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Public Member Functions

ms_unigene_entry Class Reference
[Mascot results file module]

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

#include <ms_mascotresunigene.hpp>

List of all members.

Public Member Functions

 ms_unigene_entry (FILE *f, ms_unigene &unigene)
 This constructor should only be called from within the library.
 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 ()
 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 ( 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:
fis a file pointer returned by the 'C' fopen() function
unigeneis the object that stores all the accession -> id mappings.
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:
idis the unigene id as returned by the getID() function.
titleis the unigene title as returned by the getTitle() function.
geneis the gene name as returned by the getGene() function.
cytoBandis the CYTOBAND as returned by the getCytoBand() function.
locusLinkis the LocusLink as returned by the getLocusLink() function.
expressis EXPRESS entry as returned by the getExpress() function.
chromosomeis the chromosome that contains the unignene entry as returned by the getChromosome() function.
numAccessionsis the number of accessions that comprise this unigene entry.
fileOffsetis the byte offset into the .data file for this unigene entry.

Member Function Documentation

long getChromosome (  ) const [inline]

Return the chromosome that contains the unignene entry.

Returns:
the chromosome number
std::string getCytoBand (  ) const [inline]

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

Returns:
the CYTOBAND
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.
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
std::string getGene (  ) const [inline]

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

Returns:
the gene name
std::string getID (  ) const [inline]

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

Returns:
the ID (also called accession) for the entry
std::string getLocusLink (  ) const [inline]

Return the LocusLink - e.g. 125.

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

Returns:
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
std::string getTitle (  ) const [inline]

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

Returns:
a readable name for the entry.

The documentation for this class was generated from the following files:
Copyright © 2016 Matrix Science Ltd.  All Rights Reserved. Generated on Fri Jun 2 2017 01:44:55