react-msaview 4.5.0 → 4.8.0

package/dist/seqCoordToRowSpecificGlobalCoord.test.js

@@ -1,42 +0,0 @@
-import { describe, expect, test } from 'vitest';
-import { seqCoordToRowSpecificGlobalCoord } from './seqCoordToRowSpecificGlobalCoord';
-describe('seqCoordToRowSpecificGlobalCoord', () => {
-    test('converts sequence coordinate to global coordinate with no gaps', () => {
-        const row = 'ATGCATGC';
-        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 3 })).toBe(3);
-        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 0 })).toBe(0);
-        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 8 })).toBe(8);
-    });
-    test('converts sequence coordinate to global coordinate with gaps', () => {
-        const row = 'A-TG-CA-TGC';
-        // A(0) -(1) T(2) G(3) -(4) C(5) A(6) -(7) T(8) G(9) C(10)
-        // Sequence positions: A(0) T(1) G(2) C(3) A(4) T(5) G(6) C(7)
-        // Position 0 (first A) -> Global index 0
-        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 0 })).toBe(0);
-        // Position 1 (T after first gap) -> Global index 2
-        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 1 })).toBe(2);
-        // Position 3 (C after second gap) -> Global index 5
-        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 3 })).toBe(5);
-        // Position 5 (T after third gap) -> Global index 8
-        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 5 })).toBe(8);
-        // Position 8 (end of sequence) -> Global index 11
-        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 8 })).toBe(11);
-    });
-    test('handles empty row', () => {
-        expect(seqCoordToRowSpecificGlobalCoord({ row: '', position: 0 })).toBe(0);
-    });
-    test('handles row with only gaps', () => {
-        const row = '---..--';
-        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 0 })).toBe(0);
-    });
-    test('handles mixed gap characters', () => {
-        const row = 'A-.G-C.';
-        // A(0) -(1) .(2) G(3) -(4) C(5) .(6)
-        // Sequence positions: A(0) G(1) C(2)
-        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 0 })).toBe(0);
-        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 1 })).toBe(3);
-        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 2 })).toBe(5);
-        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 3 })).toBe(7);
-    });
-});
-//# sourceMappingURL=seqCoordToRowSpecificGlobalCoord.test.js.map

package/dist/seqCoordToRowSpecificGlobalCoord.test.js.map

@@ -1 +0,0 @@
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package/src/parseGFF.ts

@@ -1,34 +0,0 @@
-export function parseGFF(str?: string) {
-  return str
-    ?.split('\n')
-    .map(f => f.trim())
-    .filter(f => !!f && !f.startsWith('#'))
-    .map(f => {
-      const [seq_id, source, type, start, end, score, strand, phase, col9] =
-        f.split('\t')
-
-      return {
-        seq_id: seq_id!,
-        source: source!,
-        type: type!,
-        start: +start!,
-        end: +end!,
-        score: +score!,
-        strand: strand!,
-        phase: phase!,
-        ...Object.fromEntries(
-          col9!
-            .split(';')
-            .map(f => f.trim())
-            .filter(f => !!f)
-            .map(f => f.split('='))
-            .map(([key, val]) => [
-              key!.trim(),
-              val
-                ? decodeURIComponent(val).trim().split(',').join(' ')
-                : undefined,
-            ]),
-        ),
-      }
-    })
-}

package/src/parseNewick.ts

@@ -1,94 +0,0 @@
-/**
- * Newick format parser in JavaScript.
- *
- * Copyright (c) Jason Davies 2010.
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in
- * all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- * THE SOFTWARE.
- *
- * Example tree (from http://en.wikipedia.org/wiki/Newick_format):
- *
- * +--0.1--A
- * F-----0.2-----B            +-------0.3----C
- * +------------------0.5-----E
- *                            +---------0.4------D
- *
- * Newick format:
- * (A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F;
- *
- * Converted to JSON:
- * {
- *   name: "F",
- *   children: [
- *     {name: "A", length: 0.1},
- *     {name: "B", length: 0.2},
- *     {
- *       name: "E",
- *       length: 0.5,
- *       children: [
- *         {name: "C", length: 0.3},
- *         {name: "D", length: 0.4}
- *       ]
- *     }
- *   ]
- * }
- *
- * Converted to JSON, but with no names or lengths:
- * {
- *   children: [
- *     {}, {}, {
- *       children: [{}, {}]
- *     }
- *   ]
- * }
- */
-export default function parse(s: string) {
-  const ancestors = []
-
-  let tree = {} as Record<string, any>
-  const tokens = s.split(/\s*(;|\(|\)|,|:)\s*/)
-  for (let i = 0; i < tokens.length; i++) {
-    const token = tokens[i]!
-    const subtree = {}
-    switch (token) {
-      case '(': // new children
-        tree.children = [subtree]
-        ancestors.push(tree)
-        tree = subtree
-        break
-      case ',': // another branch
-        ancestors.at(-1)?.children.push(subtree)
-        tree = subtree
-        break
-      case ')': // optional name next
-        tree = ancestors.pop()!
-        break
-      case ':': // optional length next
-        break
-      default: {
-        const x = tokens[i - 1]!
-        if (x === ')' || x === '(' || x === ',') {
-          tree.name = token
-        } else if (x === ':') {
-          tree.length = Number.parseFloat(token)
-        }
-      }
-    }
-  }
-  return tree
-}

package/src/parsers/A3mMSA.test.ts

@@ -1,164 +0,0 @@
-import { describe, expect, test } from 'vitest'
-
-import A3mMSA from './A3mMSA'
-
-const exampleA3M = `>example
-ETESMKTVRIREKIKKFLGDRPRNTAEILEHINSTMRHGTTSQQLGNVLSKDKDIVKVGYIKRSGILSGGYDICEWATRNWVAEHCPEWTE
->1
-----MRTTRLRQKIKKFLNERGeANTTEILEHVNSTMRHGTTPQQLGNVLSKDKDILKVATTKRGGALSGRYEICVWTLRP-----------
->2
-----MDSQNLRDLIRNYLSERPRNTIEISAWLASQMDPNSCPEDVTNILEADESIVRIGTVRKSGMRLTDLPISEWASSSWVRRHE-----
->3
-----MNSQNLRELIRNYLSERPRNTIEISTWLSSQIDPTNSPVDITSILEADDQIVRIGTVRKSGMRRSESPVSEWASNTWVKHHE-----
->4
---RDMDTEKVREIVRNYISERPRNTAEIAAWLNRH-DDGTGGSDVAAILESDGSFVRIGTVRTSGMTGNSPPLSEWATEKWIQHHER----
->5
------RTRRLREAVLVFLEEKGnANTVEVFDYLNERFRWGATMNQVGNILAKDTRFAKVGHQ-RGQFRGSVYTVCVWALS------------
->6
------RTKRLREAVRVYLAENGrSHTVDIFDHLNDRFSWGATMNQVGNILAKDNRFEKVGHVRD-FFRGARYTVCVWDLAS-----------
-`
-
-describe('A3mMSA', () => {
-  test('sniff detects A3M format', () => {
-    expect(A3mMSA.sniff(exampleA3M)).toBe(true)
-  })
-
-  test('sniff returns false for regular FASTA', () => {
-    const fasta = `>seq1
-ACDEFGHIKLMNPQRST
->seq2
-ACDEFGHIKLMNPQRST
-`
-    expect(A3mMSA.sniff(fasta)).toBe(false)
-  })
-
-  test('sniff returns false for non-FASTA formats', () => {
-    expect(A3mMSA.sniff('# STOCKHOLM 1.0\n')).toBe(false)
-    expect(A3mMSA.sniff('CLUSTAL W')).toBe(false)
-  })
-
-  test('parses A3M and expands insertions', () => {
-    const parser = new A3mMSA(exampleA3M)
-    const names = parser.getNames()
-
-    expect(names).toEqual(['example', '1', '2', '3', '4', '5', '6'])
-
-    // All sequences should have the same length after expansion
-    const widths = names.map(name => parser.getRow(name).length)
-    expect(widths.every(w => w === widths[0])).toBe(true)
-
-    // The width should be greater than the original due to expanded inserts
-    expect(parser.getWidth()).toBeGreaterThan(90)
-  })
-
-  test('lowercase inserts become uppercase after expansion', () => {
-    const parser = new A3mMSA(exampleA3M)
-
-    // The expanded sequences should not contain lowercase letters
-    for (const name of parser.getNames()) {
-      const row = parser.getRow(name)
-      expect(/[a-z]/.test(row)).toBe(false)
-    }
-  })
-
-  test('handles simple A3M with single insert', () => {
-    // In valid A3M, match columns (uppercase + - + .) must be consistent
-    // seq1 has 5 match columns + 1 insert after D
-    // seq2 has 5 match columns, no inserts
-    const simple = `>seq1
-ACDaEF
->seq2
-ACDEF
-`
-    const parser = new A3mMSA(simple)
-
-    // seq1 has an 'a' insert after 'D', seq2 doesn't
-    // After expansion, both should be same length
-    const seq1 = parser.getRow('seq1')
-    const seq2 = parser.getRow('seq2')
-
-    expect(seq1.length).toBe(seq2.length)
-    expect(seq1).toBe('ACDAEF')
-    expect(seq2).toBe('ACD.EF')
-  })
-
-  test('handles multiple inserts at different positions', () => {
-    // seq1: 6 match columns (A,C,D,E,F,I) + inserts (ab after D, gh after F)
-    // seq2: 6 match columns, no inserts
-    const multi = `>seq1
-ACDabEFghI
->seq2
-ACDEFI
-`
-    const parser = new A3mMSA(multi)
-
-    const seq1 = parser.getRow('seq1')
-    const seq2 = parser.getRow('seq2')
-
-    expect(seq1.length).toBe(seq2.length)
-    // seq1: ACD + ab (inserts) + EF + gh (inserts) + I
-    // seq2: ACD + EF + I -> needs . padding at insert positions
-    expect(seq1).toBe('ACDABEFGHI')
-    expect(seq2).toBe('ACD..EF..I')
-  })
-
-  test('handles varying insert lengths', () => {
-    const varying = `>seq1
-ACDabcEF
->seq2
-ACDaEF
->seq3
-ACDEF
-`
-    const parser = new A3mMSA(varying)
-
-    const seq1 = parser.getRow('seq1')
-    const seq2 = parser.getRow('seq2')
-    const seq3 = parser.getRow('seq3')
-
-    // All should have same length
-    expect(seq1.length).toBe(seq2.length)
-    expect(seq2.length).toBe(seq3.length)
-
-    // seq1 has 3 inserts, seq2 has 1, seq3 has 0
-    // After expansion with max 3 insert slots:
-    expect(seq1).toBe('ACDABCEF')
-    expect(seq2).toBe('ACDA..EF')
-    expect(seq3).toBe('ACD...EF')
-  })
-
-  test('getTree returns flat tree structure', () => {
-    const parser = new A3mMSA(exampleA3M)
-    const tree = parser.getTree()
-
-    expect(tree.id).toBe('root')
-    expect(tree.noTree).toBe(true)
-    expect(tree.children.length).toBe(7)
-    expect(tree.children.map(c => c.name)).toEqual([
-      'example',
-      '1',
-      '2',
-      '3',
-      '4',
-      '5',
-      '6',
-    ])
-  })
-
-  test('getWidth returns consistent width', () => {
-    const parser = new A3mMSA(exampleA3M)
-    const width = parser.getWidth()
-
-    for (const name of parser.getNames()) {
-      expect(parser.getRow(name).length).toBe(width)
-    }
-  })
-
-  test('getMSA returns parsed data', () => {
-    const parser = new A3mMSA(exampleA3M)
-    const msa = parser.getMSA()
-
-    expect(msa.seqdata).toBeDefined()
-    expect(Object.keys(msa.seqdata).length).toBe(7)
-  })
-})

package/src/parsers/A3mMSA.ts

@@ -1,321 +0,0 @@
-import type { NodeWithIds } from '../types'
-
-// Char code helpers for fast character classification
-const CODE_A = 65 // 'A'
-const CODE_Z = 90 // 'Z'
-const CODE_a = 97 // 'a'
-const CODE_z = 122 // 'z'
-const CODE_DASH = 45 // '-'
-const CODE_DOT = 46 // '.'
-
-function isUpperOrGap(code: number): boolean {
-  return (
-    (code >= CODE_A && code <= CODE_Z) ||
-    code === CODE_DASH ||
-    code === CODE_DOT
-  )
-}
-
-function isLower(code: number): boolean {
-  return code >= CODE_a && code <= CODE_z
-}
-
-/**
- * A3M format parser
- *
- * The A3M format consists of aligned fasta, in which:
- * - Insertions are shown as lowercase characters
- * - Matches are shown as uppercase characters
- * - Deletions are shown as '-'
- * - Gaps aligned to inserts are shown as '.'
- *
- * The key property is that lowercase letters (inserts) implicitly introduce
- * gaps in all other sequences that don't have an insert at that position.
- */
-export default class A3mMSA {
-  private MSA: { seqdata: Record<string, string> }
-  private orderedNames: string[]
-
-  constructor(text: string) {
-    const rawSeqs: string[] = []
-    const names: string[] = []
-
-    // First pass: parse sequences (like FASTA), preserving order
-    for (const entry of text.split('>')) {
-      if (!/\S/.test(entry)) {
-        continue
-      }
-      const newlineIdx = entry.indexOf('\n')
-      if (newlineIdx === -1) {
-        continue
-      }
-      const defLine = entry.slice(0, newlineIdx)
-      const spaceIdx = defLine.indexOf(' ')
-      const id = spaceIdx === -1 ? defLine : defLine.slice(0, spaceIdx)
-      if (id) {
-        rawSeqs.push(entry.slice(newlineIdx + 1).replaceAll(/\s/g, ''))
-        names.push(id)
-      }
-    }
-
-    this.orderedNames = names
-    this.MSA = { seqdata: this.expandA3M(rawSeqs, names) }
-  }
-
-  /**
-   * Detect if text is likely A3M format
-   */
-  static sniff(text: string): boolean {
-    if (!text.startsWith('>')) {
-      return false
-    }
-
-    const seqs: string[] = []
-    for (const entry of text.split('>')) {
-      if (!/\S/.test(entry)) {
-        continue
-      }
-      const newlineIdx = entry.indexOf('\n')
-      if (newlineIdx === -1) {
-        continue
-      }
-      const seq = entry.slice(newlineIdx + 1).replaceAll(/\s/g, '')
-      if (seq) {
-        seqs.push(seq)
-      }
-    }
-
-    if (seqs.length < 2) {
-      return false
-    }
-
-    // Check for lowercase and compute lengths in single pass per sequence
-    let hasLowercase = false
-    let firstMatchLen = -1
-    let firstRawLen = -1
-    let sameMatchLength = true
-    let differentRawLengths = false
-
-    for (const seq of seqs) {
-      let matchLen = 0
-      for (let i = 0; i < seq.length; i++) {
-        const code = seq.charCodeAt(i)
-        if (isLower(code)) {
-          hasLowercase = true
-        } else {
-          matchLen++
-        }
-      }
-
-      if (firstMatchLen === -1) {
-        firstMatchLen = matchLen
-        firstRawLen = seq.length
-      } else {
-        if (matchLen !== firstMatchLen) {
-          sameMatchLength = false
-        }
-        if (seq.length !== firstRawLen) {
-          differentRawLengths = true
-        }
-      }
-    }
-
-    return hasLowercase && sameMatchLength && differentRawLengths
-  }
-
-  /**
-   * Expand A3M format to standard aligned format.
-   *
-   * In A3M, lowercase characters are insertions that implicitly introduce
-   * gaps in sequences that don't have an insert at that position.
-   */
-  private expandA3M(
-    rawSeqs: string[],
-    names: string[],
-  ): Record<string, string> {
-    const numSeqs = names.length
-    if (numSeqs === 0) {
-      return {}
-    }
-
-    // Parse sequences into parallel arrays: matchChars and insertLengths
-    // matchChars[seqIdx] = string of match characters for that sequence
-    // insertLengths[seqIdx] = array of insert lengths after each match position
-    const matchChars: string[] = []
-    const insertLengths: number[][] = []
-
-    for (let seqIdx = 0; seqIdx < numSeqs; seqIdx++) {
-      const seq = rawSeqs[seqIdx]!
-      const matches: string[] = []
-      const insLens: number[] = []
-      let i = 0
-
-      while (i < seq.length) {
-        const code = seq.charCodeAt(i)
-
-        if (isUpperOrGap(code)) {
-          matches.push(seq[i]!)
-          // Count following lowercase inserts
-          let insLen = 0
-          let j = i + 1
-          while (j < seq.length && isLower(seq.charCodeAt(j))) {
-            insLen++
-            j++
-          }
-          insLens.push(insLen)
-          i = j
-        } else if (isLower(code)) {
-          // Leading insert before first match
-          matches.push('')
-          let insLen = 0
-          let j = i
-          while (j < seq.length && isLower(seq.charCodeAt(j))) {
-            insLen++
-            j++
-          }
-          insLens.push(insLen)
-          i = j
-        } else {
-          i++
-        }
-      }
-
-      matchChars.push(matches.join(''))
-      insertLengths.push(insLens)
-    }
-
-    // Find number of match positions and max inserts at each position
-    let numPositions = 0
-    for (let seqIdx = 0; seqIdx < numSeqs; seqIdx++) {
-      const len = insertLengths[seqIdx]!.length
-      if (len > numPositions) {
-        numPositions = len
-      }
-    }
-
-    const maxInserts = new Array<number>(numPositions).fill(0)
-    for (let seqIdx = 0; seqIdx < numSeqs; seqIdx++) {
-      const insLens = insertLengths[seqIdx]!
-      for (let pos = 0; pos < insLens.length; pos++) {
-        const len = insLens[pos]!
-        if (len > maxInserts[pos]!) {
-          maxInserts[pos] = len
-        }
-      }
-    }
-
-    // Pre-compute gap strings for common lengths (avoid repeated .repeat())
-    const gapCache: string[] = ['']
-    const maxGap = Math.max(...maxInserts, 0)
-    for (let i = 1; i <= maxGap; i++) {
-      gapCache.push('.'.repeat(i))
-    }
-
-    // Build expanded sequences
-    const expanded: Record<string, string> = {}
-
-    for (let seqIdx = 0; seqIdx < numSeqs; seqIdx++) {
-      const seq = rawSeqs[seqIdx]!
-      const matches = matchChars[seqIdx]!
-      const insLens = insertLengths[seqIdx]!
-      const result: string[] = []
-
-      // Track position in original sequence for extracting inserts
-      let seqPos = 0
-
-      for (let pos = 0; pos < numPositions; pos++) {
-        const maxIns = maxInserts[pos]!
-
-        if (pos < insLens.length) {
-          const matchChar = matches[pos]
-          const insLen = insLens[pos]!
-
-          // Add match character
-          if (matchChar) {
-            result.push(matchChar)
-            seqPos++
-          } else {
-            result.push('.')
-          }
-
-          // Extract and uppercase inserts from original sequence
-          if (insLen > 0) {
-            result.push(seq.slice(seqPos, seqPos + insLen).toUpperCase())
-            seqPos += insLen
-          }
-
-          // Pad with gaps
-          const padding = maxIns - insLen
-          if (padding > 0) {
-            result.push(gapCache[padding]!)
-          }
-        } else {
-          // This sequence is shorter - add gaps
-          result.push(gapCache[1 + maxIns]!)
-        }
-      }
-
-      expanded[names[seqIdx]!] = result.join('')
-    }
-
-    return expanded
-  }
-
-  getMSA() {
-    return this.MSA
-  }
-
-  getRowData() {
-    return undefined
-  }
-
-  getNames() {
-    return this.orderedNames
-  }
-
-  getRow(name: string) {
-    return this.MSA.seqdata[name] || ''
-  }
-
-  getWidth() {
-    const name = Object.keys(this.MSA.seqdata)[0]
-    return name ? this.getRow(name).length : 0
-  }
-
-  getStructures() {
-    return {}
-  }
-
-  get alignmentNames() {
-    return []
-  }
-
-  getHeader() {
-    return {}
-  }
-
-  getTree(): NodeWithIds {
-    return {
-      id: 'root',
-      name: 'root',
-      noTree: true,
-      children: this.getNames().map(name => ({
-        id: name,
-        children: [],
-        name,
-      })),
-    }
-  }
-
-  get seqConsensus() {
-    return undefined
-  }
-
-  get secondaryStructureConsensus() {
-    return undefined
-  }
-
-  get tracks() {
-    return []
-  }
-}