msa-parsers 5.10.0 → 6.0.0

package/dist/gff/annotationsToGFF.d.ts

@@ -0,0 +1,9 @@
+import type { Annotation } from '../types.ts';
+/**
+ * Write annotations as GFF3, one line per annotation, in list order.
+ *
+ * The source column is always `InterProScan`: an Annotation records no source
+ * of its own, and the CLI's precomputed-lookup path depends on this output
+ * matching what a real InterProScan run emits, byte for byte.
+ */
+export declare function annotationsToGFF(annotations: Annotation[]): string;

package/dist/gff/annotationsToGFF.js

@@ -0,0 +1,36 @@
+/**
+ * Write annotations as GFF3, one line per annotation, in list order.
+ *
+ * The source column is always `InterProScan`: an Annotation records no source
+ * of its own, and the CLI's precomputed-lookup path depends on this output
+ * matching what a real InterProScan run emits, byte for byte.
+ */
+export function annotationsToGFF(annotations) {
+    return [
+        '##gff-version 3',
+        ...annotations.map(annotation => {
+            const { accession, name, description, featureType } = annotation;
+            const { id, start, end, strand } = annotation;
+            return [
+                id,
+                'InterProScan',
+                // GFF-sourced annotations carry their original type; writing every
+                // feature back out as protein_match would turn an exon overlay into
+                // generic domains on the next read, losing the numbered-segment
+                // rendering and the gene arrowheads
+                featureType ?? 'protein_match',
+                start,
+                end,
+                '.',
+                strand === undefined ? '.' : strand > 0 ? '+' : '-',
+                '.',
+                [
+                    `Name=${encodeURIComponent(accession)}`,
+                    `signature_desc=${encodeURIComponent(name)}`,
+                    `description=${encodeURIComponent(description)}`,
+                ].join(';'),
+            ].join('\t');
+        }),
+    ].join('\n');
+}
+//# sourceMappingURL=annotationsToGFF.js.map

package/dist/gff/annotationsToGFF.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"annotationsToGFF.js","sourceRoot":"","sources":["../../src/gff/annotationsToGFF.ts"],"names":[],"mappings":"AAEA;;;;;;GAMG;AACH,MAAM,UAAU,gBAAgB,CAAC,WAAyB;IACxD,OAAO;QACL,iBAAiB;QACjB,GAAG,WAAW,CAAC,GAAG,CAAC,UAAU,CAAC,EAAE;YAC9B,MAAM,EAAE,SAAS,EAAE,IAAI,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,UAAU,CAAA;YAChE,MAAM,EAAE,EAAE,EAAE,KAAK,EAAE,GAAG,EAAE,MAAM,EAAE,GAAG,UAAU,CAAA;YAC7C,OAAO;gBACL,EAAE;gBACF,cAAc;gBACd,mEAAmE;gBACnE,oEAAoE;gBACpE,gEAAgE;gBAChE,oCAAoC;gBACpC,WAAW,IAAI,eAAe;gBAC9B,KAAK;gBACL,GAAG;gBACH,GAAG;gBACH,MAAM,KAAK,SAAS,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG;gBACnD,GAAG;gBACH;oBACE,QAAQ,kBAAkB,CAAC,SAAS,CAAC,EAAE;oBACvC,kBAAkB,kBAAkB,CAAC,IAAI,CAAC,EAAE;oBAC5C,eAAe,kBAAkB,CAAC,WAAW,CAAC,EAAE;iBACjD,CAAC,IAAI,CAAC,GAAG,CAAC;aACZ,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACd,CAAC,CAAC;KACH,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;AACd,CAAC"}

package/dist/gff/gffToAnnotations.d.ts

@@ -0,0 +1,9 @@
+import type { Annotation, GFFRecord } from '../types.ts';
+/**
+ * Convert GFF records to annotations, one per record, in file order.
+ *
+ * InterProScan's own GFF3 output falls out of the same mapping: it writes
+ * `Name` as the signature accession and `signature_desc` as its human-readable
+ * name, with domain positions 1-based.
+ */
+export declare function gffToAnnotations(gffRecords: GFFRecord[]): Annotation[];

package/dist/gff/gffToAnnotations.js

@@ -0,0 +1,53 @@
+// Feature types that read as a directional "gene" and get an arrowhead in the
+// overlay. Exon/CDS/UTR/domain features deliberately stay rectangular blocks —
+// turning every exon into an arrow is misleading, since exons are segments of a
+// single transcript, not independently-oriented genes.
+const GENE_LEVEL_TYPES = new Set([
+    'gene',
+    'pseudogene',
+    'mRNA',
+    'transcript',
+    'primary_transcript',
+    'ncRNA',
+    'tRNA',
+    'rRNA',
+    'snRNA',
+    'snoRNA',
+    'miRNA',
+    'lnc_RNA',
+]);
+// +1/-1 for a stranded gene-level feature, undefined otherwise (which the
+// renderer draws as a plain block).
+function geneStrand({ type, strand }) {
+    const directional = strand === '+' ? 1 : strand === '-' ? -1 : undefined;
+    return GENE_LEVEL_TYPES.has(type) ? directional : undefined;
+}
+/**
+ * Convert GFF records to annotations, one per record, in file order.
+ *
+ * InterProScan's own GFF3 output falls out of the same mapping: it writes
+ * `Name` as the signature accession and `signature_desc` as its human-readable
+ * name, with domain positions 1-based.
+ */
+export function gffToAnnotations(gffRecords) {
+    return gffRecords.map(record => {
+        const accession = record.Name ||
+            record.ID ||
+            `${record.source}_${record.start}_${record.end}`;
+        const name = record.signature_desc || record.Name || accession;
+        return {
+            id: record.seq_id,
+            accession,
+            name,
+            description: record.Ontology_term ||
+                record.description ||
+                record.Note ||
+                name,
+            featureType: record.type,
+            start: record.start,
+            end: record.end,
+            strand: geneStrand(record),
+        };
+    });
+}
+//# sourceMappingURL=gffToAnnotations.js.map

package/dist/gff/gffToAnnotations.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"gffToAnnotations.js","sourceRoot":"","sources":["../../src/gff/gffToAnnotations.ts"],"names":[],"mappings":"AAEA,8EAA8E;AAC9E,+EAA+E;AAC/E,gFAAgF;AAChF,uDAAuD;AACvD,MAAM,gBAAgB,GAAG,IAAI,GAAG,CAAC;IAC/B,MAAM;IACN,YAAY;IACZ,MAAM;IACN,YAAY;IACZ,oBAAoB;IACpB,OAAO;IACP,MAAM;IACN,MAAM;IACN,OAAO;IACP,QAAQ;IACR,OAAO;IACP,SAAS;CACV,CAAC,CAAA;AAEF,0EAA0E;AAC1E,oCAAoC;AACpC,SAAS,UAAU,CAAC,EAAE,IAAI,EAAE,MAAM,EAAa;IAC7C,MAAM,WAAW,GAAG,MAAM,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IACxE,OAAO,gBAAgB,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,SAAS,CAAA;AAC7D,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,gBAAgB,CAAC,UAAuB;IACtD,OAAO,UAAU,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE;QAC7B,MAAM,SAAS,GACZ,MAAM,CAAC,IAAe;YACtB,MAAM,CAAC,EAAa;YACrB,GAAG,MAAM,CAAC,MAAM,IAAI,MAAM,CAAC,KAAK,IAAI,MAAM,CAAC,GAAG,EAAE,CAAA;QAClD,MAAM,IAAI,GACP,MAAM,CAAC,cAAyB,IAAK,MAAM,CAAC,IAAe,IAAI,SAAS,CAAA;QAC3E,OAAO;YACL,EAAE,EAAE,MAAM,CAAC,MAAM;YACjB,SAAS;YACT,IAAI;YACJ,WAAW,EACR,MAAM,CAAC,aAAwB;gBAC/B,MAAM,CAAC,WAAsB;gBAC7B,MAAM,CAAC,IAAe;gBACvB,IAAI;YACN,WAAW,EAAE,MAAM,CAAC,IAAI;YACxB,KAAK,EAAE,MAAM,CAAC,KAAK;YACnB,GAAG,EAAE,MAAM,CAAC,GAAG;YACf,MAAM,EAAE,UAAU,CAAC,MAAM,CAAC;SAC3B,CAAA;IACH,CAAC,CAAC,CAAA;AACJ,CAAC"}

package/dist/gff/gffToAnnotations.test.js

@@ -0,0 +1,71 @@
+import { expect, test } from 'vitest';
+import { gffToAnnotations } from './gffToAnnotations.js';
+function record(fields = {}) {
+    return {
+        seq_id: 'seq1',
+        source: 'Pfam',
+        type: 'protein_match',
+        start: 10,
+        end: 50,
+        score: 0,
+        strand: '.',
+        phase: '.',
+        ...fields,
+    };
+}
+test('converts empty array', () => {
+    expect(gffToAnnotations([])).toEqual([]);
+});
+test('maps a record onto the annotation fields', () => {
+    expect(gffToAnnotations([
+        record({
+            Name: 'PF00001',
+            signature_desc: '7tm_1',
+            description: 'GPCR family',
+        }),
+    ])).toEqual([
+        {
+            id: 'seq1',
+            accession: 'PF00001',
+            name: '7tm_1',
+            description: 'GPCR family',
+            featureType: 'protein_match',
+            start: 10,
+            end: 50,
+            strand: undefined,
+        },
+    ]);
+});
+test('keeps one annotation per record, in file order', () => {
+    const annotations = gffToAnnotations([
+        record({ Name: 'PF00001', start: 10, end: 50 }),
+        record({ Name: 'PF00001', start: 100, end: 150 }),
+        record({ seq_id: 'seq2', Name: 'PF00002', start: 5, end: 40 }),
+    ]);
+    expect(annotations.map(a => [a.id, a.accession, a.start, a.end])).toEqual([
+        ['seq1', 'PF00001', 10, 50],
+        ['seq1', 'PF00001', 100, 150],
+        ['seq2', 'PF00002', 5, 40],
+    ]);
+});
+test('gives gene-level features a direction but leaves exons/domains as blocks', () => {
+    const annotations = gffToAnnotations([
+        record({ type: 'gene', strand: '+', Name: 'GENEA' }),
+        record({ type: 'mRNA', strand: '-', Name: 'GENEB' }),
+        record({ type: 'exon', strand: '+', Name: 'exon-1' }),
+        record({ type: 'protein_match', strand: '+', Name: 'PF00001' }),
+    ]);
+    expect(Object.fromEntries(annotations.map(a => [a.accession, a.strand]))).toEqual({
+        GENEA: 1, // + gene -> arrow right
+        GENEB: -1, // - gene -> arrow left
+        'exon-1': undefined, // exon stays a block even though it is stranded
+        PF00001: undefined, // protein domain stays a block
+    });
+});
+test('falls back from Name to ID to source and positions', () => {
+    expect(gffToAnnotations([
+        record({ ID: 'domain_123' }),
+        record({ source: 'CustomSource' }),
+    ]).map(a => a.accession)).toEqual(['domain_123', 'CustomSource_10_50']);
+});
+//# sourceMappingURL=gffToAnnotations.test.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"gffToAnnotations.test.js","sourceRoot":"","sources":["../../src/gff/gffToAnnotations.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAErC,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAA;AAIxD,SAAS,MAAM,CAAC,MAAM,GAAuB,EAAE;IAC7C,OAAO;QACL,MAAM,EAAE,MAAM;QACd,MAAM,EAAE,MAAM;QACd,IAAI,EAAE,eAAe;QACrB,KAAK,EAAE,EAAE;QACT,GAAG,EAAE,EAAE;QACP,KAAK,EAAE,CAAC;QACR,MAAM,EAAE,GAAG;QACX,KAAK,EAAE,GAAG;QACV,GAAG,MAAM;KACV,CAAA;AACH,CAAC;AAED,IAAI,CAAC,sBAAsB,EAAE,GAAG,EAAE;IAChC,MAAM,CAAC,gBAAgB,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAA;AAC1C,CAAC,CAAC,CAAA;AAEF,IAAI,CAAC,0CAA0C,EAAE,GAAG,EAAE;IACpD,MAAM,CACJ,gBAAgB,CAAC;QACf,MAAM,CAAC;YACL,IAAI,EAAE,SAAS;YACf,cAAc,EAAE,OAAO;YACvB,WAAW,EAAE,aAAa;SAC3B,CAAC;KACH,CAAC,CACH,CAAC,OAAO,CAAC;QACR;YACE,EAAE,EAAE,MAAM;YACV,SAAS,EAAE,SAAS;YACpB,IAAI,EAAE,OAAO;YACb,WAAW,EAAE,aAAa;YAC1B,WAAW,EAAE,eAAe;YAC5B,KAAK,EAAE,EAAE;YACT,GAAG,EAAE,EAAE;YACP,MAAM,EAAE,SAAS;SAClB;KACF,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,IAAI,CAAC,gDAAgD,EAAE,GAAG,EAAE;IAC1D,MAAM,WAAW,GAAG,gBAAgB,CAAC;QACnC,MAAM,CAAC,EAAE,IAAI,EAAE,SAAS,EAAE,KAAK,EAAE,EAAE,EAAE,GAAG,EAAE,EAAE,EAAE,CAAC;QAC/C,MAAM,CAAC,EAAE,IAAI,EAAE,SAAS,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,CAAC;QACjD,MAAM,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,SAAS,EAAE,KAAK,EAAE,CAAC,EAAE,GAAG,EAAE,EAAE,EAAE,CAAC;KAC/D,CAAC,CAAA;IACF,MAAM,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,SAAS,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC;QACxE,CAAC,MAAM,EAAE,SAAS,EAAE,EAAE,EAAE,EAAE,CAAC;QAC3B,CAAC,MAAM,EAAE,SAAS,EAAE,GAAG,EAAE,GAAG,CAAC;QAC7B,CAAC,MAAM,EAAE,SAAS,EAAE,CAAC,EAAE,EAAE,CAAC;KAC3B,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,IAAI,CAAC,0EAA0E,EAAE,GAAG,EAAE;IACpF,MAAM,WAAW,GAAG,gBAAgB,CAAC;QACnC,MAAM,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,EAAE,IAAI,EAAE,OAAO,EAAE,CAAC;QACpD,MAAM,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,EAAE,IAAI,EAAE,OAAO,EAAE,CAAC;QACpD,MAAM,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,EAAE,IAAI,EAAE,QAAQ,EAAE,CAAC;QACrD,MAAM,CAAC,EAAE,IAAI,EAAE,eAAe,EAAE,MAAM,EAAE,GAAG,EAAE,IAAI,EAAE,SAAS,EAAE,CAAC;KAChE,CAAC,CAAA;IACF,MAAM,CACJ,MAAM,CAAC,WAAW,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAClE,CAAC,OAAO,CAAC;QACR,KAAK,EAAE,CAAC,EAAE,wBAAwB;QAClC,KAAK,EAAE,CAAC,CAAC,EAAE,uBAAuB;QAClC,QAAQ,EAAE,SAAS,EAAE,gDAAgD;QACrE,OAAO,EAAE,SAAS,EAAE,+BAA+B;KACpD,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,IAAI,CAAC,oDAAoD,EAAE,GAAG,EAAE;IAC9D,MAAM,CACJ,gBAAgB,CAAC;QACf,MAAM,CAAC,EAAE,EAAE,EAAE,YAAY,EAAE,CAAC;QAC5B,MAAM,CAAC,EAAE,MAAM,EAAE,cAAc,EAAE,CAAC;KACnC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC,CACzB,CAAC,OAAO,CAAC,CAAC,YAAY,EAAE,oBAAoB,CAAC,CAAC,CAAA;AACjD,CAAC,CAAC,CAAA"}

package/dist/gff/index.d.ts

@@ -1,3 +1,4 @@
 export { parseGFF } from './parseGFF.ts';
-export { gffToInterProResponse, gffToInterProResults } from './gffToInterPro.ts';
+export { gffToAnnotations } from './gffToAnnotations.ts';
+export { annotationsToGFF } from './annotationsToGFF.ts';
 export { interProResponseToGFF, interProToGFF } from './interProToGFF.ts';

package/dist/gff/index.js

@@ -1,4 +1,5 @@
 export { parseGFF } from './parseGFF.js';
-export { gffToInterProResponse, gffToInterProResults } from './gffToInterPro.js';
+export { gffToAnnotations } from './gffToAnnotations.js';
+export { annotationsToGFF } from './annotationsToGFF.js';
 export { interProResponseToGFF, interProToGFF } from './interProToGFF.js';
 //# sourceMappingURL=index.js.map

package/dist/gff/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/gff/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AACxC,OAAO,EAAE,qBAAqB,EAAE,oBAAoB,EAAE,MAAM,oBAAoB,CAAA;AAChF,OAAO,EAAE,qBAAqB,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/gff/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AACxC,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAA;AACxD,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAA;AACxD,OAAO,EAAE,qBAAqB,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAA"}

package/dist/gff/interProToGFF.d.ts

@@ -1,9 +1,10 @@
 import type { InterProScanResults } from '../types.ts';
 /**
- * Convert InterProScan results to GFF3 format
+ * Convert InterProScan results, keyed by the row name they attach to, to GFF3.
  */
 export declare function interProToGFF(results: Record<string, InterProScanResults>): string;
 /**
- * Convert InterProScan JSON response to GFF3 format
+ * Convert a list of InterProScan results to GFF3, taking each one's row name
+ * from its xref.
  */
 export declare function interProResponseToGFF(results: InterProScanResults[]): string;

package/dist/gff/interProToGFF.js

@@ -1,52 +1,16 @@
+import { indexResultsByXref, interProScanToAnnotations, } from '../interProScanToAnnotations.js';
+import { annotationsToGFF } from './annotationsToGFF.js';
 /**
- * Convert InterProScan results to GFF3 format
+ * Convert InterProScan results, keyed by the row name they attach to, to GFF3.
  */
 export function interProToGFF(results) {
-    const lines = ['##gff-version 3'];
-    for (const [seqId, data] of Object.entries(results)) {
-        for (const match of data.matches) {
-            const entry = match.signature.entry;
-            if (!entry) {
-                continue;
-            }
-            for (const location of match.locations) {
-                const attributes = [
-                    `Name=${encodeURIComponent(entry.accession)}`,
-                    `signature_desc=${encodeURIComponent(entry.name)}`,
-                    `description=${encodeURIComponent(entry.description)}`,
-                ].join(';');
-                const line = [
-                    seqId,
-                    'InterProScan',
-                    // GFF-sourced annotations carry their original type; writing every
-                    // feature back out as protein_match would turn an exon overlay into
-                    // generic domains on the next read, losing the numbered-segment
-                    // rendering and the gene arrowheads
-                    entry.featureType ?? 'protein_match',
-                    location.start,
-                    location.end,
-                    '.',
-                    location.strand === undefined ? '.' : location.strand > 0 ? '+' : '-',
-                    '.',
-                    attributes,
-                ].join('\t');
-                lines.push(line);
-            }
-        }
-    }
-    return lines.join('\n');
+    return annotationsToGFF(interProScanToAnnotations(results));
 }
 /**
- * Convert InterProScan JSON response to GFF3 format
+ * Convert a list of InterProScan results to GFF3, taking each one's row name
+ * from its xref.
  */
 export function interProResponseToGFF(results) {
-    const resultsMap = {};
-    for (const result of results) {
-        const seqId = result.xref[0]?.id;
-        if (seqId) {
-            resultsMap[seqId] = result;
-        }
-    }
-    return interProToGFF(resultsMap);
+    return interProToGFF(indexResultsByXref(results));
 }
 //# sourceMappingURL=interProToGFF.js.map

package/dist/gff/interProToGFF.js.map

@@ -1 +1 @@
-{"version":3,"file":"interProToGFF.js","sourceRoot":"","sources":["../../src/gff/interProToGFF.ts"],"names":[],"mappings":"AAEA;;GAEG;AACH,MAAM,UAAU,aAAa,CAC3B,OAA4C;IAE5C,MAAM,KAAK,GAAa,CAAC,iBAAiB,CAAC,CAAA;IAE3C,KAAK,MAAM,CAAC,KAAK,EAAE,IAAI,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE,CAAC;QACpD,KAAK,MAAM,KAAK,IAAI,IAAI,CAAC,OAAO,EAAE,CAAC;YACjC,MAAM,KAAK,GAAG,KAAK,CAAC,SAAS,CAAC,KAAK,CAAA;YACnC,IAAI,CAAC,KAAK,EAAE,CAAC;gBACX,SAAQ;YACV,CAAC;YAED,KAAK,MAAM,QAAQ,IAAI,KAAK,CAAC,SAAS,EAAE,CAAC;gBACvC,MAAM,UAAU,GAAG;oBACjB,QAAQ,kBAAkB,CAAC,KAAK,CAAC,SAAS,CAAC,EAAE;oBAC7C,kBAAkB,kBAAkB,CAAC,KAAK,CAAC,IAAI,CAAC,EAAE;oBAClD,eAAe,kBAAkB,CAAC,KAAK,CAAC,WAAW,CAAC,EAAE;iBACvD,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;gBAEX,MAAM,IAAI,GAAG;oBACX,KAAK;oBACL,cAAc;oBACd,mEAAmE;oBACnE,oEAAoE;oBACpE,gEAAgE;oBAChE,oCAAoC;oBACpC,KAAK,CAAC,WAAW,IAAI,eAAe;oBACpC,QAAQ,CAAC,KAAK;oBACd,QAAQ,CAAC,GAAG;oBACZ,GAAG;oBACH,QAAQ,CAAC,MAAM,KAAK,SAAS,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG;oBACrE,GAAG;oBACH,UAAU;iBACX,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBAEZ,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAClB,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;AACzB,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,qBAAqB,CAAC,OAA8B;IAClE,MAAM,UAAU,GAAwC,EAAE,CAAA;IAE1D,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;QAC7B,MAAM,KAAK,GAAG,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAA;QAChC,IAAI,KAAK,EAAE,CAAC;YACV,UAAU,CAAC,KAAK,CAAC,GAAG,MAAM,CAAA;QAC5B,CAAC;IACH,CAAC;IAED,OAAO,aAAa,CAAC,UAAU,CAAC,CAAA;AAClC,CAAC"}
+{"version":3,"file":"interProToGFF.js","sourceRoot":"","sources":["../../src/gff/interProToGFF.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,kBAAkB,EAClB,yBAAyB,GAC1B,MAAM,iCAAiC,CAAA;AACxC,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAA;AAIxD;;GAEG;AACH,MAAM,UAAU,aAAa,CAC3B,OAA4C;IAE5C,OAAO,gBAAgB,CAAC,yBAAyB,CAAC,OAAO,CAAC,CAAC,CAAA;AAC7D,CAAC;AAED;;;GAGG;AACH,MAAM,UAAU,qBAAqB,CAAC,OAA8B;IAClE,OAAO,aAAa,CAAC,kBAAkB,CAAC,OAAO,CAAC,CAAC,CAAA;AACnD,CAAC"}

package/dist/gff/interProToGFF.test.js

@@ -1,5 +1,6 @@
 import { describe, expect, test } from 'vitest';
-import { gffToInterProResults } from './gffToInterPro.js';
+import { annotationsToGFF } from './annotationsToGFF.js';
+import { gffToAnnotations } from './gffToAnnotations.js';
 import { interProResponseToGFF, interProToGFF } from './interProToGFF.js';
 import { parseGFF } from './parseGFF.js';
 describe('interProToGFF', () => {
@@ -125,7 +126,7 @@ describe('interProToGFF', () => {
             'seq1\tRefSeq\tmRNA\t1\t99\t.\t+\t.\tName=NM_1',
             'seq1\tRefSeq\texon\t1\t30\t.\t+\t.\tName=exon-1',
         ].join('\n');
-        const rows = interProToGFF(gffToInterProResults(parseGFF(gff)))
+        const rows = annotationsToGFF(gffToAnnotations(parseGFF(gff)))
             .split('\n')
             .slice(1)
             .map(l => l.split('\t'));

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

@@ -1 +1 @@
-{"version":3,"file":"interProToGFF.test.js","sourceRoot":"","sources":["../../src/gff/interProToGFF.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAE/C,OAAO,EAAE,oBAAoB,EAAE,MAAM,oBAAoB,CAAA;AACzD,OAAO,EAAE,qBAAqB,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAA;AACzE,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAIxC,QAAQ,CAAC,eAAe,EAAE,GAAG,EAAE;IAC7B,IAAI,CAAC,wBAAwB,EAAE,GAAG,EAAE;QAClC,MAAM,GAAG,GAAG,aAAa,CAAC,EAAE,CAAC,CAAA;QAC7B,MAAM,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAA;IACrC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,wBAAwB,EAAE,GAAG,EAAE;QAClC,MAAM,OAAO,GAAwC;YACnD,IAAI,EAAE;gBACJ,OAAO,EAAE;oBACP;wBACE,SAAS,EAAE;4BACT,KAAK,EAAE;gCACL,SAAS,EAAE,SAAS;gCACpB,IAAI,EAAE,OAAO;gCACb,WAAW,EAAE,aAAa;6BAC3B;yBACF;wBACD,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,GAAG,EAAE,EAAE,EAAE,CAAC;qBACpC;iBACF;gBACD,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,CAAC;aACvB;SACF,CAAA;QACD,MAAM,GAAG,GAAG,aAAa,CAAC,OAAO,CAAC,CAAA;QAClC,MAAM,KAAK,GAAG,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAE7B,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAA;QACxC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,MAAM,CAAC,CAAA;QAClC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,cAAc,CAAC,CAAA;QAC1C,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,eAAe,CAAC,CAAA;QAC3C,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAChC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAChC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,cAAc,CAAC,CAAA;QAC1C,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,sBAAsB,CAAC,CAAA;QAClD,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,2BAA2B,CAAC,CAAA;IACzD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,4BAA4B,EAAE,GAAG,EAAE;QACtC,MAAM,OAAO,GAAwC;YACnD,IAAI,EAAE;gBACJ,OAAO,EAAE;oBACP;wBACE,SAAS,EAAE;4BACT,KAAK,EAAE;gCACL,SAAS,EAAE,SAAS;gCACpB,IAAI,EAAE,QAAQ;gCACd,WAAW,EAAE,MAAM;6BACpB;yBACF;wBACD,SAAS,EAAE;4BACT,EAAE,KAAK,EAAE,EAAE,EAAE,GAAG,EAAE,EAAE,EAAE;4BACtB,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE;yBACzB;qBACF;iBACF;gBACD,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,CAAC;aACvB;SACF,CAAA;QACD,MAAM,GAAG,GAAG,aAAa,CAAC,OAAO,CAAC,CAAA;QAClC,MAAM,KAAK,GAAG,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAE7B,MAAM,CAAC,KAAK,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAC7B,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAA;QACpC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,UAAU,CAAC,CAAA;IACxC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,4BAA4B,EAAE,GAAG,EAAE;QACtC,MAAM,OAAO,GAAwC;YACnD,IAAI,EAAE;gBACJ,OAAO,EAAE;oBACP;wBACE,SAAS,EAAE;4BACT,KAAK,EAAE;gCACL,SAAS,EAAE,SAAS;gCACpB,IAAI,EAAE,SAAS;gCACf,WAAW,EAAE,OAAO;6BACrB;yBACF;wBACD,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,GAAG,EAAE,EAAE,EAAE,CAAC;qBACpC;iBACF;gBACD,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,CAAC;aACvB;YACD,IAAI,EAAE;gBACJ,OAAO,EAAE;oBACP;wBACE,SAAS,EAAE;4BACT,KAAK,EAAE;gCACL,SAAS,EAAE,SAAS;gCACpB,IAAI,EAAE,SAAS;gCACf,WAAW,EAAE,OAAO;6BACrB;yBACF;wBACD,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,GAAG,EAAE,EAAE,EAAE,CAAC;qBACnC;iBACF;gBACD,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,CAAC;aACvB;SACF,CAAA;QACD,MAAM,GAAG,GAAG,aAAa,CAAC,OAAO,CAAC,CAAA;QAClC,MAAM,KAAK,GAAG,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAE7B,MAAM,CAAC,KAAK,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAC7B,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACtD,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;IACxD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,6BAA6B,EAAE,GAAG,EAAE;QACvC,MAAM,OAAO,GAAwC;YACnD,IAAI,EAAE;gBACJ,OAAO,EAAE;oBACP;wBACE,SAAS,EAAE,EAAE;wBACb,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,GAAG,EAAE,EAAE,EAAE,CAAC;qBACpC;iBACF;gBACD,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,CAAC;aACvB;SACF,CAAA;QACD,MAAM,GAAG,GAAG,aAAa,CAAC,OAAO,CAAC,CAAA;QAClC,MAAM,KAAK,GAAG,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAE7B,MAAM,CAAC,KAAK,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAC7B,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAA;IAC1C,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,qEAAqE,EAAE,GAAG,EAAE;QAC/E,MAAM,GAAG,GAAG;YACV,+CAA+C;YAC/C,iDAAiD;SAClD,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACZ,MAAM,IAAI,GAAG,aAAa,CAAC,oBAAoB,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC;aAC5D,KAAK,CAAC,IAAI,CAAC;aACX,KAAK,CAAC,CAAC,CAAC;aACR,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAA;QAE1B,yEAAyE;QACzE,4EAA4E;QAC5E,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC;YAC1C,CAAC,MAAM,EAAE,GAAG,CAAC;YACb,CAAC,MAAM,EAAE,GAAG,CAAC;SACd,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,8CAA8C,EAAE,GAAG,EAAE;QACxD,MAAM,OAAO,GAAwC;YACnD,IAAI,EAAE;gBACJ,OAAO,EAAE;oBACP;wBACE,SAAS,EAAE;4BACT,KAAK,EAAE;gCACL,SAAS,EAAE,SAAS;gCACpB,IAAI,EAAE,iBAAiB;gCACvB,WAAW,EAAE,yBAAyB;6BACvC;yBACF;wBACD,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,GAAG,EAAE,EAAE,EAAE,CAAC;qBACpC;iBACF;gBACD,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,CAAC;aACvB;SACF,CAAA;QACD,MAAM,GAAG,GAAG,aAAa,CAAC,OAAO,CAAC,CAAA;QAElC,MAAM,CAAC,GAAG,CAAC,CAAC,SAAS,CAAC,oCAAoC,CAAC,CAAA;QAC3D,MAAM,CAAC,GAAG,CAAC,CAAC,SAAS,CAAC,yCAAyC,CAAC,CAAA;IAClE,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,uBAAuB,EAAE,GAAG,EAAE;IACrC,IAAI,CAAC,2BAA2B,EAAE,GAAG,EAAE;QACrC,MAAM,OAAO,GAA0B;YACrC;gBACE,OAAO,EAAE;oBACP;wBACE,SAAS,EAAE;4BACT,KAAK,EAAE;gCACL,SAAS,EAAE,SAAS;gCACpB,IAAI,EAAE,QAAQ;gCACd,WAAW,EAAE,MAAM;6BACpB;yBACF;wBACD,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,GAAG,EAAE,EAAE,EAAE,CAAC;qBACpC;iBACF;gBACD,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,CAAC;aACvB;SACF,CAAA;QACD,MAAM,GAAG,GAAG,qBAAqB,CAAC,OAAO,CAAC,CAAA;QAE1C,MAAM,CAAC,GAAG,CAAC,CAAC,SAAS,CAAC,iBAAiB,CAAC,CAAA;QACxC,MAAM,CAAC,GAAG,CAAC,CAAC,SAAS,CAAC,MAAM,CAAC,CAAA;IAC/B,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,8BAA8B,EAAE,GAAG,EAAE;QACxC,MAAM,OAAO,GAA0B;YACrC;gBACE,OAAO,EAAE;oBACP;wBACE,SAAS,EAAE;4BACT,KAAK,EAAE;gCACL,SAAS,EAAE,SAAS;gCACpB,IAAI,EAAE,QAAQ;gCACd,WAAW,EAAE,MAAM;6BACpB;yBACF;wBACD,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,GAAG,EAAE,EAAE,EAAE,CAAC;qBACpC;iBACF;gBACD,IAAI,EAAE,EAAE;aACT;SACF,CAAA;QACD,MAAM,GAAG,GAAG,qBAAqB,CAAC,OAAO,CAAC,CAAA;QAE1C,MAAM,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAA;IACrC,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA"}
+{"version":3,"file":"interProToGFF.test.js","sourceRoot":"","sources":["../../src/gff/interProToGFF.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAE/C,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAA;AACxD,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAA;AACxD,OAAO,EAAE,qBAAqB,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAA;AACzE,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAIxC,QAAQ,CAAC,eAAe,EAAE,GAAG,EAAE;IAC7B,IAAI,CAAC,wBAAwB,EAAE,GAAG,EAAE;QAClC,MAAM,GAAG,GAAG,aAAa,CAAC,EAAE,CAAC,CAAA;QAC7B,MAAM,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAA;IACrC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,wBAAwB,EAAE,GAAG,EAAE;QAClC,MAAM,OAAO,GAAwC;YACnD,IAAI,EAAE;gBACJ,OAAO,EAAE;oBACP;wBACE,SAAS,EAAE;4BACT,KAAK,EAAE;gCACL,SAAS,EAAE,SAAS;gCACpB,IAAI,EAAE,OAAO;gCACb,WAAW,EAAE,aAAa;6BAC3B;yBACF;wBACD,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,GAAG,EAAE,EAAE,EAAE,CAAC;qBACpC;iBACF;gBACD,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,CAAC;aACvB;SACF,CAAA;QACD,MAAM,GAAG,GAAG,aAAa,CAAC,OAAO,CAAC,CAAA;QAClC,MAAM,KAAK,GAAG,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAE7B,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAA;QACxC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,MAAM,CAAC,CAAA;QAClC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,cAAc,CAAC,CAAA;QAC1C,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,eAAe,CAAC,CAAA;QAC3C,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAChC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAChC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,cAAc,CAAC,CAAA;QAC1C,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,sBAAsB,CAAC,CAAA;QAClD,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,2BAA2B,CAAC,CAAA;IACzD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,4BAA4B,EAAE,GAAG,EAAE;QACtC,MAAM,OAAO,GAAwC;YACnD,IAAI,EAAE;gBACJ,OAAO,EAAE;oBACP;wBACE,SAAS,EAAE;4BACT,KAAK,EAAE;gCACL,SAAS,EAAE,SAAS;gCACpB,IAAI,EAAE,QAAQ;gCACd,WAAW,EAAE,MAAM;6BACpB;yBACF;wBACD,SAAS,EAAE;4BACT,EAAE,KAAK,EAAE,EAAE,EAAE,GAAG,EAAE,EAAE,EAAE;4BACtB,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE;yBACzB;qBACF;iBACF;gBACD,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,CAAC;aACvB;SACF,CAAA;QACD,MAAM,GAAG,GAAG,aAAa,CAAC,OAAO,CAAC,CAAA;QAClC,MAAM,KAAK,GAAG,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAE7B,MAAM,CAAC,KAAK,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAC7B,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAA;QACpC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,UAAU,CAAC,CAAA;IACxC,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,4BAA4B,EAAE,GAAG,EAAE;QACtC,MAAM,OAAO,GAAwC;YACnD,IAAI,EAAE;gBACJ,OAAO,EAAE;oBACP;wBACE,SAAS,EAAE;4BACT,KAAK,EAAE;gCACL,SAAS,EAAE,SAAS;gCACpB,IAAI,EAAE,SAAS;gCACf,WAAW,EAAE,OAAO;6BACrB;yBACF;wBACD,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,GAAG,EAAE,EAAE,EAAE,CAAC;qBACpC;iBACF;gBACD,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,CAAC;aACvB;YACD,IAAI,EAAE;gBACJ,OAAO,EAAE;oBACP;wBACE,SAAS,EAAE;4BACT,KAAK,EAAE;gCACL,SAAS,EAAE,SAAS;gCACpB,IAAI,EAAE,SAAS;gCACf,WAAW,EAAE,OAAO;6BACrB;yBACF;wBACD,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,GAAG,EAAE,EAAE,EAAE,CAAC;qBACnC;iBACF;gBACD,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,CAAC;aACvB;SACF,CAAA;QACD,MAAM,GAAG,GAAG,aAAa,CAAC,OAAO,CAAC,CAAA;QAClC,MAAM,KAAK,GAAG,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAE7B,MAAM,CAAC,KAAK,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAC7B,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACtD,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;IACxD,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,6BAA6B,EAAE,GAAG,EAAE;QACvC,MAAM,OAAO,GAAwC;YACnD,IAAI,EAAE;gBACJ,OAAO,EAAE;oBACP;wBACE,SAAS,EAAE,EAAE;wBACb,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,GAAG,EAAE,EAAE,EAAE,CAAC;qBACpC;iBACF;gBACD,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,CAAC;aACvB;SACF,CAAA;QACD,MAAM,GAAG,GAAG,aAAa,CAAC,OAAO,CAAC,CAAA;QAClC,MAAM,KAAK,GAAG,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAE7B,MAAM,CAAC,KAAK,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAC7B,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAA;IAC1C,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,qEAAqE,EAAE,GAAG,EAAE;QAC/E,MAAM,GAAG,GAAG;YACV,+CAA+C;YAC/C,iDAAiD;SAClD,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACZ,MAAM,IAAI,GAAG,gBAAgB,CAAC,gBAAgB,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC;aAC3D,KAAK,CAAC,IAAI,CAAC;aACX,KAAK,CAAC,CAAC,CAAC;aACR,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAA;QAE1B,yEAAyE;QACzE,4EAA4E;QAC5E,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC;YAC1C,CAAC,MAAM,EAAE,GAAG,CAAC;YACb,CAAC,MAAM,EAAE,GAAG,CAAC;SACd,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,8CAA8C,EAAE,GAAG,EAAE;QACxD,MAAM,OAAO,GAAwC;YACnD,IAAI,EAAE;gBACJ,OAAO,EAAE;oBACP;wBACE,SAAS,EAAE;4BACT,KAAK,EAAE;gCACL,SAAS,EAAE,SAAS;gCACpB,IAAI,EAAE,iBAAiB;gCACvB,WAAW,EAAE,yBAAyB;6BACvC;yBACF;wBACD,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,GAAG,EAAE,EAAE,EAAE,CAAC;qBACpC;iBACF;gBACD,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,CAAC;aACvB;SACF,CAAA;QACD,MAAM,GAAG,GAAG,aAAa,CAAC,OAAO,CAAC,CAAA;QAElC,MAAM,CAAC,GAAG,CAAC,CAAC,SAAS,CAAC,oCAAoC,CAAC,CAAA;QAC3D,MAAM,CAAC,GAAG,CAAC,CAAC,SAAS,CAAC,yCAAyC,CAAC,CAAA;IAClE,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,QAAQ,CAAC,uBAAuB,EAAE,GAAG,EAAE;IACrC,IAAI,CAAC,2BAA2B,EAAE,GAAG,EAAE;QACrC,MAAM,OAAO,GAA0B;YACrC;gBACE,OAAO,EAAE;oBACP;wBACE,SAAS,EAAE;4BACT,KAAK,EAAE;gCACL,SAAS,EAAE,SAAS;gCACpB,IAAI,EAAE,QAAQ;gCACd,WAAW,EAAE,MAAM;6BACpB;yBACF;wBACD,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,GAAG,EAAE,EAAE,EAAE,CAAC;qBACpC;iBACF;gBACD,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,CAAC;aACvB;SACF,CAAA;QACD,MAAM,GAAG,GAAG,qBAAqB,CAAC,OAAO,CAAC,CAAA;QAE1C,MAAM,CAAC,GAAG,CAAC,CAAC,SAAS,CAAC,iBAAiB,CAAC,CAAA;QACxC,MAAM,CAAC,GAAG,CAAC,CAAC,SAAS,CAAC,MAAM,CAAC,CAAA;IAC/B,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,8BAA8B,EAAE,GAAG,EAAE;QACxC,MAAM,OAAO,GAA0B;YACrC;gBACE,OAAO,EAAE;oBACP;wBACE,SAAS,EAAE;4BACT,KAAK,EAAE;gCACL,SAAS,EAAE,SAAS;gCACpB,IAAI,EAAE,QAAQ;gCACd,WAAW,EAAE,MAAM;6BACpB;yBACF;wBACD,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,GAAG,EAAE,EAAE,EAAE,CAAC;qBACpC;iBACF;gBACD,IAAI,EAAE,EAAE;aACT;SACF,CAAA;QACD,MAAM,GAAG,GAAG,qBAAqB,CAAC,OAAO,CAAC,CAAA;QAE1C,MAAM,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAA;IACrC,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA"}

package/dist/index.d.ts

@@ -2,4 +2,5 @@ export type * from './types.ts';
 export { generateNodeIds } from './util.ts';
 export { A3mMSA, ClustalMSA, EmfMSA, FastaMSA, StockholmMSA, getUngappedSequence, parseEmfTree, parseMSA, parseNewick, stockholmSniff, } from './msa/index.ts';
 export type { MSAFormat, MSAParserType } from './msa/index.ts';
-export { gffToInterProResponse, gffToInterProResults, interProResponseToGFF, interProToGFF, parseGFF, } from './gff/index.ts';
+export { indexResultsByXref, interProScanResponseToAnnotations, interProScanToAnnotations, } from './interProScanToAnnotations.ts';
+export { annotationsToGFF, gffToAnnotations, interProResponseToGFF, interProToGFF, parseGFF, } from './gff/index.ts';

package/dist/index.js

@@ -2,6 +2,8 @@
 export { generateNodeIds } from './util.js';
 // MSA parsers
 export { A3mMSA, ClustalMSA, EmfMSA, FastaMSA, StockholmMSA, getUngappedSequence, parseEmfTree, parseMSA, parseNewick, stockholmSniff, } from './msa/index.js';
+// Overlay annotations: the canonical shape, and the adapters onto it
+export { indexResultsByXref, interProScanResponseToAnnotations, interProScanToAnnotations, } from './interProScanToAnnotations.js';
 // GFF parsing
-export { gffToInterProResponse, gffToInterProResults, interProResponseToGFF, interProToGFF, parseGFF, } from './gff/index.js';
+export { annotationsToGFF, gffToAnnotations, interProResponseToGFF, interProToGFF, parseGFF, } from './gff/index.js';
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAGA,YAAY;AACZ,OAAO,EAAE,eAAe,EAAE,MAAM,WAAW,CAAA;AAE3C,cAAc;AACd,OAAO,EACL,MAAM,EACN,UAAU,EACV,MAAM,EACN,QAAQ,EACR,YAAY,EACZ,mBAAmB,EACnB,YAAY,EACZ,QAAQ,EACR,WAAW,EACX,cAAc,GACf,MAAM,gBAAgB,CAAA;AAGvB,cAAc;AACd,OAAO,EACL,qBAAqB,EACrB,oBAAoB,EACpB,qBAAqB,EACrB,aAAa,EACb,QAAQ,GACT,MAAM,gBAAgB,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAGA,YAAY;AACZ,OAAO,EAAE,eAAe,EAAE,MAAM,WAAW,CAAA;AAE3C,cAAc;AACd,OAAO,EACL,MAAM,EACN,UAAU,EACV,MAAM,EACN,QAAQ,EACR,YAAY,EACZ,mBAAmB,EACnB,YAAY,EACZ,QAAQ,EACR,WAAW,EACX,cAAc,GACf,MAAM,gBAAgB,CAAA;AAGvB,qEAAqE;AACrE,OAAO,EACL,kBAAkB,EAClB,iCAAiC,EACjC,yBAAyB,GAC1B,MAAM,gCAAgC,CAAA;AAEvC,cAAc;AACd,OAAO,EACL,gBAAgB,EAChB,gBAAgB,EAChB,qBAAqB,EACrB,aAAa,EACb,QAAQ,GACT,MAAM,gBAAgB,CAAA"}

package/dist/interProScanToAnnotations.d.ts

@@ -0,0 +1,21 @@
+import type { Annotation, InterProScanResponse, InterProScanResults } from './types.ts';
+/**
+ * Key each result by its xref id, which is the row name its annotations attach
+ * to. A result without one is dropped rather than keyed `undefined`, which
+ * would draw a phantom row's worth of annotations (and rather than throwing,
+ * which would lose every other result over one malformed one).
+ */
+export declare function indexResultsByXref(results: InterProScanResults[]): {
+    [k: string]: InterProScanResults;
+};
+/**
+ * Flatten InterProScan results, keyed by the row name they attach to, into one
+ * annotation per signature location. A signature without an `entry` carries no
+ * accession or name to color, filter or label by, so it is dropped.
+ */
+export declare function interProScanToAnnotations(results: Record<string, InterProScanResults>): Annotation[];
+/**
+ * Flatten a whole InterProScan JSON response, resolving each result's row name
+ * from its xref.
+ */
+export declare function interProScanResponseToAnnotations(response: InterProScanResponse): Annotation[];

package/dist/interProScanToAnnotations.js

@@ -0,0 +1,38 @@
+/**
+ * Key each result by its xref id, which is the row name its annotations attach
+ * to. A result without one is dropped rather than keyed `undefined`, which
+ * would draw a phantom row's worth of annotations (and rather than throwing,
+ * which would lose every other result over one malformed one).
+ */
+export function indexResultsByXref(results) {
+    return Object.fromEntries(results
+        .map(r => [r.xref[0]?.id, r])
+        .filter((e) => e[0] !== undefined));
+}
+/**
+ * Flatten InterProScan results, keyed by the row name they attach to, into one
+ * annotation per signature location. A signature without an `entry` carries no
+ * accession or name to color, filter or label by, so it is dropped.
+ */
+export function interProScanToAnnotations(results) {
+    return Object.entries(results).flatMap(([id, { matches }]) => matches.flatMap(({ signature: { entry }, locations }) => entry
+        ? locations.map(({ start, end, strand }) => ({
+            id,
+            accession: entry.accession,
+            name: entry.name,
+            description: entry.description,
+            featureType: entry.featureType,
+            start,
+            end,
+            strand,
+        }))
+        : []));
+}
+/**
+ * Flatten a whole InterProScan JSON response, resolving each result's row name
+ * from its xref.
+ */
+export function interProScanResponseToAnnotations(response) {
+    return interProScanToAnnotations(indexResultsByXref(response.results));
+}
+//# sourceMappingURL=interProScanToAnnotations.js.map

package/dist/interProScanToAnnotations.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"interProScanToAnnotations.js","sourceRoot":"","sources":["../src/interProScanToAnnotations.ts"],"names":[],"mappings":"AAMA;;;;;GAKG;AACH,MAAM,UAAU,kBAAkB,CAAC,OAA8B;IAC/D,OAAO,MAAM,CAAC,WAAW,CACvB,OAAO;SACJ,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAU,CAAC;SACrC,MAAM,CAAC,CAAC,CAAC,EAAsC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,CACzE,CAAA;AACH,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,yBAAyB,CACvC,OAA4C;IAE5C,OAAO,MAAM,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,OAAO,EAAE,CAAC,EAAE,EAAE,CAC3D,OAAO,CAAC,OAAO,CAAC,CAAC,EAAE,SAAS,EAAE,EAAE,KAAK,EAAE,EAAE,SAAS,EAAE,EAAE,EAAE,CACtD,KAAK;QACH,CAAC,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,EAAE,GAAG,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,CAAC;YACzC,EAAE;YACF,SAAS,EAAE,KAAK,CAAC,SAAS;YAC1B,IAAI,EAAE,KAAK,CAAC,IAAI;YAChB,WAAW,EAAE,KAAK,CAAC,WAAW;YAC9B,WAAW,EAAE,KAAK,CAAC,WAAW;YAC9B,KAAK;YACL,GAAG;YACH,MAAM;SACP,CAAC,CAAC;QACL,CAAC,CAAC,EAAE,CACP,CACF,CAAA;AACH,CAAC;AAED;;;GAGG;AACH,MAAM,UAAU,iCAAiC,CAC/C,QAA8B;IAE9B,OAAO,yBAAyB,CAAC,kBAAkB,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAA;AACxE,CAAC"}

package/dist/types.d.ts

@@ -28,6 +28,30 @@ export interface GFFRecord {
     phase: string;
     [key: string]: string | number;
 }
+/**
+ * One annotation interval attached to an alignment row: a protein domain, an
+ * exon, a gene. This is the canonical overlay shape -- every source
+ * (InterProScan, GFF, a user upload) converts to a flat list of these, and the
+ * viewer renders nothing else.
+ */
+export interface Annotation {
+    /** name of the alignment row the interval attaches to */
+    id: string;
+    /** stable key deciding color, legend membership and filter state */
+    accession: string;
+    name: string;
+    description: string;
+    /**
+     * original GFF feature type (exon, CDS, gene, ...) when sourced from GFF;
+     * lets the viewer treat ordinal segments (exons) differently from
+     * categorical domains
+     */
+    featureType?: string;
+    /** 1-based, inclusive of both ends */
+    start: number;
+    end: number;
+    strand?: number;
+}
 export interface InterProScanMatch {
     signature: {
         entry?: {

package/dist/util.d.ts

@@ -1,2 +1,12 @@
 import type { Node, NodeWithIds } from './types.ts';
+/**
+ * Copy a parsed tree, giving every node a stable id derived from its path, and
+ * falling back to that id for an unnamed node.
+ *
+ * Iterative, like the traversals in @gmod/newick and the Newick emitter in the
+ * viewer's neighbor joining: a phylogeny can be a caterpillar whose depth equals
+ * its leaf count, and the recursive form of this overflowed the stack somewhere
+ * past 5000 deep -- which every tree reaches, since this is the last step of
+ * parsing one.
+ */
 export declare function generateNodeIds(tree: Node, parent?: string, depth?: number): NodeWithIds;

package/dist/util.js

@@ -1,10 +1,31 @@
+/**
+ * Copy a parsed tree, giving every node a stable id derived from its path, and
+ * falling back to that id for an unnamed node.
+ *
+ * Iterative, like the traversals in @gmod/newick and the Newick emitter in the
+ * viewer's neighbor joining: a phylogeny can be a caterpillar whose depth equals
+ * its leaf count, and the recursive form of this overflowed the stack somewhere
+ * past 5000 deep -- which every tree reaches, since this is the last step of
+ * parsing one.
+ */
 export function generateNodeIds(tree, parent = 'node', depth = 0) {
-    const id = `${parent}-${depth}`;
-    return {
-        ...tree,
+    const withId = (node, id) => ({
+        ...node,
         id,
-        name: tree.name || id,
-        children: tree.children?.map((b, i) => generateNodeIds(b, `${id}-${i}`, depth + 1)) || [],
-    };
+        name: node.name || id,
+        children: [],
+    });
+    const root = withId(tree, `${parent}-${depth}`);
+    const stack = [{ src: tree, out: root, depth }];
+    while (stack.length > 0) {
+        const { src, out, depth: d } = stack.pop();
+        if (src.children) {
+            out.children = src.children.map((child, i) => withId(child, `${out.id}-${i}-${d + 1}`));
+            for (const [i, child] of src.children.entries()) {
+                stack.push({ src: child, out: out.children[i], depth: d + 1 });
+            }
+        }
+    }
+    return root;
 }
 //# sourceMappingURL=util.js.map

package/dist/util.js.map

@@ -1 +1 @@
-{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,eAAe,CAC7B,IAAU,EACV,MAAM,GAAG,MAAM,EACf,KAAK,GAAG,CAAC;IAET,MAAM,EAAE,GAAG,GAAG,MAAM,IAAI,KAAK,EAAE,CAAA;IAE/B,OAAO;QACL,GAAG,IAAI;QACP,EAAE;QACF,IAAI,EAAE,IAAI,CAAC,IAAI,IAAI,EAAE;QACrB,QAAQ,EACN,IAAI,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAC1B,eAAe,CAAC,CAAC,EAAE,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE,KAAK,GAAG,CAAC,CAAC,CAC5C,IAAI,EAAE;KACV,CAAA;AACH,CAAC"}
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAEA;;;;;;;;;GASG;AACH,MAAM,UAAU,eAAe,CAC7B,IAAU,EACV,MAAM,GAAG,MAAM,EACf,KAAK,GAAG,CAAC;IAET,MAAM,MAAM,GAAG,CAAC,IAAU,EAAE,EAAU,EAAe,EAAE,CAAC,CAAC;QACvD,GAAG,IAAI;QACP,EAAE;QACF,IAAI,EAAE,IAAI,CAAC,IAAI,IAAI,EAAE;QACrB,QAAQ,EAAE,EAAE;KACb,CAAC,CAAA;IAEF,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,EAAE,GAAG,MAAM,IAAI,KAAK,EAAE,CAAC,CAAA;IAC/C,MAAM,KAAK,GAAG,CAAC,EAAE,GAAG,EAAE,IAAI,EAAE,GAAG,EAAE,IAAI,EAAE,KAAK,EAAE,CAAC,CAAA;IAC/C,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACxB,MAAM,EAAE,GAAG,EAAE,GAAG,EAAE,KAAK,EAAE,CAAC,EAAE,GAAG,KAAK,CAAC,GAAG,EAAG,CAAA;QAC3C,IAAI,GAAG,CAAC,QAAQ,EAAE,CAAC;YACjB,GAAG,CAAC,QAAQ,GAAG,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,CAAC,EAAE,EAAE,CAC3C,MAAM,CAAC,KAAK,EAAE,GAAG,GAAG,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,CACzC,CAAA;YACD,KAAK,MAAM,CAAC,CAAC,EAAE,KAAK,CAAC,IAAI,GAAG,CAAC,QAAQ,CAAC,OAAO,EAAE,EAAE,CAAC;gBAChD,KAAK,CAAC,IAAI,CAAC,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAE,EAAE,KAAK,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;YACjE,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}

package/dist/util.test.d.ts

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

package/dist/util.test.js

@@ -0,0 +1,40 @@
+import { expect, test } from 'vitest';
+import parseNewick from './msa/parseNewick.js';
+import { generateNodeIds } from './util.js';
+test('ids encode the path to each node, and name unnamed nodes', () => {
+    const tree = generateNodeIds({
+        children: [{ name: 'a' }, { name: 'b', children: [{ name: 'c' }] }],
+    });
+    expect(tree.id).toBe('node-0');
+    // an unnamed node takes its id as its name
+    expect(tree.name).toBe('node-0');
+    expect(tree.children.map(c => [c.name, c.id])).toEqual([
+        ['a', 'node-0-0-1'],
+        ['b', 'node-0-1-1'],
+    ]);
+    expect(tree.children[1].children.map(c => c.id)).toEqual(['node-0-1-1-0-2']);
+});
+test('a leaf gets an empty children array, not undefined', () => {
+    expect(generateNodeIds({ name: 'solo' }).children).toEqual([]);
+});
+// a phylogeny can be a caterpillar whose depth equals its leaf count. The
+// recursive form of generateNodeIds threw "Maximum call stack size exceeded"
+// somewhere past 5000 deep -- and every parsed tree goes through it, so a deep
+// newick took the whole viewer down.
+test('a caterpillar tree far past the recursion limit still gets ids', () => {
+    const depth = 50_000;
+    let newick = 'leaf0:0.1';
+    for (let i = 1; i <= depth; i++) {
+        newick = `(${newick},leaf${i}:0.1)`;
+    }
+    const tree = generateNodeIds(parseNewick(`${newick};`));
+    let node = tree;
+    let seen = 0;
+    while (node.children.length > 1) {
+        seen++;
+        node = node.children[0];
+    }
+    expect(seen).toBe(depth);
+    expect(node.name).toBe('leaf0');
+});
+//# sourceMappingURL=util.test.js.map

package/dist/util.test.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.test.js","sourceRoot":"","sources":["../src/util.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAErC,OAAO,WAAW,MAAM,sBAAsB,CAAA;AAC9C,OAAO,EAAE,eAAe,EAAE,MAAM,WAAW,CAAA;AAI3C,IAAI,CAAC,0DAA0D,EAAE,GAAG,EAAE;IACpE,MAAM,IAAI,GAAG,eAAe,CAAC;QAC3B,QAAQ,EAAE,CAAC,EAAE,IAAI,EAAE,GAAG,EAAE,EAAE,EAAE,IAAI,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,IAAI,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC;KACpE,CAAC,CAAA;IACF,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;IAC9B,2CAA2C;IAC3C,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;IAChC,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC;QACrD,CAAC,GAAG,EAAE,YAAY,CAAC;QACnB,CAAC,GAAG,EAAE,YAAY,CAAC;KACpB,CAAC,CAAA;IACF,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAA;AAC/E,CAAC,CAAC,CAAA;AAEF,IAAI,CAAC,oDAAoD,EAAE,GAAG,EAAE;IAC9D,MAAM,CAAC,eAAe,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAA;AAChE,CAAC,CAAC,CAAA;AAEF,0EAA0E;AAC1E,6EAA6E;AAC7E,+EAA+E;AAC/E,qCAAqC;AACrC,IAAI,CAAC,gEAAgE,EAAE,GAAG,EAAE;IAC1E,MAAM,KAAK,GAAG,MAAM,CAAA;IACpB,IAAI,MAAM,GAAG,WAAW,CAAA;IACxB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,KAAK,EAAE,CAAC,EAAE,EAAE,CAAC;QAChC,MAAM,GAAG,IAAI,MAAM,QAAQ,CAAC,OAAO,CAAA;IACrC,CAAC;IAED,MAAM,IAAI,GAAG,eAAe,CAAC,WAAW,CAAC,GAAG,MAAM,GAAG,CAAC,CAAC,CAAA;IAEvD,IAAI,IAAI,GAAgB,IAAI,CAAA;IAC5B,IAAI,IAAI,GAAG,CAAC,CAAA;IACZ,OAAO,IAAI,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAChC,IAAI,EAAE,CAAA;QACN,IAAI,GAAG,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAE,CAAA;IAC1B,CAAC;IACD,MAAM,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;IACxB,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;AACjC,CAAC,CAAC,CAAA"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "msa-parsers",
-  "version": "5.10.0",
+  "version": "6.0.0",
   "license": "MIT",
   "type": "module",
   "repository": {