ParseBlocksManager
in package
implements
ParseDatabaseInterface
Class ParseBlocksManager A BLOCKS entry describes an ungapped conserved region of a protein family, not a sequence, so this class exposes plain scalars rather than the Sequence/Feature entities of ParseDbAbstractManager.
Tags
Table of Contents
Interfaces
- ParseDatabaseInterface
- Interface ParseDatabaseInterface
Properties
- $aaTriplet : string
- $accession : string
- $description : string
- $distMax : int
- $distMin : int
- $id : string
Methods
- __construct() : mixed
- Constructor.
- getAaTriplet() : string
- getAccession() : string
- getDescription() : string
- getDistMax() : int
- Maximum distance, in residues, from the previous block of the family.
- getDistMin() : int
- Minimum distance, in residues, from the previous block of the family.
- getEntryId() : string
- Extracts the identifier uniquely naming a BLOCKS entry, read from its AC line.
- getFormat() : string
- The name this format is known by in the collection records and in DatabaseParserFactory.
- getId() : string
- isEntryEnd() : bool
- Tells whether a line closes a BLOCKS entry.
- isEntryStart() : bool
- Tells whether a line opens a new BLOCKS entry.
- parseDataFile() : Sequence
- Parses a BLOCKS data file and populates this manager's fields.
- parseAccession() : void
- Reads the AC line, which carries the accession then the distance range to the previous block.
Properties
$aaTriplet
private
string
$aaTriplet
= ""
$accession
private
string
$accession
= ""
$description
private
string
$description
= ""
$distMax
private
int
$distMax
= 0
$distMin
private
int
$distMin
= 0
$id
private
string
$id
= ""
Methods
__construct()
Constructor.
public
__construct() : mixed
getAaTriplet()
public
getAaTriplet() : string
Return values
stringgetAccession()
public
getAccession() : string
Return values
stringgetDescription()
public
getDescription() : string
Return values
stringgetDistMax()
Maximum distance, in residues, from the previous block of the family.
public
getDistMax() : int
Return values
intgetDistMin()
Minimum distance, in residues, from the previous block of the family.
public
getDistMin() : int
Return values
intgetEntryId()
Extracts the identifier uniquely naming a BLOCKS entry, read from its AC line.
public
static getEntryId(array<string|int, mixed> $aFlines, string $sLine) : string
Parameters
- $aFlines : array<string|int, mixed>
-
The whole file, buffered
- $sLine : string
-
The line opening the entry
Return values
stringgetFormat()
The name this format is known by in the collection records and in DatabaseParserFactory.
public
static getFormat() : string
Return values
stringgetId()
public
getId() : string
Return values
stringisEntryEnd()
Tells whether a line closes a BLOCKS entry.
public
static isEntryEnd(string $sLine) : bool
Parameters
- $sLine : string
-
The line to analyze
Return values
boolisEntryStart()
Tells whether a line opens a new BLOCKS entry.
public
static isEntryStart(string $sLine) : bool
Parameters
- $sLine : string
-
The line to analyze
Return values
boolparseDataFile()
Parses a BLOCKS data file and populates this manager's fields.
public
parseDataFile(array<string|int, mixed> $aFlines) : Sequence
Parameters
- $aFlines : array<string|int, mixed>
-
The lines the script has to parse
Tags
Return values
Sequence —$oSequence
parseAccession()
Reads the AC line, which carries the accession then the distance range to the previous block.
private
parseAccession(string $sData) : void
Example: AC IPB002128C; distance from previous block=(30,31)
Parameters
- $sData : string
-
The AC line, tag stripped