Class OkazakiFragment

constructor

• new OkazakiFragment(id, startPosition, endPosition, primer, isPrimerRemoved?, isLigated?): OkazakiFragment

• Creates a new Okazaki fragment.

  Parameters

  • id: string

    Unique identifier for this fragment
  • startPosition: number

    Starting position (0-based, inclusive)
  • endPosition: number

    Ending position (0-based, exclusive)
  • primer: RNAPrimer

    RNA primer that initiated this fragment
  • isPrimerRemoved: boolean = false

    Whether RNA primer has been removed
  • isLigated: boolean = false

    Whether fragment has been ligated to previous fragment

  Returns OkazakiFragment

  Throws

  Error if positions are invalid or fragment size is unrealistic

Readonly endPosition

Readonly id

isLigated

isPrimerRemoved

Readonly primer

Readonly startPosition

getDNA

• getDNA(): undefined | DNA

• Gets the DNA object for this fragment (if sequence is set).

  Returns undefined | DNA

getLength

• getLength(): number

• Gets the length of this fragment in base pairs.

  Returns number

getProcessingStatus

• getProcessingStatus(): {
      complete: boolean;
      ligated: boolean;
      nextStep: null | string;
      primerRemoved: boolean;
  }

• Gets the processing status of this fragment.

  Returns {
      complete: boolean;
      ligated: boolean;
      nextStep: null | string;
      primerRemoved: boolean;
  }

  • complete: boolean

  • ligated: boolean

  • nextStep: null | string

  • primerRemoved: boolean

getSequence

• getSequence(): undefined | string

• Gets the DNA sequence of this fragment (if set).

  Returns undefined | string

isAdjacentTo

• isAdjacentTo(other): boolean

• Checks if this fragment is adjacent to another fragment.

  Parameters

  • other: OkazakiFragment

    Other fragment to check

  Returns boolean

  True if fragments are adjacent (this fragment comes before other)

isComplete

• isComplete(): boolean

• Checks if this fragment is completely processed. A fragment is complete when its primer is removed and it's ligated.

  Returns boolean

ligate

• ligate(): void

• Marks this fragment as ligated to the previous fragment. This simulates DNA ligase activity.

  Returns void

needsProcessing

• needsProcessing(): boolean

• Checks if this fragment needs processing.

  Returns boolean

overlapsWith

• overlapsWith(other): boolean

• Checks if this fragment overlaps with another fragment.

  Parameters

  • other: OkazakiFragment

    Other fragment to check

  Returns boolean

  True if fragments overlap

removePrimer

• removePrimer(): void

• Marks the primer as removed. This simulates 5' to 3' exonuclease activity.

  Returns void

setSequence

• setSequence(sequence): void

• Sets the DNA sequence for this fragment.

  Parameters

  • sequence: string

    DNA sequence

  Returns void

  Throws

  Error if sequence length doesn't match fragment length

toString

• toString(): string

• Returns a string representation of this fragment.

  Returns string

validateForOrganism

• validateForOrganism(organism): ValidationResult<boolean>

• Validates fragment against organism-specific constraints.

  Parameters

  • organism: OrganismProfile

    Organism profile to validate against

  Returns ValidationResult<boolean>

  Validation result

Static create

• create(id, startPosition, endPosition, primer, isPrimerRemoved?, isLigated?): ValidationResult<OkazakiFragment>

• Creates an Okazaki fragment with validation.

  Parameters

  • id: string

    Unique identifier
  • startPosition: number

    Start position
  • endPosition: number

    End position
  • primer: RNAPrimer

    RNA primer
  • isPrimerRemoved: boolean = false

    Primer removal status
  • isLigated: boolean = false

    Ligation status

  Returns ValidationResult<OkazakiFragment>

  ValidationResult containing OkazakiFragment or error

Static generateRandom

• generateRandom(id, startPosition, organism): ValidationResult<OkazakiFragment>

• Generates a random Okazaki fragment for the given organism.

  Parameters

  • id: string

    Fragment identifier
  • startPosition: number

    Starting position
  • organism: OrganismProfile

    Organism profile for size constraints

  Returns ValidationResult<OkazakiFragment>

  ValidationResult containing random OkazakiFragment