Documentation

ParseEntrezManager

in package

• Amelaye
• BioPHP
• Domain
• Parser

implements ParseDatabaseInterface

Class ParseEntrezManager An Entrez genome record describes a whole genome the way GenBank describes an entry : same LOCUS columns, same 12-character label column. It carries neither a FEATURES table nor an ORIGIN sequence though, so it holds annotation only and this class exposes plain scalars and EntrezReference objects rather than the Sequence/Feature entities of ParseDbAbstractManager.

Tags

author

Amélie DUVERNET aka Amelaye amelieonline@gmail.com

Table of Contents

Interfaces

ParseDatabaseInterface

Interface ParseDatabaseInterface

Constants

REFERENCE_SUBKEYS  : mixed = ["AUTHORS", "TITLE", "JOURNAL", "MEDLINE", "PUB...

Subkeys of a REFERENCE block, indented under it.

Properties

$accession  : array<string|int, mixed>

$definition  : string

$division  : string

$entryDate  : string

$entryName  : string

$keywords  : array<string|int, mixed>

$length  : int

$molType  : string

$ncbiGiId  : string

$organism  : string

$primAcc  : string

$references  : array<string|int, EntrezReference>

$source  : string

$strands  : string

$taxonomy  : array<string|int, mixed>

$topology  : string

$version  : string

Methods

__construct()  : mixed

Constructor.

getAccession()  : array<string|int, mixed>

getDefinition()  : string

getDivision()  : string

getEntryDate()  : string

getEntryId()  : string

Extracts the identifier uniquely naming an Entrez genome record, which is its first accession number. A record short of an ACCESSION line falls back on its LOCUS name.

getEntryName()  : string

getFormat()  : string

The name this format is known by in the collection records and in DatabaseParserFactory.

getKeywords()  : array<string|int, mixed>

getLength()  : int

getMolType()  : string

getNcbiGiId()  : string

getOrganism()  : string

getPrimAcc()  : string

getReferences()  : array<string|int, EntrezReference>

getSource()  : string

getStrands()  : string

getTaxonomy()  : array<string|int, mixed>

getTopology()  : string

getVersion()  : string

isEntryEnd()  : bool

Tells whether a line closes an Entrez genome record.

isEntryStart()  : bool

Tells whether a line opens a new Entrez genome record.

parseDataFile()  : Sequence

Parses an Entrez genome data file and populates this manager's fields.

accumulate()  : string

Accumulates a field written over several lines : the data of the current line, plus every continuation line below it, joined by a space. Advances $aLines past what it reads.

fillReference()  : mixed

Fills one subkey of the reference being read. A subkey met before any REFERENCE line has no reference to belong to and is dropped.

parseLocus()  : mixed

Parses the LOCUS line, whose fields sit at fixed columns.

parseVersion()  : mixed

Parses the VERSION line.

readLabel()  : string

Reads the label a line carries in its first 12 characters. A continuation line leaves that column blank, which is how a field tells it goes on.

splitAuthors()  : array<string|int, mixed>

Splits an AUTHORS field into individual names. Names are separated by a comma and a space, the last two by "and" - the comma inside a name itself ("Sanger,F.") carries no space and holds the name together.

splitList()  : array<string|int, mixed>

Splits a field listing its values, semicolon separated and closed by a period, into its items. A field holding just the period holds nothing.

startReference()  : EntrezReference

Opens the reference a REFERENCE line announces.