Documentation

ParsePrfManager

in package

• Amelaye
• BioPHP
• Domain
• Parser

implements ParseDatabaseInterface

Class ParsePrfManager A PRF entry describes a published protein. Its layout is a twelve character label column, a blank label meaning the line continues the one above, and indented sub-keys qualifying the field they follow. This class exposes plain scalars rather than the Sequence/Feature entities of ParseDbAbstractManager. The SOURCE, KEYWORD, CROSSREF and SEQUENCE fields, which the original BioPHP parser declared without ever filling, are read here.

Tags

author

Amélie DUVERNET aka Amelaye amelieonline@gmail.com

Table of Contents

Interfaces

ParseDatabaseInterface

Interface ParseDatabaseInterface

Constants

LABEL_WIDTH  : mixed = 12

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

Properties

$authors  : array<string|int, mixed>

$comment  : string

$commonName  : string

$crossRefs  : array<string|int, mixed>

$entryCode  : string

$entryName  : string

$journal  : string

$keywords  : array<string|int, mixed>

$sequence  : string

$source  : string

$taxonomy  : array<string|int, mixed>

$title  : string

Methods

__construct()  : mixed

Constructor.

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

getComment()  : string

getCommonName()  : string

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

getEntryCode()  : string

getEntryId()  : string

Extracts the identifier uniquely naming a PRF entry.

getEntryName()  : string

getFormat()  : string

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

getJournal()  : string

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

getSequence()  : string

getSource()  : string

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

getTitle()  : string

isEntryEnd()  : bool

Tells whether a line closes a PRF entry. PRF uses a triple slash, where the GenBank family uses a double one.

isEntryStart()  : bool

Tells whether a line opens a new PRF entry.

parseDataFile()  : Sequence

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

parseCrossRefs()  : void

Cross-references are semicolon separated "DATABASE=IDENTIFIER" pairs. The same database may appear more than once, so they are returned as a list rather than keyed by name.

separatorFor()  : string

What joins a field to its continuation line. Keywords are separated by a run of at least two spaces, and the line break itself separates them too : joining those lines with a single space would weld the last keyword of one line to the first of the next.

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

Authors are written "Surname,Initial., Surname,Initial." : the separator is the period closing the initial, which has to be put back on each name.

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

Keywords sit on one line each, separated by a run of at least two spaces.

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

The taxonomy is a semicolon separated lineage, which may span several lines.