react-msaview 6.5.0 → 8.0.0

package/dist/useColorContrast.js

@@ -1,13 +0,0 @@
-import { useMemo } from 'react';
-import { useTheme } from '@mui/material';
-import { colorContrast } from './util.js';
-/**
- * Resolves the current theme and a memoized contrast-color scheme for a given
- * color scheme. Shared by the MSA and text-track canvas blocks.
- */
-export function useColorContrast(colorScheme) {
-    const theme = useTheme();
-    const contrastScheme = useMemo(() => colorContrast(colorScheme, theme), [colorScheme, theme]);
-    return { theme, contrastScheme };
-}
-//# sourceMappingURL=useColorContrast.js.map

package/dist/useColorContrast.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"useColorContrast.js","sourceRoot":"","sources":["../src/useColorContrast.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,OAAO,CAAA;AAE/B,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAExC,OAAO,EAAE,aAAa,EAAE,MAAM,WAAW,CAAA;AAEzC;;;GAGG;AACH,MAAM,UAAU,gBAAgB,CAAC,WAAmC;IAClE,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,MAAM,cAAc,GAAG,OAAO,CAC5B,GAAG,EAAE,CAAC,aAAa,CAAC,WAAW,EAAE,KAAK,CAAC,EACvC,CAAC,WAAW,EAAE,KAAK,CAAC,CACrB,CAAA;IACD,OAAO,EAAE,KAAK,EAAE,cAAc,EAAE,CAAA;AAClC,CAAC"}

package/src/clustalX.test.ts

@@ -1,74 +0,0 @@
-import { describe, expect, test } from 'vitest'
-
-import { clustalXColumnColors } from './clustalX.ts'
-import { columnCountsFromColumns } from './columnCounts.ts'
-
-// one alignment column, given top-to-bottom
-function column(letters: string) {
-  return clustalXColumnColors(columnCountsFromColumns([letters]), 0)
-}
-
-const BLUE = 'rgb(128,179,230)'
-const RED = '#d88'
-const GREEN = '#8f8'
-const GREEN_ST = 'rgb(26,204,26)'
-const ORANGE = 'rgb(240, 144, 72)'
-const YELLOW = 'rgb(204, 204, 0)'
-const CYAN = 'rgb(26, 179, 179)'
-
-describe('clustalXColumnColors', () => {
-  test('hydrophobic column (all L) colors the hydrophobic group', () => {
-    expect(column('LLLLLLLLLL')).toEqual({
-      W: BLUE,
-      L: BLUE,
-      V: BLUE,
-      A: BLUE,
-      I: BLUE,
-      M: BLUE,
-      F: BLUE,
-      C: BLUE,
-      S: GREEN_ST,
-      T: GREEN_ST,
-      H: CYAN,
-      Y: CYAN,
-    })
-  })
-
-  test('glycine is always colored when present', () => {
-    expect(column('GGGGGGGGGG')).toEqual({
-      G: ORANGE,
-    })
-  })
-
-  test('proline is always colored, and counts as hydrophobic', () => {
-    expect(column('PPPPPPPPPP')).toEqual({
-      W: BLUE,
-      L: BLUE,
-      V: BLUE,
-      A: BLUE,
-      I: BLUE,
-      M: BLUE,
-      F: BLUE,
-      C: BLUE,
-      S: GREEN_ST,
-      T: GREEN_ST,
-      P: YELLOW,
-      H: CYAN,
-      Y: CYAN,
-    })
-  })
-
-  test('positively charged column (all K)', () => {
-    expect(column('KKKKKKKKKK')).toEqual({
-      K: RED,
-      R: RED,
-      E: 'rgb(192, 72, 192)',
-      D: 'rgb(204, 77, 204)',
-      Q: GREEN,
-    })
-  })
-
-  test('unconserved column produces no colors', () => {
-    expect(column('XXXXXXXXXX')).toEqual({})
-  })
-})

package/src/colSpace.test.ts

@@ -1,67 +0,0 @@
-// @vitest-environment jsdom
-import { expect, test } from 'vitest'
-
-import MSAModelF from './model.ts'
-
-// a ragged alignment: row `a` stops early, so the alignment is as wide as `b`.
-// Column space has to follow the widest row -- the gap analysis already does --
-// or every column past the first row's end becomes unreachable: unscrollable,
-// unhoverable, and missing from the minimap.
-const msa = `>a
-ACGT
->b
-ACGTACGTAC`
-
-function makeModel() {
-  const model = MSAModelF().create({
-    id: 'col-space-test',
-    type: 'MsaView',
-    msaFormat: 'fasta',
-    data: { msa },
-  })
-  model.setWidth(800)
-  return model
-}
-
-test('column space spans the widest row', () => {
-  const model = makeModel()
-  expect(model.numColumns).toBe(10)
-  expect(model.totalWidth).toBe(10 * model.colWidth)
-})
-
-test('the last column agrees with the column statistics', () => {
-  const model = makeModel()
-  expect(model.colStats.numColumns).toBe(model.numColumns)
-  expect(model.conservation).toHaveLength(model.numColumns)
-
-  model.setMousePos(model.numColumns - 1, 1)
-  expect(model.mouseOverColumnStats?.col).toBe(9)
-  expect(model.visibleColToRowLetter('b', 9)).toBe('C')
-})
-
-// enough rows to force the vertical scrollbar, which eats into the width the
-// alignment canvas actually gets
-function makeTallModel() {
-  const names = Array.from({ length: 60 }, (_, i) => `seq${i}`)
-  const model = MSAModelF().create({
-    id: 'col-fit-test',
-    type: 'MsaView',
-    msaFormat: 'fasta',
-    height: 300,
-    data: { msa: names.map(n => `>${n}\n${'ACGT'.repeat(50)}`).join('\n') },
-  })
-  model.setWidth(800)
-  return model
-}
-
-test('fit horizontally leaves every column on screen', () => {
-  const model = makeTallModel()
-  expect(model.showVerticalScrollbar).toBe(true)
-
-  model.fitHorizontally()
-  // the canvas is the msa area minus the scrollbar; fitting to the msa area
-  // alone pushed the last columns past the right edge, with no minimap to
-  // show that anything was cut off
-  expect(model.totalWidth).toBeLessThanOrEqual(model.msaCanvasWidth)
-  expect(model.showHorizontalScrollbar).toBe(false)
-})

package/src/collapseLogic.test.ts

@@ -1,115 +0,0 @@
-import { describe, expect, test } from 'vitest'
-
-import { collapse, find, hierarchy, leaves, sort, sum } from './hierarchy.ts'
-
-import type { NodeWithIds } from './types.ts'
-
-function buildRoot(tree: NodeWithIds, collapsed: string[], showOnly?: string) {
-  let hier = hierarchy(tree, d => d.children)
-  sum(hier, d => (d.children.length > 0 ? 0 : 1))
-  sort(hier, (a, b) => (a.data.length ?? 1) - (b.data.length ?? 1))
-
-  if (showOnly) {
-    const res = find(hier, n => n.data.id === showOnly)
-    if (res) {
-      hier = res
-    }
-  }
-
-  for (const collapsedId of collapsed) {
-    const node = find(hier, n => n.data.id === collapsedId)
-    if (!node) {
-      continue
-    }
-    if (node.children) {
-      collapse(node)
-    } else if (node.parent?.children) {
-      node.parent.children = node.parent.children.filter(
-        c => c.data.id !== collapsedId,
-      )
-    }
-  }
-
-  return hier
-}
-
-function simpleTree(): NodeWithIds {
-  return {
-    id: 'root',
-    name: 'root',
-    children: [
-      {
-        id: 'clade1',
-        name: 'clade1',
-        children: [
-          { id: 'seq1', name: 'seq1', children: [] },
-          { id: 'seq2', name: 'seq2', children: [] },
-        ],
-      },
-      {
-        id: 'clade2',
-        name: 'clade2',
-        children: [
-          { id: 'seq3', name: 'seq3', children: [] },
-          { id: 'seq4', name: 'seq4', children: [] },
-        ],
-      },
-    ],
-  }
-}
-
-describe('collapse logic (mirrors model.root getter)', () => {
-  test('no collapsed nodes returns all leaves', () => {
-    const root = buildRoot(simpleTree(), [])
-    expect(leaves(root).map(n => n.data.name)).toEqual([
-      'seq1',
-      'seq2',
-      'seq3',
-      'seq4',
-    ])
-  })
-
-  test('collapsing a branch hides its children', () => {
-    const root = buildRoot(simpleTree(), ['clade1'])
-    const l = leaves(root).map(n => n.data.name)
-    expect(l).toEqual(['clade1', 'seq3', 'seq4'])
-  })
-
-  test('collapsing a leaf node removes it', () => {
-    const root = buildRoot(simpleTree(), ['seq2'])
-    const l = leaves(root).map(n => n.data.name)
-    expect(l).toEqual(['seq1', 'seq3', 'seq4'])
-  })
-
-  test('collapsing multiple leaves', () => {
-    const root = buildRoot(simpleTree(), ['seq1', 'seq4'])
-    const l = leaves(root).map(n => n.data.name)
-    expect(l).toEqual(['seq2', 'seq3'])
-  })
-
-  test('collapsing a branch and a leaf in another branch', () => {
-    const root = buildRoot(simpleTree(), ['clade1', 'seq3'])
-    const l = leaves(root).map(n => n.data.name)
-    expect(l).toEqual(['clade1', 'seq4'])
-  })
-
-  test('collapsing nonexistent id is a no-op', () => {
-    const root = buildRoot(simpleTree(), ['doesnotexist'])
-    expect(leaves(root).map(n => n.data.name)).toEqual([
-      'seq1',
-      'seq2',
-      'seq3',
-      'seq4',
-    ])
-  })
-
-  test('showOnly focuses on a subtree', () => {
-    const root = buildRoot(simpleTree(), [], 'clade2')
-    expect(leaves(root).map(n => n.data.name)).toEqual(['seq3', 'seq4'])
-  })
-
-  test('showOnly + collapse within subtree', () => {
-    const root = buildRoot(simpleTree(), ['seq3'], 'clade2')
-    expect(leaves(root).map(n => n.data.name)).toEqual(['seq4'])
-  })
-})

package/src/colorSchemes.docs.test.ts

@@ -1,57 +0,0 @@
-import { readFileSync } from 'node:fs'
-
-import { expect, test } from 'vitest'
-
-import colorSchemes from './colorSchemes.ts'
-
-// Guard against doc drift: every color-scheme name listed in the JS embedding
-// docs (USAGE.md) must be a real registered scheme, so a rename or removal in
-// colorSchemes.ts can't silently leave a dead name in the docs that users copy.
-// (Subset check only — a registered scheme may intentionally go undocumented.)
-test('color schemes listed in USAGE.md all exist', () => {
-  const registered = new Set(Object.keys(colorSchemes))
-  const usage = readFileSync(
-    new URL('../../../USAGE.md', import.meta.url),
-    'utf8',
-  )
-
-  const section = /## Color schemes\n([\s\S]*?)\n## /.exec(usage)?.[1]
-  expect(section, 'could not find the "## Color schemes" section').toBeTruthy()
-
-  // drop the bold labels (**Protein:**, **Dynamic (per-column):**, …), leaving
-  // just the comma-separated scheme names
-  const names = section!.replace(/\*\*[^*]+\*\*/g, '').match(/[a-z][a-z0-9_]+/g)
-  expect(names?.length).toBeGreaterThan(0)
-
-  const unknown = names!.filter(name => !registered.has(name))
-  expect(
-    unknown,
-    `documented but not registered: ${unknown.join(', ')}`,
-  ).toEqual([])
-})
-
-// Same guard for the R package docs, whose color_scheme names pass straight
-// through as colorSchemeName with no remapping — a name that isn't registered
-// silently renders with no coloring.
-test('color schemes listed in the R README all exist', () => {
-  const registered = new Set(Object.keys(colorSchemes))
-  const readme = readFileSync(
-    new URL('../../r-msaview/README.md', import.meta.url),
-    'utf8',
-  )
-
-  const section = /## Color schemes\n([\s\S]*?)\n## /.exec(readme)?.[1]
-  expect(section, 'could not find the "## Color schemes" section').toBeTruthy()
-
-  // names are backtick-quoted, e.g. `jalview_taylor`
-  const names = [...section!.matchAll(/`([a-z][a-z0-9_]+)`/g)].flatMap(m =>
-    m[1] ? [m[1]] : [],
-  )
-  expect(names.length).toBeGreaterThan(0)
-
-  const unknown = names.filter(name => !registered.has(name))
-  expect(
-    unknown,
-    `documented but not registered: ${unknown.join(', ')}`,
-  ).toEqual([])
-})

package/src/columnCounts.test.ts

@@ -1,73 +0,0 @@
-import { describe, expect, test } from 'vitest'
-
-import {
-  columnCountsFromColumns,
-  columnCountsFromRows,
-  letterOfResidueSlot,
-} from './columnCounts.ts'
-
-describe('columnCounts', () => {
-  test('tallies residues and gaps per column', () => {
-    const counts = columnCountsFromRows(['AC-', 'AG.', 'AC-'])
-    expect(counts.numColumns).toBe(3)
-    expect(counts.count(0, 'A')).toBe(3)
-    expect(counts.count(1, 'C')).toBe(2)
-    expect(counts.count(1, 'G')).toBe(1)
-    expect(counts.total(2)).toBe(3)
-    expect(counts.gapCount(2)).toBe(3)
-    expect(counts.gapCount(0)).toBe(0)
-  })
-
-  test('counts both gap characters, and neither as a residue', () => {
-    const counts = columnCountsFromColumns(['-.A'])
-    expect(counts.count(0, '-')).toBe(1)
-    expect(counts.count(0, '.')).toBe(1)
-    expect(counts.gapCount(0)).toBe(2)
-    expect(counts.residueEntries(0)).toEqual([['A', 1]])
-    expect(counts.lettersPresent).toEqual(new Set(['A']))
-  })
-
-  test('folds case, so lowercase (a3m insertions) counts as its residue', () => {
-    const counts = columnCountsFromColumns(['aA'])
-    expect(counts.count(0, 'A')).toBe(2)
-  })
-
-  test('digits and punctuation do not land on letter slots', () => {
-    // a plain `code & 31` would fold '0' onto 'P' and '!' onto 'A'
-    const counts = columnCountsFromColumns(['0!'])
-    expect(counts.count(0, 'P')).toBe(0)
-    expect(counts.count(0, 'A')).toBe(0)
-    expect(counts.residueEntries(0)).toEqual([['?', 2]])
-  })
-
-  test('ragged rows: the widest row sets the column count', () => {
-    const counts = columnCountsFromRows(['AAAA', 'AA'])
-    expect(counts.numColumns).toBe(4)
-    expect(counts.total(0)).toBe(2)
-    expect(counts.total(3)).toBe(1)
-  })
-
-  test('entropy is taken over the non-gap residues only', () => {
-    const counts = columnCountsFromColumns(['AAAA', 'AACC', 'ACGT', 'AC--'])
-    // fully conserved: no choice left to make
-    expect(counts.entropy(0)).toBeCloseTo(0, 10)
-    // even two-way and four-way splits
-    expect(counts.entropy(1)).toBeCloseTo(1, 10)
-    expect(counts.entropy(2)).toBeCloseTo(2, 10)
-    // the two gaps do not turn a 1-bit choice into a 2-bit one
-    expect(counts.entropy(3)).toBeCloseTo(1, 10)
-  })
-
-  test('an all-gap column has no entropy rather than NaN', () => {
-    expect(columnCountsFromColumns(['----']).entropy(0)).toBe(0)
-  })
-
-  test('residue slots round-trip to their letters', () => {
-    const counts = columnCountsFromColumns(['WY'])
-    const slots: number[] = []
-    counts.forEachResidue(0, slot => {
-      slots.push(slot)
-    })
-    expect(slots.map(letterOfResidueSlot)).toEqual(['W', 'Y'])
-  })
-})

package/src/columnStats.test.ts

@@ -1,94 +0,0 @@
-// @vitest-environment jsdom
-import { beforeAll, describe, expect, test } from 'vitest'
-
-import MSAModelF from './model.ts'
-
-beforeAll(() => {
-  HTMLCanvasElement.prototype.getContext = function () {
-    let font = '10px sans-serif'
-    return {
-      get font() {
-        return font
-      },
-      set font(v: string) {
-        font = v
-      },
-      measureText(t: string) {
-        const size = Number.parseFloat(font) || 10
-        return { width: t.length * size * 0.6 } as TextMetrics
-      },
-    } as unknown as CanvasRenderingContext2D
-  } as unknown as typeof HTMLCanvasElement.prototype.getContext
-})
-
-// col0 is invariant M; col3 varies V/V/A (all hydrophobic) so property
-// conservation stays high while identity conservation drops
-const protein = `>a
-MKLVIL
->b
-MRLVIL
->c
-MKLAIL`
-
-const dna = `>a
-ACGTAC
->b
-ACGTAG
->c
-ACGAAC`
-
-function make(msa: string, id: string) {
-  return MSAModelF().create({
-    id,
-    type: 'MsaView',
-    msaFormat: 'fasta',
-    data: { msa },
-  })
-}
-
-describe('property conservation track', () => {
-  test('present for protein alignments', () => {
-    const ids = make(protein, 'p').tracks.map(t => t.model.id)
-    expect(ids).toContain('conservation')
-    expect(ids).toContain('property-conservation')
-  })
-
-  test('omitted for nucleotide alignments', () => {
-    const ids = make(dna, 'd').tracks.map(t => t.model.id)
-    expect(ids).toContain('conservation')
-    expect(ids).not.toContain('property-conservation')
-  })
-
-  test('conservative-substitution column: property beats identity', () => {
-    const model = make(protein, 'pc')
-    // col3 = V/V/A: same property class, different identity
-    expect(model.propertyConservation[3]!).toBeGreaterThan(
-      model.conservation[3]!,
-    )
-  })
-})
-
-describe('mouseOverColumnStats', () => {
-  test('undefined when nothing hovered', () => {
-    expect(make(protein, 'm0').mouseOverColumnStats).toBeUndefined()
-  })
-
-  test('reports consensus, gaps and distribution for hovered column', () => {
-    const model = make(protein, 'm1')
-    model.setMousePos(0, 0)
-    const s = model.mouseOverColumnStats
-    expect(s?.consensusLetter).toBe('M')
-    expect(s?.consensusFraction).toBe(1)
-    expect(s?.gapFraction).toBe(0)
-    expect(s?.total).toBe(3)
-  })
-
-  test('mixed column reports the majority residue as consensus', () => {
-    const model = make(protein, 'm2')
-    // col1 = K/R/K -> consensus K at 2/3
-    model.setMousePos(1, 0)
-    const s = model.mouseOverColumnStats
-    expect(s?.consensusLetter).toBe('K')
-    expect(s?.consensusCount).toBe(2)
-  })
-})

package/src/columnTracks.test.ts

@@ -1,97 +0,0 @@
-import { getSnapshot } from '@jbrowse/mobx-state-tree'
-import { expect, test } from 'vitest'
-
-import stateModelFactory from './model.ts'
-
-import type { ColumnTrackSpec } from './types.ts'
-
-const MsaView = stateModelFactory()
-
-// s1 has a gap at column 1 and s2 a gap at column 3, and every row is gapped at
-// column 5, so hiding gappy columns drops that one
-const msa = '>s1\nA-CDE-F\n>s2\nAB-DE-F\n>s3\nABCDE-F\n'
-
-function makeModel(columnTracks: ColumnTrackSpec[]) {
-  return MsaView.create({
-    type: 'MsaView',
-    msaFormat: 'fasta',
-    data: { msa },
-    columnTracks,
-  })
-}
-
-test('column-indexed values normalize by max and clamp to 0..1', () => {
-  const model = makeModel([
-    { id: 't', name: 'T', kind: 'bar', values: [1, 2, 4, -1], max: 2 },
-  ])
-  expect(model.columnTrackContent.get('t')?.values).toEqual([0.5, 1, 1, 0])
-})
-
-test('row-indexed values land on the residues of that row', () => {
-  const model = makeModel([
-    { id: 't', name: 'T', kind: 'bar', values: [0.1, 0.2, 0.3], row: 's1' },
-  ])
-  // residues 1..3 of s1 are A, C, D at global columns 0, 2, 3
-  expect(model.columnTrackContent.get('t')?.values).toEqual([
-    0.1, 0, 0.2, 0.3, 0, 0, 0,
-  ])
-})
-
-test('a row-indexed text track spreads its letters the same way', () => {
-  const model = makeModel([
-    { id: 'f', name: 'Frame', kind: 'text', data: '123', row: 's2' },
-  ])
-  // residues of s2 sit at columns 0, 1, 3
-  expect(model.columnTrackContent.get('f')?.data).toBe('12 3   ')
-})
-
-test('hiding gappy columns drops them from the values and the text', () => {
-  const model = makeModel([
-    { id: 't', name: 'T', kind: 'bar', values: [1, 2, 3, 4, 5, 6, 7], max: 7 },
-    { id: 'f', name: 'F', kind: 'text', data: 'abcdefg' },
-  ])
-  model.setHideGaps(true)
-  model.setAllowedGappyness(99)
-  expect(model.blanks).toEqual([5])
-  expect(model.columnTrackContent.get('t')?.values).toHaveLength(6)
-  expect(model.columnTrackContent.get('f')?.data).toBe('abcdeg')
-})
-
-test('data tracks join the track list with their own color and height', () => {
-  const model = makeModel([
-    { id: 't', name: 'dN/dS', kind: 'bar', values: [1], color: 'red' },
-    { id: 'f', name: 'Frame', kind: 'text', data: '1', colors: { 1: 'blue' } },
-  ])
-  const ids = model.tracks.map(t => t.model.id)
-  expect(ids).toContain('t')
-  expect(ids).toContain('f')
-  const bar = model.tracks.find(t => t.model.id === 't')!.model
-  expect(bar.barColor).toBe('red')
-  expect(bar.height).toBe(model.conservationTrackHeight)
-  const text = model.tracks.find(t => t.model.id === 'f')!.model
-  expect(text.customColorScheme).toEqual({ 1: 'blue' })
-  expect(text.height).toBe(model.rowHeight)
-  expect(text.data).toBe('1')
-
-  expect(model.turnedOnTracks.map(t => t.model.id)).toContain('t')
-  model.toggleTrack('t')
-  expect(model.turnedOnTracks.map(t => t.model.id)).not.toContain('t')
-})
-
-test('setColumnTracks replaces the set and the snapshot carries it', () => {
-  const model = makeModel([])
-  expect(getSnapshot(model)).not.toHaveProperty('columnTracks')
-  model.setColumnTracks([{ id: 't', name: 'T', kind: 'bar', values: [0.5] }])
-  expect(getSnapshot(model).columnTracks).toEqual([
-    { id: 't', name: 'T', kind: 'bar', values: [0.5] },
-  ])
-})
-
-test('a track too large to share leaves the snapshot but keeps drawing', () => {
-  const model = makeModel([
-    { id: 'big', name: 'Big', kind: 'bar', values: Array(20_000).fill(0.5) },
-    { id: 'small', name: 'Small', kind: 'bar', values: [0.5] },
-  ])
-  expect(model.columnTrackContent.get('big')?.values).toHaveLength(20_000)
-  expect(getSnapshot(model).columnTracks?.map(t => t.id)).toEqual(['small'])
-})