ms_unigene_entry Class Reference

This class encapsulates a single entry from a unigene file. More...

#include <ms_unigene.hpp>

Public Member Functions
	ms_unigene_entry (const std::string &id, const std::string &title, const std::string &gene, const std::string &cytoBand, const std::string &locusLink, const std::string &express, const long chromosome, const int numAccessions, const OFFSET64_T fileOffset)
	This constructor should only be called from within the library.
	ms_unigene_entry (FILE *f, ms_unigene &unigene)
	This constructor should only be called from within the library.
	~ms_unigene_entry ()
	Destructor.
long	getChromosome () const
	Return the chromosome that contains the unignene entry.
std::string	getCytoBand () const
	Return the CYTOBAND - e.g. 4q21-q23.
std::string	getExpress () const
	Return the EXPRESS entry. Can be very long - 5000 bytes.
OFFSET64_T	getFileOffset () const
	Return the offset into the unigene data file for this entry.
std::string	getGene () const
	Return the gene name for this entry - e.g. "ADH1B".
std::string	getID () const
	Return the 'ID' of this entry - e.g. Hs.4.
std::string	getLocusLink () const
	Return the LocusLink - e.g. 125.
int	getNumAccessions () const
	Return the number of accessions (gi numbers or EMBL accessions) that comprise this entry.
std::string	getTitle () const
	Return the 'title' of this entry - e.g. "alcohol dehydrogenase...".

Detailed Description

This class encapsulates a single entry from a unigene file.

A number of objects of this class will be created when a ms_unigene object is created.

Constructor & Destructor Documentation

ms_unigene_entry() [1/2]

ms_unigene_entry	(	FILE *	f,
		ms_unigene &	unigene
	)

This constructor should only be called from within the library.

Reads lines in the file up to the next // and fills the object.

If the id_ value is empty, (use getID()) or the number of accessions (use getNumAccessions()) then the object has not been initialised correcty

Parameters

f	is a file pointer returned by the 'C' fopen() function
unigene	is the object that stores all the accession -> id mappings.

ms_unigene_entry() [2/2]

ms_unigene_entry	(	const std::string &	id,
		const std::string &	title,
		const std::string &	gene,
		const std::string &	cytoBand,
		const std::string &	locusLink,
		const std::string &	express,
		const long	chromosome,
		const int	numAccessions,
		const OFFSET64_T	fileOffset
	)

This constructor should only be called from within the library.

Parameters

id	is the unigene id as returned by the getID() function.
title	is the unigene title as returned by the getTitle() function.
gene	is the gene name as returned by the getGene() function.
cytoBand	is the CYTOBAND as returned by the getCytoBand() function.
locusLink	is the LocusLink as returned by the getLocusLink() function.
express	is EXPRESS entry as returned by the getExpress() function.
chromosome	is the chromosome that contains the unignene entry as returned by the getChromosome() function.
numAccessions	is the number of accessions that comprise this unigene entry.
fileOffset	is the byte offset into the .data file for this unigene entry.

Member Function Documentation

getChromosome()

long getChromosome ( ) const

inline

Return the chromosome that contains the unignene entry.

Returns

the chromosome number

getCytoBand()

std::string getCytoBand ( ) const

inline

Return the CYTOBAND - e.g. 4q21-q23.

Returns

the CYTOBAND

getExpress()

std::string getExpress ( ) const

inline

Return the EXPRESS entry. Can be very long - 5000 bytes.

For example, can be of the form:

adipose tissue| blood| bone marrow| brain| connective tissue| dorsal

Returns

the express entry string.

getFileOffset()

OFFSET64_T getFileOffset ( ) const

inline

Return the offset into the unigene data file for this entry.

This function returns quickly if an index file has been created.

Returns

the number of bytes into the file where this entry starts

getGene()

std::string getGene ( ) const

inline

Return the gene name for this entry - e.g. "ADH1B".

Returns

the gene name

getID()

std::string getID ( ) const

inline

Return the 'ID' of this entry - e.g. Hs.4.

Returns

the ID (also called accession) for the entry

getLocusLink()

std::string getLocusLink ( ) const

inline

Return the LocusLink - e.g. 125.

Seems to be identical to the gene number in most cases?

Returns

getNumAccessions()

int getNumAccessions ( ) const

inline

Return the number of accessions (gi numbers or EMBL accessions) that comprise this entry.

The accessions themselves cannot be returned from this object. See ms_unigene::findEntry

Returns

The number of accessions

getTitle()

std::string getTitle ( ) const

inline

Return the 'title' of this entry - e.g. "alcohol dehydrogenase...".

Returns

a readable name for the entry.

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

• ms_unigene.hpp
• ms_unigene.cpp