msa-parsers 8.1.0 → 8.3.0

package/dist/gff/annotationTextToGFF.d.ts

@@ -0,0 +1,5 @@
+/**
+ * An annotation file's text as GFF3: GFF passes through, and the JSON an
+ * InterProScan run returns converts, taking each result's row from its xref.
+ */
+export declare function annotationTextToGFF(text: string): string;

package/dist/gff/annotationTextToGFF.js

@@ -0,0 +1,15 @@
+import { interProScanResponseToAnnotations } from '../interProScanToAnnotations.js';
+import { annotationsToGFF } from './annotationsToGFF.js';
+/**
+ * An annotation file's text as GFF3: GFF passes through, and the JSON an
+ * InterProScan run returns converts, taking each result's row from its xref.
+ */
+export function annotationTextToGFF(text) {
+    const trimmed = text.trimStart();
+    if (!trimmed.startsWith('{')) {
+        return text;
+    }
+    const response = JSON.parse(trimmed);
+    return annotationsToGFF(interProScanResponseToAnnotations(response));
+}
+//# sourceMappingURL=annotationTextToGFF.js.map

package/dist/gff/annotationTextToGFF.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"annotationTextToGFF.js","sourceRoot":"","sources":["../../src/gff/annotationTextToGFF.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,iCAAiC,EAAE,MAAM,iCAAiC,CAAA;AACnF,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAA;AAIxD;;;GAGG;AACH,MAAM,UAAU,mBAAmB,CAAC,IAAY;IAC9C,MAAM,OAAO,GAAG,IAAI,CAAC,SAAS,EAAE,CAAA;IAChC,IAAI,CAAC,OAAO,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;QAC7B,OAAO,IAAI,CAAA;IACb,CAAC;IACD,MAAM,QAAQ,GAAyB,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IAC1D,OAAO,gBAAgB,CAAC,iCAAiC,CAAC,QAAQ,CAAC,CAAC,CAAA;AACtE,CAAC"}

package/dist/gff/annotationsToGFF.js

@@ -15,7 +15,7 @@ export function annotationsToGFF(annotations, header = []) {
             const { accession, name, description, featureType } = annotation;
             const { id, start, end, strand } = annotation;
             return [
-                id,
+                id.replaceAll(/[%\t\n\r]/g, encodeURIComponent),
                 'InterProScan',
                 // GFF-sourced annotations carry their original type; writing every
                 // feature back out as protein_match would turn an exon overlay into

package/dist/gff/annotationsToGFF.js.map

@@ -1 +1 @@
-{"version":3,"file":"annotationsToGFF.js","sourceRoot":"","sources":["../../src/gff/annotationsToGFF.ts"],"names":[],"mappings":"AAEA;;;;;;;;GAQG;AACH,MAAM,UAAU,gBAAgB,CAC9B,WAAyB,EACzB,MAAM,GAAa,EAAE;IAErB,OAAO;QACL,iBAAiB;QACjB,GAAG,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,KAAK,IAAI,EAAE,CAAC;QAClC,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"}
+{"version":3,"file":"annotationsToGFF.js","sourceRoot":"","sources":["../../src/gff/annotationsToGFF.ts"],"names":[],"mappings":"AAEA;;;;;;;;GAQG;AACH,MAAM,UAAU,gBAAgB,CAC9B,WAAyB,EACzB,MAAM,GAAa,EAAE;IAErB,OAAO;QACL,iBAAiB;QACjB,GAAG,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,KAAK,IAAI,EAAE,CAAC;QAClC,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,CAAC,UAAU,CAAC,YAAY,EAAE,kBAAkB,CAAC;gBAC/C,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.js

@@ -1,9 +1,9 @@
-// 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.
+// Feature types drawn with an arrowhead for their strand. A prokaryotic GFF
+// writes each gene as a CDS row. Exon, UTR and domain features stay blocks,
+// since an exon is a segment of one transcript.
 const GENE_LEVEL_TYPES = new Set([
     'gene',
+    'CDS',
     'pseudogene',
     'mRNA',
     'transcript',

package/dist/gff/gffToAnnotations.js.map

@@ -1 +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,+EAA+E;AAC/E,WAAW;AACX,MAAM,WAAW,GAAG,IAAI,GAAG,CAAC;IAC1B,QAAQ;IACR,QAAQ;IACR,MAAM;IACN,OAAO;IACP,KAAK;IACL,OAAO;IACP,QAAQ;IACR,OAAO;CACR,CAAC,CAAA;AAEF,SAAS,YAAY,CAAC,MAAiB;IACrC,MAAM,OAAO,GAAG,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,MAAM,CAC3C,CAAC,CAAC,GAAG,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,CAAC,WAAW,CAAC,GAAG,CAAC,GAAG,CAAC,IAAI,OAAO,KAAK,KAAK,QAAQ,CAC/C,CAAA;IACvB,OAAO,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,WAAW,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;AACrE,CAAC;AAED,8EAA8E;AAC9E,+EAA+E;AAC/E,6BAA6B;AAC7B,MAAM,UAAU,GAAG,2CAA2C,CAAA;AAE9D,SAAS,QAAQ,CAAC,MAAiB;IACjC,MAAM,KAAK,GAAG,CAAC,MAAM,CAAC,KAAK;QACzB,MAAM,CAAC,MAAM;QACb,MAAM,CAAC,KAAK;QACZ,MAAM,CAAC,MAAM,CAAuB,CAAA;IACtC,IAAI,CAAC,KAAK,EAAE,CAAC;QACX,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,MAAM,GAAG,UAAU,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAA;IAC5C,OAAO,MAAM,CAAC,CAAC,CAAC,OAAO,MAAM,CAAC,CAAC,CAAC,IAAI,MAAM,CAAC,CAAC,CAAC,IAAI,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,IAAI,EAAE,CAAA;AAC9E,CAAC;AAED,4EAA4E;AAC5E,6EAA6E;AAC7E,oDAAoD;AACpD,MAAM,oBAAoB,GAAG,IAAI,GAAG,CAAC,CAAC,aAAa,EAAE,cAAc,CAAC,CAAC,CAAA;AAErE;;;;;;GAMG;AACH,MAAM,UAAU,gBAAgB,CAAC,UAAuB;IACtD,OAAO,UAAU;SACd,MAAM,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC,oBAAoB,CAAC,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;SACxD,GAAG,CAAC,MAAM,CAAC,EAAE;QACZ,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;YAChC,MAAM,CAAC,IAAe;YACvB,SAAS,CAAA;QACX,OAAO;YACL,EAAE,EAAE,MAAM,CAAC,MAAM;YACjB,SAAS;YACT,IAAI;YACJ,kEAAkE;YAClE,4DAA4D;YAC5D,8CAA8C;YAC9C,WAAW,EACR,MAAM,CAAC,WAAsB;gBAC7B,MAAM,CAAC,IAAe;gBACtB,MAAM,CAAC,cAAyB;gBACjC,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;YAC1B,KAAK,EAAE,QAAQ,CAAC,MAAM,CAAC;YACvB,UAAU,EAAE,YAAY,CAAC,MAAM,CAAC;SACjC,CAAA;IACH,CAAC,CAAC,CAAA;AACN,CAAC"}
+{"version":3,"file":"gffToAnnotations.js","sourceRoot":"","sources":["../../src/gff/gffToAnnotations.ts"],"names":[],"mappings":"AAEA,4EAA4E;AAC5E,4EAA4E;AAC5E,gDAAgD;AAChD,MAAM,gBAAgB,GAAG,IAAI,GAAG,CAAC;IAC/B,MAAM;IACN,KAAK;IACL,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,+EAA+E;AAC/E,WAAW;AACX,MAAM,WAAW,GAAG,IAAI,GAAG,CAAC;IAC1B,QAAQ;IACR,QAAQ;IACR,MAAM;IACN,OAAO;IACP,KAAK;IACL,OAAO;IACP,QAAQ;IACR,OAAO;CACR,CAAC,CAAA;AAEF,SAAS,YAAY,CAAC,MAAiB;IACrC,MAAM,OAAO,GAAG,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,MAAM,CAC3C,CAAC,CAAC,GAAG,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,CAAC,WAAW,CAAC,GAAG,CAAC,GAAG,CAAC,IAAI,OAAO,KAAK,KAAK,QAAQ,CAC/C,CAAA;IACvB,OAAO,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,WAAW,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;AACrE,CAAC;AAED,8EAA8E;AAC9E,+EAA+E;AAC/E,6BAA6B;AAC7B,MAAM,UAAU,GAAG,2CAA2C,CAAA;AAE9D,SAAS,QAAQ,CAAC,MAAiB;IACjC,MAAM,KAAK,GAAG,CAAC,MAAM,CAAC,KAAK;QACzB,MAAM,CAAC,MAAM;QACb,MAAM,CAAC,KAAK;QACZ,MAAM,CAAC,MAAM,CAAuB,CAAA;IACtC,IAAI,CAAC,KAAK,EAAE,CAAC;QACX,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,MAAM,GAAG,UAAU,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAA;IAC5C,OAAO,MAAM,CAAC,CAAC,CAAC,OAAO,MAAM,CAAC,CAAC,CAAC,IAAI,MAAM,CAAC,CAAC,CAAC,IAAI,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,IAAI,EAAE,CAAA;AAC9E,CAAC;AAED,4EAA4E;AAC5E,6EAA6E;AAC7E,oDAAoD;AACpD,MAAM,oBAAoB,GAAG,IAAI,GAAG,CAAC,CAAC,aAAa,EAAE,cAAc,CAAC,CAAC,CAAA;AAErE;;;;;;GAMG;AACH,MAAM,UAAU,gBAAgB,CAAC,UAAuB;IACtD,OAAO,UAAU;SACd,MAAM,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC,oBAAoB,CAAC,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;SACxD,GAAG,CAAC,MAAM,CAAC,EAAE;QACZ,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;YAChC,MAAM,CAAC,IAAe;YACvB,SAAS,CAAA;QACX,OAAO;YACL,EAAE,EAAE,MAAM,CAAC,MAAM;YACjB,SAAS;YACT,IAAI;YACJ,kEAAkE;YAClE,4DAA4D;YAC5D,8CAA8C;YAC9C,WAAW,EACR,MAAM,CAAC,WAAsB;gBAC7B,MAAM,CAAC,IAAe;gBACtB,MAAM,CAAC,cAAyB;gBACjC,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;YAC1B,KAAK,EAAE,QAAQ,CAAC,MAAM,CAAC;YACvB,UAAU,EAAE,YAAY,CAAC,MAAM,CAAC;SACjC,CAAA;IACH,CAAC,CAAC,CAAA;AACN,CAAC"}

package/dist/gff/parseGFF.js

@@ -17,28 +17,22 @@ function parseAttributes(col9) {
     if (!col9) {
         return {};
     }
-    return Object.fromEntries(col9
-        .split(';')
-        .map(f => f.trim())
-        .filter(f => !!f)
-        .map(f => {
-        const eq = f.indexOf('=');
-        const key = (eq === -1 ? f : f.slice(0, eq)).trim();
-        const val = eq === -1 ? undefined : f.slice(eq + 1);
+    const attributes = {};
+    for (const field of col9.split(';')) {
+        const eq = field.indexOf('=');
+        const key = field.slice(0, eq).trim();
+        const val = field.slice(eq + 1);
         // split on comma (the GFF3 multi-value separator) BEFORE decoding, so a
         // literal comma encoded as %2C survives the split and isn't mistaken
         // for a separator
-        return [
-            key,
-            val
-                ? val
-                    .split(',')
-                    .map(v => unquote(safeDecode(v).trim()))
-                    .join(' ')
-                : undefined,
-        ];
-    })
-        .filter(([key]) => key !== ''));
+        if (eq !== -1 && key && val) {
+            attributes[key] = val
+                .split(',')
+                .map(v => unquote(safeDecode(v).trim()))
+                .join(' ');
+        }
+    }
+    return attributes;
 }
 export function parseGFF(str) {
     if (!str) {
@@ -66,7 +60,7 @@ export function parseGFF(str) {
         // "start=") can't turn a number field into a string
         return {
             ...parseAttributes(col9),
-            seq_id: seq_id ?? '',
+            seq_id: safeDecode(seq_id ?? ''),
             source: source ?? '',
             type: type ?? '',
             start: Number(start) || 0,

package/dist/gff/parseGFF.js.map

@@ -1 +1 @@
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package/dist/index.d.ts

@@ -4,3 +4,4 @@ export { A3mMSA, ClustalMSA, EmfMSA, FastaMSA, StockholmMSA, getUngappedSequence
 export type { MSAFormat, MSAParserType } from './msa/index.ts';
 export { indexResultsByXref, interProScanResponseToAnnotations, interProScanToAnnotations, } from './interProScanToAnnotations.ts';
 export { annotationsToGFF, gffToAnnotations, interProResponseToGFF, interProToGFF, parseGFF, } from './gff/index.ts';
+export { annotationTextToGFF } from './gff/annotationTextToGFF.ts';

package/dist/index.js

@@ -6,4 +6,5 @@ export { A3mMSA, ClustalMSA, EmfMSA, FastaMSA, StockholmMSA, getUngappedSequence
 export { indexResultsByXref, interProScanResponseToAnnotations, interProScanToAnnotations, } from './interProScanToAnnotations.js';
 // GFF parsing
 export { annotationsToGFF, gffToAnnotations, interProResponseToGFF, interProToGFF, parseGFF, } from './gff/index.js';
+export { annotationTextToGFF } from './gff/annotationTextToGFF.js';
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

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

@@ -1,12 +1,6 @@
 import BaseMSA from './BaseMSA.ts';
+import type { FastaRecord } from './fastaRecords.ts';
 export default class A3mMSA extends BaseMSA {
-    private MSA;
-    private orderedNames;
-    constructor(text: string);
-    static sniff(text: string): boolean;
-    getMSA(): {
-        seqdata: Record<string, string>;
-    };
-    getNames(): string[];
-    getRow(name: string): string;
+    constructor(input: string | FastaRecord[]);
+    static sniff(input: string | FastaRecord[]): boolean;
 }

package/dist/msa/A3mMSA.js

@@ -1,5 +1,5 @@
 import BaseMSA from './BaseMSA.js';
-import { fastaSniff, splitFastaRecords } from './fastaRecords.js';
+import { fastaSniff, toRecords } from './fastaRecords.js';
 /**
  * A3M Format Parser
  *
@@ -50,21 +50,16 @@ function parseRow(seq) {
     return { matches, inserts };
 }
 export default class A3mMSA extends BaseMSA {
-    MSA;
-    orderedNames;
-    constructor(text) {
-        super();
-        const records = splitFastaRecords(text);
-        this.orderedNames = records.map(r => r.id);
-        this.MSA = {
-            seqdata: expandA3M(records.map(r => r.seq), this.orderedNames),
-        };
+    constructor(input) {
+        const records = toRecords(input);
+        const expanded = expandA3M(records.map(r => r.seq));
+        super(records.map((r, i) => [r.id, expanded[i]]));
     }
-    static sniff(text) {
-        if (!fastaSniff(text)) {
+    static sniff(input) {
+        if (typeof input === 'string' && !fastaSniff(input)) {
             return false;
         }
-        const seqs = splitFastaRecords(text)
+        const seqs = toRecords(input)
             .map(r => r.seq)
             .filter(s => !!s);
         if (seqs.length < 2) {
@@ -78,19 +73,25 @@ export default class A3mMSA extends BaseMSA {
         if (new Set(seqs.map(s => s.length)).size === 1) {
             return false;
         }
-        const rows = seqs.map(parseRow);
-        const hasLowercase = rows.some(r => r.inserts.some(i => !!i));
-        const sameMatchLength = new Set(rows.map(r => r.matches.length)).size === 1;
-        return hasLowercase && sameMatchLength;
-    }
-    getMSA() {
-        return this.MSA;
-    }
-    getNames() {
-        return this.orderedNames;
-    }
-    getRow(name) {
-        return this.MSA.seqdata[name] ?? '';
+        let hasLowercase = false;
+        let matchCount;
+        for (const seq of seqs) {
+            let matches = 0;
+            for (let i = 0; i < seq.length; i++) {
+                const code = seq.charCodeAt(i);
+                if (isMatch(code)) {
+                    matches++;
+                }
+                else if (isLower(code)) {
+                    hasLowercase = true;
+                }
+            }
+            if (matchCount !== undefined && matches !== matchCount) {
+                return false;
+            }
+            matchCount = matches;
+        }
+        return hasLowercase;
     }
 }
 /**
@@ -98,7 +99,7 @@ export default class A3mMSA extends BaseMSA {
  * the longest insert any row places there, and rows without one are padded with
  * '.' so all rows stay in register.
  */
-function expandA3M(rawSeqs, names) {
+function expandA3M(rawSeqs) {
     const rows = rawSeqs.map(parseRow);
     // a loop, not Math.max(...): an a3m from an hhblits search routinely carries
     // six figures of hits, and spreading one argument per row throws
@@ -114,8 +115,7 @@ function expandA3M(rawSeqs, names) {
             maxInserts[pos] = Math.max(maxInserts[pos], ins.length);
         }
     }
-    const expanded = Object.create(null);
-    for (const [seqIdx, { matches, inserts }] of rows.entries()) {
+    return rows.map(({ matches, inserts }) => {
         const result = [];
         for (let pos = 0; pos <= numPositions; pos++) {
             const ins = inserts[pos] ?? '';
@@ -125,8 +125,7 @@ function expandA3M(rawSeqs, names) {
                 result.push(matches[pos] ?? '-');
             }
         }
-        expanded[names[seqIdx]] = result.join('');
-    }
-    return expanded;
+        return result.join('');
+    });
 }
 //# sourceMappingURL=A3mMSA.js.map

package/dist/msa/A3mMSA.js.map

@@ -1 +1 @@
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+{"version":3,"file":"A3mMSA.js","sourceRoot":"","sources":["../../src/msa/A3mMSA.ts"],"names":[],"mappings":"AAAA,OAAO,OAAO,MAAM,cAAc,CAAA;AAClC,OAAO,EAAE,UAAU,EAAE,SAAS,EAAE,MAAM,mBAAmB,CAAA;AAIzD;;;;;;;;;;;;;;;;;;;;GAoBG;AAEH,MAAM,MAAM,GAAG,EAAE,CAAA,CAAC,MAAM;AACxB,MAAM,MAAM,GAAG,EAAE,CAAA,CAAC,MAAM;AACxB,MAAM,MAAM,GAAG,EAAE,CAAA,CAAC,MAAM;AACxB,MAAM,MAAM,GAAG,GAAG,CAAA,CAAC,MAAM;AACzB,MAAM,SAAS,GAAG,EAAE,CAAA,CAAC,MAAM;AAE3B,SAAS,OAAO,CAAC,IAAY;IAC3B,OAAO,IAAI,IAAI,MAAM,IAAI,IAAI,IAAI,MAAM,CAAA;AACzC,CAAC;AAED,SAAS,OAAO,CAAC,IAAY;IAC3B,OAAO,CAAC,IAAI,IAAI,MAAM,IAAI,IAAI,IAAI,MAAM,CAAC,IAAI,IAAI,KAAK,SAAS,CAAA;AACjE,CAAC;AAYD,SAAS,QAAQ,CAAC,GAAW;IAC3B,MAAM,OAAO,GAAa,EAAE,CAAA;IAC5B,MAAM,OAAO,GAAG,CAAC,EAAE,CAAC,CAAA;IAEpB,KAAK,MAAM,EAAE,IAAI,GAAG,EAAE,CAAC;QACrB,MAAM,IAAI,GAAG,EAAE,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;QAC7B,IAAI,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC;YAClB,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;YAChB,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;QAClB,CAAC;aAAM,IAAI,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC;YACzB,OAAO,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,WAAW,EAAE,CAAA;QACjD,CAAC;QACD,0EAA0E;QAC1E,wDAAwD;IAC1D,CAAC;IAED,OAAO,EAAE,OAAO,EAAE,OAAO,EAAE,CAAA;AAC7B,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,MAAO,SAAQ,OAAO;IACzC,YAAY,KAA6B;QACvC,MAAM,OAAO,GAAG,SAAS,CAAC,KAAK,CAAC,CAAA;QAChC,MAAM,QAAQ,GAAG,SAAS,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;QACnD,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,EAAE,QAAQ,CAAC,CAAC,CAAE,CAAC,CAAC,CAAC,CAAA;IACpD,CAAC;IAED,MAAM,CAAC,KAAK,CAAC,KAA6B;QACxC,IAAI,OAAO,KAAK,KAAK,QAAQ,IAAI,CAAC,UAAU,CAAC,KAAK,CAAC,EAAE,CAAC;YACpD,OAAO,KAAK,CAAA;QACd,CAAC;QAED,MAAM,IAAI,GAAG,SAAS,CAAC,KAAK,CAAC;aAC1B,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC;aACf,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAEnB,IAAI,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACpB,OAAO,KAAK,CAAA;QACd,CAAC;QAED,sEAAsE;QACtE,4EAA4E;QAC5E,6EAA6E;QAC7E,4EAA4E;QAC5E,2BAA2B;QAC3B,IAAI,IAAI,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,EAAE,CAAC;YAChD,OAAO,KAAK,CAAA;QACd,CAAC;QAED,IAAI,YAAY,GAAG,KAAK,CAAA;QACxB,IAAI,UAA8B,CAAA;QAClC,KAAK,MAAM,GAAG,IAAI,IAAI,EAAE,CAAC;YACvB,IAAI,OAAO,GAAG,CAAC,CAAA;YACf,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;gBACpC,MAAM,IAAI,GAAG,GAAG,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;gBAC9B,IAAI,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC;oBAClB,OAAO,EAAE,CAAA;gBACX,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC;oBACzB,YAAY,GAAG,IAAI,CAAA;gBACrB,CAAC;YACH,CAAC;YACD,IAAI,UAAU,KAAK,SAAS,IAAI,OAAO,KAAK,UAAU,EAAE,CAAC;gBACvD,OAAO,KAAK,CAAA;YACd,CAAC;YACD,UAAU,GAAG,OAAO,CAAA;QACtB,CAAC;QACD,OAAO,YAAY,CAAA;IACrB,CAAC;CACF;AAED;;;;GAIG;AACH,SAAS,SAAS,CAAC,OAAiB;IAClC,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAA;IAClC,6EAA6E;IAC7E,iEAAiE;IACjE,kEAAkE;IAClE,IAAI,YAAY,GAAG,CAAC,CAAA;IACpB,KAAK,MAAM,EAAE,OAAO,EAAE,IAAI,IAAI,EAAE,CAAC;QAC/B,YAAY,GAAG,IAAI,CAAC,GAAG,CAAC,YAAY,EAAE,OAAO,CAAC,MAAM,CAAC,CAAA;IACvD,CAAC;IAED,mEAAmE;IACnE,MAAM,UAAU,GAAG,IAAI,KAAK,CAAS,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IAC9D,KAAK,MAAM,EAAE,OAAO,EAAE,IAAI,IAAI,EAAE,CAAC;QAC/B,KAAK,MAAM,CAAC,GAAG,EAAE,GAAG,CAAC,IAAI,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC;YAC3C,UAAU,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,GAAG,CAAE,EAAE,GAAG,CAAC,MAAM,CAAC,CAAA;QAC1D,CAAC;IACH,CAAC;IAED,OAAO,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,OAAO,EAAE,OAAO,EAAE,EAAE,EAAE;QACvC,MAAM,MAAM,GAAa,EAAE,CAAA;QAC3B,KAAK,IAAI,GAAG,GAAG,CAAC,EAAE,GAAG,IAAI,YAAY,EAAE,GAAG,EAAE,EAAE,CAAC;YAC7C,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,IAAI,EAAE,CAAA;YAC9B,MAAM,CAAC,IAAI,CAAC,GAAG,EAAE,GAAG,CAAC,MAAM,CAAC,UAAU,CAAC,GAAG,CAAE,GAAG,GAAG,CAAC,MAAM,CAAC,CAAC,CAAA;YAC3D,IAAI,GAAG,GAAG,YAAY,EAAE,CAAC;gBACvB,+DAA+D;gBAC/D,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,IAAI,GAAG,CAAC,CAAA;YAClC,CAAC;QACH,CAAC;QACD,OAAO,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;IACxB,CAAC,CAAC,CAAA;AACJ,CAAC"}

package/dist/msa/BaseMSA.d.ts

@@ -1,9 +1,15 @@
 import type { MSATrack, NodeWithIds } from '../types.ts';
 export default abstract class BaseMSA {
-    abstract getMSA(): unknown;
-    abstract getRow(name: string): string;
-    abstract getNames(): string[];
+    protected rows: Map<string, string>;
+    private names;
     private width?;
+    /**
+     * A repeated name keeps its first row: names index the rows, so listing the
+     * name twice would render a phantom duplicate row.
+     */
+    constructor(rows: Iterable<readonly [string, string]>);
+    getRow(name: string): string;
+    getNames(): string[];
     /**
      * Column count of the alignment: the length of its widest row, since a
      * hand-edited fasta or some aligners leave rows short. The viewer's gap

package/dist/msa/BaseMSA.js

@@ -1,5 +1,25 @@
 export default class BaseMSA {
+    rows = new Map();
+    names;
     width;
+    /**
+     * A repeated name keeps its first row: names index the rows, so listing the
+     * name twice would render a phantom duplicate row.
+     */
+    constructor(rows) {
+        for (const [name, seq] of rows) {
+            if (!this.rows.has(name)) {
+                this.rows.set(name, seq);
+            }
+        }
+        this.names = [...this.rows.keys()];
+    }
+    getRow(name) {
+        return this.rows.get(name) ?? '';
+    }
+    getNames() {
+        return this.names;
+    }
     /**
      * Column count of the alignment: the length of its widest row, since a
      * hand-edited fasta or some aligners leave rows short. The viewer's gap

package/dist/msa/BaseMSA.js.map

@@ -1 +1 @@
-{"version":3,"file":"BaseMSA.js","sourceRoot":"","sources":["../../src/msa/BaseMSA.ts"],"names":[],"mappings":"AAEA,MAAM,CAAC,OAAO,OAAgB,OAAO;IAK3B,KAAK,CAAS;IAEtB;;;;OAIG;IACH,QAAQ;QACN,IAAI,CAAC,KAAK,KAAK,IAAI,CAAC,QAAQ,EAAE,CAAC,MAAM,CACnC,CAAC,GAAG,EAAE,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC,EACtD,CAAC,CACF,CAAA;QACD,OAAO,IAAI,CAAC,KAAK,CAAA;IACnB,CAAC;IAED,OAAO;QACL,OAAO;YACL,EAAE,EAAE,MAAM;YACV,IAAI,EAAE,MAAM;YACZ,MAAM,EAAE,IAAI;YACZ,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACrC,EAAE,EAAE,IAAI;gBACR,QAAQ,EAAE,EAAE;gBACZ,IAAI;aACL,CAAC,CAAC;SACJ,CAAA;IACH,CAAC;IAED,UAAU,CACR,KAAa;QAEb,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,aAAa;QACX,OAAO,EAAE,CAAA;IACX,CAAC;IAED,SAAS;QACP,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,YAAY;QACd,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,2BAA2B;QAC7B,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,MAAM;QACR,OAAO,EAAE,CAAA;IACX,CAAC;CACF"}
+{"version":3,"file":"BaseMSA.js","sourceRoot":"","sources":["../../src/msa/BaseMSA.ts"],"names":[],"mappings":"AAEA,MAAM,CAAC,OAAO,OAAgB,OAAO;IACzB,IAAI,GAAG,IAAI,GAAG,EAAkB,CAAA;IAClC,KAAK,CAAU;IACf,KAAK,CAAS;IAEtB;;;OAGG;IACH,YAAY,IAAyC;QACnD,KAAK,MAAM,CAAC,IAAI,EAAE,GAAG,CAAC,IAAI,IAAI,EAAE,CAAC;YAC/B,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC;gBACzB,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,CAAA;YAC1B,CAAC;QACH,CAAC;QACD,IAAI,CAAC,KAAK,GAAG,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAC,CAAA;IACpC,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;IAClC,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,KAAK,CAAA;IACnB,CAAC;IAED;;;;OAIG;IACH,QAAQ;QACN,IAAI,CAAC,KAAK,KAAK,IAAI,CAAC,QAAQ,EAAE,CAAC,MAAM,CACnC,CAAC,GAAG,EAAE,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC,EACtD,CAAC,CACF,CAAA;QACD,OAAO,IAAI,CAAC,KAAK,CAAA;IACnB,CAAC;IAED,OAAO;QACL,OAAO;YACL,EAAE,EAAE,MAAM;YACV,IAAI,EAAE,MAAM;YACZ,MAAM,EAAE,IAAI;YACZ,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACrC,EAAE,EAAE,IAAI;gBACR,QAAQ,EAAE,EAAE;gBACZ,IAAI;aACL,CAAC,CAAC;SACJ,CAAA;IACH,CAAC;IAED,UAAU,CACR,KAAa;QAEb,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,aAAa;QACX,OAAO,EAAE,CAAA;IACX,CAAC;IAED,SAAS;QACP,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,YAAY;QACd,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,2BAA2B;QAC7B,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,MAAM;QACR,OAAO,EAAE,CAAA;IACX,CAAC;CACF"}

package/dist/msa/ClustalMSA.d.ts

@@ -1,24 +1,10 @@
 import BaseMSA from './BaseMSA.ts';
 export default class ClustalMSA extends BaseMSA {
     private MSA;
-    private byName;
     constructor(text: string);
-    getMSA(): {
-        consensus: string;
-        alns: {
-            id: string;
-            seq: string;
-        }[];
-        header: {
-            info: string;
-            version: string | undefined;
-        };
-    };
-    getRow(name: string): string;
     getHeader(): {
         info: string;
         version: string | undefined;
     };
-    getNames(): string[];
     get seqConsensus(): string;
 }

package/dist/msa/ClustalMSA.js

@@ -2,34 +2,14 @@ import { parse } from 'clustal-js';
 import BaseMSA from './BaseMSA.js';
 export default class ClustalMSA extends BaseMSA {
     MSA;
-    // getRow is called once per leaf on every render pass, so a linear scan of
-    // alns makes a full pass quadratic in the row count
-    byName;
     constructor(text) {
-        super();
-        this.MSA = parse(text);
-        this.byName = new Map();
-        for (const aln of this.MSA.alns) {
-            // first wins, as the find() this replaced did
-            if (!this.byName.has(aln.id)) {
-                this.byName.set(aln.id, aln.seq);
-            }
-        }
-    }
-    getMSA() {
-        return this.MSA;
-    }
-    getRow(name) {
-        return this.byName.get(name) ?? '';
+        const msa = parse(text);
+        super(msa.alns.map(aln => [aln.id, aln.seq]));
+        this.MSA = msa;
     }
     getHeader() {
         return this.MSA.header;
     }
-    // deduped, matching the first-wins byName map: emitting a repeated id twice
-    // renders a phantom duplicate row showing the first record's residues
-    getNames() {
-        return [...this.byName.keys()];
-    }
     get seqConsensus() {
         return this.MSA.consensus;
     }

package/dist/msa/ClustalMSA.js.map

@@ -1 +1 @@
-{"version":3,"file":"ClustalMSA.js","sourceRoot":"","sources":["../../src/msa/ClustalMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,YAAY,CAAA;AAElC,OAAO,OAAO,MAAM,cAAc,CAAA;AAElC,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,OAAO;IACrC,GAAG,CAA0B;IAErC,2EAA2E;IAC3E,oDAAoD;IAC5C,MAAM,CAAqB;IAEnC,YAAY,IAAY;QACtB,KAAK,EAAE,CAAA;QACP,IAAI,CAAC,GAAG,GAAG,KAAK,CAAC,IAAI,CAAC,CAAA;QACtB,IAAI,CAAC,MAAM,GAAG,IAAI,GAAG,EAAE,CAAA;QACvB,KAAK,MAAM,GAAG,IAAI,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,CAAC;YAChC,8CAA8C;YAC9C,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,CAAC;gBAC7B,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,CAAC,GAAG,CAAC,CAAA;YAClC,CAAC;QACH,CAAC;IACH,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;IACpC,CAAC;IAED,SAAS;QACP,OAAO,IAAI,CAAC,GAAG,CAAC,MAAM,CAAA;IACxB,CAAC;IAED,4EAA4E;IAC5E,sEAAsE;IACtE,QAAQ;QACN,OAAO,CAAC,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,CAAC,CAAA;IAChC,CAAC;IAED,IAAI,YAAY;QACd,OAAO,IAAI,CAAC,GAAG,CAAC,SAAS,CAAA;IAC3B,CAAC;CACF"}
+{"version":3,"file":"ClustalMSA.js","sourceRoot":"","sources":["../../src/msa/ClustalMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,YAAY,CAAA;AAElC,OAAO,OAAO,MAAM,cAAc,CAAA;AAElC,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,OAAO;IACrC,GAAG,CAA0B;IAErC,YAAY,IAAY;QACtB,MAAM,GAAG,GAAG,KAAK,CAAC,IAAI,CAAC,CAAA;QACvB,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;QAC7C,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;IAChB,CAAC;IAED,SAAS;QACP,OAAO,IAAI,CAAC,GAAG,CAAC,MAAM,CAAA;IACxB,CAAC;IAED,IAAI,YAAY;QACd,OAAO,IAAI,CAAC,GAAG,CAAC,SAAS,CAAA;IAC3B,CAAC;CACF"}

package/dist/msa/EmfMSA.d.ts

@@ -1,19 +1,4 @@
 import BaseMSA from './BaseMSA.ts';
 export default class EmfMSA extends BaseMSA {
-    private MSA;
-    private byName;
     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;
-    getNames(): string[];
 }

package/dist/msa/EmfMSA.js

@@ -1,31 +1,8 @@
 import { parseEmfAln } from 'emf-js';
 import BaseMSA from './BaseMSA.js';
 export default class EmfMSA extends BaseMSA {
-    MSA;
-    // getRow is called once per leaf on every render pass, so a linear scan of
-    // the alignment makes a full pass quadratic in the row count
-    byName;
     constructor(text) {
-        super();
-        this.MSA = parseEmfAln(text);
-        this.byName = new Map();
-        for (const aln of this.MSA) {
-            // first wins, as the find() this replaced did
-            if (!this.byName.has(aln.protein)) {
-                this.byName.set(aln.protein, aln.seq);
-            }
-        }
-    }
-    getMSA() {
-        return this.MSA;
-    }
-    getRow(name) {
-        return this.byName.get(name) ?? '';
-    }
-    // deduped, matching the first-wins byName map: emitting a repeated id twice
-    // renders a phantom duplicate row showing the first record's residues
-    getNames() {
-        return [...this.byName.keys()];
+        super(parseEmfAln(text).map(aln => [aln.protein, aln.seq]));
     }
 }
 //# sourceMappingURL=EmfMSA.js.map

package/dist/msa/EmfMSA.js.map

@@ -1 +1 @@
-{"version":3,"file":"EmfMSA.js","sourceRoot":"","sources":["../../src/msa/EmfMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,QAAQ,CAAA;AAEpC,OAAO,OAAO,MAAM,cAAc,CAAA;AAElC,MAAM,CAAC,OAAO,OAAO,MAAO,SAAQ,OAAO;IACjC,GAAG,CAAgC;IAE3C,2EAA2E;IAC3E,6DAA6D;IACrD,MAAM,CAAqB;IAEnC,YAAY,IAAY;QACtB,KAAK,EAAE,CAAA;QACP,IAAI,CAAC,GAAG,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;QAC5B,IAAI,CAAC,MAAM,GAAG,IAAI,GAAG,EAAE,CAAA;QACvB,KAAK,MAAM,GAAG,IAAI,IAAI,CAAC,GAAG,EAAE,CAAC;YAC3B,8CAA8C;YAC9C,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC;gBAClC,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,GAAG,CAAC,OAAO,EAAE,GAAG,CAAC,GAAG,CAAC,CAAA;YACvC,CAAC;QACH,CAAC;IACH,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;IACpC,CAAC;IAED,4EAA4E;IAC5E,sEAAsE;IACtE,QAAQ;QACN,OAAO,CAAC,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,CAAC,CAAA;IAChC,CAAC;CACF"}
+{"version":3,"file":"EmfMSA.js","sourceRoot":"","sources":["../../src/msa/EmfMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,QAAQ,CAAA;AAEpC,OAAO,OAAO,MAAM,cAAc,CAAA;AAElC,MAAM,CAAC,OAAO,OAAO,MAAO,SAAQ,OAAO;IACzC,YAAY,IAAY;QACtB,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,OAAO,EAAE,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;IAC7D,CAAC;CACF"}

package/dist/msa/FastaMSA.d.ts

@@ -1,12 +1,7 @@
 import BaseMSA from './BaseMSA.ts';
+import type { FastaRecord } from './fastaRecords.ts';
 export default class FastaMSA extends BaseMSA {
-    private MSA;
-    private orderedNames;
-    constructor(text: string);
-    getMSA(): {
-        seqdata: Record<string, string>;
-        colonNormalized: Record<string, string>;
-    };
-    getNames(): string[];
+    private colonNormalized;
+    constructor(input: string | FastaRecord[]);
     getRow(name: string): string;
 }

package/dist/msa/FastaMSA.js

@@ -1,33 +1,20 @@
 import BaseMSA from './BaseMSA.js';
-import { splitFastaRecords } from './fastaRecords.js';
+import { toRecords } from './fastaRecords.js';
 export default class FastaMSA extends BaseMSA {
-    MSA;
-    // explicit insertion-ordered ids: object key order reorders integer-like
-    // keys (e.g. a numeric ">123" defline) to the front, scrambling row order
-    orderedNames;
-    constructor(text) {
-        super();
-        const records = splitFastaRecords(text);
-        const seqdata = Object.create(null);
-        const colonNormalized = Object.create(null);
-        for (const { id, seq } of records) {
-            seqdata[id] = seq;
+    // Newick tools write a colon in a name as an underscore
+    colonNormalized = new Map();
+    constructor(input) {
+        const records = toRecords(input);
+        super(records.map(r => [r.id, r.seq]));
+        for (const { id } of records) {
             if (id.includes(':')) {
-                colonNormalized[id.replaceAll(':', '_')] = id;
+                this.colonNormalized.set(id.replaceAll(':', '_'), id);
             }
         }
-        this.orderedNames = records.map(r => r.id);
-        this.MSA = { seqdata, colonNormalized };
-    }
-    getMSA() {
-        return this.MSA;
-    }
-    getNames() {
-        return this.orderedNames;
     }
     getRow(name) {
-        return (this.MSA.seqdata[name] ??
-            this.MSA.seqdata[this.MSA.colonNormalized[name] ?? ''] ??
+        return (this.rows.get(name) ??
+            this.rows.get(this.colonNormalized.get(name) ?? '') ??
             '');
     }
 }

package/dist/msa/FastaMSA.js.map

@@ -1 +1 @@
-{"version":3,"file":"FastaMSA.js","sourceRoot":"","sources":["../../src/msa/FastaMSA.ts"],"names":[],"mappings":"AAAA,OAAO,OAAO,MAAM,cAAc,CAAA;AAClC,OAAO,EAAE,iBAAiB,EAAE,MAAM,mBAAmB,CAAA;AAErD,MAAM,CAAC,OAAO,OAAO,QAAS,SAAQ,OAAO;IACnC,GAAG,CAGV;IAED,yEAAyE;IACzE,0EAA0E;IAClE,YAAY,CAAU;IAE9B,YAAY,IAAY;QACtB,KAAK,EAAE,CAAA;QACP,MAAM,OAAO,GAAG,iBAAiB,CAAC,IAAI,CAAC,CAAA;QACvC,MAAM,OAAO,GAA2B,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;QAC3D,MAAM,eAAe,GAA2B,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;QAEnE,KAAK,MAAM,EAAE,EAAE,EAAE,GAAG,EAAE,IAAI,OAAO,EAAE,CAAC;YAClC,OAAO,CAAC,EAAE,CAAC,GAAG,GAAG,CAAA;YACjB,IAAI,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;gBACrB,eAAe,CAAC,EAAE,CAAC,UAAU,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,GAAG,EAAE,CAAA;YAC/C,CAAC;QACH,CAAC;QAED,IAAI,CAAC,YAAY,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAA;QAC1C,IAAI,CAAC,GAAG,GAAG,EAAE,OAAO,EAAE,eAAe,EAAE,CAAA;IACzC,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,YAAY,CAAA;IAC1B,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,CACL,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,CAAC;YACtB,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,eAAe,CAAC,IAAI,CAAC,IAAI,EAAE,CAAC;YACtD,EAAE,CACH,CAAA;IACH,CAAC;CACF"}
+{"version":3,"file":"FastaMSA.js","sourceRoot":"","sources":["../../src/msa/FastaMSA.ts"],"names":[],"mappings":"AAAA,OAAO,OAAO,MAAM,cAAc,CAAA;AAClC,OAAO,EAAE,SAAS,EAAE,MAAM,mBAAmB,CAAA;AAI7C,MAAM,CAAC,OAAO,OAAO,QAAS,SAAQ,OAAO;IAC3C,wDAAwD;IAChD,eAAe,GAAG,IAAI,GAAG,EAAkB,CAAA;IAEnD,YAAY,KAA6B;QACvC,MAAM,OAAO,GAAG,SAAS,CAAC,KAAK,CAAC,CAAA;QAChC,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;QACtC,KAAK,MAAM,EAAE,EAAE,EAAE,IAAI,OAAO,EAAE,CAAC;YAC7B,IAAI,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;gBACrB,IAAI,CAAC,eAAe,CAAC,GAAG,CAAC,EAAE,CAAC,UAAU,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC,CAAA;YACvD,CAAC;QACH,CAAC;IACH,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,CACL,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC;YACnB,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,eAAe,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,EAAE,CAAC;YACnD,EAAE,CACH,CAAA;IACH,CAAC;CACF"}

package/dist/msa/StockholmMSA.d.ts

@@ -6,7 +6,6 @@ export default class StockholmMSA extends BaseMSA {
     private MSA;
     constructor(text: string, currentAlignment: number);
     getMSA(): StockholmData;
-    getRow(name: string): string;
     get alignmentNames(): string[];
     getHeader(): {
         General: Record<string, string[]>;
@@ -22,7 +21,6 @@ export default class StockholmMSA extends BaseMSA {
         accession: string | undefined;
         dbxref: string | undefined;
     };
-    getNames(): string[];
     getStructures(): Record<string, {
         pdb: string;
         chain: string;

package/dist/msa/StockholmMSA.js

@@ -6,21 +6,18 @@ export default class StockholmMSA extends BaseMSA {
     data;
     MSA;
     constructor(text, currentAlignment) {
-        super();
         const res = parseAll(text);
-        this.data = res;
         const aln = res[currentAlignment] ?? res[0];
         if (!aln) {
             throw new Error('No alignments found in Stockholm file');
         }
+        super(aln.seqname.map(name => [name, aln.seqdata[name] ?? '']));
+        this.data = res;
         this.MSA = aln;
     }
     getMSA() {
         return this.MSA;
     }
-    getRow(name) {
-        return this.MSA.seqdata[name] ?? '';
-    }
     get alignmentNames() {
         return this.data.map((aln, idx) => aln.gf.DE?.[0] ?? `Alignment ${idx + 1}`);
     }
@@ -40,11 +37,6 @@ export default class StockholmMSA extends BaseMSA {
             dbxref: this.MSA.gs.DR?.[rowName]?.join('; '),
         };
     }
-    getNames() {
-        // seqname, not Object.keys(seqdata): object key order hoists integer-like
-        // keys (a numeric sequence name) to the front, scrambling row order
-        return this.MSA.seqname;
-    }
     getStructures() {
         const pdbRegex = /PDB; +(\S+) +([^;\s]+); *(-?[0-9]+)-(-?[0-9]+)/;
         const drEntries = this.MSA.gs.DR ?? {};