Documentation

ParsePirManager

in package

• Amelaye
• BioPHP
• Domain
• Parser

implements ParseDatabaseInterface

Class ParsePirManager A PIR entry qualifies most of its fields with "#key value" pairs, a pattern this class reads once and reuses everywhere. It exposes plain scalars rather than the Sequence/Feature entities of ParseDbAbstractManager.

Tags

author

Amélie DUVERNET aka Amelaye amelieonline@gmail.com

Table of Contents

Interfaces

ParseDatabaseInterface

Interface ParseDatabaseInterface

Constants

LABEL_WIDTH  : mixed = 16

Width of the label column, the data starting right after it.

Properties

$accessions  : array<string|int, mixed>

$checksum  : string

$createDate  : string

$entryName  : string

$entryType  : string

$keywords  : array<string|int, mixed>

$length  : int

$molwt  : float

$organism  : string

$seqrevDate  : string

$species  : string

$title  : string

$txtchgDate  : string

Methods

__construct()  : mixed

Constructor.

getAccessions()  : array<string|int, mixed>

getChecksum()  : string

getCreateDate()  : string

getEntryId()  : string

Extracts the identifier uniquely naming a PIR entry, which is the entry name preceding the qualifiers.

getEntryName()  : string

getEntryType()  : string

getFormat()  : string

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

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

getLength()  : int

getMolwt()  : float

getOrganism()  : string

The common name of the source organism.

getSeqrevDate()  : string

getSpecies()  : string

The scientific name of the source organism.

getTitle()  : string

getTxtchgDate()  : string

isEntryEnd()  : bool

Tells whether a line closes a PIR entry.

isEntryStart()  : bool

Tells whether a line opens a new PIR entry.

parseDataFile()  : Sequence

Parses a PIR data file and populates this manager's fields.

readDates()  : void

Example: DATE 15-Jun-2001 #sequence_revision 15-Jun-2001 #text_change 15-Jun-2001

readEntry()  : void

Example: ENTRY RHTDTO #type complete

readOrganism()  : void

Example: ORGANISM #formal_name Oryctolagus cuniculus #common_name domestic rabbit

readSummary()  : void

Example: SUMMARY #length 3 #molecular-weight 380 #checksum 465

splitList()  : array<string|int, mixed>

Accessions and keywords are semicolon separated lists which may run over several lines.

splitQualifiers()  : array<string|int, mixed>

Splits a "value #key1 val1 #key2 val2" string into its leading value and its qualifiers.