msa-parsers 1.0.5 → 5.0.3

package/dist/msa/index.test.js

@@ -1,60 +0,0 @@
-import { describe, expect, test } from 'vitest';
-import A3mMSA from './A3mMSA';
-import ClustalMSA from './ClustalMSA';
-import FastaMSA from './FastaMSA';
-import { getUngappedSequence, parseMSA } from './index';
-describe('parseMSA', () => {
-    test('parses FASTA format', () => {
-        const fasta = `>seq1
-ACDEF
->seq2
-GHIKL`;
-        const msa = parseMSA(fasta);
-        expect(msa).toBeInstanceOf(FastaMSA);
-        expect(msa.getNames()).toEqual(['seq1', 'seq2']);
-    });
-    test('parses A3M format', () => {
-        const a3m = `>seq1
-ACDEFghiKLMNPQ
->seq2
-ACDEF---KLMNPQ`;
-        const msa = parseMSA(a3m);
-        expect(msa).toBeInstanceOf(A3mMSA);
-    });
-    test('parses Clustal format', () => {
-        const clustal = `CLUSTAL W (1.83) multiple sequence alignment
-
-seq1      ACDEFGHIKL
-seq2      ACDEFGHIKL
-          **********`;
-        const msa = parseMSA(clustal);
-        expect(msa).toBeInstanceOf(ClustalMSA);
-    });
-    test('defaults to Clustal for unknown format', () => {
-        const unknown = `some unknown format
-that doesn't match anything`;
-        const msa = parseMSA(unknown);
-        expect(msa).toBeInstanceOf(ClustalMSA);
-    });
-});
-describe('getUngappedSequence', () => {
-    test('removes dashes', () => {
-        expect(getUngappedSequence('AC--DEF')).toBe('ACDEF');
-    });
-    test('removes dots', () => {
-        expect(getUngappedSequence('AC..DEF')).toBe('ACDEF');
-    });
-    test('removes mixed gaps', () => {
-        expect(getUngappedSequence('A-C.D--E..F')).toBe('ACDEF');
-    });
-    test('handles empty string', () => {
-        expect(getUngappedSequence('')).toBe('');
-    });
-    test('handles string with only gaps', () => {
-        expect(getUngappedSequence('---...')).toBe('');
-    });
-    test('handles string with no gaps', () => {
-        expect(getUngappedSequence('ACDEF')).toBe('ACDEF');
-    });
-});
-//# sourceMappingURL=index.test.js.map

package/dist/msa/index.test.js.map

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

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

package/dist/msa/stockholmParser.test.js

@@ -1,111 +0,0 @@
-import { describe, expect, test } from 'vitest';
-import { parse, parseAll, sniff } from './stockholmParser';
-describe('stockholmParser', () => {
-    describe('sniff', () => {
-        test('returns true for Stockholm format', () => {
-            expect(sniff('# STOCKHOLM 1.0\n')).toBe(true);
-        });
-        test('returns false for non-Stockholm format', () => {
-            expect(sniff('>seq1\nACDEF')).toBe(false);
-            expect(sniff('CLUSTAL W')).toBe(false);
-        });
-    });
-    describe('parseAll', () => {
-        test('parses simple Stockholm file', () => {
-            const stockholm = `# STOCKHOLM 1.0
-seq1  ACDEFGHIKL
-seq2  ACDEFGHIKL
-//`;
-            const result = parseAll(stockholm);
-            expect(result).toHaveLength(1);
-            expect(result[0]?.seqdata).toEqual({
-                seq1: 'ACDEFGHIKL',
-                seq2: 'ACDEFGHIKL',
-            });
-            expect(result[0]?.seqname).toEqual(['seq1', 'seq2']);
-        });
-        test('parses GF lines', () => {
-            const stockholm = `# STOCKHOLM 1.0
-#=GF DE Description of the alignment
-#=GF NH (A:0.1,B:0.2);
-seq1  ACDEF
-//`;
-            const result = parseAll(stockholm);
-            expect(result[0]?.gf.DE).toEqual(['Description of the alignment']);
-            expect(result[0]?.gf.NH).toEqual(['(A:0.1,B:0.2);']);
-        });
-        test('parses GC lines', () => {
-            const stockholm = `# STOCKHOLM 1.0
-seq1          ACDEF
-#=GC seq_cons *****
-#=GC SS_cons  <<>>>
-//`;
-            const result = parseAll(stockholm);
-            expect(result[0]?.gc.seq_cons).toBe('*****');
-            expect(result[0]?.gc.SS_cons).toBe('<<>>>');
-        });
-        test('parses GS lines', () => {
-            const stockholm = `# STOCKHOLM 1.0
-#=GS seq1 AC P12345
-#=GS seq1 DR PDB; 1ABC A; 1-100
-seq1  ACDEF
-//`;
-            const result = parseAll(stockholm);
-            expect(result[0]?.gs.AC?.seq1).toEqual(['P12345']);
-            expect(result[0]?.gs.DR?.seq1).toEqual(['PDB; 1ABC A; 1-100']);
-        });
-        test('parses multiple alignments', () => {
-            const stockholm = `# STOCKHOLM 1.0
-seq1  ACDEF
-//
-# STOCKHOLM 1.0
-seq2  GHIKL
-//`;
-            const result = parseAll(stockholm);
-            expect(result).toHaveLength(2);
-            expect(result[0]?.seqdata.seq1).toBe('ACDEF');
-            expect(result[1]?.seqdata.seq2).toBe('GHIKL');
-        });
-        test('concatenates interleaved sequence blocks', () => {
-            const stockholm = `# STOCKHOLM 1.0
-seq1  ACDEF
-seq2  GHIKL
-
-seq1  MNOPQ
-seq2  RSTUV
-//`;
-            const result = parseAll(stockholm);
-            expect(result[0]?.seqdata.seq1).toBe('ACDEFMNOPQ');
-            expect(result[0]?.seqdata.seq2).toBe('GHIKLRSTUV');
-        });
-        test('handles file without trailing //', () => {
-            const stockholm = `# STOCKHOLM 1.0
-seq1  ACDEF`;
-            const result = parseAll(stockholm);
-            expect(result).toHaveLength(1);
-            expect(result[0]?.seqdata.seq1).toBe('ACDEF');
-        });
-    });
-    describe('parse', () => {
-        test('returns single alignment', () => {
-            const stockholm = `# STOCKHOLM 1.0
-seq1  ACDEF
-//`;
-            const result = parse(stockholm);
-            expect(result.seqdata.seq1).toBe('ACDEF');
-        });
-        test('throws on empty input', () => {
-            expect(() => parse('')).toThrow('No alignments found');
-        });
-        test('throws on multiple alignments', () => {
-            const stockholm = `# STOCKHOLM 1.0
-seq1  ACDEF
-//
-# STOCKHOLM 1.0
-seq2  GHIKL
-//`;
-            expect(() => parse(stockholm)).toThrow('More than one alignment found');
-        });
-    });
-});
-//# sourceMappingURL=stockholmParser.test.js.map

package/dist/msa/stockholmParser.test.js.map

@@ -1 +0,0 @@
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