pgb_liv\php_ms\Core\Identification

Class for spectra identification object, provides storage for assigning a modifiable sequence and scoring.

Synopsis

class Identification {
}

Coverage

Methods 100% 12 / 12
Lines 100% 23 / 23

Violations

Checkstyle

Line Column Severity Message
159 1 error Multi-line function call not indented correctly; expected 12 spaces but found 16
159 101 error Closing parenthesis of a multi-line function call must be on a line by itself
185 1 error Multi-line function call not indented correctly; expected 12 spaces but found 16
185 94 error Closing parenthesis of a multi-line function call must be on a line by itself

Members

private

  • $ionsMatched — int
    Number of ions matched from a search result
  • $rank — int
    The rank of this identification in a collection
  • $scores — array
    Map of identification scores
  • $sequence — pgb_liv\php_ms\Core\ModifiableSequenceInterface
    Sequence assigned to this identification

Methods

public

  • clearScores() — Clears all scores held by this instance.
  • getIonsMatched() — Gets the number of ions matched
  • getPeptide() — Gets the peptide associated with this identification
  • getRank() — Gets the rank value for this instance
  • getScore() — Gets the value for a score identified by the key that was set when setScore was called.
  • getScores() — Gets the scores for this identification as an associative array.
  • getSequence() — Gets the sequence associated with this identification
  • setIonsMatched() — Sets the the number of fragment ions matched
  • setPeptide() — Sets the peptide for this identification
  • setRank() — Sets the rank for this instance
  • setScore() — Sets the score for this identification, a key must be specified that can be used for retreiving the score type later.
  • setSequence() — Sets the sequence for this identification

History