react-msaview 6.4.2 → 7.0.0

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'])
-})

package/src/components/dialogs/InterProScanDialog.tsx

@@ -1,214 +0,0 @@
-import React, { useState } from 'react'
-
-import { Dialog } from '@jbrowse/core/ui'
-import { getSession } from '@jbrowse/core/util'
-import { Button, DialogActions, DialogContent, Typography } from '@mui/material'
-import { observer } from 'mobx-react'
-import { getUngappedSequence } from 'msa-parsers'
-
-import { launchInterProScan } from '../../launchInterProScan.ts'
-
-import type { MsaViewModel } from '../../model.ts'
-
-const FAMILIES = 'Families, domains, sites & repeats'
-const FEATURES = 'Other sequence features'
-const STRUCTURAL = 'Structural domains'
-const OTHER = 'Other category'
-
-// The analyses the EBI iprscan5 endpoint accepts, all on by default. Static, so
-// it lives out here rather than being rebuilt on every render of the dialog.
-const interProScanPrograms = [
-  {
-    name: 'NCBIfam',
-    category: FAMILIES,
-    description: 'NCBI RefSeq FAMs including TIGRFAMs',
-  },
-  {
-    name: 'SFLD',
-    category: FAMILIES,
-    description: 'Structure function linkage database',
-  },
-  {
-    name: 'Phobius',
-    category: FEATURES,
-    description:
-      'A combined transmembrane topology and signal peptide predictor',
-  },
-  { name: 'SignalP', category: FEATURES },
-  { name: 'SignalP_EUK', category: OTHER },
-  { name: 'SignalP_GRAM_POSITIVE', category: OTHER },
-  { name: 'SignalP_GRAM_NEGATIVE', category: OTHER },
-  { name: 'SuperFamily', category: STRUCTURAL },
-  { name: 'Panther', category: FAMILIES },
-  { name: 'Gene3d', category: STRUCTURAL },
-  { name: 'HAMAP', category: FAMILIES },
-  { name: 'PrositeProfiles', category: FAMILIES },
-  { name: 'PrositePatterns', category: FAMILIES },
-  { name: 'Coils', category: FEATURES },
-  { name: 'SMART', category: FAMILIES },
-  {
-    name: 'CDD',
-    category: FAMILIES,
-    description: 'Conserved Domains Database',
-  },
-  { name: 'PRINTS', category: FAMILIES },
-  { name: 'PfamA', category: FAMILIES },
-  { name: 'MobiDBLite', category: FEATURES },
-  { name: 'PIRSF', category: OTHER },
-  { name: 'TMHMM', category: FEATURES },
-  { name: 'AntiFam', category: OTHER },
-  { name: 'FunFam', category: OTHER },
-  { name: 'PIRSR', category: FAMILIES },
-].map(program => ({ ...program, checked: true }))
-
-const InterProScanDialog = observer(function ({
-  handleClose,
-  model,
-}: {
-  handleClose: () => void
-  model: MsaViewModel
-}) {
-  const [vals, setVals] = useState(interProScanPrograms)
-
-  const programs = vals.filter(e => e.checked).map(e => e.name)
-  const [show, setShow] = useState(false)
-
-  return (
-    <Dialog
-      maxWidth="xl"
-      title="Query InterProScan API for domains"
-      onClose={() => {
-        handleClose()
-      }}
-      open
-    >
-      <DialogContent>
-        <Typography>
-          This will run InterProScan via the InterProScan API on all rows of the
-          current MSA
-        </Typography>
-        <Button
-          onClick={() => {
-            setShow(!show)
-          }}
-        >
-          {show ? 'Hide' : 'Show'} advanced options
-        </Button>
-        {show ? (
-          <div>
-            <Typography>Select algorithms for InterProScan to run</Typography>
-            <div>
-              <Button
-                variant="contained"
-                color="secondary"
-                onClick={() => {
-                  setVals(vals.map(v => ({ ...v, checked: false })))
-                }}
-              >
-                Select none
-              </Button>
-              <Button
-                variant="contained"
-                color="primary"
-                onClick={() => {
-                  setVals(vals.map(v => ({ ...v, checked: true })))
-                }}
-              >
-                Select all
-              </Button>
-            </div>
-            <table>
-              <tbody>
-                {vals
-                  .toSorted((a, b) => a.category.localeCompare(b.category))
-                  .map(({ name, checked, category, description }) => (
-                    <tr key={name}>
-                      <td>
-                        <input
-                          type="checkbox"
-                          checked={checked}
-                          onChange={() => {
-                            setVals(
-                              vals.map(e =>
-                                e.name === name
-                                  ? { ...e, checked: !e.checked }
-                                  : e,
-                              ),
-                            )
-                          }}
-                        />
-                      </td>
-                      <td title={description}>{name}</td>
-                      <td>{category}</td>
-                    </tr>
-                  ))}
-              </tbody>
-            </table>
-          </div>
-        ) : null}
-      </DialogContent>
-      <DialogActions>
-        <Button
-          variant="contained"
-          color="secondary"
-          onClick={() => {
-            handleClose()
-          }}
-        >
-          Cancel
-        </Button>
-        <Button
-          variant="contained"
-          color="primary"
-          onClick={() => {
-            const controller = new AbortController()
-            // eslint-disable-next-line @typescript-eslint/no-floating-promises
-            ;(async () => {
-              try {
-                const { rows } = model
-                if (rows.length > 140) {
-                  throw new Error(
-                    'Too many sequences, please run InterProScan offline',
-                  )
-                }
-                await launchInterProScan({
-                  algorithm: 'interproscan',
-                  programs: programs,
-                  seq: rows
-                    .map(row => [row[0], getUngappedSequence(row[1])])
-                    .filter(f => !!f[1])
-                    .map(row => `>${row[0]}\n${row[1]}`)
-                    .join('\n'),
-                  onProgress: arg => {
-                    model.setStatus(
-                      arg
-                        ? {
-                            ...arg,
-                            onCancel: () => {
-                              controller.abort()
-                            },
-                          }
-                        : undefined,
-                    )
-                  },
-                  model,
-                  signal: controller.signal,
-                })
-              } catch (e) {
-                console.error(e)
-                getSession(model).notifyError(`${e}`, e)
-              } finally {
-                model.setStatus()
-              }
-            })()
-            handleClose()
-          }}
-        >
-          Send sequences to InterProScan
-        </Button>
-      </DialogActions>
-    </Dialog>
-  )
-})
-
-export default InterProScanDialog

package/src/components/dialogs/InterProScanFileDialog.tsx

@@ -1,138 +0,0 @@
-import React, { useState } from 'react'
-
-import { Dialog } from '@jbrowse/core/ui'
-import { getSession } from '@jbrowse/core/util'
-import {
-  Button,
-  DialogActions,
-  DialogContent,
-  FormControl,
-  FormControlLabel,
-  Radio,
-  RadioGroup,
-  TextField,
-  Typography,
-} from '@mui/material'
-import { observer } from 'mobx-react'
-import { interProScanResponseToAnnotations } from 'msa-parsers'
-
-import { jsonfetch } from '../../fetchUtils.ts'
-
-import type { MsaViewModel } from '../../model.ts'
-import type { InterProScanResponse } from 'msa-parsers'
-
-const InterProScanFileDialog = observer(function ({
-  handleClose,
-  model,
-}: {
-  handleClose: () => void
-  model: MsaViewModel
-}) {
-  const [file, setFile] = useState<File>()
-  const [choice, setChoice] = useState('file')
-  const [interProURL, setInterProURL] = useState('')
-
-  return (
-    <Dialog
-      maxWidth="xl"
-      title="Open InterProScan results"
-      onClose={() => {
-        handleClose()
-      }}
-      open
-    >
-      <DialogContent>
-        <div>
-          <Typography>
-            Open a JSON file of InterProScan results that you run remotely on
-            EBI servers or locally
-          </Typography>
-
-          <div style={{ display: 'flex', margin: 30 }}>
-            <FormControl component="fieldset">
-              <RadioGroup
-                value={choice}
-                onChange={event => {
-                  setChoice(event.target.value)
-                }}
-              >
-                <FormControlLabel value="url" control={<Radio />} label="URL" />
-                <FormControlLabel
-                  value="file"
-                  control={<Radio />}
-                  label="File"
-                />
-              </RadioGroup>
-            </FormControl>
-            {choice === 'url' ? (
-              <div>
-                <Typography>
-                  Open a InterProScan JSON file remote URL
-                </Typography>
-                <TextField
-                  label="URL"
-                  value={interProURL}
-                  onChange={event => {
-                    setInterProURL(event.target.value)
-                  }}
-                />
-              </div>
-            ) : null}
-            {choice === 'file' ? (
-              <div style={{ paddingTop: 20 }}>
-                <Typography>
-                  Open a InterProScan JSON file file from your local drive
-                </Typography>
-                <Button variant="outlined" component="label">
-                  Choose File
-                  <input
-                    type="file"
-                    hidden
-                    onChange={({ target }) => {
-                      const file = target.files?.[0]
-                      if (file) {
-                        setFile(file)
-                      }
-                    }}
-                  />
-                </Button>
-              </div>
-            ) : null}
-          </div>
-        </div>
-      </DialogContent>
-      <DialogActions>
-        <Button
-          variant="contained"
-          color="primary"
-          onClick={() => {
-            // eslint-disable-next-line @typescript-eslint/no-floating-promises
-            ;(async () => {
-              try {
-                const ret: InterProScanResponse = file
-                  ? JSON.parse(await file.text())
-                  : await jsonfetch(interProURL)
-
-                model.setAnnotations(interProScanResponseToAnnotations(ret))
-                getSession(model).notify(
-                  'Loaded interproscan results',
-                  'success',
-                )
-              } catch (e) {
-                console.error(e)
-                getSession(model).notifyError(`${e}`, e)
-              } finally {
-                model.setStatus()
-              }
-            })()
-            handleClose()
-          }}
-        >
-          Open results
-        </Button>
-      </DialogActions>
-    </Dialog>
-  )
-})
-
-export default InterProScanFileDialog