pgb_liv\php_ms\Core\Peptide

A peptide object that encapsulates a modifiable sequence and provides additional properties

Synopsis

class Peptide implements ModifiableSequenceInterface {
  • // constants
  • const AMINO_ACID_X_MASS = 0;
  • const AMINO_ACID_B_MASS = 0;
  • const AMINO_ACID_Z_MASS = 0;
  • const HYDROGEN_MASS = ChemicalConstants::HYDROGEN_MASS;
  • const OXYGEN_MASS = ChemicalConstants::OXYGEN_MASS;
  • const NITROGEN_MASS = ChemicalConstants::NITROGEN_MASS;
  • const PROTON_MASS = PhysicalConstants::PROTON_MASS;
  • const N_TERM_MASS = 1.007875;
  • const C_TERM_MASS = 17.00278;
}

Hierarchy

Uses

Implements

Coverage

Methods 80% 4 / 5
Lines 95.83% 46 / 48

Violations

PHPMessDetector

Line Rule Message
132 StaticAccess Avoid using static access to class 'pgb_liv\php_ms\Core\AminoAcidComposition' in method 'getMolecularFormula'.

Checkstyle

Line Column Severity Message
92 1 error Multi-line function call not indented correctly; expected 12 spaces but found 16
92 90 error Closing parenthesis of a multi-line function call must be on a line by itself

Tasks

Line Task
276+ This method does not yet respect modification absolute location data

Constants

Name Value
AMINO_ACID_X_MASS 0
AMINO_ACID_B_MASS 0
AMINO_ACID_Z_MASS 0
HYDROGEN_MASS ChemicalConstants::HYDROGEN_MASS
OXYGEN_MASS ChemicalConstants::OXYGEN_MASS
NITROGEN_MASS ChemicalConstants::NITROGEN_MASS
PROTON_MASS PhysicalConstants::PROTON_MASS
N_TERM_MASS 1.007875
C_TERM_MASS 17.00278

Members

private

  • $missedCleavageCount

Methods

public

Inherited from pgb_liv\php_ms\Core\ModifiableSequenceTrait

public

Inherited from pgb_liv\php_ms\Core\ProteinTrait

public

  • addProtein() — Add a new protein mapping to this object.
  • addProteinEntry() — This provides direct access to add new entity records and should be used when subclasses are expected
  • getProteins() — Gets the set of proteins that this object links to

History