Properties

$accession

$accession : array

Type

array

$authors

$authors : array

Type

array

$features

$features : array

Type

array

$keywords

$keywords : array

Type

array

$references

$references : array

Type

array

$spDatabank

$spDatabank : array

Type

array

$aLines

$aLines : array

Type

array

Methods

__construct()

__construct() 

Constructor.

getAccession()

getAccession() : array

Returns

array

getAuthors()

getAuthors() : array

Returns

array

getFeatures()

getFeatures() : array

Returns

array

getKeywords()

getKeywords() : array

Returns

array

getReferences()

getReferences() : array

Returns

array

getSpDatabank()

getSpDatabank() : array

Returns

array

setAccession()

setAccession(array  $accession) 

Parameters

array $accession

setAuthors()

setAuthors(array  $authors) 

Parameters

array $authors

setFeatures()

setFeatures(array  $features) 

Parameters

array $features

setKeywords()

setKeywords(array  $keywords) 

Parameters

array $keywords

setReferences()

setReferences(array  $references) 

Parameters

array $references

setSpDatabank()

setSpDatabank(array  $spDatabank) 

Parameters

array $spDatabank

parseDataFile()

parseDataFile(array  $aFlines) : \App\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

\App\Domain\Sequence\Entity\Sequence

$oSequence

left()

left(string  $str, integer  $numchars) : boolean|string

Returns the first $numchars characters of a string.

Parameters

string $str
integer $numchars

Returns

boolean|string

right()

right(string  $str, integer  $numchars) : boolean|string

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

Parameters

string $str
integer $numchars

Returns

boolean|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(integer  $x, integer  $y, integer  $z) : integer

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

integer $x
integer $y
integer $z

Returns

integer

rem_right()

rem_right(string  $str, integer  $charcount = 1) : boolean|string

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

Parameters

string $str
integer $charcount

Returns

boolean|string

trim_element()

trim_element(  $value,   $key) 

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

parseReferences()

parseReferences(array  $aFlines) 

Parameters

array $aFlines

The lines the script has to parse

Throws

\Exception

seekReferences()

seekReferences(string  $sReferenceProperty) : string

Parse every multi-line fields from REFERENCES

Parameters

string $sReferenceProperty

The references part

Throws

\Exception

Returns

string

parseOrganism()

parseOrganism(  $flines) 

Parses information about organism

Parameters

$flines

Throws

\Exception

parseLocus()

parseLocus() : mixed

Parses line LOCUS

Throws

\Exception

Returns

mixed

parseDefinition()

parseDefinition(  $flines) 

Parses DEFINITION field @ param array $flines

Parameters

$flines

Throws

\Exception

parseVersion()

parseVersion() 

Parses VERSION field

Throws

\Exception

parseKeywords()

parseKeywords() 

Parses KEYWORDS field

Throws

\Exception

parseAccession()

parseAccession() 

Parses ACCESSION field

Throws

\Exception

parseFeatures()

parseFeatures(array  $aFlines, string  $sField) 

Parses each fields for FEATURES

Parameters

array $aFlines
string $sField

Throws

\Exception

buildFeature()

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

Creates Feature object

Parameters

string $sLine
string $sKey
array $aBounds