Documentation

ParseKeggOrthologManager extends ParseKeggAbstractManager

in package

• Amelaye
• BioPHP
• Domain
• Parser

Class ParseKeggOrthologManager An ortholog record groups the genes of different organisms that descend from one common ancestral gene and do the same job, which is what lets a pathway be carried from one species to another.

Tags

author

Amélie DUVERNET aka Amelaye amelieonline@gmail.com

Table of Contents

Properties

$entry  : string

$names  : array<string|int, mixed>

$classification  : array<string|int, mixed>

$dbLinks  : array<string|int, mixed>

$definition  : string

$genes  : array<string|int, mixed>

One entry per organism, e.g. "HSA: 3101 3098".

Methods

__construct()  : mixed

Constructor.

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

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

getDefinition()  : string

getEntry()  : string

getEntryId()  : string

Extracts the identifier uniquely naming a KEGG record.

getFormat()  : string

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

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

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.

parseDataFile()  : Sequence

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

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.

readData()  : string

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

readEntryId()  : string

Reads the identifier out of an ENTRY line. Its last word names the kind of record rather than the record itself - "C00031 Compound", "EC 2.7.1.1 Enzyme" - so the identifier is what comes before it, which for an enzyme is the two words "EC" and its number.

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.

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.