Documentation

ParsePmdManager

in package

• Amelaye
• BioPHP
• Domain
• Parser

implements ParseDatabaseInterface

Class ParsePmdManager A PMD entry describes a mutation reported in the literature, not a sequence, so this class 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

$articleNo  : string

$authors  : array<string|int, mixed>

$entryNo  : string

$entryType  : string

$journal  : string

$medlineNo  : string

$mutationType  : string

$title  : string

Methods

__construct()  : mixed

Constructor.

getArticleNo()  : string

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

getEntryId()  : string

Extracts the identifier uniquely naming a PMD entry, which is the entry type followed by its number.

getEntryNo()  : string

getEntryType()  : string

getFormat()  : string

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

getJournal()  : string

getMedlineNo()  : string

getMutationType()  : string

getTitle()  : string

isEntryEnd()  : bool

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

isEntryStart()  : bool

Tells whether a line opens a new PMD entry.

parseDataFile()  : Sequence

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

parseEntry()  : void

Reads the ENTRY line. The entry type is its first character and the entry number the six that follow, both at fixed positions.

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

Authors are written as a list separated by commas and closed by an ampersand.