\Amelaye\BioPHP\Domain\Database\ServiceParseDbAbstractManager

Class ParseDbAbstractManager

Summary

Methods

Properties

Constants

left()
right()
intrim()
getmin()
rem_right()
trim_element()
__construct()
getAccession()
getSequence()
getAuthors()
getGbSequence()
getFeatures()
getKeywords()
getReferences()
getSrcForm()
getSpDatabank()
setAccession()
setSequence()
setAuthors()
setFeatures()
setKeywords()
setReferences()
setSrcForm()
setGbSequence()
setSpDatabank()
parseDataFile()

No public properties found

No constants found

No protected methods found

$accession
$sequence
$authors
$features
$keywords
$references
$srcForm
$gbSequence
$spDatabank

N/A

No private methods found

No private properties found

N/A

abstract

File: Domain/Database/Service/ParseDbAbstractManager.php
Package: Database\Service
Class hierarchy: \Amelaye\BioPHP\Domain\Database\Service\ParseDbAbstractManager
Implements: \Amelaye\BioPHP\Domain\Database\Interfaces\ParseDatabaseInterface
Uses traits: \Amelaye\BioPHP\Domain\Sequence\Traits\FormatsTrait

Properties

$accession

$accession : array

Type

normal

$sequence

$sequence : \Amelaye\BioPHP\Domain\Sequence\Entity\Sequence

Type

normal

$authors

$authors : array

Type

normal

$features

$features : array

Type

normal

$keywords

$keywords : array

Type

normal

$references

$references : array

Type

normal

$srcForm

$srcForm : \Amelaye\BioPHP\Domain\Sequence\Entity\SrcForm

Type

normal

$gbSequence

$gbSequence : \Amelaye\BioPHP\Domain\Sequence\Entity\GbSequence

Type

normal

$spDatabank

$spDatabank : array

Type

normal

Methods

left()

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

Returns the first $numchars characters of a string.

Parameters

string	$str
int	$numchars

Returns

bool|string

right()

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

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

Parameters

string	$str
int	$numchars

Returns

bool|string

intrim()

intrim(string  $string) : mixed

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

Parameters

string

$string

Returns

mixed

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

int	$x
int	$y
int	$z

Returns

int

rem_right()

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

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

Parameters

string	$str
int	$charcount

Returns

bool|string

trim_element()

trim_element( $value,  $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

	$value
	$key

Returns

mixed

__construct()

__construct() : mixed

Constructor.

Returns

mixed

getAccession()

getAccession() : array

Returns

array

getSequence()

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

Returns

\Amelaye\BioPHP\Domain\Sequence\Entity\Sequence

getAuthors()

getAuthors() : array

Returns

array

getGbSequence()

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

Returns

\Amelaye\BioPHP\Domain\Sequence\Entity\GbSequence

getFeatures()

getFeatures() : array

Returns

array

getKeywords()

getKeywords() : array

Returns

array

getReferences()

getReferences() : array

Returns

array

getSrcForm()

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

Returns

\Amelaye\BioPHP\Domain\Sequence\Entity\SrcForm

getSpDatabank()

getSpDatabank() : array

Returns

array

setAccession()

setAccession(array  $accession) : void

Parameters

array

$accession

setSequence()

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

Parameters

\Amelaye\BioPHP\Domain\Sequence\Entity\Sequence

$sequence

setAuthors()

setAuthors(array  $authors) : void

Parameters

array

$authors

setFeatures()

setFeatures(array  $features) : void

Parameters

array

$features

setKeywords()

setKeywords(array  $keywords) : void

Parameters

array

$keywords

setReferences()

setReferences(array  $references) : void

Parameters

array

$references

setSrcForm()

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

Parameters

\Amelaye\BioPHP\Domain\Sequence\Entity\SrcForm

$srcForm

setGbSequence()

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

Parameters

\Amelaye\BioPHP\Domain\Sequence\Entity\GbSequence

$gbSequence

setSpDatabank()

setSpDatabank(array  $spDatabank) : void

Parameters

array

$spDatabank

parseDataFile()

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

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

Parameters

array

$aFlines

The lines the script has to parse

Throws

\Exception

Returns

\Amelaye\BioPHP\Domain\Sequence\Entity\Sequence —

$oSequence