\Amelaye\BioPHP\Domain\Parser\Service ParseKeggEnzymeManager

getFormat()

getFormat() : string

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

Returns

parseDataFile()

parseDataFile(array  $aFlines) : \Amelaye\BioPHP\Domain\Sequence\Entity\Sequence

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

Parameters

Throws

\Exception

Returns

$oSequence

getClassification()

getClassification() : array

Returns

getSysname()

getSysname() : string

Returns

getReactions()

getReactions() : array

Returns

getSubstrates()

getSubstrates() : array

Returns

getProducts()

getProducts() : array

Returns

getComment()

getComment() : string

Returns

getPathways()

getPathways() : array

Returns

getOrthologs()

getOrthologs() : array

Returns

getGenes()

getGenes() : array

Returns

getDiseases()

getDiseases() : array

Returns

getMotifs()

getMotifs() : array

Returns

getStructures()

getStructures() : array

Returns

getDbLinks()

getDbLinks() : array

Returns

__construct()

__construct() : mixed

Constructor.

Returns

isEntryStart()

isEntryStart(string  $sLine) : bool

Tells whether a line opens a new KEGG record.

Parameters

Returns

isEntryEnd()

isEntryEnd(string  $sLine) : bool

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

Parameters

Returns

getEntryId()

getEntryId(array  $aFlines, string  $sLine) : string

Extracts the identifier uniquely naming a KEGG record.

Parameters

Returns

getEntry()

getEntry() : string

Returns

getNames()

getNames() : array

Returns

readEntryId()

readEntryId(string  $sData) : 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.

Parameters

Returns

readLabel()

readLabel(string  $sLine) : string

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

Parameters

Returns

readData()

readData(string  $sLine) : string

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

Parameters

Returns

readFields()

readFields(array  $aFlines) : array

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

Parameters

Returns

joinLines()

joinLines(array  $aLines) : 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.

Parameters

Returns

splitTokens()

splitTokens(array  $aLines) : array

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

Parameters

Returns

parsePathways()

parsePathways(array  $aLines) : array

Reads a PATHWAY field into pairs of map identifier and pathway name.

Format : PATHWAY PATH: map00010 Glycolysis / Gluconeogenesis

Parameters

Returns

parseDbLinks()

parseDbLinks(array  $aLines) : array

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

Format : DBLINKS CAS: 50-99-7

Parameters

Returns

splitLines()

splitLines(array  $aLines) : array

Reads a field listing one item per line, a long item wrapping onto the next : a wrapped line is indented past the column the items start at.

Parameters

Returns

splitStructures()

splitStructures(array  $aLines) : array

Reads the STRUCTURES field, which names the database holding the structures before listing them : only the identifiers are kept.

Format : STRUCTURES PDB: 1HKB 1HKC 1IG8

Parameters

Returns

splitClasses()

splitClasses(array  $aLines) : array

Reads the CLASS field, whose levels are separated by semicolons and may wrap over lines.

Parameters

Returns