react-msaview 4.5.0 → 4.8.0

package/src/util.ts

@@ -2,7 +2,7 @@ import { colord, extend } from 'colord'
 import namesPlugin from 'colord/plugins/names'
 import { max } from 'd3-array'
 
-import type { Node, NodeWithIds } from './types'
+import type { NodeWithIds } from './types'
 import type { Theme } from '@mui/material'
 import type { HierarchyNode } from 'd3-hierarchy'
 
@@ -15,24 +15,6 @@ export function transform<T>(
   return Object.fromEntries(Object.entries(obj).map(cb))
 }
 
-export function generateNodeIds(
-  tree: Node,
-  parent = 'node',
-  depth = 0,
-): NodeWithIds {
-  const id = `${parent}-${depth}`
-
-  return {
-    ...tree,
-    id,
-    name: tree.name || id,
-    children:
-      tree.children?.map((b, i) =>
-        generateNodeIds(b, `${id}-${i}`, depth + 1),
-      ) || [],
-  }
-}
-
 export function colorContrast(
   colorScheme: Record<string, string>,
   theme: Theme,

package/src/version.ts

@@ -1 +1 @@
-export const version = '4.4.7'
+export const version = '4.7.0'

package/dist/parseGFF.d.ts

@@ -1,10 +0,0 @@
-export declare function parseGFF(str?: string): {
-    seq_id: string;
-    source: string;
-    type: string;
-    start: number;
-    end: number;
-    score: number;
-    strand: string;
-    phase: string;
-}[] | undefined;

package/dist/parseGFF.js

@@ -1,31 +0,0 @@
-export function parseGFF(str) {
-    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,
-            ])),
-        };
-    });
-}
-//# sourceMappingURL=parseGFF.js.map

package/dist/parseGFF.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"parseGFF.js","sourceRoot":"","sources":["../src/parseGFF.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,QAAQ,CAAC,GAAY;IACnC,OAAO,GAAG;QACR,EAAE,KAAK,CAAC,IAAI,CAAC;SACZ,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC;SACtC,GAAG,CAAC,CAAC,CAAC,EAAE;QACP,MAAM,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,IAAI,CAAC,GAClE,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAEf,OAAO;YACL,MAAM,EAAE,MAAO;YACf,MAAM,EAAE,MAAO;YACf,IAAI,EAAE,IAAK;YACX,KAAK,EAAE,CAAC,KAAM;YACd,GAAG,EAAE,CAAC,GAAI;YACV,KAAK,EAAE,CAAC,KAAM;YACd,MAAM,EAAE,MAAO;YACf,KAAK,EAAE,KAAM;YACb,GAAG,MAAM,CAAC,WAAW,CACnB,IAAK;iBACF,KAAK,CAAC,GAAG,CAAC;iBACV,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;iBAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;iBAChB,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;iBACtB,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC;gBACnB,GAAI,CAAC,IAAI,EAAE;gBACX,GAAG;oBACD,CAAC,CAAC,kBAAkB,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC;oBACrD,CAAC,CAAC,SAAS;aACd,CAAC,CACL;SACF,CAAA;IACH,CAAC,CAAC,CAAA;AACN,CAAC"}

package/dist/parseNewick.d.ts

@@ -1,60 +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): Record<string, any>;

package/dist/parseNewick.js

@@ -1,95 +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) {
-    const ancestors = [];
-    let tree = {};
-    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;
-}
-//# sourceMappingURL=parseNewick.js.map

package/dist/parseNewick.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"parseNewick.js","sourceRoot":"","sources":["../src/parseNewick.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA0DG;AACH,MAAM,CAAC,OAAO,UAAU,KAAK,CAAC,CAAS;IACrC,MAAM,SAAS,GAAG,EAAE,CAAA;IAEpB,IAAI,IAAI,GAAG,EAAyB,CAAA;IACpC,MAAM,MAAM,GAAG,CAAC,CAAC,KAAK,CAAC,qBAAqB,CAAC,CAAA;IAC7C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACvC,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAE,CAAA;QACxB,MAAM,OAAO,GAAG,EAAE,CAAA;QAClB,QAAQ,KAAK,EAAE,CAAC;YACd,KAAK,GAAG,EAAE,eAAe;gBACvB,IAAI,CAAC,QAAQ,GAAG,CAAC,OAAO,CAAC,CAAA;gBACzB,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBACpB,IAAI,GAAG,OAAO,CAAA;gBACd,MAAK;YACP,KAAK,GAAG,EAAE,iBAAiB;gBACzB,SAAS,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACxC,IAAI,GAAG,OAAO,CAAA;gBACd,MAAK;YACP,KAAK,GAAG,EAAE,qBAAqB;gBAC7B,IAAI,GAAG,SAAS,CAAC,GAAG,EAAG,CAAA;gBACvB,MAAK;YACP,KAAK,GAAG,EAAE,uBAAuB;gBAC/B,MAAK;YACP,OAAO,CAAC,CAAC,CAAC;gBACR,MAAM,CAAC,GAAG,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,CAAA;gBACxB,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;oBACxC,IAAI,CAAC,IAAI,GAAG,KAAK,CAAA;gBACnB,CAAC;qBAAM,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;oBACrB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAC,UAAU,CAAC,KAAK,CAAC,CAAA;gBACxC,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}

package/dist/parsers/A3mMSA.d.ts

@@ -1,43 +0,0 @@
-import type { NodeWithIds } from '../types';
-/**
- * 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;
-    private orderedNames;
-    constructor(text: string);
-    /**
-     * Detect if text is likely A3M format
-     */
-    static sniff(text: string): boolean;
-    /**
-     * 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;
-    getMSA(): {
-        seqdata: Record<string, string>;
-    };
-    getRowData(): undefined;
-    getNames(): string[];
-    getRow(name: string): string;
-    getWidth(): number;
-    getStructures(): {};
-    get alignmentNames(): never[];
-    getHeader(): {};
-    getTree(): NodeWithIds;
-    get seqConsensus(): undefined;
-    get secondaryStructureConsensus(): undefined;
-    get tracks(): never[];
-}

package/dist/parsers/A3mMSA.js

@@ -1,277 +0,0 @@
-// 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) {
-    return ((code >= CODE_A && code <= CODE_Z) ||
-        code === CODE_DASH ||
-        code === CODE_DOT);
-}
-function isLower(code) {
-    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 {
-    MSA;
-    orderedNames;
-    constructor(text) {
-        const rawSeqs = [];
-        const names = [];
-        // 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) {
-        if (!text.startsWith('>')) {
-            return false;
-        }
-        const seqs = [];
-        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.
-     */
-    expandA3M(rawSeqs, names) {
-        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 = [];
-        const insertLengths = [];
-        for (let seqIdx = 0; seqIdx < numSeqs; seqIdx++) {
-            const seq = rawSeqs[seqIdx];
-            const matches = [];
-            const insLens = [];
-            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(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 = [''];
-        const maxGap = Math.max(...maxInserts, 0);
-        for (let i = 1; i <= maxGap; i++) {
-            gapCache.push('.'.repeat(i));
-        }
-        // Build expanded sequences
-        const expanded = {};
-        for (let seqIdx = 0; seqIdx < numSeqs; seqIdx++) {
-            const seq = rawSeqs[seqIdx];
-            const matches = matchChars[seqIdx];
-            const insLens = insertLengths[seqIdx];
-            const result = [];
-            // 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) {
-        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() {
-        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 [];
-    }
-}
-//# sourceMappingURL=A3mMSA.js.map

package/dist/parsers/A3mMSA.js.map

@@ -1 +0,0 @@
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