react-msaview 4.4.5 → 4.5.0

package/src/neighborJoining.test.ts

@@ -0,0 +1,129 @@
+import { describe, expect, test } from 'vitest'
+
+import { calculateNeighborJoiningTree } from './neighborJoining'
+
+describe('calculateNeighborJoiningTree', () => {
+  test('generates valid Newick tree for 2 sequences', () => {
+    const rows: [string, string][] = [
+      ['seq1', 'MKAA'],
+      ['seq2', 'MKAA'],
+    ]
+    const tree = calculateNeighborJoiningTree(rows)
+
+    expect(tree).toMatch(/;$/)
+    expect(tree).toContain('seq1')
+    expect(tree).toContain('seq2')
+  })
+
+  test('generates valid Newick tree for 3 sequences', () => {
+    const rows: [string, string][] = [
+      ['human', 'MKAAYLSMFG'],
+      ['mouse', 'MKAAYLSMFG'],
+      ['chicken', 'MKAAFLSMFG'],
+    ]
+    const tree = calculateNeighborJoiningTree(rows)
+
+    expect(tree).toMatch(/;$/)
+    expect(tree).toContain('human')
+    expect(tree).toContain('mouse')
+    expect(tree).toContain('chicken')
+    expect(tree).toContain('(')
+    expect(tree).toContain(')')
+  })
+
+  test('generates valid Newick tree for 4 sequences', () => {
+    const rows: [string, string][] = [
+      ['A', 'MKAAYLSMFGKED'],
+      ['B', 'MKAAYLSMFGKED'],
+      ['C', 'MKAAFLSMFGKEE'],
+      ['D', 'MKAAFLSMFGKEE'],
+    ]
+    const tree = calculateNeighborJoiningTree(rows)
+
+    expect(tree).toMatch(/;$/)
+    expect(tree).toContain('A')
+    expect(tree).toContain('B')
+    expect(tree).toContain('C')
+    expect(tree).toContain('D')
+  })
+
+  test('includes branch lengths in tree', () => {
+    const rows: [string, string][] = [
+      ['seq1', 'MKAAYLSMFG'],
+      ['seq2', 'MKAAFLSMFG'],
+      ['seq3', 'MKBBFLSMFG'],
+    ]
+    const tree = calculateNeighborJoiningTree(rows)
+
+    // Branch lengths are formatted as :0.123456
+    expect(tree).toMatch(/:\d+\.\d+/)
+  })
+
+  test('throws error for less than 2 sequences', () => {
+    const rows: [string, string][] = [['seq1', 'MKAA']]
+    expect(() => calculateNeighborJoiningTree(rows)).toThrow(
+      'Need at least 2 sequences',
+    )
+  })
+
+  test('handles sequences with gaps', () => {
+    const rows: [string, string][] = [
+      ['seq1', 'MK-AYLSMFG'],
+      ['seq2', 'MKAAYLSMFG'],
+      ['seq3', 'MKA-YLSMFG'],
+    ]
+    const tree = calculateNeighborJoiningTree(rows)
+
+    expect(tree).toMatch(/;$/)
+    expect(tree).toContain('seq1')
+    expect(tree).toContain('seq2')
+    expect(tree).toContain('seq3')
+  })
+
+  test('handles special characters in sequence names', () => {
+    const rows: [string, string][] = [
+      ['seq:1', 'MKAA'],
+      ['seq(2)', 'MKAA'],
+    ]
+    const tree = calculateNeighborJoiningTree(rows)
+
+    expect(tree).toMatch(/;$/)
+    // Special characters should be escaped
+    expect(tree).not.toMatch(/seq:1/)
+    expect(tree).not.toMatch(/seq\(2\)/)
+  })
+
+  test('identical sequences have zero distance', () => {
+    const rows: [string, string][] = [
+      ['seq1', 'MKAAYLSMFG'],
+      ['seq2', 'MKAAYLSMFG'],
+    ]
+    const tree = calculateNeighborJoiningTree(rows)
+
+    // Identical sequences should have equal branch lengths
+    const match = tree.match(/:(\d+\.\d+)/g)
+    expect(match).not.toBeNull()
+    if (match) {
+      const lengths = match.map(m => parseFloat(m.slice(1)))
+      // Branch lengths should be small or zero for identical sequences
+      for (const len of lengths) {
+        expect(len).toBeGreaterThanOrEqual(0)
+      }
+    }
+  })
+
+  test('more divergent sequences have larger distances', () => {
+    const rows: [string, string][] = [
+      ['similar1', 'MKAAYLSMFGKED'],
+      ['similar2', 'MKAAYLSMFGKED'],
+      ['different', 'WWWWWWWWWWWWW'],
+    ]
+    const tree = calculateNeighborJoiningTree(rows)
+
+    expect(tree).toMatch(/;$/)
+    // The tree should be valid even with very different sequences
+    expect(tree).toContain('similar1')
+    expect(tree).toContain('similar2')
+    expect(tree).toContain('different')
+  })
+})