Class ReplicationFork

constructor

• new ReplicationFork(position?, dnaLength, organism): ReplicationFork

• Creates a new replication fork.

  Parameters

  • position: number = 0

    Current position of the fork (0-based)
  • dnaLength: number

    Total length of DNA being replicated
  • organism: OrganismProfile

    Organism profile for biological constraints

  Returns ReplicationFork

  Throws

  Error if parameters are invalid

Readonly dnaLength

Readonly organism

position

advance

• advance(basePairs): number

• Advances the fork by the specified number of base pairs.

  Parameters

  • basePairs: number

    Number of base pairs to advance

  Returns number

  New position after advancement

  Throws

  Error if advancement would exceed DNA length

canAdvance

• canAdvance(): boolean

• Checks if replication can advance further.

  Returns boolean

copy

• copy(): ReplicationFork

• Creates a copy of this replication fork.

  Returns ReplicationFork

equals

• equals(other): boolean

• Compares this fork with another for equality.

  Parameters

  • other: ReplicationFork

  Returns boolean

getCompletionPercentage

• getCompletionPercentage(): number

• Gets the completion percentage of replication (0-100).

  Returns number

getCurrentSpeed

• getCurrentSpeed(): number

• Gets the current replication speed based on organism profile. Returns speed in base pairs per second.

  Returns number

getEstimatedCompletionTime

• getEstimatedCompletionTime(): number

• Gets the theoretical time to complete replication at maximum speed. Returns time in seconds.

  Returns number

getExpectedFragmentCount

• getExpectedFragmentCount(): number

• Calculates how many Okazaki fragments are expected for the remaining distance.

  Returns number

getExpectedFragmentSize

• getExpectedFragmentSize(): number

• Gets an expected Okazaki fragment size for this organism. Returns a random size within the organism's biological range.

  Returns number

getExpectedPrimerLength

• getExpectedPrimerLength(): number

• Gets an expected RNA primer length for this organism. Returns a random length within the organism's biological range.

  Returns number

getRemainingDistance

• getRemainingDistance(): number

• Gets the remaining distance to replicate.

  Returns number

getStatistics

• getStatistics(): {
      completionPercentage: number;
      estimatedTimeRemaining: number;
      expectedFragmentsRemaining: number;
      organismType: string;
      position: number;
      remainingDistance: number;
      speed: number;
      totalLength: number;
  }

• Gets current replication statistics.

  Returns {
      completionPercentage: number;
      estimatedTimeRemaining: number;
      expectedFragmentsRemaining: number;
      organismType: string;
      position: number;
      remainingDistance: number;
      speed: number;
      totalLength: number;
  }

  • completionPercentage: number

  • estimatedTimeRemaining: number

  • expectedFragmentsRemaining: number

  • organismType: string

  • position: number

  • remainingDistance: number

  • speed: number

  • totalLength: number

isComplete

• isComplete(): boolean

• Checks if replication is complete.

  Returns boolean

isConsistentWith

• isConsistentWith(fragmentEnd): boolean

• Checks if the fork position is valid relative to fragment boundaries.

  Parameters

  • fragmentEnd: number

    End position of the last completed fragment

  Returns boolean

  True if fork position is consistent

safeAdvance

• safeAdvance(basePairs): number

• Safely advances the fork, capping at DNA length.

  Parameters

  • basePairs: number

    Number of base pairs to advance

  Returns number

  Actual distance advanced

toString

• toString(): string

• Returns a string representation of this replication fork.

  Returns string

Static create

• create(position, dnaLength, organism): ValidationResult<ReplicationFork>

• Creates a replication fork with validation.

  Parameters

  • position: number

    Starting position
  • dnaLength: number

    Total DNA length
  • organism: OrganismProfile

    Organism profile

  Returns ValidationResult<ReplicationFork>

  ValidationResult containing ReplicationFork or error