interface for file readers More...

#include <Reader.hpp>

Inheritance diagram for pwiz::msdata::Reader:

Classes
struct	Config
	Reader configuration. More...

Public Member Functions
bool	accept (const std::string &filename, const std::string &head) const
	return true iff Reader recognizes the file as one it should handle
virtual std::string	identify (const std::string &filename, const std::string &head) const =0
	return file type iff Reader recognizes the file, else empty;
virtual void	read (const std::string &filename, const std::string &head, MSData &result, int runIndex=0, const Config &config=Config()) const =0
	fill in the MSData structure from the first (or only) sample
virtual void	read (const std::string &filename, const std::string &head, std::vector< MSDataPtr > &results, const Config &config=Config()) const =0
	fill in a vector of MSData structures; provides support for multi-run input files
virtual void	readIds (const std::string &filename, const std::string &head, std::vector< std::string > &dataIds, const Config &config=Config()) const
	fill in a vector of MSData.Id values; provides support for multi-run input files
virtual const char *	getType () const =0
	returns a unique string identifying the reader type
virtual	~Reader ()

Detailed Description

interface for file readers

Definition at line 37 of file Reader.hpp.

Constructor & Destructor Documentation

virtual pwiz::msdata::Reader::~Reader ( )

inlinevirtual

Definition at line 93 of file Reader.hpp.

{}

Member Function Documentation

bool pwiz::msdata::Reader::accept	(	const std::string &	filename,
		const std::string &	head
	)		const

inline

return true iff Reader recognizes the file as one it should handle

that's not to say one it CAN handle, necessarily, as in Thermo on linux, see comment for identify() below

Definition at line 57 of file Reader.hpp.

Referenced by testAccept(), and testRead().

        {
                return (identify(filename,head).length() != 0);
        }

virtual std::string pwiz::msdata::Reader::identify	(	const std::string &	filename,
		const std::string &	head
	)		const

pure virtual

return file type iff Reader recognizes the file, else empty;

note: for formats requiring a 3rd party DLL identify() should return non-empty if it recognized the format, even though reading may fail if the 3rd party DLL isn't actually present Reader may filter based on filename and/or head of the file

Implemented in pwiz::msdata::ReaderList, pwiz::msdata::Reader_mz5, pwiz::msdata::Reader_BTDX, pwiz::msdata::Reader_MSn, pwiz::msdata::Reader_MGF, pwiz::msdata::Reader_mzXML, pwiz::msdata::Reader_ABI, pwiz::msdata::Reader_ABI_T2D, pwiz::msdata::Reader_Waters, pwiz::msdata::Reader_Agilent, pwiz::msdata::Reader_Bruker, pwiz::msdata::Reader_Thermo, and pwiz::msdata::Reader_mzML.

virtual void pwiz::msdata::Reader::read	(	const std::string &	filename,
		const std::string &	head,
		MSData &	result,
		int	runIndex = `0`,
		const Config &	config = `Config()`
	)		const

pure virtual

fill in the MSData structure from the first (or only) sample

Implemented in pwiz::msdata::ReaderList, pwiz::msdata::Reader_mz5, pwiz::msdata::Reader_BTDX, pwiz::msdata::Reader_MSn, pwiz::msdata::Reader_MGF, pwiz::msdata::Reader_mzXML, pwiz::msdata::Reader_ABI, pwiz::msdata::Reader_ABI_T2D, pwiz::msdata::Reader_Waters, pwiz::msdata::Reader_Agilent, pwiz::msdata::Reader_Bruker, pwiz::msdata::Reader_Thermo, and pwiz::msdata::Reader_mzML.

virtual void pwiz::msdata::Reader::read	(	const std::string &	filename,
		const std::string &	head,
		std::vector< MSDataPtr > &	results,
		const Config &	config = `Config()`
	)		const

pure virtual

fill in a vector of MSData structures; provides support for multi-run input files

Implemented in pwiz::msdata::ReaderList, pwiz::msdata::Reader_mz5, pwiz::msdata::Reader_BTDX, pwiz::msdata::Reader_MSn, pwiz::msdata::Reader_MGF, pwiz::msdata::Reader_ABI_T2D, pwiz::msdata::Reader_ABI, pwiz::msdata::Reader_Waters, pwiz::msdata::Reader_mzXML, pwiz::msdata::Reader_Agilent, pwiz::msdata::Reader_Bruker, pwiz::msdata::Reader_Thermo, and pwiz::msdata::Reader_mzML.

virtual void pwiz::msdata::Reader::readIds	(	const std::string &	filename,
		const std::string &	head,
		std::vector< std::string > &	dataIds,
		const Config &	config = `Config()`
	)		const

virtual

fill in a vector of MSData.Id values; provides support for multi-run input files

Reimplemented in pwiz::msdata::ReaderList, and pwiz::msdata::Reader_ABI.

virtual const char* pwiz::msdata::Reader::getType ( ) const

pure virtual

returns a unique string identifying the reader type

Implemented in pwiz::msdata::ReaderList, pwiz::msdata::Reader_mz5, pwiz::msdata::Reader_BTDX, pwiz::msdata::Reader_MSn, pwiz::msdata::Reader_MGF, pwiz::msdata::Reader_ABI, pwiz::msdata::Reader_ABI_T2D, pwiz::msdata::Reader_Waters, pwiz::msdata::Reader_Agilent, pwiz::msdata::Reader_Bruker, pwiz::msdata::Reader_Thermo, pwiz::msdata::Reader_mzXML, and pwiz::msdata::Reader_mzML.

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

/Users/parag/_Research/pwiz/svn/trunk/pwiz/pwiz/data/msdata/Reader.hpp

Classes

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation