Documentation

ParseBlocksManager

in package

• Amelaye
• BioPHP
• Domain
• Parser
• Service

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

author

Amélie DUVERNET aka Amelaye amelieonline@gmail.com

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.

readLabel()  : string

Reads the label of a field line : two letters followed by three blanks. A sequence line of a block opens on its protein name in the first column, which may begin like a label (IDHP_HUMAN, ACON_YEAST, BLAC_ECOLX) and is no field.