react-msaview 4.5.0 → 4.8.0

package/dist/parsers/A3mMSA.test.js

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

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

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package/dist/parsers/ClustalMSA.d.ts

@@ -1,30 +0,0 @@
-import type { NodeWithIds } from '../types';
-export default class ClustalMSA {
-    private MSA;
-    constructor(text: string);
-    getMSA(): {
-        consensus: string;
-        alns: {
-            id: string | undefined;
-            seq: string;
-        }[];
-        header: {
-            info: string;
-            version: string | undefined;
-        };
-    };
-    getRow(name: string): string;
-    getWidth(): number;
-    getRowData(): undefined;
-    getHeader(): {
-        info: string;
-        version: string | undefined;
-    };
-    getNames(): (string | undefined)[];
-    getStructures(): {};
-    get alignmentNames(): never[];
-    getTree(): NodeWithIds;
-    get seqConsensus(): string;
-    get secondaryStructureConsensus(): undefined;
-    get tracks(): never[];
-}

package/dist/parsers/ClustalMSA.js

@@ -1,55 +0,0 @@
-import { parse } from 'clustal-js';
-export default class ClustalMSA {
-    MSA;
-    constructor(text) {
-        this.MSA = parse(text);
-    }
-    getMSA() {
-        return this.MSA;
-    }
-    getRow(name) {
-        return this.MSA.alns.find(aln => aln.id === name)?.seq || '';
-    }
-    getWidth() {
-        return this.MSA.alns[0].seq.length;
-    }
-    getRowData() {
-        return undefined;
-    }
-    getHeader() {
-        return this.MSA.header;
-    }
-    getNames() {
-        return this.MSA.alns.map(aln => aln.id);
-    }
-    getStructures() {
-        return {};
-    }
-    get alignmentNames() {
-        return [];
-    }
-    getTree() {
-        return {
-            id: 'root',
-            name: 'root',
-            noTree: true,
-            children: this.getNames()
-                .filter((name) => name !== undefined)
-                .map(name => ({
-                id: name,
-                name,
-                children: [],
-            })),
-        };
-    }
-    get seqConsensus() {
-        return this.MSA.consensus;
-    }
-    get secondaryStructureConsensus() {
-        return undefined;
-    }
-    get tracks() {
-        return [];
-    }
-}
-//# sourceMappingURL=ClustalMSA.js.map

package/dist/parsers/ClustalMSA.js.map

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

@@ -1,27 +0,0 @@
-import type { NodeWithIds } from '../types';
-export default class EmfMSA {
-    private MSA;
-    constructor(text: string);
-    getMSA(): {
-        species: string;
-        protein: string;
-        chr: string;
-        start: number;
-        end: number;
-        strand: number;
-        geneId: string;
-        unknown: string;
-        seq: string;
-    }[];
-    getRow(name: string): string;
-    getWidth(): number;
-    getRowData(): undefined;
-    getHeader(): string;
-    getNames(): string[];
-    getStructures(): {};
-    get alignmentNames(): never[];
-    getTree(): NodeWithIds;
-    get seqConsensus(): undefined;
-    get secondaryStructureConsensus(): undefined;
-    get tracks(): never[];
-}

package/dist/parsers/EmfMSA.js

@@ -1,53 +0,0 @@
-import { parseEmfAln } from 'emf-js';
-export default class EmfMSA {
-    MSA;
-    constructor(text) {
-        this.MSA = parseEmfAln(text);
-    }
-    getMSA() {
-        return this.MSA;
-    }
-    getRow(name) {
-        return this.MSA.find(aln => aln.protein === name)?.seq || '';
-    }
-    getWidth() {
-        return this.MSA[0].seq.length;
-    }
-    getRowData() {
-        return undefined;
-    }
-    getHeader() {
-        return '';
-    }
-    getNames() {
-        return this.MSA.map(aln => aln.protein);
-    }
-    getStructures() {
-        return {};
-    }
-    get alignmentNames() {
-        return [];
-    }
-    getTree() {
-        return {
-            id: 'root',
-            name: 'root',
-            noTree: true,
-            children: this.getNames().map(name => ({
-                id: name,
-                name,
-                children: [],
-            })),
-        };
-    }
-    get seqConsensus() {
-        return undefined;
-    }
-    get secondaryStructureConsensus() {
-        return undefined;
-    }
-    get tracks() {
-        return [];
-    }
-}
-//# sourceMappingURL=EmfMSA.js.map

package/dist/parsers/EmfMSA.js.map

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

@@ -1,5 +0,0 @@
-import { parseEmfTree } from 'emf-js';
-export default class EmfTree {
-    data: ReturnType<typeof parseEmfTree>;
-    constructor(text: string);
-}

package/dist/parsers/EmfTree.js

@@ -1,8 +0,0 @@
-import { parseEmfTree } from 'emf-js';
-export default class EmfTree {
-    data;
-    constructor(text) {
-        this.data = parseEmfTree(text);
-    }
-}
-//# sourceMappingURL=EmfTree.js.map

package/dist/parsers/EmfTree.js.map

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

@@ -1,19 +0,0 @@
-import type { NodeWithIds } from '../types';
-export default class FastaMSA {
-    private MSA;
-    constructor(text: string);
-    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/FastaMSA.js

@@ -1,69 +0,0 @@
-export default class FastaMSA {
-    MSA;
-    constructor(text) {
-        const seqdata = {};
-        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) {
-                seqdata[id] = entry.slice(newlineIdx + 1).replaceAll(/\s/g, '');
-            }
-        }
-        this.MSA = { seqdata };
-    }
-    getMSA() {
-        return this.MSA;
-    }
-    getRowData() {
-        return undefined;
-    }
-    getNames() {
-        return Object.keys(this.MSA.seqdata);
-    }
-    getRow(name) {
-        return this.MSA.seqdata[name] || '';
-    }
-    getWidth() {
-        const name = Object.keys(this.MSA.seqdata)[0];
-        return this.getRow(name).length;
-    }
-    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=FastaMSA.js.map

package/dist/parsers/FastaMSA.js.map

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

@@ -1,68 +0,0 @@
-import type { NodeWithIds } from '../types';
-interface StockholmEntry {
-    gf: {
-        DE?: string[];
-        NH?: string[];
-    };
-    gs?: {
-        AC: Record<string, string>;
-        DR?: Record<string, string>;
-    };
-    gc?: {
-        SS_cons?: string;
-        seq_cons?: string;
-    };
-    seqdata: Record<string, string>;
-}
-export default class StockholmMSA {
-    private data;
-    private MSA;
-    constructor(text: string, currentAlignment: number);
-    getMSA(): StockholmEntry;
-    getRow(name: string): string;
-    getWidth(): number;
-    get alignmentNames(): string[];
-    getHeader(): {
-        General: {
-            DE?: string[];
-            NH?: string[];
-        };
-        Accessions: Record<string, string> | undefined;
-        Dbxref: Record<string, string> | undefined;
-    };
-    getRowData(rowName: string): {
-        name: string;
-        accession: string | undefined;
-        dbxref: string | undefined;
-    };
-    getNames(): string[];
-    getSeqCoords(): void;
-    getStructures(): Record<string, Omit<{
-        id: string;
-        pdb: string;
-        chain: string;
-        startPos: number;
-        endPos: number;
-    }, "id">[]>;
-    getTree(): NodeWithIds;
-    get seqConsensus(): string | undefined;
-    get secondaryStructureConsensus(): string | undefined;
-    get tracks(): ({
-        id: string;
-        name: string;
-        data: string | undefined;
-        customColorScheme: {
-            '>'?: undefined;
-            '<'?: undefined;
-        };
-    } | {
-        id: string;
-        name: string;
-        data: string | undefined;
-        customColorScheme: {
-            '>': string;
-            '<': string;
-        };
-    })[];
-}
-export {};

package/dist/parsers/StockholmMSA.js

@@ -1,107 +0,0 @@
-import Stockholm from 'stockholm-js';
-import parseNewick from '../parseNewick';
-import { generateNodeIds } from '../util';
-export default class StockholmMSA {
-    data;
-    MSA;
-    constructor(text, currentAlignment) {
-        const res = Stockholm.parseAll(text);
-        this.data = res;
-        this.MSA = res[currentAlignment];
-    }
-    getMSA() {
-        return this.MSA;
-    }
-    getRow(name) {
-        return this.MSA.seqdata[name] || '';
-    }
-    getWidth() {
-        const name = Object.keys(this.MSA.seqdata)[0];
-        return this.getRow(name).length;
-    }
-    get alignmentNames() {
-        return this.data.map((aln, idx) => aln.gf.DE?.[0] || `Alignment ${idx + 1}`);
-    }
-    getHeader() {
-        return {
-            General: this.MSA.gf,
-            Accessions: this.MSA.gs?.AC,
-            Dbxref: this.MSA.gs?.DR,
-        };
-    }
-    getRowData(rowName) {
-        return {
-            name: rowName,
-            accession: this.MSA.gs?.AC[rowName],
-            dbxref: this.MSA.gs?.DR?.[rowName],
-        };
-    }
-    getNames() {
-        return Object.keys(this.MSA.seqdata);
-    }
-    getSeqCoords() { }
-    getStructures() {
-        const pdbRegex = /PDB; +(\S+) +(\S); ([0-9]+)-([0-9]+)/;
-        const ent = this.MSA;
-        const args = Object.entries(ent.gs?.DR || {})
-            .map(([id, dr]) => [id, pdbRegex.exec(dr)])
-            .filter((item) => !!item[1])
-            .map(([id, match]) => {
-            const pdb = match[1].toLowerCase();
-            const chain = match[2];
-            const startPos = +match[3];
-            const endPos = +match[4];
-            return { id, pdb, chain, startPos, endPos };
-        });
-        const ret = {};
-        for (const entry of args) {
-            const { id, ...rest } = entry;
-            if (!ret[id]) {
-                ret[id] = [];
-            }
-            ret[id].push(rest);
-        }
-        return ret;
-    }
-    getTree() {
-        const tree = this.MSA.gf.NH?.[0];
-        return tree
-            ? generateNodeIds(parseNewick(tree))
-            : {
-                id: 'root',
-                name: 'root',
-                noTree: true,
-                children: this.getNames().map(name => ({
-                    id: name,
-                    children: [],
-                    name,
-                })),
-            };
-    }
-    get seqConsensus() {
-        return this.MSA.gc?.seq_cons;
-    }
-    get secondaryStructureConsensus() {
-        return this.MSA.gc?.SS_cons;
-    }
-    get tracks() {
-        return [
-            {
-                id: 'seqConsensus',
-                name: 'Sequence consensus',
-                data: this.seqConsensus,
-                customColorScheme: {},
-            },
-            {
-                id: 'secondaryStruct',
-                name: 'Secondary-structure',
-                data: this.secondaryStructureConsensus,
-                customColorScheme: {
-                    '>': 'pink',
-                    '<': 'lightblue',
-                },
-            },
-        ];
-    }
-}
-//# sourceMappingURL=StockholmMSA.js.map

package/dist/parsers/StockholmMSA.js.map

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package/dist/seqCoordToRowSpecificGlobalCoord.d.ts

@@ -1,4 +0,0 @@
-export declare function seqCoordToRowSpecificGlobalCoord({ row, position, }: {
-    row: string;
-    position: number;
-}): number;

package/dist/seqCoordToRowSpecificGlobalCoord.js

@@ -1,19 +0,0 @@
-import { isBlank } from './util';
-export function seqCoordToRowSpecificGlobalCoord({ row, position, }) {
-    let k = 0;
-    let i = 0;
-    // Find the position-th non-gap character
-    while (i < row.length) {
-        if (!isBlank(row[i])) {
-            if (k === position) {
-                return i;
-            }
-            k++;
-        }
-        i++;
-    }
-    // If position is 0 and we didn't find any non-gap character, return 0
-    // Otherwise return i (which is row.length at this point)
-    return position === 0 ? 0 : i;
-}
-//# sourceMappingURL=seqCoordToRowSpecificGlobalCoord.js.map

package/dist/seqCoordToRowSpecificGlobalCoord.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"seqCoordToRowSpecificGlobalCoord.js","sourceRoot":"","sources":["../src/seqCoordToRowSpecificGlobalCoord.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,QAAQ,CAAA;AAEhC,MAAM,UAAU,gCAAgC,CAAC,EAC/C,GAAG,EACH,QAAQ,GAIT;IACC,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,yCAAyC;IACzC,OAAO,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC;QACtB,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;YACrB,IAAI,CAAC,KAAK,QAAQ,EAAE,CAAC;gBACnB,OAAO,CAAC,CAAA;YACV,CAAC;YACD,CAAC,EAAE,CAAA;QACL,CAAC;QACD,CAAC,EAAE,CAAA;IACL,CAAC;IACD,sEAAsE;IACtE,yDAAyD;IACzD,OAAO,QAAQ,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AAC/B,CAAC"}

package/dist/seqCoordToRowSpecificGlobalCoord.test.d.ts

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