msa-parsers 5.0.3 → 5.0.5

package/dist/gff/gffToInterPro.test.d.ts

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+export {};

package/dist/gff/gffToInterPro.test.js

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+import { describe, expect, test } from 'vitest';
+import { gffToInterProResponse, gffToInterProResults } from "./gffToInterPro.js";
+describe('gffToInterProResults', () => {
+    test('converts empty array', () => {
+        expect(gffToInterProResults([])).toEqual({});
+    });
+    test('converts single GFF record', () => {
+        const records = [
+            {
+                seq_id: 'seq1',
+                source: 'Pfam',
+                type: 'protein_match',
+                start: 10,
+                end: 50,
+                score: 0,
+                strand: '.',
+                phase: '.',
+                Name: 'PF00001',
+                signature_desc: '7tm_1',
+                description: 'GPCR family',
+            },
+        ];
+        const result = gffToInterProResults(records);
+        expect(result).toHaveProperty('seq1');
+        expect(result.seq1?.matches).toHaveLength(1);
+        expect(result.seq1?.matches[0]?.signature.entry).toEqual({
+            accession: 'PF00001',
+            name: '7tm_1',
+            description: 'GPCR family',
+        });
+        expect(result.seq1?.matches[0]?.locations).toEqual([{ start: 10, end: 50 }]);
+        expect(result.seq1?.xref).toEqual([{ id: 'seq1' }]);
+    });
+    test('groups multiple records for same sequence', () => {
+        const records = [
+            {
+                seq_id: 'seq1',
+                source: 'Pfam',
+                type: 'protein_match',
+                start: 10,
+                end: 50,
+                score: 0,
+                strand: '.',
+                phase: '.',
+                Name: 'PF00001',
+            },
+            {
+                seq_id: 'seq1',
+                source: 'SMART',
+                type: 'protein_match',
+                start: 60,
+                end: 100,
+                score: 0,
+                strand: '.',
+                phase: '.',
+                Name: 'SM00001',
+            },
+        ];
+        const result = gffToInterProResults(records);
+        expect(Object.keys(result)).toHaveLength(1);
+        expect(result.seq1?.matches).toHaveLength(2);
+    });
+    test('handles multiple sequences', () => {
+        const records = [
+            {
+                seq_id: 'seq1',
+                source: 'Pfam',
+                type: 'protein_match',
+                start: 10,
+                end: 50,
+                score: 0,
+                strand: '.',
+                phase: '.',
+                Name: 'PF00001',
+            },
+            {
+                seq_id: 'seq2',
+                source: 'Pfam',
+                type: 'protein_match',
+                start: 5,
+                end: 40,
+                score: 0,
+                strand: '.',
+                phase: '.',
+                Name: 'PF00002',
+            },
+        ];
+        const result = gffToInterProResults(records);
+        expect(Object.keys(result)).toHaveLength(2);
+        expect(result).toHaveProperty('seq1');
+        expect(result).toHaveProperty('seq2');
+    });
+    test('combines locations for same accession', () => {
+        const records = [
+            {
+                seq_id: 'seq1',
+                source: 'Pfam',
+                type: 'protein_match',
+                start: 10,
+                end: 50,
+                score: 0,
+                strand: '.',
+                phase: '.',
+                Name: 'PF00001',
+            },
+            {
+                seq_id: 'seq1',
+                source: 'Pfam',
+                type: 'protein_match',
+                start: 100,
+                end: 150,
+                score: 0,
+                strand: '.',
+                phase: '.',
+                Name: 'PF00001',
+            },
+        ];
+        const result = gffToInterProResults(records);
+        expect(result.seq1?.matches).toHaveLength(1);
+        expect(result.seq1?.matches[0]?.locations).toHaveLength(2);
+        expect(result.seq1?.matches[0]?.locations).toEqual([
+            { start: 10, end: 50 },
+            { start: 100, end: 150 },
+        ]);
+    });
+    test('uses ID as fallback for Name', () => {
+        const records = [
+            {
+                seq_id: 'seq1',
+                source: 'Source',
+                type: 'protein_match',
+                start: 10,
+                end: 50,
+                score: 0,
+                strand: '.',
+                phase: '.',
+                ID: 'domain_123',
+            },
+        ];
+        const result = gffToInterProResults(records);
+        expect(result.seq1?.matches[0]?.signature.entry?.accession).toBe('domain_123');
+    });
+    test('generates fallback accession from source and positions', () => {
+        const records = [
+            {
+                seq_id: 'seq1',
+                source: 'CustomSource',
+                type: 'protein_match',
+                start: 10,
+                end: 50,
+                score: 0,
+                strand: '.',
+                phase: '.',
+            },
+        ];
+        const result = gffToInterProResults(records);
+        expect(result.seq1?.matches[0]?.signature.entry?.accession).toBe('CustomSource_10_50');
+    });
+});
+describe('gffToInterProResponse', () => {
+    test('wraps results in response format', () => {
+        const records = [
+            {
+                seq_id: 'seq1',
+                source: 'Pfam',
+                type: 'protein_match',
+                start: 10,
+                end: 50,
+                score: 0,
+                strand: '.',
+                phase: '.',
+                Name: 'PF00001',
+            },
+        ];
+        const response = gffToInterProResponse(records);
+        expect(response).toHaveProperty('results');
+        expect(response.results).toHaveLength(1);
+        expect(response.results[0]?.xref[0]?.id).toBe('seq1');
+    });
+});
+//# sourceMappingURL=gffToInterPro.test.js.map

package/dist/gff/gffToInterPro.test.js.map

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package/dist/gff/interProToGFF.test.d.ts

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+export {};

package/dist/gff/interProToGFF.test.js

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+import { describe, expect, test } from 'vitest';
+import { interProResponseToGFF, interProToGFF } from "./interProToGFF.js";
+describe('interProToGFF', () => {
+    test('converts empty results', () => {
+        const gff = interProToGFF({});
+        expect(gff).toBe('##gff-version 3');
+    });
+    test('converts single result', () => {
+        const results = {
+            seq1: {
+                matches: [
+                    {
+                        signature: {
+                            entry: {
+                                accession: 'PF00001',
+                                name: '7tm_1',
+                                description: 'GPCR family',
+                            },
+                        },
+                        locations: [{ start: 10, end: 50 }],
+                    },
+                ],
+                xref: [{ id: 'seq1' }],
+            },
+        };
+        const gff = interProToGFF(results);
+        const lines = gff.split('\n');
+        expect(lines[0]).toBe('##gff-version 3');
+        expect(lines[1]).toContain('seq1');
+        expect(lines[1]).toContain('InterProScan');
+        expect(lines[1]).toContain('protein_match');
+        expect(lines[1]).toContain('10');
+        expect(lines[1]).toContain('50');
+        expect(lines[1]).toContain('Name=PF00001');
+        expect(lines[1]).toContain('signature_desc=7tm_1');
+        expect(lines[1]).toContain('description=GPCR%20family');
+    });
+    test('handles multiple locations', () => {
+        const results = {
+            seq1: {
+                matches: [
+                    {
+                        signature: {
+                            entry: {
+                                accession: 'PF00001',
+                                name: 'domain',
+                                description: 'test',
+                            },
+                        },
+                        locations: [
+                            { start: 10, end: 50 },
+                            { start: 100, end: 150 },
+                        ],
+                    },
+                ],
+                xref: [{ id: 'seq1' }],
+            },
+        };
+        const gff = interProToGFF(results);
+        const lines = gff.split('\n');
+        expect(lines).toHaveLength(3);
+        expect(lines[1]).toContain('10\t50');
+        expect(lines[2]).toContain('100\t150');
+    });
+    test('handles multiple sequences', () => {
+        const results = {
+            seq1: {
+                matches: [
+                    {
+                        signature: {
+                            entry: {
+                                accession: 'PF00001',
+                                name: 'domain1',
+                                description: 'test1',
+                            },
+                        },
+                        locations: [{ start: 10, end: 50 }],
+                    },
+                ],
+                xref: [{ id: 'seq1' }],
+            },
+            seq2: {
+                matches: [
+                    {
+                        signature: {
+                            entry: {
+                                accession: 'PF00002',
+                                name: 'domain2',
+                                description: 'test2',
+                            },
+                        },
+                        locations: [{ start: 5, end: 40 }],
+                    },
+                ],
+                xref: [{ id: 'seq2' }],
+            },
+        };
+        const gff = interProToGFF(results);
+        const lines = gff.split('\n');
+        expect(lines).toHaveLength(3);
+        expect(lines.some(l => l.includes('seq1'))).toBe(true);
+        expect(lines.some(l => l.includes('seq2'))).toBe(true);
+    });
+    test('skips matches without entry', () => {
+        const results = {
+            seq1: {
+                matches: [
+                    {
+                        signature: {},
+                        locations: [{ start: 10, end: 50 }],
+                    },
+                ],
+                xref: [{ id: 'seq1' }],
+            },
+        };
+        const gff = interProToGFF(results);
+        const lines = gff.split('\n');
+        expect(lines).toHaveLength(1);
+        expect(lines[0]).toBe('##gff-version 3');
+    });
+    test('URL-encodes special characters in attributes', () => {
+        const results = {
+            seq1: {
+                matches: [
+                    {
+                        signature: {
+                            entry: {
+                                accession: 'PF00001',
+                                name: 'test;name=value',
+                                description: 'description with spaces',
+                            },
+                        },
+                        locations: [{ start: 10, end: 50 }],
+                    },
+                ],
+                xref: [{ id: 'seq1' }],
+            },
+        };
+        const gff = interProToGFF(results);
+        expect(gff).toContain('signature_desc=test%3Bname%3Dvalue');
+        expect(gff).toContain('description=description%20with%20spaces');
+    });
+});
+describe('interProResponseToGFF', () => {
+    test('converts array of results', () => {
+        const results = [
+            {
+                matches: [
+                    {
+                        signature: {
+                            entry: {
+                                accession: 'PF00001',
+                                name: 'domain',
+                                description: 'test',
+                            },
+                        },
+                        locations: [{ start: 10, end: 50 }],
+                    },
+                ],
+                xref: [{ id: 'seq1' }],
+            },
+        ];
+        const gff = interProResponseToGFF(results);
+        expect(gff).toContain('##gff-version 3');
+        expect(gff).toContain('seq1');
+    });
+    test('handles results without xref', () => {
+        const results = [
+            {
+                matches: [
+                    {
+                        signature: {
+                            entry: {
+                                accession: 'PF00001',
+                                name: 'domain',
+                                description: 'test',
+                            },
+                        },
+                        locations: [{ start: 10, end: 50 }],
+                    },
+                ],
+                xref: [],
+            },
+        ];
+        const gff = interProResponseToGFF(results);
+        expect(gff).toBe('##gff-version 3');
+    });
+});
+//# sourceMappingURL=interProToGFF.test.js.map

package/dist/gff/interProToGFF.test.js.map

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

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

package/dist/gff/parseGFF.test.js

@@ -0,0 +1,92 @@
+import { describe, expect, test } from 'vitest';
+import { parseGFF } from "./parseGFF.js";
+describe('parseGFF', () => {
+    test('parses empty string', () => {
+        expect(parseGFF('')).toEqual([]);
+        expect(parseGFF(undefined)).toEqual([]);
+    });
+    test('parses basic GFF3 line', () => {
+        const gff = 'seq1\tInterProScan\tprotein_match\t10\t50\t.\t+\t.\tName=PF00001';
+        const result = parseGFF(gff);
+        expect(result).toHaveLength(1);
+        expect(result[0]).toEqual({
+            seq_id: 'seq1',
+            source: 'InterProScan',
+            type: 'protein_match',
+            start: 10,
+            end: 50,
+            score: 0,
+            strand: '+',
+            phase: '.',
+            Name: 'PF00001',
+        });
+    });
+    test('parses multiple attributes', () => {
+        const gff = 'seq1\tPfam\tprotein_match\t10\t50\t1.5\t.\t.\tName=PF00001;signature_desc=7tm_1;description=GPCR';
+        const result = parseGFF(gff);
+        expect(result[0]).toMatchObject({
+            Name: 'PF00001',
+            signature_desc: '7tm_1',
+            description: 'GPCR',
+        });
+    });
+    test('handles URL-encoded attribute values', () => {
+        const gff = 'seq1\tSource\ttype\t1\t10\t.\t.\t.\tNote=Hello%20World%3B%3D';
+        const result = parseGFF(gff);
+        expect(result[0]?.Note).toBe('Hello World;=');
+    });
+    test('skips comment lines', () => {
+        const gff = `##gff-version 3
+# This is a comment
+seq1\tSource\ttype\t1\t10\t.\t.\t.\tName=test`;
+        const result = parseGFF(gff);
+        expect(result).toHaveLength(1);
+        expect(result[0]?.seq_id).toBe('seq1');
+    });
+    test('skips empty lines', () => {
+        const gff = `seq1\tSource\ttype\t1\t10\t.\t.\t.\tName=test1
+
+seq2\tSource\ttype\t20\t30\t.\t.\t.\tName=test2`;
+        const result = parseGFF(gff);
+        expect(result).toHaveLength(2);
+    });
+    test('handles missing attributes column', () => {
+        const gff = 'seq1\tSource\ttype\t1\t10\t.\t.\t.';
+        const result = parseGFF(gff);
+        expect(result).toHaveLength(1);
+        expect(result[0]?.seq_id).toBe('seq1');
+    });
+    test('handles partial GFF lines gracefully', () => {
+        const gff = 'seq1\tSource\ttype';
+        const result = parseGFF(gff);
+        expect(result).toHaveLength(1);
+        expect(result[0]).toMatchObject({
+            seq_id: 'seq1',
+            source: 'Source',
+            type: 'type',
+            start: 0,
+            end: 0,
+        });
+    });
+    test('parses numeric score', () => {
+        const gff = 'seq1\tSource\ttype\t1\t10\t45.6\t.\t.\tName=test';
+        const result = parseGFF(gff);
+        expect(result[0]?.score).toBe(45.6);
+    });
+    test('handles comma-separated values in attributes', () => {
+        const gff = 'seq1\tSource\ttype\t1\t10\t.\t.\t.\tOntology_term=GO:0001,GO:0002';
+        const result = parseGFF(gff);
+        expect(result[0]?.Ontology_term).toBe('GO:0001 GO:0002');
+    });
+    test('parses multiple lines', () => {
+        const gff = `seq1\tPfam\tprotein_match\t10\t50\t.\t.\t.\tName=PF00001
+seq1\tSMART\tprotein_match\t60\t100\t.\t.\t.\tName=SM00001
+seq2\tPfam\tprotein_match\t5\t40\t.\t.\t.\tName=PF00002`;
+        const result = parseGFF(gff);
+        expect(result).toHaveLength(3);
+        expect(result[0]?.seq_id).toBe('seq1');
+        expect(result[1]?.seq_id).toBe('seq1');
+        expect(result[2]?.seq_id).toBe('seq2');
+    });
+});
+//# sourceMappingURL=parseGFF.test.js.map

package/dist/gff/parseGFF.test.js.map

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

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

package/dist/msa/A3mMSA.test.js

@@ -0,0 +1,155 @@
+import { describe, expect, test } from 'vitest';
+import A3mMSA from "./A3mMSA.js";
+describe('A3mMSA', () => {
+    describe('sniff', () => {
+        test('returns false for non-FASTA text', () => {
+            expect(A3mMSA.sniff('not fasta')).toBe(false);
+            expect(A3mMSA.sniff('CLUSTAL W')).toBe(false);
+        });
+        test('returns false for regular FASTA', () => {
+            const fasta = `>seq1
+ACDEFGHIKLMNPQRSTVWY
+>seq2
+ACDEFGHIKLMNPQRSTVWY`;
+            expect(A3mMSA.sniff(fasta)).toBe(false);
+        });
+        test('returns true for A3M format', () => {
+            const a3m = `>seq1
+ACDEFghiKLMNPQ
+>seq2
+ACDEF---KLMNPQ`;
+            expect(A3mMSA.sniff(a3m)).toBe(true);
+        });
+        test('returns false for single sequence', () => {
+            const a3m = `>seq1
+ACDEFghiKLMNPQ`;
+            expect(A3mMSA.sniff(a3m)).toBe(false);
+        });
+    });
+    describe('parsing', () => {
+        test('parses simple A3M', () => {
+            const a3m = `>seq1
+ACDEFghiKLMNPQ
+>seq2
+ACDEF---KLMNPQ`;
+            const msa = new A3mMSA(a3m);
+            expect(msa.getNames()).toEqual(['seq1', 'seq2']);
+            const seq1 = msa.getRow('seq1');
+            const seq2 = msa.getRow('seq2');
+            expect(seq1.length).toBe(seq2.length);
+            expect(seq1).toContain('GHI');
+        });
+        test('expands lowercase insertions', () => {
+            const a3m = `>seq1
+ACabc
+>seq2
+AC---`;
+            const msa = new A3mMSA(a3m);
+            const seq1 = msa.getRow('seq1');
+            const seq2 = msa.getRow('seq2');
+            expect(seq1).toBe('ACABC');
+            expect(seq2).toBe('AC...');
+        });
+        test('handles multiple insertions', () => {
+            const a3m = `>seq1
+AabcDdefG
+>seq2
+A---D---G`;
+            const msa = new A3mMSA(a3m);
+            const seq1 = msa.getRow('seq1');
+            const seq2 = msa.getRow('seq2');
+            expect(seq1.length).toBe(seq2.length);
+        });
+        test('getWidth returns correct width', () => {
+            const a3m = `>seq1
+ACDEF
+>seq2
+ACDEF`;
+            const msa = new A3mMSA(a3m);
+            expect(msa.getWidth()).toBe(5);
+        });
+        test('getMSA returns seqdata', () => {
+            const a3m = `>seq1
+ACDEF
+>seq2
+GHIKL`;
+            const msa = new A3mMSA(a3m);
+            const data = msa.getMSA();
+            expect(data.seqdata).toHaveProperty('seq1');
+            expect(data.seqdata).toHaveProperty('seq2');
+        });
+        test('getTree returns noTree structure', () => {
+            const a3m = `>seq1
+ACDEF
+>seq2
+GHIKL`;
+            const msa = new A3mMSA(a3m);
+            const tree = msa.getTree();
+            expect(tree.noTree).toBe(true);
+            expect(tree.children).toHaveLength(2);
+        });
+        test('handles empty sequences', () => {
+            const a3m = `>seq1
+ACDEF`;
+            const msa = new A3mMSA(a3m);
+            expect(msa.getNames()).toEqual(['seq1']);
+        });
+        test('handles sequences with only ID on defline', () => {
+            const a3m = `>seq1 description here
+ACDEF
+>seq2 another description
+GHIKL`;
+            const msa = new A3mMSA(a3m);
+            expect(msa.getNames()).toEqual(['seq1', 'seq2']);
+        });
+        test('preserves sequence order', () => {
+            const a3m = `>z_seq
+AAAAA
+>a_seq
+CCCCC
+>m_seq
+DDDDD`;
+            const msa = new A3mMSA(a3m);
+            expect(msa.getNames()).toEqual(['z_seq', 'a_seq', 'm_seq']);
+        });
+    });
+    describe('properties', () => {
+        test('alignmentNames is empty array', () => {
+            const a3m = `>seq1
+ACDEF`;
+            const msa = new A3mMSA(a3m);
+            expect(msa.alignmentNames).toEqual([]);
+        });
+        test('seqConsensus is undefined', () => {
+            const a3m = `>seq1
+ACDEF`;
+            const msa = new A3mMSA(a3m);
+            expect(msa.seqConsensus).toBeUndefined();
+        });
+        test('secondaryStructureConsensus is undefined', () => {
+            const a3m = `>seq1
+ACDEF`;
+            const msa = new A3mMSA(a3m);
+            expect(msa.secondaryStructureConsensus).toBeUndefined();
+        });
+        test('tracks is empty array', () => {
+            const a3m = `>seq1
+ACDEF`;
+            const msa = new A3mMSA(a3m);
+            expect(msa.tracks).toEqual([]);
+        });
+        test('getStructures returns empty object', () => {
+            const a3m = `>seq1
+ACDEF`;
+            const msa = new A3mMSA(a3m);
+            expect(msa.getStructures()).toEqual({});
+        });
+        test('getHeader returns empty object', () => {
+            const a3m = `>seq1
+ACDEF`;
+            const msa = new A3mMSA(a3m);
+            expect(msa.getHeader()).toEqual({});
+        });
+    });
+});
+//# sourceMappingURL=A3mMSA.test.js.map

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

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package/dist/msa/index.test.d.ts

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

package/dist/msa/index.test.js

@@ -0,0 +1,60 @@
+import { describe, expect, test } from 'vitest';
+import A3mMSA from "./A3mMSA.js";
+import ClustalMSA from "./ClustalMSA.js";
+import FastaMSA from "./FastaMSA.js";
+import { getUngappedSequence, parseMSA } from "./index.js";
+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

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

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

package/dist/msa/stockholmParser.test.js

@@ -0,0 +1,111 @@
+import { describe, expect, test } from 'vitest';
+import { parse, parseAll, sniff } from "./stockholmParser.js";
+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

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "msa-parsers",
-  "version": "5.0.3",
+  "version": "5.0.5",
   "license": "MIT",
   "type": "module",
   "exports": {