AminoAcidSequence
extends AbstractMolecularSequence
in package
Accepts the twenty amino acids in single-letter format, plus the two symbols already handled by SequenceManager::charge() and SequenceManager::chemicalGroup() : X for an unknown residue and the asterisk for a stop codon.
Class AminoAcidSequence
Tags
Table of Contents
Constants
- STOP : mixed = "*"
- The symbol marking the end of the translation.
- ALPHABET : mixed = "ACDEFGHIKLMNPQRSTVWYX*"
- Symbols accepted by the value object, overridden by each concrete class.
- MOL_TYPE : mixed = "PROTEIN"
- Molecule type of the value object, overridden by each concrete class.
Methods
- __construct() : mixed
- AbstractMolecularSequence constructor.
- __toString() : string
- Allows the value object to be used wherever the library still expects a raw string.
- countSymbol() : int
- Counts how many times a symbol occurs in the sequence.
- equals() : bool
- Two value objects are equal when they are of the same kind and hold the same symbols.
- getAlphabet() : string
- The symbols accepted by this kind of sequence.
- getLength() : int
- Number of symbols held by the sequence.
- getMolType() : string
- The molecule type, as used by SequenceManager (DNA, RNA, PROTEIN).
- getValue() : string
- The wrapped sequence, normalized.
- hasStop() : bool
- Tells whether the chain holds a stop codon.
- hasUnknownResidue() : bool
- Tells whether the chain holds an unknown residue.
- isEmpty() : bool
- isValid() : bool
- Tells whether every symbol of a string belongs to the alphabet of the value object, without building an instance.
- reverse() : static
- Returns the sequence read from the last symbol to the first one.
- subSequence() : static
- Extracts a portion of the sequence, keeping the same kind of value object.
- truncateAtStop() : AminoAcidSequence
- Returns the residues preceding the first stop codon, the whole chain when there is none.
Constants
STOP
The symbol marking the end of the translation.
public
mixed
STOP
= "*"
ALPHABET
Symbols accepted by the value object, overridden by each concrete class.
protected
mixed
ALPHABET
= "ACDEFGHIKLMNPQRSTVWYX*"
Tags
MOL_TYPE
Molecule type of the value object, overridden by each concrete class.
protected
mixed
MOL_TYPE
= "PROTEIN"
Tags
Methods
__construct()
AbstractMolecularSequence constructor.
public
__construct(string $sSequence) : mixed
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
- $sSequence : string
-
The raw sequence string
Tags
__toString()
Allows the value object to be used wherever the library still expects a raw string.
public
__toString() : string
Return values
stringcountSymbol()
Counts how many times a symbol occurs in the sequence.
public
countSymbol(string $sSymbol) : int
Parameters
- $sSymbol : string
-
A single symbol, case insensitive
Return values
intequals()
Two value objects are equal when they are of the same kind and hold the same symbols.
public
equals(AbstractMolecularSequence $oOther) : bool
Parameters
- $oOther : AbstractMolecularSequence
Return values
boolgetAlphabet()
The symbols accepted by this kind of sequence.
public
getAlphabet() : string
Return values
stringgetLength()
Number of symbols held by the sequence.
public
getLength() : int
Return values
intgetMolType()
The molecule type, as used by SequenceManager (DNA, RNA, PROTEIN).
public
getMolType() : string
Return values
stringgetValue()
The wrapped sequence, normalized.
public
getValue() : string
Return values
stringhasStop()
Tells whether the chain holds a stop codon.
public
hasStop() : bool
Return values
boolhasUnknownResidue()
Tells whether the chain holds an unknown residue.
public
hasUnknownResidue() : bool
Return values
boolisEmpty()
public
isEmpty() : bool
Return values
boolisValid()
Tells whether every symbol of a string belongs to the alphabet of the value object, without building an instance.
public
static isValid(string $sSequence) : bool
Parameters
- $sSequence : string
Return values
boolreverse()
Returns the sequence read from the last symbol to the first one.
public
reverse() : static
Tags
Return values
staticsubSequence()
Extracts a portion of the sequence, keeping the same kind of value object.
public
subSequence(int $iStart[, int|null $iLength = null ]) : static
Parameters
- $iStart : int
-
Zero-based position of the first symbol
- $iLength : int|null = null
-
Number of symbols, until the end when omitted
Tags
Return values
statictruncateAtStop()
Returns the residues preceding the first stop codon, the whole chain when there is none.
public
truncateAtStop() : AminoAcidSequence