ParseUnigeneManager
in package
implements
ParseDatabaseInterface
Class ParseUnigeneManager A UniGene entry groups the sequences believed to come from one gene. It carries no sequence of its own, so this class exposes plain scalars rather than the Sequence/Feature entities of ParseDbAbstractManager. The PROTSIM lines are kept raw, as ParsePrositeManager does for its matrix field: their layout varies and the original BioPHP parser never decomposed them.
Tags
Table of Contents
Interfaces
- ParseDatabaseInterface
- Interface ParseDatabaseInterface
Properties
- $clusterId : string
- $expression : array<string|int, mixed>
- $protSims : array<string|int, mixed>
- $seqCount : int
- $title : string
Methods
- __construct() : mixed
- Constructor.
- getClusterId() : string
- getEntryId() : string
- Extracts the identifier uniquely naming a UniGene entry.
- getExpression() : array<string|int, mixed>
- The tissues the cluster was observed in, one entry per semicolon separated item.
- getFormat() : string
- The name this format is known by in the collection records and in DatabaseParserFactory.
- getProtSims() : array<string|int, mixed>
- The PROTSIM lines, kept as written.
- getSeqCount() : int
- getTitle() : string
- isEntryEnd() : bool
- Tells whether a line closes a UniGene entry.
- isEntryStart() : bool
- Tells whether a line opens a new UniGene entry.
- parseDataFile() : Sequence
- Parses a UniGene data file and populates this manager's fields.
Properties
$clusterId
private
string
$clusterId
= ""
$expression
private
array<string|int, mixed>
$expression
= []
$protSims
private
array<string|int, mixed>
$protSims
= []
$seqCount
private
int
$seqCount
= 0
$title
private
string
$title
= ""
Methods
__construct()
Constructor.
public
__construct() : mixed
getClusterId()
public
getClusterId() : string
Return values
stringgetEntryId()
Extracts the identifier uniquely naming a UniGene entry.
public
static getEntryId(array<string|int, mixed> $aFlines, string $sLine) : string
Parameters
- $aFlines : array<string|int, mixed>
-
The whole file, buffered
- $sLine : string
-
The line opening the entry
Return values
stringgetExpression()
The tissues the cluster was observed in, one entry per semicolon separated item.
public
getExpression() : array<string|int, mixed>
Return values
array<string|int, mixed>getFormat()
The name this format is known by in the collection records and in DatabaseParserFactory.
public
static getFormat() : string
Return values
stringgetProtSims()
The PROTSIM lines, kept as written.
public
getProtSims() : array<string|int, mixed>
Return values
array<string|int, mixed>getSeqCount()
public
getSeqCount() : int
Return values
intgetTitle()
public
getTitle() : string
Return values
stringisEntryEnd()
Tells whether a line closes a UniGene entry.
public
static isEntryEnd(string $sLine) : bool
Parameters
- $sLine : string
-
The line to analyze
Return values
boolisEntryStart()
Tells whether a line opens a new UniGene entry.
public
static isEntryStart(string $sLine) : bool
Parameters
- $sLine : string
-
The line to analyze
Return values
boolparseDataFile()
Parses a UniGene data file and populates this manager's fields.
public
parseDataFile(array<string|int, mixed> $aFlines) : Sequence
Parameters
- $aFlines : array<string|int, mixed>
-
The lines the script has to parse
Tags
Return values
Sequence —$oSequence