var data = require('../lib/data')
var test = require('tape')
var needleman = require('../lib/index')

test('run', function (t) {
  let v = 'GCATGCU'
  let w = 'GATTACA'
  let scores = { match: +1, mismatch: -1 }
  let scoringMatrix = data.scoringMatrix({ v, w, scores })
  let res = needleman.run(v, w, { scoringMatrix })
  t.equal(res.score, 0)
  t.equal(res.vAligned, 'GCA-TGCU')
  t.equal(res.wAligned, 'G-ATTACA')

  scoringMatrix = data.scoringMatrix({ v, w, name: 'PAM250' })
  res = needleman.run(v, w, { scoringMatrix })
  t.equal(res.score, 20)
  t.equal(res.vAligned, 'GCA-TGCU')
  t.equal(res.wAligned, 'G-ATTACA')

  t.end()
})

var data = require('../lib/data')
var test = require('tape')
var needleman = require('../lib/index')

test('run', function (t) {
  let v = 'GCATGCU'
  let w = 'GATTACA'
  let scores = { match: +1, mismatch: -1 }
  let scoringMatrix = data.scoringMatrix({ v, w, scores })
  let res = needleman.run(v, w, { scoringMatrix })
  t.equal(res.score, 0)
  t.equal(res.vAligned, 'GCA-TGCU')
  t.equal(res.wAligned, 'G-ATTACA')
  t.end()
})

--- 
+++ 
@@ -11,5 +11,12 @@
   t.equal(res.score, 0)
   t.equal(res.vAligned, 'GCA-TGCU')
   t.equal(res.wAligned, 'G-ATTACA')
+
+  scoringMatrix = data.scoringMatrix({ v, w, name: 'PAM250' })
+  res = needleman.run(v, w, { scoringMatrix })
+  t.equal(res.score, 20)
+  t.equal(res.vAligned, 'GCA-TGCU')
+  t.equal(res.wAligned, 'G-ATTACA')
+
   t.end()
 })
Test a run with PAM250
