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\Amelaye\BioPHP\Domain\Sequence\ValueObject DnaSequence

Accepts the four deoxyribonucleotides and the IUPAC degenerated symbols already tolerated by SequenceTrait::cleanSequence().

Class DnaSequence

Summary

Methods
Properties
Constants
toRna
__construct
getValue
__toString
getMolType
getAlphabet
getLength
isEmpty
equals
subSequence
reverse
countSymbol
isValid
complement
reverseComplement
getGcContent
No public properties found
No public constants found
No protected methods found
No protected properties found
ALPHABET
MOL_TYPE
COMPLEMENTS
No private methods found
No private properties found
No private constants found

Constant

ALPHABET

ALPHABET = ""

Symbols accepted by the value object, overridden by each concrete class.

MOL_TYPE

MOL_TYPE = ""

Molecule type of the value object, overridden by each concrete class.

COMPLEMENTS

COMPLEMENTS = []

Complement of each symbol of the alphabet, overridden by each concrete class.

Methods

toRna()

toRna() : \Amelaye\BioPHP\Domain\Sequence\ValueObject\RnaSequence

Transcribes the sequence, thymine becoming uracil.

Throws

\Amelaye\BioPHP\Domain\Sequence\ValueObject\InvalidSequenceException

Returns

\Amelaye\BioPHP\Domain\Sequence\ValueObject\RnaSequence —

__construct()

__construct(string  $sSequence) : mixed

AbstractMolecularSequence constructor.

Whitespace is stripped and the remaining symbols are upper-cased before validation, so raw lines coming from a GenBank, EMBL or FASTA file can be wrapped as they are read.

Parameters

string $sSequence

The raw sequence string

Throws

\Amelaye\BioPHP\Domain\Sequence\ValueObject\InvalidSequenceException

When a symbol does not belong to the alphabet

Returns

mixed —

getValue()

getValue() : string

The wrapped sequence, normalized.

Returns

string —

__toString()

__toString() : string

Allows the value object to be used wherever the library still expects a raw string.

Returns

string —

getMolType()

getMolType() : string

The molecule type, as used by SequenceManager (DNA, RNA, PROTEIN).

Returns

string —

getAlphabet()

getAlphabet() : string

The symbols accepted by this kind of sequence.

Returns

string —

getLength()

getLength() : int

Number of symbols held by the sequence.

Returns

int —

isEmpty()

isEmpty() : bool

Returns

bool —

equals()

equals(\Amelaye\BioPHP\Domain\Sequence\ValueObject\AbstractMolecularSequence  $oOther) : bool

Two value objects are equal when they are of the same kind and hold the same symbols.

Parameters

\Amelaye\BioPHP\Domain\Sequence\ValueObject\AbstractMolecularSequence $oOther

Returns

bool —

subSequence()

subSequence(int  $iStart, int|null  $iLength = null) : static

Extracts a portion of the sequence, keeping the same kind of value object.

Parameters

int $iStart

Zero-based position of the first symbol
int|null $iLength

Number of symbols, until the end when omitted

Throws

\Amelaye\BioPHP\Domain\Sequence\ValueObject\InvalidSequenceException

Returns

static —

reverse()

reverse() : static

Returns the sequence read from the last symbol to the first one.

Throws

\Amelaye\BioPHP\Domain\Sequence\ValueObject\InvalidSequenceException

Returns

static —

countSymbol()

countSymbol(string  $sSymbol) : int

Counts how many times a symbol occurs in the sequence.

Parameters

string $sSymbol

A single symbol, case insensitive

Returns

int —

isValid()

isValid(string  $sSequence) : bool

Tells whether every symbol of a string belongs to the alphabet of the value object, without building an instance.

Parameters

string $sSequence

Returns

bool —

complement()

complement() : static

Returns the genetic complement of the sequence, degenerated symbols included.

Throws

\Amelaye\BioPHP\Domain\Sequence\ValueObject\InvalidSequenceException

Returns

static —

reverseComplement()

reverseComplement() : static

Returns the complement of the sequence read backwards, which is the strand facing it.

Throws

\Amelaye\BioPHP\Domain\Sequence\ValueObject\InvalidSequenceException

Returns

static —

getGcContent()

getGcContent() : float

Proportion of guanine and cytosine in the sequence, expressed as a percentage. The degenerated symbol S, which stands for G or C, is counted as well.

Returns

float —

0 when the sequence is empty