Documentation

ParseKeggAbstractManager

in package

• Amelaye
• BioPHP
• Domain
• Parser
• Service

implements ParseDatabaseInterface

Class ParseKeggAbstractManager KEGG describes metabolism through several files - compound, enzyme, reaction, ortholog, genome - written in one same grammar : a label in the first twelve columns, its data from the thirteenth, a line leaving the label column blank continuing the field above it, and "///" closing the record. That grammar and the ENTRY and NAME fields every record carries live here; each subclass adds the fields of its own file.

Tags

author

Amélie DUVERNET aka Amelaye amelieonline@gmail.com

Table of Contents

Interfaces

ParseDatabaseInterface

Interface ParseDatabaseInterface

Properties

$entry  : string

$names  : array<string|int, mixed>

$rawFields  : array<string|int, mixed>

The lines of each field as readFields() gathered them, but with the indentation past the thirteenth column kept : it tells a wrapped line from a new item.

Methods

__construct()  : mixed

Constructor.

getEntry()  : string

getEntryId()  : string

Extracts the identifier uniquely naming a KEGG record.

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

isEntryEnd()  : bool

Tells whether a line closes a KEGG record. KEGG closes on three slashes where most flat files use two.

isEntryStart()  : bool

Tells whether a line opens a new KEGG record.

joinLines()  : string

Joins the lines of a field into one string. A line opening with "$" continues the word the line above broke off, so it joins without a space.

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

Reads a DBLINKS field into pairs of database name and identifier, one per line.

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

Reads a PATHWAY field into pairs of map identifier and pathway name, one per line : the identifier is the first word (map00010, ec00010, ko00010...), behind a "PATH:" tag in the files before 2008. A line not opening on an identifier continues the name above it.

readData()  : string

Reads the data a line carries, which starts at its thirteenth column.

readEntryId()  : string

Reads the identifier out of an ENTRY line. The words after it name the kind of record rather than the record itself - "C00031 Compound", "T01001 Complete Genome" - so the identifier is the first word, or for an enzyme the two words "EC" and its number ("EC 2.7.1.1 Enzyme").

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

Gathers a record into its fields : one entry per label, holding the data of its own line and of every continuation line below it.

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

Reads a field listing one item per line, a trailing ";" dropped. A long item wraps onto a line indented past the column the items start at, which continues it.

readLabel()  : string

Reads the label a line carries in its first twelve columns.

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

Splits the lines of a field into the whitespace-separated identifiers they list.

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

Reads the NAME field, which gives the record its preferred name first and its synonyms after. A semicolon separates them, whether they sit on one line or on several.