Documentation

ParseSwissprotManager extends ParseDbAbstractManager
in package

Amelaye

BioPHP

Domain

Parser

FinalYes

Class ParseSwissprotManager

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 : array<string|int, mixed>
$geneNames : array<string|int, mixed>: Gene names, as groups of synonyms: ( (GNAME1, GNAME2), (GNAME3) ).
$notupdDate : string: Date of the last annotation update, read from the DT lines.
$sequpdDate : string: Date of the last sequence update, read from the DT lines. The Sequence entity only carries the creation date, so the two other DT dates stay on the parser.

Methods

__construct() : mixed: Constructor.
getAccession() : array<string|int, mixed>
getAuthors() : array<string|int, mixed>
getEntryId() : string: Extracts the identifier uniquely naming a Swiss-Prot entry.
getFeatures() : array<string|int, mixed>
getFormat() : string: The name this format is known by in the collection records and in DatabaseParserFactory.
getGbSequence() : GbSequence
getGeneNames() : array<string|int, mixed>: Gene names (GN line), as groups of synonyms.
getKeywords() : array<string|int, mixed>
getmin() : int: Gets the minimum of three (usually numeric) values $x, $y, and $z.
getNotupdDate() : string: Date of the last annotation update (DT line).
getReferences() : array<string|int, mixed>
getSequence() : Sequence
getSequpdDate() : string: Date of the last sequence update (DT line).
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 Swiss-Prot entry.
isEntryStart() : bool: Tells whether a line opens a new Swiss-Prot entry.
left() : bool|string: Returns the first $numchars characters of a string.
parseDataFile() : Sequence: Parses a Swissprot 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.
parseLocationBounds() : array<string|int, mixed>: 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.
buildACFields() : array<string|int, mixed>: Parses AC line Format : AC P01375;
buildDEFields() : mixed: Parses DE line Format : DE TUMOR NECROSIS FACTOR PRECURSOR (TNF-ALPHA) (CACHECTIN).
buildDRField() : mixed: 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.
buildDTFields() : mixed: Parses DT Line Format : DT 21-JUL-1986 (REL. 01, LAST SEQUENCE UPDATE)
buildFTField() : mixed: Parses FT lines Format : FT KEY START END COMMENT.
buildGNField() : mixed: Parses GN line - GN is always exactly one line.
buildIDFields() : mixed: Parses ID line Format : ID PROTNAME_PROTSOURCE DATA_CLASS; MOL_TYPE; LENGTH AA.
buildKWFields() : mixed: Parses KW Fields Format : KW WORD1; WORD2; WORD3; etc .
buildOCField() : mixed: Parses OC lines Format : OC EUKARYOTA; METAZOA; CHORDATA; VERTEBRATA; TETRAPODA; MAMMALIA; OC EUTHERIA; PRIMATES.
buildOSFields() : mixed: Parses OS line Format : OS HOMO SAPIENS (HUMAN).
buildRNField() : mixed: Parses RN lines - This is a paragraph which contains several lines Example : RN [8] RP X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS).
buildSQField() : mixed: Parses SQ lines and below SQ SEQUENCE XXXX AA; XXXXX MW; XXXXX CN;
makeRefArray() : mixed: Creates references array

$accession


        protected
            array<string|int, mixed>
    $accession

$authors


        protected
            array<string|int, mixed>
    $authors

$features


        protected
            array<string|int, mixed>
    $features

$gbSequence


        protected
            GbSequence
    $gbSequence

$keywords


        protected
            array<string|int, mixed>
    $keywords

$references


        protected
            array<string|int, mixed>
    $references

$sequence


        protected
            Sequence
    $sequence

$spDatabank


        protected
            array<string|int, mixed>
    $spDatabank

$srcForm


        protected
            SrcForm
    $srcForm

$aLines


        private
            array<string|int, mixed>
    $aLines

$geneNames

Gene names, as groups of synonyms: ( (GNAME1, GNAME2), (GNAME3) ).


        private
            array<string|int, mixed>
    $geneNames
     = []

$notupdDate

Date of the last annotation update, read from the DT lines.


        private
            string
    $notupdDate
     = ""

$sequpdDate

Date of the last sequence update, read from the DT lines. The Sequence entity only carries the creation date, so the two other DT dates stay on the parser.


        private
            string
    $sequpdDate
     = ""

__construct()

Constructor.


    public
                    __construct() : mixed

getAccession()


    public
                    getAccession() : array<string|int, mixed>

Return values

array<string|int, mixed>

getAuthors()


    public
                    getAuthors() : array<string|int, mixed>

Return values

array<string|int, mixed>

getEntryId()

Extracts the identifier uniquely naming a Swiss-Prot entry.


    public
            static        getEntryId(array<string|int, mixed> $aFlines, string $sLine) : string

Parameters

$aFlines : array<string|int, mixed>: The whole file, buffered
$sLine : string: The line opening the entry

Return values

string

getFeatures()


    public
                    getFeatures() : array<string|int, mixed>

Return values

array<string|int, mixed>

getFormat()

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


    public
            static        getFormat() : string

Return values

string

getGbSequence()


    public
                    getGbSequence() : GbSequence

Return values

GbSequence

getGeneNames()

Gene names (GN line), as groups of synonyms.


    public
                    getGeneNames() : array<string|int, mixed>

Return values

array<string|int, mixed>

getKeywords()


    public
                    getKeywords() : array<string|int, mixed>

Return values

array<string|int, mixed>

getmin()

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


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

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

Parameters

$x : int
$y : int
$z : int

Return values

int

getNotupdDate()

Date of the last annotation update (DT line).


    public
                    getNotupdDate() : string

Return values

string

getReferences()


    public
                    getReferences() : array<string|int, mixed>

Return values

array<string|int, mixed>

getSequence()


    public
                    getSequence() : Sequence

Return values

Sequence

getSequpdDate()

Date of the last sequence update (DT line).


    public
                    getSequpdDate() : string

Return values

string

getSpDatabank()


    public
                    getSpDatabank() : array<string|int, mixed>

Return values

array<string|int, mixed>

getSrcForm()


    public
                    getSrcForm() : SrcForm

Return values

SrcForm

intrim()

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


    public
                    intrim(string $string) : mixed

Parameters

$string : string

isEntryEnd()

Tells whether a line closes a Swiss-Prot entry.


    public
            static        isEntryEnd(string $sLine) : bool

Parameters

$sLine : string: The line to analyze

Return values

bool

isEntryStart()

Tells whether a line opens a new Swiss-Prot entry.


    public
            static        isEntryStart(string $sLine) : bool

Parameters

$sLine : string: The line to analyze

Return values

bool

left()

Returns the first $numchars characters of a string.


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

Parameters

$str : string
$numchars : int

Return values

bool|string

parseDataFile()

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


    public
                    parseDataFile(array<string|int, mixed> $aFlines) : Sequence

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

$aFlines : array<string|int, mixed>

Return values

Sequence —

$oSequence

rem_right()

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


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

Parameters

$str : string
$charcount : int = 1

Return values

bool|string

right()

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


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

Parameters

$str : string
$numchars : int

Return values

bool|string

setAccession()


    public
                    setAccession(array<string|int, mixed> $accession) : void

Parameters

$accession : array<string|int, mixed>

setAuthors()


    public
                    setAuthors(array<string|int, mixed> $authors) : void

Parameters

$authors : array<string|int, mixed>

setFeatures()


    public
                    setFeatures(array<string|int, mixed> $features) : void

Parameters

$features : array<string|int, mixed>

setGbSequence()


    public
                    setGbSequence(GbSequence $gbSequence) : void

Parameters

$gbSequence : GbSequence

setKeywords()


    public
                    setKeywords(array<string|int, mixed> $keywords) : void

Parameters

$keywords : array<string|int, mixed>

setReferences()


    public
                    setReferences(array<string|int, mixed> $references) : void

Parameters

$references : array<string|int, mixed>

setSequence()


    public
                    setSequence(Sequence $sequence) : void

Parameters

$sequence : Sequence

setSpDatabank()


    public
                    setSpDatabank(array<string|int, mixed> $spDatabank) : void

Parameters

$spDatabank : array<string|int, mixed>

setSrcForm()


    public
                    setSrcForm(SrcForm $srcForm) : void

Parameters

$srcForm : SrcForm

trim_element()

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.


    public
                    trim_element(mixed &$value, mixed $key) : mixed

Parameters

$value : mixed
$key : mixed

parseLocationBounds()

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.


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

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

$sLocation : string: The raw location text, e.g. "complement(join(<1..10,50..>60))".

Return values

array<string|int, mixed> —

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

buildACFields()

Parses AC line Format : AC P01375;


    private
                    buildACFields(array<string|int, mixed> &$aAccess) : array<string|int, mixed>

Parameters

$aAccess : array<string|int, mixed>

Return values

array<string|int, mixed>

buildDEFields()

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


    private
                    buildDEFields(string &$sDescription, int &$iDescCpt) : mixed

Parameters

$sDescription : string
$iDescCpt : int

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.


    private
                    buildDRField() : mixed

( 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.

buildDTFields()

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


    private
                    buildDTFields() : mixed

buildFTField()

Parses FT lines Format : FT KEY START END COMMENT.


    private
                    buildFTField() : mixed

buildGNField()

Parses GN line - GN is always exactly one line.


    private
                    buildGNField() : mixed

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:

Split expressions by " AND ".
Test each "token" if in between parentheses or not.
If not, then token is a singleton, else it's a multiple-ton.
Singletons are translated into (GNAME1). Multiple-tons are translated into (GNAME1, GNAME 2).
Push gene name array into larger array. Go to next token.

buildIDFields()

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


    private
                    buildIDFields() : mixed

buildKWFields()

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


    private
                    buildKWFields(string &$sKeywords) : mixed

Parameters

$sKeywords : string

buildOCField()

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


    private
                    buildOCField(string &$sOrganism, int &$iOrgaCpt) : mixed

Parameters

$sOrganism : string
$iOrgaCpt : int

buildOSFields()

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


    private
                    buildOSFields(string &$sSource, int &$iSourceCpt) : mixed

Parameters

$sSource : string
$iSourceCpt : int

buildRNField()

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


    private
                    buildRNField(array<string|int, mixed> $aFlines, array<string|int, mixed> &$aReferences, array<string|int, mixed> &$aAuthors) : mixed

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

Parameters

$aFlines : array<string|int, mixed>
$aReferences : array<string|int, mixed>
$aAuthors : array<string|int, mixed>

buildSQField()

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


    private
                    buildSQField() : mixed

makeRefArray()

Creates references array


    private
                    makeRefArray(array<string|int, mixed> $aReferences) : mixed

Parameters

$aReferences : array<string|int, mixed>

ParseSwissprotManager extends ParseDbAbstractManager in package Amelaye BioPHP Domain Parser

Tags

Table of Contents

Properties

Methods

Properties

$accession

$authors

$features

$gbSequence

$keywords

$references

$sequence

$spDatabank

$srcForm

$aLines

$geneNames

$notupdDate

$sequpdDate

Methods

__construct()

getAccession()

Return values

getAuthors()

Return values

getEntryId()

Parameters

Return values

getFeatures()

Return values

getFormat()

Return values

getGbSequence()

Return values

getGeneNames()

Return values

getKeywords()

Return values

getmin()

Parameters

Return values

getNotupdDate()

Return values

getReferences()

Return values

getSequence()

Return values

getSequpdDate()

Return values

getSpDatabank()

Return values

getSrcForm()

Return values

intrim()

Parameters

isEntryEnd()

Parameters

Return values

isEntryStart()

Parameters

Return values

left()

Parameters

Return values

parseDataFile()

Parameters

Tags

Return values

rem_right()

Parameters

Return values

right()

Parameters

Return values

setAccession()

Parameters

setAuthors()

Parameters

setFeatures()

Parameters

ParseSwissprotManager extends ParseDbAbstractManager
in package

Amelaye

BioPHP

Domain

Parser