jbrowse-plugin-msaview 2.2.2 → 2.2.4

package/src/MsaViewPanel/pairwiseAlignment.test.ts

@@ -0,0 +1,140 @@
+import { describe, expect, test } from 'vitest'
+
+import {
+  buildAlignmentMaps,
+  needlemanWunsch,
+  runPairwiseAlignment,
+} from './pairwiseAlignment'
+
+describe('needlemanWunsch', () => {
+  test('identical sequences align perfectly', () => {
+    const result = needlemanWunsch('MKAA', 'MKAA')
+    expect(result.alignedSeq1).toBe('MKAA')
+    expect(result.alignedSeq2).toBe('MKAA')
+    expect(result.score).toBeGreaterThan(0)
+  })
+
+  test('aligned sequences have same length', () => {
+    const result = needlemanWunsch('MKAAYLSMFG', 'MKAYLSMFG')
+    expect(result.alignedSeq1.length).toBe(result.alignedSeq2.length)
+  })
+
+  test('aligned sequences preserve original characters', () => {
+    const seq1 = 'MKAAYLSMFG'
+    const seq2 = 'MKAYLSMFG'
+    const result = needlemanWunsch(seq1, seq2)
+    expect(result.alignedSeq1.replaceAll('-', '')).toBe(seq1)
+    expect(result.alignedSeq2.replaceAll('-', '')).toBe(seq2)
+  })
+
+  test('handles empty sequences', () => {
+    const result = needlemanWunsch('', '')
+    expect(result.alignedSeq1).toBe('')
+    expect(result.alignedSeq2).toBe('')
+  })
+
+  test('handles one empty sequence', () => {
+    const result = needlemanWunsch('MKA', '')
+    expect(result.alignedSeq1.replaceAll('-', '')).toBe('MKA')
+    expect(result.alignedSeq2.replaceAll('-', '')).toBe('')
+    expect(result.alignedSeq1.length).toBe(result.alignedSeq2.length)
+  })
+})
+
+describe('runPairwiseAlignment', () => {
+  test('returns PairwiseAlignment format', () => {
+    const result = runPairwiseAlignment('MKAA', 'MKAA')
+    expect(result.consensus).toBeDefined()
+    expect(result.alns).toHaveLength(2)
+    expect(result.alns[0].id).toBe('msa')
+    expect(result.alns[1].id).toBe('structure')
+  })
+
+  test('consensus marks matches with pipe', () => {
+    const result = runPairwiseAlignment('MKAA', 'MKAA')
+    expect(result.consensus).toBe('||||')
+  })
+
+  test('consensus marks gaps with space', () => {
+    const result = runPairwiseAlignment('MKAA', 'MKA')
+    expect(result.consensus).toContain(' ')
+  })
+
+  test('consensus marks mismatches with space', () => {
+    const result = runPairwiseAlignment('MKAA', 'MKBA')
+    // A vs B should be a space in consensus
+    expect(result.consensus).toContain(' ')
+  })
+})
+
+describe('buildAlignmentMaps', () => {
+  test('builds bidirectional maps for identical sequences', () => {
+    const alignment = runPairwiseAlignment('MKAA', 'MKAA')
+    const { seq1ToSeq2, seq2ToSeq1 } = buildAlignmentMaps(alignment)
+
+    expect(seq1ToSeq2.get(0)).toBe(0)
+    expect(seq1ToSeq2.get(1)).toBe(1)
+    expect(seq1ToSeq2.get(2)).toBe(2)
+    expect(seq1ToSeq2.get(3)).toBe(3)
+
+    expect(seq2ToSeq1.get(0)).toBe(0)
+    expect(seq2ToSeq1.get(1)).toBe(1)
+    expect(seq2ToSeq1.get(2)).toBe(2)
+    expect(seq2ToSeq1.get(3)).toBe(3)
+  })
+
+  test('maps are inverses of each other for matched positions', () => {
+    const alignment = runPairwiseAlignment('MKAAYLSMFG', 'MKAYLSMFG')
+    const { seq1ToSeq2, seq2ToSeq1 } = buildAlignmentMaps(alignment)
+
+    // For every mapped position, the inverse should return the original
+    for (const [pos1, pos2] of seq1ToSeq2) {
+      expect(seq2ToSeq1.get(pos2)).toBe(pos1)
+    }
+  })
+
+  test('handles gaps correctly - positions without counterpart are not in map', () => {
+    // Aligning 'MKAAA' with 'MKA' should result in gaps
+    const alignment = runPairwiseAlignment('MKAAA', 'MKA')
+    const { seq1ToSeq2 } = buildAlignmentMaps(alignment)
+
+    // seq1 has 5 positions, seq2 has 3
+    // Only matched positions should be in the map
+    expect(seq1ToSeq2.size).toBeLessThanOrEqual(3)
+  })
+
+  test('handles real protein sequence alignment', () => {
+    const msaSeq = 'MKAAYLSMFGKEDHKPFGDDEVELFRAVPGLKLKIAG'
+    const structureSeq = 'MKAAYLSMFGKEDHKPFGDDEVELFRAVPGLKLKIAG'
+
+    const alignment = runPairwiseAlignment(msaSeq, structureSeq)
+    const { seq1ToSeq2, seq2ToSeq1 } = buildAlignmentMaps(alignment)
+
+    // Identical sequences should have 1:1 mapping
+    expect(seq1ToSeq2.size).toBe(msaSeq.length)
+    expect(seq2ToSeq1.size).toBe(structureSeq.length)
+
+    // Check a few positions
+    expect(seq1ToSeq2.get(0)).toBe(0)
+    expect(seq1ToSeq2.get(10)).toBe(10)
+    expect(seq2ToSeq1.get(20)).toBe(20)
+  })
+
+  test('handles sequences with insertions/deletions', () => {
+    // MSA sequence has an extra 'X' in the middle
+    const msaSeq = 'MKAXYLSMFG'
+    const structureSeq = 'MKAYLSMFG'
+
+    const alignment = runPairwiseAlignment(msaSeq, structureSeq)
+    const { seq1ToSeq2 } = buildAlignmentMaps(alignment)
+
+    // Positions before the insertion should map correctly
+    expect(seq1ToSeq2.get(0)).toBe(0) // M
+    expect(seq1ToSeq2.get(1)).toBe(1) // K
+    expect(seq1ToSeq2.get(2)).toBe(2) // A
+
+    // The mapping should handle the offset after insertion
+    // (exact behavior depends on alignment algorithm)
+    expect(seq1ToSeq2.size).toBeLessThanOrEqual(structureSeq.length)
+  })
+})