This class encapsulates a single entry from a unigene file. More...
#include <ms_mascotresunigene.hpp>
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...". |
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.
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
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 | ( | 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.
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. |
long getChromosome | ( | ) | const [inline] |
Return the chromosome that contains the unignene entry.
std::string getCytoBand | ( | ) | const [inline] |
Return the CYTOBAND - e.g. 4q21-q23.
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
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.
std::string getGene | ( | ) | const [inline] |
Return the gene name for this entry - e.g. "ADH1B".
std::string getID | ( | ) | const [inline] |
Return the 'ID' of this entry - e.g. Hs.4.
std::string getLocusLink | ( | ) | const [inline] |
Return the LocusLink - e.g. 125.
Seems to be identical to the gene number in most cases?
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
std::string getTitle | ( | ) | const [inline] |
Return the 'title' of this entry - e.g. "alcohol dehydrogenase...".
Copyright © 2022 Matrix Science Ltd. All Rights Reserved. Generated on Thu Mar 31 2022 01:12:39 |