTitle () const

OBConversion * GetAuxConv () const

void SetAuxConv (OBConversion *pConv)

Supported file format

std::vector< std::string > GetSupportedInputFormat ()

std::vector< std::string > GetSupportedOutputFormat ()

Conversion

int Convert (std::istream *is, std::ostream *os)

int Convert ()

int FullConvert (std::vector< std::string > &FileList, std::string &OutputFileName, std::vector< std::string > &OutputFileList)

Conversion loop control

int AddChemObject (OBBase *pOb)

OBBase * GetChemObject ()

bool IsFirstInput ()

void SetFirstInput (bool b=true)

int GetOutputIndex () const

void SetOutputIndex (int indx)

void SetMoreFilesToCome ()

void SetOneObjectOnly (bool b=true)

void SetLast (bool b)

bool IsLastFile ()

Static Public Member Functions

static NsMapType & Namespaces ()

static void RegisterXMLFormat (XMLBaseFormat *pFormat, bool IsDefault=false, const char *uri=NULL)

static XMLConversion * GetDerived (OBConversion *pConv, bool ForReading=true)

static XMLBaseFormat * GetDefaultXMLClass ()

static int ReadStream (void *context, char *buffer, int len)

static int WriteStream (void *context, const char *buffer, int len)

Collection of formats

static int RegisterFormat (const char *ID, OBFormat *pFormat, const char *MIME=NULL)

static OBFormat * FindFormat (const char *ID)

static OBFormat * FormatFromExt (const char *filename)

static OBFormat * FormatFromMIME (const char *MIME)

static bool GetNextFormat (Formatpos &itr, const char *&str, OBFormat *&pFormat)

Information

static const char * Description ()

Public Attributes

bool _SkipNextRead

Protected Types

typedef std::map< std::string,
int > OPAMapType

typedef
FilteringInputStreambuf
< LineEndingExtractor > LErdbuf

Protected Member Functions

bool SetStartAndEnd ()

bool OpenAndSetFormat (bool SetFormat, std::ifstream *is)

Static Protected Member Functions

static OPAMapType & OptionParamArray (Option_type typ)

static int LoadFormatFiles ()

Protected Attributes

std::string InFilename

std::istream * pInStream

std::ostream * pOutStream

OBFormat * pInFormat

OBFormat * pOutFormat

std::map< std::string,
std::string > OptionsArray [3]

int Index

unsigned int StartNumber

unsigned int EndNumber

int Count

bool m_IsFirstInput

bool m_IsLast

bool MoreFilesToCome

bool OneObjectOnly

bool ReadyToInput

bool CheckedForGzip

bool NeedToFreeInStream

bool NeedToFreeOutStream

LErdbuf * pLineEndBuf

OBBase * pOb1

std::streampos wInpos

std::streampos rInpos

size_t wInlen

size_t rInlen

OBConversion * pAuxConv

std::vector< std::string > SupportedInputFormat

std::vector< std::string > SupportedOutputFormat

Static Protected Attributes

static OBFormat * pDefaultFormat

static int FormatFilesLoaded = 0

Detailed Description

A subclass for conversion of XML formats.

An extended OBConversion class which includes a libxml2 reader for use with XML formats. Copies an OBConversion and then extends it with a XML parser. Instances made on the heap are deleted when the original OBConversion object is.

This class is not intended to be used externally -- instead use OBConversion which will find both XML and non-XML OBFormats.

Instead, this subclass also has support for handling specific needs in XML formats. For example, an XML file may include multiple namespaces, and the conversion should call appropriate XMLBaseFormat formats as needed.

Member Typedef Documentation

typedef std::map<std::string, XMLBaseFormat*> NsMapType

typedef std::map<std::string,int> OPAMapType [protected, inherited]

typedef FilteringInputStreambuf< LineEndingExtractor > LErdbuf [protected, inherited]

Member Enumeration Documentation

enum Option_type [inherited]

Three types of options set on the the command line by -a? , -x? , or -?

Enumerator:

INOPTIONS
OUTOPTIONS
GENOPTIONS
ALL

Constructor & Destructor Documentation

XMLConversion ( OBConversion * pConv )

Existing OBConversion instance copied.

~XMLConversion ( )

Frees reader and writer if necessary.

Member Function Documentation

bool SetupReader ( )

opens libxml2 reader

bool SetupWriter ( )

opens libxml2 writer

bool ReadXML	(	XMLBaseFormat *	pFormat,
		OBBase *	pOb
	)

Parses the input xml stream and sends each element to the format's callback routines.

Referenced by XMLMoleculeFormat::ReadMolecule().

int SkipXML ( const char * ctag )

Read and discard XML text up to the next occurrence of the tag e.g."/molecule>" This is left as the current node. Returns 1 on success, 0 if not found, -1 if failed.

Referenced by XMLBaseFormat::SkipObjects().

static NsMapType& Namespaces ( ) [inline, static]

This static function returns a reference to the map Avoids "static initialization order fiasco"

static void RegisterXMLFormat	(	XMLBaseFormat *	pFormat,
		bool	IsDefault = `false`,
		const char *	uri = `NULL`
	)			`[static]`

static XMLConversion* GetDerived	(	OBConversion *	pConv,
		bool	ForReading = `true`
	)			`[static]`

Returns the extended OBConversion class, making it if necessary.

Referenced by XMLMoleculeFormat::ReadMolecule(), and XMLBaseFormat::SkipObjects().

bool IsLast ( ) [inline]

Because OBConversion::Convert is still using the unextended OBConversion object we need to obtain the conversion paramters from it when requested

Reimplemented from OBConversion.

int GetOutputIndex ( ) [inline]

xmlTextReaderPtr GetReader ( ) const [inline]

Referenced by XMLBaseFormat::reader().

xmlTextWriterPtr GetWriter ( ) const [inline]

Referenced by XMLBaseFormat::writer().

void OutputToStream ( ) [inline]

Referenced by XMLBaseFormat::OutputToStream().

static XMLBaseFormat* GetDefaultXMLClass ( ) [inline, static]

void LookForNamespace ( ) [inline]

static int ReadStream	(	void *	context,
		char *	buffer,
		int	len
	)			`[static]`

Static callback functions for xmlReaderForIO().

static int WriteStream	(	void *	context,
		const char *	buffer,
		int	len
	)			`[static]`

std::string GetAttribute ( const char * attrname )

std::string GetContent ( )

Sets value to element content. Returns false if there is no content.

bool GetContentInt ( int & value )

Sets value to element content as an integer. Returns false if there is no content.

bool GetContentDouble ( double & value )

Sets value to element content as an double. Returns false if there is no content.

int RegisterFormat	(	const char *	ID,
		OBFormat *	pFormat,
		const char *	MIME = `NULL`
	)			`[static, inherited]`

Called once by each format class.

Class information on formats is collected by making an instance of the class derived from OBFormat(only one is usually required). RegisterFormat() is called from its constructor.

If the compiled format is stored separately, like in a DLL or shared library, the initialization code makes an instance of the imported OBFormat class.

OBFormat * FindFormat ( const char * ID ) [static, inherited]

Searches registered formats.

Referenced by OBConversion::FormatFromExt(), OBConversion::SetInFormat(), and OBConversion::SetOutFormat().

OBFormat * FormatFromExt ( const char * filename ) [static, inherited]

Searches registered formats for an ID the same as the file extension.

Referenced by OBConversion::OpenAndSetFormat().

OBFormat * FormatFromMIME ( const char * MIME ) [static, inherited]

Searches registered formats for a MIME the same as the chemical MIME type passed.

bool GetNextFormat	(	Formatpos &	itr,
		const char *&	str,
		OBFormat *&	pFormat
	)			`[static, inherited]`

Deprecated!.Repeatedly called to recover available Formats.

const char * Description ( ) [static, inherited]

std::istream* GetInStream ( ) const [inline, inherited]

Referenced by OBMoleculeFormat::DeferMolOutput(), and OBMoleculeFormat::ReadChemObjectImpl().

std::ostream* GetOutStream ( ) const [inline, inherited]

void SetInStream ( std::istream * pIn ) [inline, inherited]

Referenced by OBConversion::FullConvert().

void SetOutStream ( std::ostream * pOut ) [inline, inherited]

Referenced by OBConversion::FullConvert().

bool SetInAndOutFormats	(	const char *	inID,
		const char *	outID
	)			`[inherited]`

Sets the formats from their ids, e g CML.

Sets the formats from their ids, e g CML. If inID is NULL, the input format is left unchanged. Similarly for outID Returns true if both formats have been successfully set at sometime

bool SetInAndOutFormats	(	OBFormat *	pIn,
		OBFormat *	pOut
	)			`[inherited]`

bool SetInFormat ( const char * inID ) [inherited]

Sets the input format from an id e.g. CML.

Referenced by OBMoleculeFormat::ReadNameIndex(), and OBConversion::SetInAndOutFormats().

bool SetInFormat ( OBFormat * pIn ) [inherited]

bool SetOutFormat ( const char * outID ) [inherited]

Sets the output format from an id e.g. CML.

Referenced by OBConversion::SetInAndOutFormats().

bool SetOutFormat ( OBFormat * pOut ) [inherited]

OBFormat* GetInFormat ( ) const [inline, inherited]

OBFormat* GetOutFormat ( ) const [inline, inherited]

Referenced by OBMoleculeFormat::OutputDeferredMols().

std::string GetInFilename ( ) const [inline, inherited]

std::streampos GetInPos ( ) const [inline, inherited]

Get the position in the input stream of the object being read.

size_t GetInLen ( ) const [inline, inherited]

Get the length in the input stream of the object being read.

const char * GetTitle ( ) const [inherited]

Returns:: a default title which is the filename

OBConversion* GetAuxConv ( ) const [inline, inherited]

Extension method: deleted in ~OBConversion().

void SetAuxConv ( OBConversion * pConv ) [inline, inherited]

const char * IsOption	(	const char *	opt,
		Option_type	opttyp = `OUTOPTIONS`
	)			`[inherited]`

Determine whether an option is set.

Returns:: NULL if option not and a pointer to the associated text if it is

Referenced by OBConversion::Convert(), OBConversion::FullConvert(), OBMoleculeFormat::ReadChemObjectImpl(), OBConversion::SetStartAndEnd(), OBConversion::Write(), and OBMoleculeFormat::WriteChemObjectImpl().

const std::map<std::string,std::string>* GetOptions ( Option_type opttyp ) [inline, inherited]

Access the map with option name as key and any associated text as value.

Referenced by OBMoleculeFormat::OutputDeferredMols(), and OBMoleculeFormat::ReadChemObjectImpl().

void AddOption	(	const char *	opt,
		Option_type	opttyp = `OUTOPTIONS`,
		const char *	txt = `NULL`
	)			`[inherited]`

Set an option of specified type, with optional text.

bool RemoveOption	(	const char *	opt,
		Option_type	optype
	)			`[inherited]`

void SetOptions	(	const char *	options,
		Option_type	opttyp
	)			`[inherited]`

Set several single character options of specified type from string like ab"btext"c"ctext".

void RegisterOptionParam	(	std::string	name,
		OBFormat *	pFormat,
		int	numberParams = `0`,
		Option_type	typ = `OUTOPTIONS`
	)			`[static, inherited]`

For example -h takes 0 parameters; -f takes 1. Call in a format constructor.

Referenced by OBConversion::OBConversion(), and OBMoleculeFormat::OBMoleculeFormat().

int GetOptionParams	(	std::string	name,
		Option_type	typ
	)			`[static, inherited]`

Returns:: the number of parameters registered for the option, or 0 if not found

void CopyOptions	(	OBConversion *	pSourceConv,
		Option_type	typ = `ALL`
	)			`[inherited]`

Copies the options (by default of all types) from one OBConversion Object to another.

std::vector< std::string > GetSupportedInputFormat ( ) [inherited]

Returns the list of supported input format

std::vector< std::string > GetSupportedOutputFormat ( ) [inherited]

Returns the list of supported output format

int Convert	(	std::istream *	is,
		std::ostream *	os
	)			`[inherited]`

Conversion for single input and output stream.

int Convert ( ) [inherited]

Conversion with existing streams.

Actions the "convert" interface. Calls the OBFormat class's ReadMolecule() which

makes a new chemical object of its chosen type (e.g. OBMol)
reads an object from the input file
subjects the chemical object to 'transformations' as specified by the Options
calls AddChemObject to add it to a buffer. The previous object is first output via the output Format's WriteMolecule(). During the output process calling IsFirst() and GetIndex() (the number of objects including the current one already output. allows more control, for instance writing <cml> and </cml> tags for multiple molecule outputs only.

AddChemObject does not save the object passed to it if it is NULL (as a result of a DoTransformation()) or if the number of the object is outside the range defined by StartNumber and EndNumber.This means the start and end counts apply to all chemical objects found whether or not they are output.

If ReadMolecule returns false the input conversion loop is exited.

Referenced by OBConversion::Convert(), and OBConversion::FullConvert().

int FullConvert	(	std::vector< std::string > &	FileList,
		std::string &	OutputFileName,
		std::vector< std::string > &	OutputFileList
	)			`[inherited]`

Conversion with multiple input/output files: makes input and output streams, and carries out normal, batch, aggregation, and splitting conversion.

Makes input and output streams, and carries out normal, batch, aggregation, and splitting conversion.

Normal Done if FileList contains a single file name and OutputFileName does not contain a *.

Aggregation Done if FileList has more than one file name and OutputFileName does not contain * . All the chemical objects are converted and sent to the single output file.

Splitting Done if FileList contains a single file name and OutputFileName contains a * . Each chemical object in the input file is converted and sent to a separate file whose name is OutputFileName with the replaced by 1, 2, 3, etc. OutputFileName must have at least one character other than the * before the extension. For example, if OutputFileName is NEW*.smi then the output files are NEW1.smi, NEW2.smi, etc.

Batch Conversion Done if FileList has more than one file name and contains a * . Each input file is converted to an output file whose name is OutputFileName with the * replaced by the inputfile name without its path and extension. So if the input files were inpath/First.cml, inpath/Second.cml and OutputFileName was NEW*.mol, the output files would be NEWFirst.mol, NEWSecond.mol.

If FileList is empty, the input stream that has already been set (usually in the constructor) is used. If OutputFileName is empty, the output stream already set is used.

On exit, OutputFileList contains the names of the output files.

Returns the number of Chemical objects converted.

int AddChemObject ( OBBase * pOb ) [inherited]

Adds to internal array during input.

Called by ReadMolecule() to deliver an object it has read from an input stream. Used in two modes:

When Count is negative it is left negative and the routine is just a store for an OBBase object. The negative value returned tells the calling routine that no more objects are required.
When count is >=0, probably set by Convert(), it acts as a queue of 2: writing the currently stored value before accepting the supplied one. This delay allows output routines to respond differently when the written object is the last. Count is incremented with each call, even if pOb=NULL. Objects are not added to the queue if the count is outside the range StartNumber to EndNumber. There is no upper limit if EndNumber is zero. The return value is Count ((>0) or 0 if WriteChemObject returned false.

Referenced by OBMoleculeFormat::ReadChemObjectImpl().

OBBase * GetChemObject ( ) [inherited]

Retrieve from internal array during output.

Retrieves an object stored by AddChemObject() during output

Referenced by OBMoleculeFormat::WriteChemObjectImpl().

bool IsFirstInput ( ) [inherited]

True if the first input object is being processed.

Referenced by OBMoleculeFormat::DeferMolOutput(), and OBMoleculeFormat::ReadChemObjectImpl().

void SetFirstInput ( bool b = true ) [inherited]

Setwhether or not is the first input.

Referenced by OBConversion::Convert(), and OBConversion::FullConvert().

int GetOutputIndex ( ) const [inherited]

Retrieves number of ChemObjects that have been actually output.

Returns the number of objects which have been output or are currently being output. The outputindex is incremented when an object for output is fetched by GetChemObject(). So the function will return 1 if called from WriteMolecule() during output of the first object.

Referenced by XMLConversion::GetOutputIndex().

void SetOutputIndex ( int indx ) [inherited]

Sets ouput index (maybe to control whether seen as first object).

Referenced by OBConversion::FullConvert(), OBMoleculeFormat::OutputDeferredMols(), and OBMoleculeFormat::WriteChemObjectImpl().

void SetMoreFilesToCome ( ) [inherited]

Used with multiple input files. Off by default.

Referenced by OBConversion::FullConvert().

void SetOneObjectOnly ( bool b = true ) [inherited]

Used with multiple input files. Off by default.

Referenced by OBConversion::FullConvert(), OBMoleculeFormat::OutputDeferredMols(), and OBConversion::Write().

void SetLast ( bool b ) [inline, inherited]

Synonym for SetOneObjectOnly().

bool IsLastFile ( ) [inline, inherited]

True if no more files to be read.

static OBFormat* GetDefaultFormat ( ) [inline, static, inherited]

The default format is set in a single OBFormat class (generally it is OBMol).

bool Write	(	OBBase *	pOb,
		std::ostream *	pout = `NULL`
	)			`[inherited]`

Outputs an object of a class derived from OBBase.

Part of "API" interface. The output stream can be specified and the change is retained in the OBConversion instance

Writes the object pOb but does not delete it afterwards. The output stream is lastingly changed if pos is not NULL Returns true if successful.

Referenced by OBConversion::WriteFile(), and OBConversion::WriteString().

std::string WriteString	(	OBBase *	pOb,
		bool	trimWhitespace = `false`
	)			`[inherited]`

Outputs an object of a class derived from OBBase as a string.

Part of "API" interface. The output stream is temporarily changed to the string and then restored This method is primarily intended for scripting languages without "stream" classes The optional "trimWhitespace" parameter allows trailing whitespace to be removed (e.g., in a SMILES string or InChI, etc.)

Writes the object pOb but does not delete it afterwards. The output stream not changed (since we cannot write to this string later) Returns true if successful.

bool WriteFile	(	OBBase *	pOb,
		std::string	filePath
	)			`[inherited]`

Outputs an object of a class derived from OBBase as a file (with the supplied path).

Part of "API" interface. The output stream is changed to the supplied file and the change is retained in the OBConversion instance. This method is primarily intended for scripting languages without "stream" classes

Writes the object pOb but does not delete it afterwards. The output stream is lastingly changed to point to the file Returns true if successful.

void CloseOutFile ( ) [inherited]

Manually closes and deletes the output stream The file is closed anyway when in the OBConversion destructor or when WriteFile is called again.

Since:: version 2.1

bool Read	(	OBBase *	pOb,
		std::istream *	pin = `NULL`
	)			`[inherited]`

Reads an object of a class derived from OBBase into pOb.

Part of "API" interface. The input stream can be specified and the change is retained in the OBConversion instance

Returns:: false and pOb=NULL on error

Referenced by OBConversion::ReadFile(), OBMoleculeFormat::ReadNameIndex(), and OBConversion::ReadString().

bool ReadString	(	OBBase *	pOb,
		std::string	input
	)			`[inherited]`

Reads an object of a class derived from OBBase into pOb from the supplied string.

Part of "API" interface. The input stream can be specified and the change is retained in the OBConversion instance

Returns:: NULL on error Part of "API" interface.
false and pOb=NULL on error This method is primarily intended for scripting languages without "stream" classes

bool ReadFile	(	OBBase *	pOb,
		std::string	filePath
	)			`[inherited]`

Reads an object of a class derived from OBBase into pOb from the file specified.

Part of "API" interface. The output stream is changed to the supplied file and the change is retained in the OBConversion instance.

Returns:: false and pOb=NULL on error This method is primarily intended for scripting languages without "stream" classes

bool OpenInAndOutFiles	(	std::string	infilepath,
		std::string	outfilepath
	)			`[inherited]`

Part of the "Convert" interface Open the files and update the streams in the OBConversion object. This method is primarily intended for scripting languages without "stream" classes and will usually followed by a call to Convert()

Returns:: false if unsucessful.

void ReportNumberConverted	(	int	count,
		OBFormat *	pFormat = `NULL`
	)			`[inherited]`

Sends a message like "2 molecules converted" to clog The type of object is taken from the TargetClassDescription of the specified class (or the output format if not specified)and is appropriately singular or plural.

string BatchFileName	(	std::string &	BaseName,
		std::string &	InFile
	)			`[static, protected, inherited]`

Replaces * in BaseName by InFile without extension and path.

Referenced by OBConversion::FullConvert().

string IncrementedFileName	(	std::string &	BaseName,
		const int	Count
	)			`[static, protected, inherited]`

Replaces * in BaseName by Count.

Referenced by OBConversion::FullConvert().

bool CheckForUnintendedBatch	(	const std::string &	infile,
		const std::string &	outfile
	)			`[static, protected, inherited]`

Checks for misunderstandings when using the -m option.

Referenced by OBConversion::FullConvert().

void InstallStreamFilter ( ) [protected, inherited]

Adds a filtering rdbuffer to handle line endings if not already installed and not a binary or xml format.

Referenced by OBConversion::Convert(), and OBConversion::Read().

bool SetStartAndEnd ( ) [protected, inherited]

Referenced by OBConversion::Convert().

OBConversion::OPAMapType & OptionParamArray ( Option_type typ ) [static, protected, inherited]

Referenced by OBConversion::GetOptionParams(), and OBConversion::RegisterOptionParam().

int LoadFormatFiles ( ) [static, protected, inherited]

Referenced by OBConversion::OBConversion().

bool OpenAndSetFormat	(	bool	SetFormat,
		std::ifstream *	is
	)			`[protected, inherited]`

Referenced by OBConversion::FullConvert().

Member Data Documentation

bool _SkipNextRead

std::string InFilename [protected, inherited]

Referenced by OBConversion::FullConvert(), OBConversion::GetTitle(), OBConversion::OBConversion(), OBConversion::OpenAndSetFormat(), OBConversion::OpenInAndOutFiles(), and OBConversion::ReadFile().

std::istream* pInStream [protected, inherited]

Referenced by OBConversion::AddChemObject(), OBConversion::Convert(), OBConversion::InstallStreamFilter(), OBConversion::OBConversion(), OBConversion::OpenInAndOutFiles(), OBConversion::Read(), OBConversion::ReadFile(), OBConversion::ReadString(), and OBConversion::~OBConversion().

std::ostream* pOutStream [protected, inherited]

Referenced by OBConversion::CloseOutFile(), OBConversion::Convert(), OBConversion::OBConversion(), OBConversion::OpenInAndOutFiles(), OBConversion::Write(), OBConversion::WriteFile(), OBConversion::WriteString(), and OBConversion::~OBConversion().

OBFormat* pDefaultFormat [static, protected, inherited]

OBFormat* pInFormat [protected, inherited]

Referenced by OBConversion::Convert(), OBConversion::FullConvert(), OBConversion::InstallStreamFilter(), OBConversion::OBConversion(), OBConversion::OpenAndSetFormat(), OBConversion::Read(), OBConversion::ReadFile(), OBConversion::SetInFormat(), and OBConversion::SetStartAndEnd().

OBFormat* pOutFormat [protected, inherited]

Referenced by OBConversion::AddChemObject(), OBConversion::Convert(), OBConversion::FullConvert(), OBConversion::OBConversion(), OBConversion::ReportNumberConverted(), OBConversion::SetOutFormat(), OBConversion::Write(), OBConversion::WriteFile(), and OBConversion::WriteString().

std::map<std::string,std::string> OptionsArray[3] [protected, inherited]

Referenced by OBConversion::AddOption(), OBConversion::CopyOptions(), OBConversion::IsOption(), OBConversion::OBConversion(), OBConversion::RemoveOption(), and OBConversion::SetOptions().

int Index [protected, inherited]

Referenced by OBConversion::AddChemObject(), OBConversion::Convert(), OBConversion::GetChemObject(), OBConversion::GetOutputIndex(), OBConversion::OBConversion(), and OBConversion::SetOutputIndex().

unsigned int StartNumber [protected, inherited]

Referenced by OBConversion::AddChemObject(), OBConversion::Convert(), OBConversion::OBConversion(), and OBConversion::SetStartAndEnd().

unsigned int EndNumber [protected, inherited]

Referenced by OBConversion::AddChemObject(), OBConversion::Convert(), OBConversion::OBConversion(), and OBConversion::SetStartAndEnd().

int Count [protected, inherited]

Referenced by OBConversion::AddChemObject(), OBConversion::Convert(), OBConversion::FullConvert(), OBConversion::OBConversion(), and OBConversion::SetStartAndEnd().

bool m_IsFirstInput [protected, inherited]

Referenced by OBConversion::IsFirstInput(), OBConversion::OBConversion(), and OBConversion::SetFirstInput().

bool m_IsLast [protected, inherited]

Referenced by OBConversion::Convert(), OBConversion::IsLast(), OBConversion::OBConversion(), and OBConversion::SetOneObjectOnly().

bool MoreFilesToCome [protected, inherited]

Referenced by OBConversion::Convert(), OBConversion::OBConversion(), and OBConversion::SetMoreFilesToCome().

bool OneObjectOnly [protected, inherited]

Referenced by OBConversion::Convert(), OBConversion::OBConversion(), and OBConversion::SetOneObjectOnly().

bool ReadyToInput [protected, inherited]

Referenced by OBConversion::AddChemObject(), OBConversion::Convert(), and OBConversion::OBConversion().

bool CheckedForGzip [protected, inherited]

input stream is gzip-encoded

Referenced by OBConversion::Convert(), OBConversion::FullConvert(), OBConversion::OBConversion(), and OBConversion::Read().

bool NeedToFreeInStream [protected, inherited]

Referenced by OBConversion::OBConversion(), OBConversion::OpenInAndOutFiles(), OBConversion::ReadFile(), OBConversion::ReadString(), and OBConversion::~OBConversion().

bool NeedToFreeOutStream [protected, inherited]

Referenced by OBConversion::CloseOutFile(), OBConversion::OBConversion(), OBConversion::OpenInAndOutFiles(), OBConversion::WriteFile(), and OBConversion::~OBConversion().

LErdbuf* pLineEndBuf [protected, inherited]

Referenced by OBConversion::InstallStreamFilter(), and OBConversion::OBConversion().

int FormatFilesLoaded = 0 [static, protected, inherited]

Referenced by OBConversion::OBConversion().

OBBase* pOb1 [protected, inherited]

Referenced by OBConversion::AddChemObject(), OBConversion::Convert(), OBConversion::GetChemObject(), and OBConversion::OBConversion().

std::streampos wInpos [protected, inherited]

position in the input stream of the object being written

Referenced by OBConversion::AddChemObject(), and OBConversion::OBConversion().

std::streampos rInpos [protected, inherited]

position in the input stream of the object being read

Referenced by OBConversion::AddChemObject(), OBConversion::Convert(), and OBConversion::OBConversion().

size_t wInlen [protected, inherited]

length in the input stream of the object being written

Referenced by OBConversion::AddChemObject(), OBConversion::Convert(), and OBConversion::OBConversion().

size_t rInlen [protected, inherited]

length in the input stream of the object being read

Referenced by OBConversion::AddChemObject(), and OBConversion::OBConversion().

OBConversion* pAuxConv [protected, inherited]

Way to extend OBConversion.

Referenced by OBConversion::OBConversion(), and OBConversion::~OBConversion().

std::vector<std::string> SupportedInputFormat [protected, inherited]

list of supported input format

std::vector<std::string> SupportedOutputFormat [protected, inherited]

list of supported output format

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

xml.h


Option handling
enum	Option_type { INOPTIONS, OUTOPTIONS, GENOPTIONS, ALL }
const char *	IsOption (const char *opt, Option_type opttyp=OUTOPTIONS)
const std::map< std::string, std::string > *	GetOptions (Option_type opttyp)
void	AddOption (const char opt, Option_type opttyp=OUTOPTIONS, const char txt=NULL)
bool	RemoveOption (const char *opt, Option_type optype)
void	SetOptions (const char *options, Option_type opttyp)
static void	RegisterOptionParam (std::string name, OBFormat *pFormat, int numberParams=0, Option_type typ=OUTOPTIONS)
static int	GetOptionParams (std::string name, Option_type typ)
Convenience functions
bool	Write (OBBase pOb, std::ostream pout=NULL)
std::string	WriteString (OBBase *pOb, bool trimWhitespace=false)
bool	WriteFile (OBBase *pOb, std::string filePath)
void	CloseOutFile ()
bool	Read (OBBase pOb, std::istream pin=NULL)
bool	ReadString (OBBase *pOb, std::string input)
bool	ReadFile (OBBase *pOb, std::string filePath)
bool	OpenInAndOutFiles (std::string infilepath, std::string outfilepath)
void	ReportNumberConverted (int count, OBFormat *pFormat=NULL)
static OBFormat *	GetDefaultFormat ()
static std::string	BatchFileName (std::string &BaseName, std::string &InFile)
static std::string	IncrementedFileName (std::string &BaseName, const int Count)
static bool	CheckForUnintendedBatch (const std::string &infile, const std::string &outfile)
void	InstallStreamFilter ()
Public Types
typedef std::map< std::string, XMLBaseFormat * >	NsMapType
Public Member Functions
	XMLConversion (OBConversion *pConv)
	~XMLConversion ()
bool	SetupReader ()
bool	SetupWriter ()
bool	ReadXML (XMLBaseFormat pFormat, OBBase pOb)
int	SkipXML (const char *ctag)
bool	IsLast ()
int	GetOutputIndex ()
xmlTextReaderPtr	GetReader () const
xmlTextWriterPtr	GetWriter () const
void	OutputToStream ()
void	LookForNamespace ()
std::string	GetAttribute (const char *attrname)
std::string	GetContent ()
bool	GetContentInt (int &value)
bool	GetContentDouble (double &value)
void	CopyOptions (OBConversion *pSourceConv, Option_type typ=ALL)
Parameter get and set
std::istream *	GetInStream () const
std::ostream *	GetOutStream () const
void	SetInStream (std::istream *pIn)
void	SetOutStream (std::ostream *pOut)
bool	SetInAndOutFormats (const char inID, const char outID)
bool	SetInAndOutFormats (OBFormat pIn, OBFormat pOut)
bool	SetInFormat (const char *inID)
bool	SetInFormat (OBFormat *pIn)
bool	SetOutFormat (const char *outID)
bool	SetOutFormat (OBFormat *pOut)
OBFormat *	GetInFormat () const
OBFormat *	GetOutFormat () const
std::string	GetInFilename () const
std::streampos	GetInPos () const
size_t	GetInLen () const
const char *	GetTitle () const
OBConversion *	GetAuxConv () const
void	SetAuxConv (OBConversion *pConv)
Supported file format
std::vector< std::string >	GetSupportedInputFormat ()
std::vector< std::string >	GetSupportedOutputFormat ()
Conversion
int	Convert (std::istream is, std::ostream os)
int	Convert ()
int	FullConvert (std::vector< std::string > &FileList, std::string &OutputFileName, std::vector< std::string > &OutputFileList)
Conversion loop control
int	AddChemObject (OBBase *pOb)
OBBase *	GetChemObject ()
bool	IsFirstInput ()
void	SetFirstInput (bool b=true)
int	GetOutputIndex () const
void	SetOutputIndex (int indx)
void	SetMoreFilesToCome ()
void	SetOneObjectOnly (bool b=true)
void	SetLast (bool b)
bool	IsLastFile ()
Static Public Member Functions
static NsMapType &	Namespaces ()
static void	RegisterXMLFormat (XMLBaseFormat pFormat, bool IsDefault=false, const char uri=NULL)
static XMLConversion *	GetDerived (OBConversion *pConv, bool ForReading=true)
static XMLBaseFormat *	GetDefaultXMLClass ()
static int	ReadStream (void context, char buffer, int len)
static int	WriteStream (void context, const char buffer, int len)
Collection of formats
static int	RegisterFormat (const char ID, OBFormat pFormat, const char *MIME=NULL)
static OBFormat *	FindFormat (const char *ID)
static OBFormat *	FormatFromExt (const char *filename)
static OBFormat *	FormatFromMIME (const char *MIME)
static bool	GetNextFormat (Formatpos &itr, const char &str, OBFormat &pFormat)
Information
static const char *	Description ()
Public Attributes
bool	_SkipNextRead
Protected Types
typedef std::map< std::string, int >	OPAMapType
typedef FilteringInputStreambuf < LineEndingExtractor >	LErdbuf
Protected Member Functions
bool	SetStartAndEnd ()
bool	OpenAndSetFormat (bool SetFormat, std::ifstream *is)
Static Protected Member Functions
static OPAMapType &	OptionParamArray (Option_type typ)
static int	LoadFormatFiles ()
Protected Attributes
std::string	InFilename
std::istream *	pInStream
std::ostream *	pOutStream
OBFormat *	pInFormat
OBFormat *	pOutFormat
std::map< std::string, std::string >	OptionsArray [3]
int	Index
unsigned int	StartNumber
unsigned int	EndNumber
int	Count
bool	m_IsFirstInput
bool	m_IsLast
bool	MoreFilesToCome
bool	OneObjectOnly
bool	ReadyToInput
bool	CheckedForGzip
bool	NeedToFreeInStream
bool	NeedToFreeOutStream
LErdbuf *	pLineEndBuf
OBBase *	pOb1
std::streampos	wInpos
std::streampos	rInpos
size_t	wInlen
size_t	rInlen
OBConversion *	pAuxConv
std::vector< std::string >	SupportedInputFormat
std::vector< std::string >	SupportedOutputFormat
Static Protected Attributes
static OBFormat *	pDefaultFormat
static int	FormatFilesLoaded = 0