\Amelaye\BioPHP\Domain\Parser\Service ParseGenbankManager

getFormat()

getFormat() : string

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

Returns

isEntryStart()

isEntryStart(string  $sLine) : bool

Tells whether a line opens a new GenBank entry.

Parameters

Returns

isEntryEnd()

isEntryEnd(string  $sLine) : bool

Tells whether a line closes a GenBank entry.

Parameters

Returns

getEntryId()

getEntryId(array  $aFlines, string  $sLine) : string

Extracts the identifier uniquely naming a GenBank entry.

Parameters

Returns

parseDataFile()

parseDataFile(array  $aFlines) : \Amelaye\BioPHP\Domain\Sequence\Entity\Sequence

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

Parameters

Throws

\Exception

Returns

$oSequence

left()

left(string  $str, int  $numchars) : bool|string

Returns the first $numchars characters of a string.

Parameters

Returns

right()

right(string  $str, int  $numchars) : bool|string

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

Parameters

Returns

intrim()

intrim(string  $string) : mixed

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

Parameters

Returns

getmin()

getmin(int  $x, int  $y, int  $z) : int

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

For now, this can't handle situations when one or more arguments is FALSE.

Parameters

Returns

rem_right()

rem_right(string  $str, int  $charcount = 1) : bool|string

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

Parameters

Returns

trim_element()

trim_element(mixed  $value, mixed  $key) : 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.

Parameters

Returns

__construct()

__construct() : mixed

Constructor.

Returns

getAccession()

getAccession() : array

Returns

getSequence()

getSequence() : \Amelaye\BioPHP\Domain\Sequence\Entity\Sequence

Returns

getAuthors()

getAuthors() : array

Returns

getGbSequence()

getGbSequence() : \Amelaye\BioPHP\Domain\Sequence\Entity\GbSequence

Returns

getFeatures()

getFeatures() : array

Returns

getKeywords()

getKeywords() : array

Returns

getReferences()

getReferences() : array

Returns

getSrcForm()

getSrcForm() : \Amelaye\BioPHP\Domain\Sequence\Entity\SrcForm

Returns

getSpDatabank()

getSpDatabank() : array

Returns

setAccession()

setAccession(array  $accession) : void

Parameters

Returns

setSequence()

setSequence(\Amelaye\BioPHP\Domain\Sequence\Entity\Sequence  $sequence) : void

Parameters

Returns

setAuthors()

setAuthors(array  $authors) : void

Parameters

Returns

setFeatures()

setFeatures(array  $features) : void

Parameters

Returns

setKeywords()

setKeywords(array  $keywords) : void

Parameters

Returns

setReferences()

setReferences(array  $references) : void

Parameters

Returns

setSrcForm()

setSrcForm(\Amelaye\BioPHP\Domain\Sequence\Entity\SrcForm  $srcForm) : void

Parameters

Returns

setGbSequence()

setGbSequence(\Amelaye\BioPHP\Domain\Sequence\Entity\GbSequence  $gbSequence) : void

Parameters

Returns

setSpDatabank()

setSpDatabank(array  $spDatabank) : void

Parameters

Returns

parseLocationBounds()

parseLocationBounds(string  $sLocation) : array

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.

For a join() of several comma-separated segments (a spliced feature), Feature has no room to keep each exon separately, so this returns the lowest start and the highest end across every segment.

Parameters

Returns

[$iFrom, $iTo, $sStrand] - $sStrand is "-" when the location was wrapped in complement(...), "+" otherwise.

parseReferences()

parseReferences(array  $aFlines) : mixed

Parameters

Throws

\Exception

Returns

seekReferences()

seekReferences(string  $sReferenceProperty) : string

Parse every multi-line fields from REFERENCES

Parameters

Throws

\Exception

Returns

parseOrganism()

parseOrganism(mixed  $flines) : mixed

Parses information about organism

Parameters

Throws

\Exception

Returns

parseLocus()

parseLocus() : mixed

Parses line LOCUS

Throws

\Exception

Returns

parseDefinition()

parseDefinition(mixed  $flines) : mixed

Parses DEFINITION field @ param array $flines

Parameters

Throws

\Exception

Returns

parseVersion()

parseVersion() : mixed

Parses VERSION field

Throws

\Exception

Returns

parseKeywords()

parseKeywords() : mixed

Parses KEYWORDS field

Throws

\Exception

Returns

parseAccession()

parseAccession() : mixed

Parses ACCESSION field

Throws

\Exception

Returns

parseFeatures()

parseFeatures(array  $aFlines, string  $sField) : mixed

Parses each fields for FEATURES

Parameters

Throws

\Exception

Returns

buildFeature()

buildFeature(string  $sLine, string  $sKey, array  $aBounds) : mixed

Creates Feature object

Parameters

Returns