Documentation

ParseGenbankManager extends ParseDbAbstractManager

in package

• Amelaye
• BioPHP
• Domain
• Parser

Class ParseGenbankManager

Tags

author

Amélie DUVERNET aka Amelaye amelieonline@gmail.com

Table of Contents

Properties

$accession  : array<string|int, mixed>

$authors  : array<string|int, mixed>

$features  : array<string|int, mixed>

$gbSequence  : GbSequence

$keywords  : array<string|int, mixed>

$references  : array<string|int, mixed>

$sequence  : Sequence

$spDatabank  : array<string|int, mixed>

$srcForm  : SrcForm

$aLines  : array<string|int, mixed>

Methods

__construct()  : mixed

Constructor.

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

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

getEntryId()  : string

Extracts the identifier uniquely naming a GenBank entry.

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

getFormat()  : string

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

getGbSequence()  : GbSequence

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

getmin()  : int

Gets the minimum of three (usually numeric) values $x, $y, and $z.

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

getSequence()  : Sequence

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

getSrcForm()  : SrcForm

intrim()  : mixed

Removes "internal spaces" (as opposed to leading and trailing spaces) from a string.

isEntryEnd()  : bool

Tells whether a line closes a GenBank entry.

isEntryStart()  : bool

Tells whether a line opens a new GenBank entry.

left()  : bool|string

Returns the first $numchars characters of a string.

parseDataFile()  : Sequence

Parses a GenBank data file and returns a Seq object containing parsed data.

rem_right()  : bool|string

Removes $charcount characters from the right (end) of a string.

right()  : bool|string

Returns the substring beginning at $numchars characters from the right end of a string.

setAccession()  : void

setAuthors()  : void

setFeatures()  : void

setGbSequence()  : void

setKeywords()  : void

setReferences()  : void

setSequence()  : void

setSpDatabank()  : void

setSrcForm()  : void

trim_element()  : mixed

trim_element() removes leading and trailing spaces from a string. In conjunction with the array_walk() function, it removes spaces from each element of an array.

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

Parses an INSDC feature location (shared by GenBank and EMBL) into its outer bounds and strand. Strips the complement()/join() wrappers and the "<"/">" fuzzy-boundary markers.

buildFeature()  : mixed

Creates Feature object

parseAccession()  : mixed

Parses ACCESSION field

parseDefinition()  : mixed

Parses DEFINITION field @ param array $flines

parseFeatures()  : mixed

Parses each fields for FEATURES

parseKeywords()  : mixed

Parses KEYWORDS field

parseLocus()  : mixed

Parses line LOCUS

parseOrganism()  : mixed

Parses information about organism

parseReferences()  : mixed

parseVersion()  : mixed

Parses VERSION field

seekReferences()  : string

Parse every multi-line fields from REFERENCES