\AppBundle\Service\IOParseSwissprotManager

__construct()

__construct() 

Constructor.

getAccession()

getAccession() : array

Returns

getSequence()

getSequence() : \AppBundle\Entity\Sequencing\Sequence

Returns

getAuthors()

getAuthors() : array

Returns

getGbSequence()

getGbSequence() : \AppBundle\Entity\Sequencing\GbSequence

Returns

getFeatures()

getFeatures() : array

Returns

getKeywords()

getKeywords() : array

Returns

getReferences()

getReferences() : array

Returns

getSrcForm()

getSrcForm() : \AppBundle\Entity\Sequencing\SrcForm

Returns

getSpDatabank()

getSpDatabank() : array

Returns

setAccession()

setAccession(array  $accession) 

Parameters

setSequence()

setSequence(\AppBundle\Entity\Sequencing\Sequence  $sequence) 

Parameters

setAuthors()

setAuthors(array  $authors) 

Parameters

setFeatures()

setFeatures(array  $features) 

Parameters

setKeywords()

setKeywords(array  $keywords) 

Parameters

setReferences()

setReferences(array  $references) 

Parameters

setSrcForm()

setSrcForm(\AppBundle\Entity\Sequencing\SrcForm  $srcForm) 

Parameters

setGbSequence()

setGbSequence(\AppBundle\Entity\Sequencing\GbSequence  $gbSequence) 

Parameters

setSpDatabank()

setSpDatabank(array  $spDatabank) 

Parameters

parseDataFile()

parseDataFile(array  $aFlines) : \AppBundle\Service\IO\Sequence

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

Parses the Feature Table lines (those that begin with FT) in a Swissprot data file, extracts the feature key name, from endpoint, to endpoint, and description, and stores them in a (simple) array.

Parameters

Throws

\Exception

Returns

$oSequence

left()

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

Returns the first $numchars characters of a string.

Parameters

Returns

right()

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

Returns

rem_right()

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

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

Parameters

Returns

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

buildIDFields()

buildIDFields() 

Parses ID line Format : ID PROTNAME_PROTSOURCE DATA_CLASS; MOL_TYPE; LENGTH AA.

Throws

\Exception

buildACFields()

buildACFields(array  $aAccess) : array

Parses AC line Format : AC P01375;

Parameters

Throws

\Exception

Returns

buildDTFields()

buildDTFields() 

Parses DT Line Format : DT 21-JUL-1986 (REL. 01, LAST SEQUENCE UPDATE)

Throws

\Exception

buildDEFields()

buildDEFields(string  $sDescription, integer  $iDescCpt) 

Parses DE line Format : DE TUMOR NECROSIS FACTOR PRECURSOR (TNF-ALPHA) (CACHECTIN).

Parameters

Throws

\Exception

buildKWFields()

buildKWFields(string  $sKeywords) 

Parses KW Fields Format : KW WORD1; WORD2; WORD3; etc .

..

Parameters

Throws

\Exception

buildOSFields()

buildOSFields(string  $sSource, integer  $iSourceCpt) 

Parses OS line Format : OS HOMO SAPIENS (HUMAN).

Parameters

Throws

\Exception

buildOCField()

buildOCField(string  $sOrganism, integer  $iOrgaCpt) 

Parses OC lines Format : OC EUKARYOTA; METAZOA; CHORDATA; VERTEBRATA; TETRAPODA; MAMMALIA; OC EUTHERIA; PRIMATES.

Parameters

Throws

\Exception

buildFTField()

buildFTField() 

Parses FT lines Format : FT KEY START END COMMENT.

Throws

\Exception

buildDRField()

buildDRField() 

Parses DR lines Format : DR DATA_BANK_IDENTIFIER; PRIMARY_IDENTIFIER; SECONDARY_IDENTIFIER We assume that all three data items are mandatory/present in all DR entries.

( refno => ( (dbname1, pid1, sid1), (dbname2, pid2, sid2), ... ), 1 => ( ... ) ) ( 0 => ( (REBASE, pid1, sid1), (WORPEP, pid2, sid2), ... ), 1 => ( ... ) ) ( rn => ( "rp" => "my rp", "rc" => ("tok1" => "value", ...) ) ) ( 10 => ( "RP" => "my rp", "RC" => ("PLASMID" => "PLA_VAL", ... ) ) ) Example: DR AARHUS/GHENT-2DPAGE; 8006; IEF.

Throws

\Exception

buildRNField()

buildRNField(array  $aFlines, array  $aReferences, array  $aAuthors) 

Parses RN lines - This is a paragraph which contains several lines Example : RN [8] RP X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS).

RX MEDLINE; 90008932. RA ECK M.J., SPRANG S.R.; RL J. BIOL. CHEM. 264:17595-17605(1989).

Parameters

Throws

\Exception

buildGNField()

buildGNField(  $aGename) 

Parses GN line - GN is always exactly one line.

GNAME1 OR GNAME2 ( (GNAME1, GNAME2) ) GNAME1 AND GNAME2 ( (GNAME1), (GNAME2) ) GNAME1 AND (GNAME2 OR GNAME3) ( (GNAME1), (GNAME2, GNAME3) ) GNAME1 OR (GNAME2 AND GNAME3) NOT POSSIBLE!!! ALGORITHM: 1) Split expressions by " AND ". 2) Test each "token" if in between parentheses or not. 3) If not, then token is a singleton, else it's a multiple-ton. 4) Singletons are translated into (GNAME1). Multiple-tons are translated into (GNAME1, GNAME 2). 5) Push gene name array into larger array. Go to next token.

Parameters

Throws

\Exception

buildSQField()

buildSQField() 

Parses SQ lines and below SQ SEQUENCE XXXX AA; XXXXX MW; XXXXX CN;

Throws

\Exception

makeRefArray()

makeRefArray(array  $aReferences) 

Creates references array

Parameters

Throws

\Exception