Documentation

ParseEmblManager extends ParseDbAbstractManager

in package

• Amelaye
• BioPHP
• Domain
• Parser

Class ParseEmblManager EMBL flat files use the same "one field per record type, feature table shared with GenBank" shape as GenBank's LOCUS/DEFINITION/ACCESSION/.../FEATURES/ORIGIN, only the line tags differ (2-char codes like ID/AC/DE/OS/OC/RN/FT/SQ instead of full keywords).

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  : ArrayIterator

$bAccessionLineSeen  : bool

Whether an AC line has already been parsed for the entry being read. Only the very first accession of the very first AC line is the entry's primary accession (already captured from the ID line); every accession on every AC line after that, continuation lines included, is a genuine secondary accession and must be kept.

Methods

__construct()  : mixed

Constructor.

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

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

getEntryId()  : string

Extracts the identifier uniquely naming a EMBL 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 EMBL entry.

isEntryStart()  : bool

Tells whether a line opens a new EMBL entry.

left()  : bool|string

Returns the first $numchars characters of a string.

parseDataFile()  : Sequence

Parses an EMBL 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.

parseAccession()  : mixed

Parses AC line(s).

parseDate()  : mixed

Parses DT lines - only the "Created" one is kept, to mirror GenBank's single date field.

parseDescription()  : mixed

Parses DE line(s), possibly on several lines.

parseFeatures()  : mixed

Parses one feature: the FT key/location line, then every /qualifier="value" line that follows it until the next feature key or the end of the feature table.

parseId()  : mixed

Parses the ID line.

parseKeywords()  : mixed

Parses KW line(s).

parseOrganism()  : mixed

Parses the OS line and the OC lines that follow it.

parseReferences()  : mixed

Parses a reference block: RN, then optionally RP, RX, RA, RT, RL.

parseSequence()  : mixed

Parses the SQ header line and every sequence data line that follows it, up to "//".