import { describe, expect, it } from 'vitest'
import { useSequenceUtils } from '../../composables/useSequenceUtils'

const { findSequenceProblems } = useSequenceUtils()

describe('useSequenceUtils findSequenceProblems', () => {
  it('should name each invalid character once in upper case when the sequence has characters outside the alphabet', () => {
    expect(findSequenceProblems('ATGxXZ', 'dna').invalidCharacters).toEqual(['X', 'Z'])
  })

  it('should not report whitespace as invalid when the sequence is formatted', () => {
    expect(findSequenceProblems('ATG CA\nTT', 'dna').invalidCharacters).toEqual([])
  })

  it('should count N bases as ambiguous when the sequence is DNA', () => {
    expect(findSequenceProblems('ATNnG', 'dna').ambiguousBases).toBe(2)
  })

  it('should not count N as ambiguous when the sequence is protein', () => {
    expect(findSequenceProblems('MNNK', 'protein').ambiguousBases).toBe(0)
  })
})

describe('useSequenceUtils detectSequenceType', () => {
  it('should detect DNA when a DNA sequence is split across lines', () => {
    expect(useSequenceUtils().detectSequenceType('ACGT\nACGT')).toBe('dna')
  })
})