Documentation

ParseEmblManager extends ParseDbAbstractManager

in package

• Amelaye
• BioPHP
• Domain
• Parser
• Service

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.

parseInsdcFeature()  : mixed

Parses one feature of an INSDC feature table, shared by GenBank and EMBL, whose columns are the same : the key from column 6, the location (possibly wrapped over several lines) and the /qualifier lines from column 22. $aFlines is read ahead to find where the feature ends : a line holding something in its first 12 columns starts another feature or section, so EMBL hands its lines with their "FT" tag blanked out.

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

Parses an INSDC feature location (shared by GenBank and EMBL) into its outer bounds and strand, 1-based and inclusive. The location as written is kept apart (Feature::getFtLocation()) : these bounds only frame it.

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.

parseId()  : mixed

Parses the ID line.

parseKeywords()  : mixed

Parses KW line(s).

parseOldId()  : mixed

Parses the ID line of the layout used before release 87, which has no sequence version. Its first word is the entry name (HSERPG), a mnemonic, not the accession : the primary accession is the first one of the AC line (see parseAccession()).

parseOrganism()  : mixed

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

parseReferences()  : mixed

Parses a reference block : the RN line, then RC, RP, RX, RG, RA, RT and RL lines, in that order and each optional, any of them but RN possibly continued on several lines.

parseSequence()  : mixed

Parses the SQ header line and every sequence data line that follows it, up to "//" or the end of the lines, a record cut short having none.