Search Toolkit Book for CGeneInfoFileReader

#include <objtools/blast/gene_info_reader/gene_info_reader.hpp>

Inheritance diagram for CGeneInfoFileReader:

Collaboration diagram for CGeneInfoFileReader:

Public Member Functions
	CGeneInfoFileReader (const string &strGi2GeneFile, const string &strGene2OffsetFile, const string &strGi2OffsetFile, const string &strAllGeneDataFile, const string &strGene2GiFile, bool bGiToOffsetLookup=true)
	Construct using direct paths. More...

	CGeneInfoFileReader (bool bGiToOffsetLookup=true)
	Construct using paths read from an environment variable. More...

virtual	~CGeneInfoFileReader ()
	Destructor. More...

virtual bool	GetGeneIdsForGi (TGi gi, TGeneIdList &geneIdList)
	GetGeneIdsForGi implementation, see IGeneInfoInput. More...

virtual bool	GetRNAGisForGeneId (int geneId, TGiList &giList)
	GetRNAGisForGeneId implementation, see IGeneInfoInput. More...

virtual bool	GetProteinGisForGeneId (int geneId, TGiList &giList)
	GetProteinGisForGeneId implementation, see IGeneInfoInput. More...

virtual bool	GetGenomicGisForGeneId (int geneId, TGiList &giList)
	GetGenomicGisForGeneId implementation, see IGeneInfoInput. More...

virtual bool	GetGeneInfoForGi (TGi gi, TGeneInfoList &infoList)
	GetGeneInfoForGi implementation, see IGeneInfoInput. More...

virtual bool	GetGeneInfoForId (int geneId, TGeneInfoList &infoList)
	GetGeneInfoForId implementation, see IGeneInfoInput. More...

Public Member Functions inherited from IGeneInfoInput
virtual	~IGeneInfoInput ()
	Destructor. More...

Private Member Functions
void	x_MapMemFiles ()
	Memory-map all the files. More...

void	x_UnmapMemFiles ()
	Unmap all the memory-mapped files. More...

bool	x_GiToGeneId (TGi gi, list< int > &listGeneIds)
	Fill the Gene ID list given a Gi. More...

bool	x_GeneIdToOffset (int geneId, int &nOffset)
	Set the offset value given a Gene ID. More...

bool	x_GiToOffset (TGi gi, list< int > &listOffsets)
	Set the offset value given a Gi. More...

bool	x_GeneIdToGi (int geneId, int iGiField, list< TGi > &listGis)
	Fill the Gi list given a Gene ID, and the Gi field index, which represents the Gi type to be read from the file. More...

bool	x_OffsetToInfo (int nOffset, CRef< CGeneInfo > &info)
	Read Gene data at the given offset and create the info object. More...

Private Attributes
string	m_strGi2GeneFile
	Path to the Gi to Gene ID file. More...

string	m_strGene2OffsetFile
	Path to the Gene ID to Offset file. More...

string	m_strGi2OffsetFile
	Path to the Gi to Offset file. More...

string	m_strGene2GiFile
	Path to the Gene ID to Gi file. More...

string	m_strAllGeneDataFile
	Path to the file containing all the Gene data. More...

bool	m_bGiToOffsetLookup
	Perform Gi to Offset lookups directly. More...

unique_ptr< CMemoryFile >	m_memGi2GeneFile
	Memory-mapped Gi to Gene ID file. More...

unique_ptr< CMemoryFile >	m_memGene2OffsetFile
	Memory-mapped Gene ID to Offset file. More...

unique_ptr< CMemoryFile >	m_memGi2OffsetFile
	Memory-mapped Gi to Offset file. More...

unique_ptr< CMemoryFile >	m_memGene2GiFile
	Memory-mapped Gene ID to Gi file. More...

CNcbiIfstream	m_inAllData
	Input stream for the Gene data file. More...

TGeneIdToGeneInfoMap	m_mapIdToInfo
	Cached map of looked up Gene Info objects. More...

Additional Inherited Members
Public Types inherited from IGeneInfoInput
typedef list< TGi >	TGiList
	List of Gis. More...

typedef list< int >	TGeneIdList
	List of Gene IDs. More...

typedef map< int, CRef< CGeneInfo > >	TGeneIdToGeneInfoMap
	Gene ID to Gene Information map. More...

typedef vector< CRef< CGeneInfo > >	TGeneInfoList
	List of Gene Information objects. More...

Static Public Member Functions inherited from CGeneFileUtils
static bool	CheckDirExistence (const string &strDir)
	Check if a directory exists, given its name. More...

static bool	CheckExistence (const string &strFile)
	Check if a file exists, given its name. More...

static Int8	GetLength (const string &strFile)
	Get the length of a file, given its name. More...

static bool	OpenTextInputFile (const string &strFileName, CNcbiIfstream &in)
	Open the given text file for reading. More...

static bool	OpenBinaryInputFile (const string &strFileName, CNcbiIfstream &in)
	Open the given binary file for reading. More...

static bool	OpenTextOutputFile (const string &strFileName, CNcbiOfstream &out)
	Open the given text file for writing. More...

static bool	OpenBinaryOutputFile (const string &strFileName, CNcbiOfstream &out)
	Open the given binary file for writing. More...

static void	WriteRecord (CNcbiOfstream &out, STwoIntRecord &record)
	Write a pair of integers to the file. More...

static void	ReadRecord (CNcbiIfstream &in, STwoIntRecord &record)
	Read a pair of integers from the file. More...

template<int k_nFields>
static void	WriteRecord (CNcbiOfstream &out, SMultiIntRecord< k_nFields > &record)
	Write an n-tuple of integers to the file. More...

template<int k_nFields>
static void	ReadRecord (CNcbiIfstream &in, SMultiIntRecord< k_nFields > &record)
	Read an n-tuple of integers from the file. More...

static void	WriteGeneInfo (CNcbiOfstream &out, CRef< CGeneInfo > info, int &nCurrentOffset)
	Write a Gene info object to the file. More...

static void	ReadGeneInfo (CNcbiIfstream &in, int nOffset, CRef< CGeneInfo > &info)
	Read a Gene info object from the file. More...

Detailed Description

CGeneInfoFileReader.

Class implementing the IGeneInfoInput interface using binary files.

CGeneInfoFileReader reads and memory-maps sorted binary files for fast Gi to Gene ID, Gene ID to Gene Info, Gi to Gene Info, and Gene ID to Gi conversions. The Gene Info lookup is represented by two files, one contains (Gi, Offset) or (Gene ID, Offset) pairs, the other one contains all the Gene data. The lookup is performed in two steps: first, the offset to the Gene data is obtained, then the Gene data line is read, parsed, and the corresponding CGeneInfo object is constructed. The paths to the pre-computed and sorted files are either provided directly to the constructor, or the class attempts to read them from a path stored in an environment variable (the preferred approach).

Definition at line 85 of file gene_info_reader.hpp.

Constructor & Destructor Documentation

◆ CGeneInfoFileReader() [1/2]

CGeneInfoFileReader::CGeneInfoFileReader	(	const string &	strGi2GeneFile,
		const string &	strGene2OffsetFile,
		const string &	strGi2OffsetFile,
		const string &	strAllGeneDataFile,
		const string &	strGene2GiFile,
		bool	bGiToOffsetLookup = `true`
	)

Construct using direct paths.

This version of the constructor takes the paths to the pre-computed binary files and attempts to open and map the files.

Parameters

strGi2GeneFile	Path to the Gi to Gene ID file
strGene2OffsetFile	Path to the Gene ID to Offset file.
strGi2OffsetFile	Path to the Gi to Offset file.
strAllGeneDataFile	Path to the Gene data file.
strGene2GiFile	Path to the Gene ID to Gi file.
bGiToOffsetLookup	Perform Gi to Offset lookups directly.

◆ CGeneInfoFileReader() [2/2]

CGeneInfoFileReader::CGeneInfoFileReader ( bool bGiToOffsetLookup = true )

Construct using paths read from an environment variable.

This version of the constructor reads the paths to the pre-computed binary files from an environment variable and attempts to open and map the files.

Parameters

bGiToOffsetLookup Perform Gi to Offset lookups directly.

◆ ~CGeneInfoFileReader()

virtual CGeneInfoFileReader::~CGeneInfoFileReader ( )

virtual

Destructor.

Member Function Documentation

◆ GetGeneIdsForGi()

virtual bool CGeneInfoFileReader::GetGeneIdsForGi	(	TGi	gi,
		TGeneIdList &	geneIdList
	)

virtual

GetGeneIdsForGi implementation, see IGeneInfoInput.

Implements IGeneInfoInput.

◆ GetGeneInfoForGi()

virtual bool CGeneInfoFileReader::GetGeneInfoForGi	(	TGi	gi,
		TGeneInfoList &	infoList
	)

virtual

GetGeneInfoForGi implementation, see IGeneInfoInput.

Implements IGeneInfoInput.

◆ GetGeneInfoForId()

virtual bool CGeneInfoFileReader::GetGeneInfoForId	(	int	geneId,
		TGeneInfoList &	infoList
	)

virtual

GetGeneInfoForId implementation, see IGeneInfoInput.

Implements IGeneInfoInput.

◆ GetGenomicGisForGeneId()

virtual bool CGeneInfoFileReader::GetGenomicGisForGeneId	(	int	geneId,
		TGiList &	giList
	)

virtual

GetGenomicGisForGeneId implementation, see IGeneInfoInput.

Implements IGeneInfoInput.

◆ GetProteinGisForGeneId()

virtual bool CGeneInfoFileReader::GetProteinGisForGeneId	(	int	geneId,
		TGiList &	giList
	)

virtual

GetProteinGisForGeneId implementation, see IGeneInfoInput.

Implements IGeneInfoInput.

◆ GetRNAGisForGeneId()

virtual bool CGeneInfoFileReader::GetRNAGisForGeneId	(	int	geneId,
		TGiList &	giList
	)

virtual

GetRNAGisForGeneId implementation, see IGeneInfoInput.

Implements IGeneInfoInput.

◆ x_GeneIdToGi()

bool CGeneInfoFileReader::x_GeneIdToGi	(	int	geneId,
		int	iGiField,
		list< TGi > &	listGis
	)

private

Fill the Gi list given a Gene ID, and the Gi field index, which represents the Gi type to be read from the file.

◆ x_GeneIdToOffset()

bool CGeneInfoFileReader::x_GeneIdToOffset	(	int	geneId,
		int &	nOffset
	)

private

Set the offset value given a Gene ID.

◆ x_GiToGeneId()

bool CGeneInfoFileReader::x_GiToGeneId	(	TGi	gi,
		list< int > &	listGeneIds
	)

private

Fill the Gene ID list given a Gi.

◆ x_GiToOffset()

bool CGeneInfoFileReader::x_GiToOffset	(	TGi	gi,
		list< int > &	listOffsets
	)

private

Set the offset value given a Gi.

◆ x_MapMemFiles()

void CGeneInfoFileReader::x_MapMemFiles ( )

private

Memory-map all the files.

◆ x_OffsetToInfo()

bool CGeneInfoFileReader::x_OffsetToInfo	(	int	nOffset,
		CRef< CGeneInfo > &	info
	)

private

Read Gene data at the given offset and create the info object.

◆ x_UnmapMemFiles()

void CGeneInfoFileReader::x_UnmapMemFiles ( )

private

Unmap all the memory-mapped files.

Member Data Documentation

◆ m_bGiToOffsetLookup

bool CGeneInfoFileReader::m_bGiToOffsetLookup

private

Perform Gi to Offset lookups directly.

Definition at line 105 of file gene_info_reader.hpp.

◆ m_inAllData

CNcbiIfstream CGeneInfoFileReader::m_inAllData

private

Input stream for the Gene data file.

Definition at line 120 of file gene_info_reader.hpp.

◆ m_mapIdToInfo

TGeneIdToGeneInfoMap CGeneInfoFileReader::m_mapIdToInfo

private

Cached map of looked up Gene Info objects.

Definition at line 123 of file gene_info_reader.hpp.

◆ m_memGene2GiFile

unique_ptr<CMemoryFile> CGeneInfoFileReader::m_memGene2GiFile

private

Memory-mapped Gene ID to Gi file.

Definition at line 117 of file gene_info_reader.hpp.

◆ m_memGene2OffsetFile

unique_ptr<CMemoryFile> CGeneInfoFileReader::m_memGene2OffsetFile

private

Memory-mapped Gene ID to Offset file.

Definition at line 111 of file gene_info_reader.hpp.

◆ m_memGi2GeneFile

unique_ptr<CMemoryFile> CGeneInfoFileReader::m_memGi2GeneFile

private

Memory-mapped Gi to Gene ID file.

Definition at line 108 of file gene_info_reader.hpp.

◆ m_memGi2OffsetFile

unique_ptr<CMemoryFile> CGeneInfoFileReader::m_memGi2OffsetFile

private

Memory-mapped Gi to Offset file.

Definition at line 114 of file gene_info_reader.hpp.

◆ m_strAllGeneDataFile

string CGeneInfoFileReader::m_strAllGeneDataFile

private

Path to the file containing all the Gene data.

Definition at line 102 of file gene_info_reader.hpp.

◆ m_strGene2GiFile

string CGeneInfoFileReader::m_strGene2GiFile

private

Path to the Gene ID to Gi file.

Definition at line 99 of file gene_info_reader.hpp.

◆ m_strGene2OffsetFile

string CGeneInfoFileReader::m_strGene2OffsetFile

private

Path to the Gene ID to Offset file.

Definition at line 93 of file gene_info_reader.hpp.

◆ m_strGi2GeneFile

string CGeneInfoFileReader::m_strGi2GeneFile

private

Path to the Gi to Gene ID file.

Definition at line 90 of file gene_info_reader.hpp.

◆ m_strGi2OffsetFile

string CGeneInfoFileReader::m_strGi2OffsetFile

private

Path to the Gi to Offset file.

Definition at line 96 of file gene_info_reader.hpp.

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

include/objtools/blast/gene_info_reader/gene_info_reader.hpp

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CGeneInfoFileReader() [1/2]

◆ CGeneInfoFileReader() [2/2]

◆ ~CGeneInfoFileReader()

Member Function Documentation

◆ GetGeneIdsForGi()

◆ GetGeneInfoForGi()

◆ GetGeneInfoForId()

◆ GetGenomicGisForGeneId()

◆ GetProteinGisForGeneId()

◆ GetRNAGisForGeneId()

◆ x_GeneIdToGi()

◆ x_GeneIdToOffset()

◆ x_GiToGeneId()

◆ x_GiToOffset()

◆ x_MapMemFiles()

◆ x_OffsetToInfo()

◆ x_UnmapMemFiles()

Member Data Documentation

◆ m_bGiToOffsetLookup

◆ m_inAllData

◆ m_mapIdToInfo

◆ m_memGene2GiFile

◆ m_memGene2OffsetFile

◆ m_memGi2GeneFile

◆ m_memGi2OffsetFile

◆ m_strAllGeneDataFile

◆ m_strGene2GiFile

◆ m_strGene2OffsetFile

◆ m_strGi2GeneFile

◆ m_strGi2OffsetFile