react-msaview 4.4.5 → 4.5.0

package/dist/neighborJoining.js.map

@@ -0,0 +1 @@
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package/dist/neighborJoining.test.d.ts

@@ -0,0 +1 @@
+export {};

package/dist/neighborJoining.test.js

@@ -0,0 +1,110 @@
+import { describe, expect, test } from 'vitest';
+import { calculateNeighborJoiningTree } from './neighborJoining';
+describe('calculateNeighborJoiningTree', () => {
+    test('generates valid Newick tree for 2 sequences', () => {
+        const rows = [
+            ['seq1', 'MKAA'],
+            ['seq2', 'MKAA'],
+        ];
+        const tree = calculateNeighborJoiningTree(rows);
+        expect(tree).toMatch(/;$/);
+        expect(tree).toContain('seq1');
+        expect(tree).toContain('seq2');
+    });
+    test('generates valid Newick tree for 3 sequences', () => {
+        const rows = [
+            ['human', 'MKAAYLSMFG'],
+            ['mouse', 'MKAAYLSMFG'],
+            ['chicken', 'MKAAFLSMFG'],
+        ];
+        const tree = calculateNeighborJoiningTree(rows);
+        expect(tree).toMatch(/;$/);
+        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 = [
+            ['A', 'MKAAYLSMFGKED'],
+            ['B', 'MKAAYLSMFGKED'],
+            ['C', 'MKAAFLSMFGKEE'],
+            ['D', 'MKAAFLSMFGKEE'],
+        ];
+        const tree = calculateNeighborJoiningTree(rows);
+        expect(tree).toMatch(/;$/);
+        expect(tree).toContain('A');
+        expect(tree).toContain('B');
+        expect(tree).toContain('C');
+        expect(tree).toContain('D');
+    });
+    test('includes branch lengths in tree', () => {
+        const rows = [
+            ['seq1', 'MKAAYLSMFG'],
+            ['seq2', 'MKAAFLSMFG'],
+            ['seq3', 'MKBBFLSMFG'],
+        ];
+        const tree = calculateNeighborJoiningTree(rows);
+        // Branch lengths are formatted as :0.123456
+        expect(tree).toMatch(/:\d+\.\d+/);
+    });
+    test('throws error for less than 2 sequences', () => {
+        const rows = [['seq1', 'MKAA']];
+        expect(() => calculateNeighborJoiningTree(rows)).toThrow('Need at least 2 sequences');
+    });
+    test('handles sequences with gaps', () => {
+        const rows = [
+            ['seq1', 'MK-AYLSMFG'],
+            ['seq2', 'MKAAYLSMFG'],
+            ['seq3', 'MKA-YLSMFG'],
+        ];
+        const tree = calculateNeighborJoiningTree(rows);
+        expect(tree).toMatch(/;$/);
+        expect(tree).toContain('seq1');
+        expect(tree).toContain('seq2');
+        expect(tree).toContain('seq3');
+    });
+    test('handles special characters in sequence names', () => {
+        const rows = [
+            ['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 = [
+            ['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 = [
+            ['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');
+    });
+});
+//# sourceMappingURL=neighborJoining.test.js.map

package/dist/neighborJoining.test.js.map

@@ -0,0 +1 @@
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package/dist/parsers/A3mMSA.d.ts

@@ -0,0 +1,43 @@
+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

@@ -0,0 +1,277 @@
+// 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

@@ -0,0 +1 @@
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package/dist/parsers/A3mMSA.test.d.ts

@@ -0,0 +1 @@
+export {};

package/dist/parsers/A3mMSA.test.js

@@ -0,0 +1,138 @@
+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);
+    });
+});
+//# sourceMappingURL=A3mMSA.test.js.map

package/dist/parsers/A3mMSA.test.js.map

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