msa-parsers 5.7.2 → 5.7.3

package/dist/gff/gffToInterPro.js

@@ -33,16 +33,7 @@ function geneStrand({ type, strand }) {
     return GENE_LEVEL_TYPES.has(type) ? directional : undefined;
 }
 export function gffToInterProResults(gffRecords) {
-    const bySequence = new Map();
-    for (const record of gffRecords) {
-        const existing = bySequence.get(record.seq_id);
-        if (existing) {
-            existing.push(record);
-        }
-        else {
-            bySequence.set(record.seq_id, [record]);
-        }
-    }
+    const bySequence = Map.groupBy(gffRecords, record => record.seq_id);
     const results = {};
     for (const [seqId, records] of bySequence) {
         const matchesByAccession = new Map();
@@ -66,31 +57,22 @@ export function gffToInterProResults(gffRecords) {
                     featureType: record.type,
                 });
             }
-            const location = {
+            let locations = matchesByAccession.get(accession);
+            if (!locations) {
+                locations = [];
+                matchesByAccession.set(accession, locations);
+            }
+            locations.push({
                 start: record.start,
                 end: record.end,
                 strand: geneStrand(record),
-            };
-            const locations = matchesByAccession.get(accession);
-            if (locations) {
-                locations.push(location);
-            }
-            else {
-                matchesByAccession.set(accession, [location]);
-            }
-        }
-        const matches = [];
-        for (const [accession, locations] of matchesByAccession) {
-            const info = matchInfo.get(accession);
-            matches.push({
-                signature: {
-                    entry: info,
-                },
-                locations,
             });
         }
         results[seqId] = {
-            matches,
+            matches: [...matchesByAccession].map(([accession, locations]) => ({
+                signature: { entry: matchInfo.get(accession) },
+                locations,
+            })),
             xref: [{ id: seqId }],
         };
     }

package/dist/gff/gffToInterPro.js.map

@@ -1 +1 @@
-{"version":3,"file":"gffToInterPro.js","sourceRoot":"","sources":["../../src/gff/gffToInterPro.ts"],"names":[],"mappings":"AAMA;;;;;;;;;GASG;AACH,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,MAAM,UAAU,oBAAoB,CAClC,UAAuB;IAEvB,MAAM,UAAU,GAAG,IAAI,GAAG,EAAuB,CAAA;IAEjD,KAAK,MAAM,MAAM,IAAI,UAAU,EAAE,CAAC;QAChC,MAAM,QAAQ,GAAG,UAAU,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QAC9C,IAAI,QAAQ,EAAE,CAAC;YACb,QAAQ,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QACvB,CAAC;aAAM,CAAC;YACN,UAAU,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,MAAM,CAAC,CAAC,CAAA;QACzC,CAAC;IACH,CAAC;IAED,MAAM,OAAO,GAAwC,EAAE,CAAA;IAEvD,KAAK,MAAM,CAAC,KAAK,EAAE,OAAO,CAAC,IAAI,UAAU,EAAE,CAAC;QAC1C,MAAM,kBAAkB,GAAG,IAAI,GAAG,EAG/B,CAAA;QACH,MAAM,SAAS,GAAG,IAAI,GAAG,EAQtB,CAAA;QAEH,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;YAC7B,MAAM,SAAS,GACZ,MAAM,CAAC,IAAe;gBACtB,MAAM,CAAC,EAAa;gBACrB,GAAG,MAAM,CAAC,MAAM,IAAI,MAAM,CAAC,KAAK,IAAI,MAAM,CAAC,GAAG,EAAE,CAAA;YAClD,MAAM,IAAI,GACP,MAAM,CAAC,cAAyB;gBAChC,MAAM,CAAC,IAAe;gBACvB,SAAS,CAAA;YACX,MAAM,WAAW,GACd,MAAM,CAAC,aAAwB;gBAC/B,MAAM,CAAC,WAAsB;gBAC7B,MAAM,CAAC,IAAe;gBACvB,IAAI,CAAA;YAEN,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,CAAC;gBAC9B,SAAS,CAAC,GAAG,CAAC,SAAS,EAAE;oBACvB,IAAI;oBACJ,WAAW;oBACX,SAAS;oBACT,WAAW,EAAE,MAAM,CAAC,IAAI;iBACzB,CAAC,CAAA;YACJ,CAAC;YAED,MAAM,QAAQ,GAAG;gBACf,KAAK,EAAE,MAAM,CAAC,KAAK;gBACnB,GAAG,EAAE,MAAM,CAAC,GAAG;gBACf,MAAM,EAAE,UAAU,CAAC,MAAM,CAAC;aAC3B,CAAA;YACD,MAAM,SAAS,GAAG,kBAAkB,CAAC,GAAG,CAAC,SAAS,CAAC,CAAA;YACnD,IAAI,SAAS,EAAE,CAAC;gBACd,SAAS,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;YAC1B,CAAC;iBAAM,CAAC;gBACN,kBAAkB,CAAC,GAAG,CAAC,SAAS,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAA;YAC/C,CAAC;QACH,CAAC;QAED,MAAM,OAAO,GAAG,EAAE,CAAA;QAClB,KAAK,MAAM,CAAC,SAAS,EAAE,SAAS,CAAC,IAAI,kBAAkB,EAAE,CAAC;YACxD,MAAM,IAAI,GAAG,SAAS,CAAC,GAAG,CAAC,SAAS,CAAE,CAAA;YACtC,OAAO,CAAC,IAAI,CAAC;gBACX,SAAS,EAAE;oBACT,KAAK,EAAE,IAAI;iBACZ;gBACD,SAAS;aACV,CAAC,CAAA;QACJ,CAAC;QAED,OAAO,CAAC,KAAK,CAAC,GAAG;YACf,OAAO;YACP,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC;SACtB,CAAA;IACH,CAAC;IAED,OAAO,OAAO,CAAA;AAChB,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,qBAAqB,CACnC,UAAuB;IAEvB,MAAM,UAAU,GAAG,oBAAoB,CAAC,UAAU,CAAC,CAAA;IACnD,OAAO;QACL,OAAO,EAAE,MAAM,CAAC,MAAM,CAAC,UAAU,CAAC;KACnC,CAAA;AACH,CAAC"}
+{"version":3,"file":"gffToInterPro.js","sourceRoot":"","sources":["../../src/gff/gffToInterPro.ts"],"names":[],"mappings":"AAMA;;;;;;;;;GASG;AACH,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,MAAM,UAAU,oBAAoB,CAClC,UAAuB;IAEvB,MAAM,UAAU,GAAG,GAAG,CAAC,OAAO,CAAC,UAAU,EAAE,MAAM,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;IACnE,MAAM,OAAO,GAAwC,EAAE,CAAA;IAEvD,KAAK,MAAM,CAAC,KAAK,EAAE,OAAO,CAAC,IAAI,UAAU,EAAE,CAAC;QAC1C,MAAM,kBAAkB,GAAG,IAAI,GAAG,EAG/B,CAAA;QACH,MAAM,SAAS,GAAG,IAAI,GAAG,EAQtB,CAAA;QAEH,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;YAC7B,MAAM,SAAS,GACZ,MAAM,CAAC,IAAe;gBACtB,MAAM,CAAC,EAAa;gBACrB,GAAG,MAAM,CAAC,MAAM,IAAI,MAAM,CAAC,KAAK,IAAI,MAAM,CAAC,GAAG,EAAE,CAAA;YAClD,MAAM,IAAI,GACP,MAAM,CAAC,cAAyB;gBAChC,MAAM,CAAC,IAAe;gBACvB,SAAS,CAAA;YACX,MAAM,WAAW,GACd,MAAM,CAAC,aAAwB;gBAC/B,MAAM,CAAC,WAAsB;gBAC7B,MAAM,CAAC,IAAe;gBACvB,IAAI,CAAA;YAEN,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,CAAC;gBAC9B,SAAS,CAAC,GAAG,CAAC,SAAS,EAAE;oBACvB,IAAI;oBACJ,WAAW;oBACX,SAAS;oBACT,WAAW,EAAE,MAAM,CAAC,IAAI;iBACzB,CAAC,CAAA;YACJ,CAAC;YAED,IAAI,SAAS,GAAG,kBAAkB,CAAC,GAAG,CAAC,SAAS,CAAC,CAAA;YACjD,IAAI,CAAC,SAAS,EAAE,CAAC;gBACf,SAAS,GAAG,EAAE,CAAA;gBACd,kBAAkB,CAAC,GAAG,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;YAC9C,CAAC;YACD,SAAS,CAAC,IAAI,CAAC;gBACb,KAAK,EAAE,MAAM,CAAC,KAAK;gBACnB,GAAG,EAAE,MAAM,CAAC,GAAG;gBACf,MAAM,EAAE,UAAU,CAAC,MAAM,CAAC;aAC3B,CAAC,CAAA;QACJ,CAAC;QAED,OAAO,CAAC,KAAK,CAAC,GAAG;YACf,OAAO,EAAE,CAAC,GAAG,kBAAkB,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,SAAS,EAAE,SAAS,CAAC,EAAE,EAAE,CAAC,CAAC;gBAChE,SAAS,EAAE,EAAE,KAAK,EAAE,SAAS,CAAC,GAAG,CAAC,SAAS,CAAE,EAAE;gBAC/C,SAAS;aACV,CAAC,CAAC;YACH,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC;SACtB,CAAA;IACH,CAAC;IAED,OAAO,OAAO,CAAA;AAChB,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,qBAAqB,CACnC,UAAuB;IAEvB,MAAM,UAAU,GAAG,oBAAoB,CAAC,UAAU,CAAC,CAAA;IACnD,OAAO;QACL,OAAO,EAAE,MAAM,CAAC,MAAM,CAAC,UAAU,CAAC;KACnC,CAAA;AACH,CAAC"}

package/dist/gff/parseGFF.js

@@ -47,7 +47,10 @@ export function parseGFF(str) {
         const parts = f.split('\t');
         const [seq_id, source, type, start, end, score, strand, phase] = parts;
         const col9 = parts[8];
+        // attributes first, so a column-9 key colliding with a core column (e.g.
+        // "start=") can't turn a number field into a string
         return {
+            ...parseAttributes(col9),
             seq_id: seq_id ?? '',
             source: source ?? '',
             type: type ?? '',
@@ -56,7 +59,6 @@ export function parseGFF(str) {
             score: Number(score) || 0,
             strand: strand ?? '.',
             phase: phase ?? '.',
-            ...parseAttributes(col9),
         };
     });
 }

package/dist/gff/parseGFF.js.map

@@ -1 +1 @@
-{"version":3,"file":"parseGFF.js","sourceRoot":"","sources":["../../src/gff/parseGFF.ts"],"names":[],"mappings":"AAEA,8EAA8E;AAC9E,kEAAkE;AAClE,SAAS,UAAU,CAAC,GAAW;IAC7B,IAAI,CAAC;QACH,OAAO,kBAAkB,CAAC,GAAG,CAAC,CAAA;IAChC,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,GAAG,CAAA;IACZ,CAAC;AACH,CAAC;AAED,SAAS,eAAe,CAAC,IAAa;IACpC,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,OAAO,EAAE,CAAA;IACX,CAAC;IACD,OAAO,MAAM,CAAC,WAAW,CACvB,IAAI;SACD,KAAK,CAAC,GAAG,CAAC;SACV,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,GAAG,CAAC,CAAC,CAAC,EAAE;QACP,MAAM,EAAE,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;QACzB,MAAM,GAAG,GAAG,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAA;QACnD,MAAM,GAAG,GAAG,EAAE,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,GAAG,CAAC,CAAC,CAAA;QACnD,wEAAwE;QACxE,qEAAqE;QACrE,kBAAkB;QAClB,OAAO;YACL,GAAG;YACH,GAAG;gBACD,CAAC,CAAC,GAAG;qBACA,KAAK,CAAC,GAAG,CAAC;qBACV,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;qBAC9B,IAAI,CAAC,GAAG,CAAC;gBACd,CAAC,CAAC,SAAS;SACd,CAAA;IACH,CAAC,CAAC;SACD,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,CACjC,CAAA;AACH,CAAC;AAED,MAAM,UAAU,QAAQ,CAAC,GAAY;IACnC,IAAI,CAAC,GAAG,EAAE,CAAC;QACT,OAAO,EAAE,CAAA;IACX,CAAC;IACD,OAAO,GAAG;SACP,KAAK,CAAC,IAAI,CAAC;SACX,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC;SACtC,GAAG,CAAC,CAAC,CAAC,EAAE;QACP,MAAM,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC3B,MAAM,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,CAAC,GAAG,KAAK,CAAA;QACtE,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;QAErB,OAAO;YACL,MAAM,EAAE,MAAM,IAAI,EAAE;YACpB,MAAM,EAAE,MAAM,IAAI,EAAE;YACpB,IAAI,EAAE,IAAI,IAAI,EAAE;YAChB,KAAK,EAAE,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC;YACzB,GAAG,EAAE,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC;YACrB,KAAK,EAAE,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC;YACzB,MAAM,EAAE,MAAM,IAAI,GAAG;YACrB,KAAK,EAAE,KAAK,IAAI,GAAG;YACnB,GAAG,eAAe,CAAC,IAAI,CAAC;SACzB,CAAA;IACH,CAAC,CAAC,CAAA;AACN,CAAC"}
+{"version":3,"file":"parseGFF.js","sourceRoot":"","sources":["../../src/gff/parseGFF.ts"],"names":[],"mappings":"AAEA,8EAA8E;AAC9E,kEAAkE;AAClE,SAAS,UAAU,CAAC,GAAW;IAC7B,IAAI,CAAC;QACH,OAAO,kBAAkB,CAAC,GAAG,CAAC,CAAA;IAChC,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,GAAG,CAAA;IACZ,CAAC;AACH,CAAC;AAED,SAAS,eAAe,CAAC,IAAa;IACpC,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,OAAO,EAAE,CAAA;IACX,CAAC;IACD,OAAO,MAAM,CAAC,WAAW,CACvB,IAAI;SACD,KAAK,CAAC,GAAG,CAAC;SACV,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,GAAG,CAAC,CAAC,CAAC,EAAE;QACP,MAAM,EAAE,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;QACzB,MAAM,GAAG,GAAG,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAA;QACnD,MAAM,GAAG,GAAG,EAAE,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,GAAG,CAAC,CAAC,CAAA;QACnD,wEAAwE;QACxE,qEAAqE;QACrE,kBAAkB;QAClB,OAAO;YACL,GAAG;YACH,GAAG;gBACD,CAAC,CAAC,GAAG;qBACA,KAAK,CAAC,GAAG,CAAC;qBACV,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;qBAC9B,IAAI,CAAC,GAAG,CAAC;gBACd,CAAC,CAAC,SAAS;SACd,CAAA;IACH,CAAC,CAAC;SACD,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,CACjC,CAAA;AACH,CAAC;AAED,MAAM,UAAU,QAAQ,CAAC,GAAY;IACnC,IAAI,CAAC,GAAG,EAAE,CAAC;QACT,OAAO,EAAE,CAAA;IACX,CAAC;IACD,OAAO,GAAG;SACP,KAAK,CAAC,IAAI,CAAC;SACX,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC;SACtC,GAAG,CAAC,CAAC,CAAC,EAAE;QACP,MAAM,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC3B,MAAM,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,CAAC,GAAG,KAAK,CAAA;QACtE,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;QAErB,yEAAyE;QACzE,oDAAoD;QACpD,OAAO;YACL,GAAG,eAAe,CAAC,IAAI,CAAC;YACxB,MAAM,EAAE,MAAM,IAAI,EAAE;YACpB,MAAM,EAAE,MAAM,IAAI,EAAE;YACpB,IAAI,EAAE,IAAI,IAAI,EAAE;YAChB,KAAK,EAAE,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC;YACzB,GAAG,EAAE,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC;YACrB,KAAK,EAAE,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC;YACzB,MAAM,EAAE,MAAM,IAAI,GAAG;YACrB,KAAK,EAAE,KAAK,IAAI,GAAG;SACpB,CAAA;IACH,CAAC,CAAC,CAAA;AACN,CAAC"}

package/dist/msa/A3mMSA.d.ts

@@ -4,7 +4,6 @@ export default class A3mMSA extends BaseMSA {
     private orderedNames;
     constructor(text: string);
     static sniff(text: string): boolean;
-    private expandA3M;
     getMSA(): {
         seqdata: Record<string, string>;
     };

package/dist/msa/A3mMSA.js

@@ -1,4 +1,5 @@
 import BaseMSA from './BaseMSA.js';
+import { splitFastaRecords } from './fastaRecords.js';
 /**
  * A3M Format Parser
  *
@@ -25,54 +26,47 @@ const CODE_Z = 90; // 'Z'
 const CODE_a = 97; // 'a'
 const CODE_z = 122; // 'z'
 const CODE_DASH = 45; // '-'
-const CODE_DOT = 46; // '.'
 function isLower(code) {
     return code >= CODE_a && code <= CODE_z;
 }
+function isMatch(code) {
+    return (code >= CODE_A && code <= CODE_Z) || code === CODE_DASH;
+}
+function parseRow(seq) {
+    const matches = [];
+    const inserts = [''];
+    for (const ch of seq) {
+        const code = ch.charCodeAt(0);
+        if (isMatch(code)) {
+            matches.push(ch);
+            inserts.push('');
+        }
+        else if (isLower(code)) {
+            inserts[inserts.length - 1] += ch.toUpperCase();
+        }
+        // '.' is padding aligned to some other row's insert, and anything else is
+        // unrecognized -- neither carries alignment information
+    }
+    return { matches, inserts };
+}
 export default class A3mMSA extends BaseMSA {
     MSA;
     orderedNames;
     constructor(text) {
         super();
-        const rawSeqs = [];
-        const names = [];
-        for (const entry of text.split('>')) {
-            if (!/\S/.test(entry)) {
-                continue;
-            }
-            const newlineIdx = entry.indexOf('\n');
-            if (newlineIdx === -1) {
-                continue;
-            }
-            const defLine = entry.slice(0, newlineIdx).replace(/\r$/, '');
-            const spaceIdx = defLine.indexOf(' ');
-            const id = spaceIdx === -1 ? defLine : defLine.slice(0, spaceIdx);
-            if (id) {
-                rawSeqs.push(entry.slice(newlineIdx + 1).replaceAll(/\s/g, ''));
-                names.push(id);
-            }
-        }
-        this.orderedNames = names;
-        this.MSA = { seqdata: this.expandA3M(rawSeqs, names) };
+        const records = splitFastaRecords(text);
+        this.orderedNames = records.map(r => r.id);
+        this.MSA = {
+            seqdata: expandA3M(records.map(r => r.seq), this.orderedNames),
+        };
     }
     static sniff(text) {
         if (!text.startsWith('>')) {
             return false;
         }
-        const seqs = [];
-        for (const entry of text.split('>')) {
-            if (!/\S/.test(entry)) {
-                continue;
-            }
-            const newlineIdx = entry.indexOf('\n');
-            if (newlineIdx === -1) {
-                continue;
-            }
-            const seq = entry.slice(newlineIdx + 1).replaceAll(/\s/g, '');
-            if (seq) {
-                seqs.push(seq);
-            }
-        }
+        const seqs = splitFastaRecords(text)
+            .map(r => r.seq)
+            .filter(s => !!s);
         if (seqs.length < 2) {
             return false;
         }
@@ -84,131 +78,11 @@ export default class A3mMSA extends BaseMSA {
         if (new Set(seqs.map(s => s.length)).size === 1) {
             return false;
         }
-        let hasLowercase = false;
-        let firstMatchLen = -1;
-        let sameMatchLength = true;
-        for (const seq of seqs) {
-            let matchLen = 0;
-            for (let i = 0; i < seq.length; i++) {
-                const code = seq.charCodeAt(i);
-                if (isLower(code)) {
-                    hasLowercase = true;
-                }
-                else if ((code >= CODE_A && code <= CODE_Z) || code === CODE_DASH) {
-                    matchLen++;
-                }
-            }
-            if (firstMatchLen === -1) {
-                firstMatchLen = matchLen;
-            }
-            else {
-                if (matchLen !== firstMatchLen) {
-                    sameMatchLength = 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;
     }
-    expandA3M(rawSeqs, names) {
-        const numSeqs = names.length;
-        if (numSeqs === 0) {
-            return {};
-        }
-        const matchChars = [];
-        const insertContent = [];
-        for (let seqIdx = 0; seqIdx < numSeqs; seqIdx++) {
-            const seq = rawSeqs[seqIdx];
-            const matches = [];
-            const inserts = [];
-            let i = 0;
-            while (i < seq.length) {
-                const code = seq.charCodeAt(i);
-                if ((code >= CODE_A && code <= CODE_Z) || code === CODE_DASH) {
-                    matches.push(seq[i]);
-                    let ins = '';
-                    let j = i + 1;
-                    while (j < seq.length) {
-                        const c = seq.charCodeAt(j);
-                        if (isLower(c) || c === CODE_DOT) {
-                            ins += seq[j];
-                            j++;
-                        }
-                        else {
-                            break;
-                        }
-                    }
-                    inserts.push(ins);
-                    i = j;
-                }
-                else if (code === CODE_DOT) {
-                    i++;
-                }
-                else if (isLower(code)) {
-                    let ins = '';
-                    while (i < seq.length && isLower(seq.charCodeAt(i))) {
-                        ins += seq[i];
-                        i++;
-                    }
-                    matches.push('');
-                    inserts.push(ins);
-                }
-                else {
-                    i++;
-                }
-            }
-            matchChars.push(matches);
-            insertContent.push(inserts);
-        }
-        const numPositions = Math.max(...matchChars.map(m => m.length), 0);
-        const maxInserts = new Array(numPositions).fill(0);
-        for (let seqIdx = 0; seqIdx < numSeqs; seqIdx++) {
-            const inserts = insertContent[seqIdx];
-            for (let pos = 0; pos < inserts.length; pos++) {
-                let lcCount = 0;
-                for (const c of inserts[pos]) {
-                    if (isLower(c.charCodeAt(0))) {
-                        lcCount++;
-                    }
-                }
-                if (lcCount > maxInserts[pos]) {
-                    maxInserts[pos] = lcCount;
-                }
-            }
-        }
-        const expanded = {};
-        for (let seqIdx = 0; seqIdx < numSeqs; seqIdx++) {
-            const matches = matchChars[seqIdx];
-            const inserts = insertContent[seqIdx];
-            const result = [];
-            for (let pos = 0; pos < numPositions; pos++) {
-                const maxIns = maxInserts[pos];
-                if (pos < matches.length) {
-                    const matchChar = matches[pos];
-                    const insContent = inserts[pos] || '';
-                    result.push(matchChar || '-');
-                    let lcContent = '';
-                    for (const c of insContent) {
-                        if (isLower(c.charCodeAt(0))) {
-                            lcContent += c.toUpperCase();
-                        }
-                    }
-                    result.push(lcContent);
-                    const padding = maxIns - lcContent.length;
-                    if (padding > 0) {
-                        result.push('.'.repeat(padding));
-                    }
-                }
-                else {
-                    result.push('-');
-                    if (maxIns > 0) {
-                        result.push('.'.repeat(maxIns));
-                    }
-                }
-            }
-            expanded[names[seqIdx]] = result.join('');
-        }
-        return expanded;
-    }
     getMSA() {
         return this.MSA;
     }
@@ -216,11 +90,41 @@ export default class A3mMSA extends BaseMSA {
         return this.orderedNames;
     }
     getRow(name) {
-        return this.MSA.seqdata[name] || '';
+        return this.MSA.seqdata[name] ?? '';
     }
     getWidth() {
-        const name = Object.keys(this.MSA.seqdata)[0];
-        return name ? this.getRow(name).length : 0;
+        const name = this.orderedNames[0];
+        return name === undefined ? 0 : this.getRow(name).length;
+    }
+}
+/**
+ * Expand A3M rows into a rectangular alignment: every insert slot is widened to
+ * the longest insert any row places there, and rows without one are padded with
+ * '.' so all rows stay in register.
+ */
+function expandA3M(rawSeqs, names) {
+    const rows = rawSeqs.map(parseRow);
+    const numPositions = Math.max(...rows.map(r => r.matches.length), 0);
+    // one insert slot before each match column, plus one trailing slot
+    const maxInserts = new Array(numPositions + 1).fill(0);
+    for (const { inserts } of rows) {
+        for (const [pos, ins] of inserts.entries()) {
+            maxInserts[pos] = Math.max(maxInserts[pos], ins.length);
+        }
+    }
+    const expanded = {};
+    for (const [seqIdx, { matches, inserts }] of rows.entries()) {
+        const result = [];
+        for (let pos = 0; pos <= numPositions; pos++) {
+            const ins = inserts[pos] ?? '';
+            result.push(ins, '.'.repeat(maxInserts[pos] - ins.length));
+            if (pos < numPositions) {
+                // a row with fewer match columns than the widest is padded out
+                result.push(matches[pos] ?? '-');
+            }
+        }
+        expanded[names[seqIdx]] = result.join('');
     }
+    return expanded;
 }
 //# sourceMappingURL=A3mMSA.js.map

package/dist/msa/A3mMSA.js.map

@@ -1 +1 @@
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package/dist/msa/A3mMSA.test.js

@@ -198,6 +198,50 @@ ACDEFghiKLMNPQ
             expect(seq1).toBe('ACDEFGHIKLMNPQ');
             expect(seq2).toBe('--DEF...KLM--Q');
         });
+        test('a leading insert does not shift the row out of register', () => {
+            // seq2 opens with a lowercase insert. That insert belongs in a new column
+            // BEFORE match column 0 -- it must not consume a match column, or every
+            // one of seq2's residues lands one column left of its true partner.
+            const a3m = `>query
+ABC
+>seq2
+aABC`;
+            const msa = new A3mMSA(a3m);
+            // query: . + A + B + C   (dot padding for seq2's insert)
+            // seq2:  A + A + B + C   (insert uppercased)
+            expect(msa.getRow('query')).toBe('.ABC');
+            expect(msa.getRow('seq2')).toBe('AABC');
+        });
+        test('a trailing insert widens only the final column', () => {
+            const a3m = `>query
+ABC
+>seq2
+ABCde`;
+            const msa = new A3mMSA(a3m);
+            expect(msa.getRow('query')).toBe('ABC..');
+            expect(msa.getRow('seq2')).toBe('ABCDE');
+        });
+        test('dots in the input are padding, not columns', () => {
+            // '.' marks a gap aligned to another row's insert, so a row already
+            // carrying them must expand to the same width as one without
+            const a3m = `>query
+AC..DEF
+>seq2
+ACghDEF`;
+            const msa = new A3mMSA(a3m);
+            expect(msa.getRow('query')).toBe('AC..DEF');
+            expect(msa.getRow('seq2')).toBe('ACGHDEF');
+        });
+        test('keeps the first record when a name repeats', () => {
+            // ids index the row data, so a repeated defline must not emit two rows
+            const a3m = `>seq1
+ACDEF
+>seq1
+GHIKL`;
+            const msa = new A3mMSA(a3m);
+            expect(msa.getNames()).toEqual(['seq1']);
+            expect(msa.getRow('seq1')).toBe('ACDEF');
+        });
         test('getWidth returns correct width', () => {
             const a3m = `>seq1
 ACDEF

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

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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;IAMnC,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,CAAC,KAAa;QACtB,OAAO,SAEM,CAAA;IACf,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;QAMR,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;IAMnC,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;QAMR,OAAO,EAAE,CAAA;IACX,CAAC;CACF"}

package/dist/msa/FastaMSA.js

@@ -1,32 +1,22 @@
 import BaseMSA from './BaseMSA.js';
+import { splitFastaRecords } 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 = [];
+    orderedNames;
     constructor(text) {
         super();
+        const records = splitFastaRecords(text);
         const seqdata = {};
         const colonNormalized = {};
-        for (const entry of text.split('>')) {
-            if (!/\S/.test(entry)) {
-                continue;
-            }
-            const newlineIdx = entry.indexOf('\n');
-            if (newlineIdx === -1) {
-                continue;
-            }
-            const defLine = entry.slice(0, newlineIdx).replace(/\r$/, '');
-            const spaceIdx = defLine.indexOf(' ');
-            const id = spaceIdx === -1 ? defLine : defLine.slice(0, spaceIdx);
-            if (id) {
-                seqdata[id] = entry.slice(newlineIdx + 1).replaceAll(/\s/g, '');
-                this.orderedNames.push(id);
-                if (id.includes(':')) {
-                    colonNormalized[id.replaceAll(':', '_')] = id;
-                }
+        for (const { id, seq } of records) {
+            seqdata[id] = seq;
+            if (id.includes(':')) {
+                colonNormalized[id.replaceAll(':', '_')] = id;
             }
         }
+        this.orderedNames = records.map(r => r.id);
         this.MSA = { seqdata, colonNormalized };
     }
     getMSA() {

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;AAElC,MAAM,CAAC,OAAO,OAAO,QAAS,SAAQ,OAAO;IACnC,GAAG,CAGV;IAED,yEAAyE;IACzE,0EAA0E;IAClE,YAAY,GAAa,EAAE,CAAA;IAEnC,YAAY,IAAY;QACtB,KAAK,EAAE,CAAA;QACP,MAAM,OAAO,GAA2B,EAAE,CAAA;QAC1C,MAAM,eAAe,GAA2B,EAAE,CAAA;QAClD,KAAK,MAAM,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC;YACpC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;gBACtB,SAAQ;YACV,CAAC;YACD,MAAM,UAAU,GAAG,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;YACtC,IAAI,UAAU,KAAK,CAAC,CAAC,EAAE,CAAC;gBACtB,SAAQ;YACV,CAAC;YACD,MAAM,OAAO,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,UAAU,CAAC,CAAC,OAAO,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;YAC7D,MAAM,QAAQ,GAAG,OAAO,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;YACrC,MAAM,EAAE,GAAG,QAAQ,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAA;YACjE,IAAI,EAAE,EAAE,CAAC;gBACP,OAAO,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,KAAK,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,UAAU,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;gBAC/D,IAAI,CAAC,YAAY,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;gBAC1B,IAAI,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;oBACrB,eAAe,CAAC,EAAE,CAAC,UAAU,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,GAAG,EAAE,CAAA;gBAC/C,CAAC;YACH,CAAC;QACH,CAAC;QACD,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;IAED,QAAQ;QACN,MAAM,IAAI,GAAG,IAAI,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QACjC,OAAO,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,CAAA;IAC1D,CAAC;CACF"}
+{"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,EAAE,CAAA;QAC1C,MAAM,eAAe,GAA2B,EAAE,CAAA;QAElD,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;IAED,QAAQ;QACN,MAAM,IAAI,GAAG,IAAI,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QACjC,OAAO,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,CAAA;IAC1D,CAAC;CACF"}

package/dist/msa/StockholmMSA.js

@@ -22,7 +22,7 @@ export default class StockholmMSA extends BaseMSA {
         return this.MSA.seqdata[name] ?? '';
     }
     getWidth() {
-        const name = Object.keys(this.MSA.seqdata)[0];
+        const name = this.MSA.seqname[0];
         return name === undefined ? 0 : this.getRow(name).length;
     }
     get alignmentNames() {
@@ -45,7 +45,9 @@ export default class StockholmMSA extends BaseMSA {
         };
     }
     getNames() {
-        return Object.keys(this.MSA.seqdata);
+        // 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]+)/;

package/dist/msa/StockholmMSA.js.map

@@ -1 +1 @@
-{"version":3,"file":"StockholmMSA.js","sourceRoot":"","sources":["../../src/msa/StockholmMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,eAAe,EAAE,MAAM,YAAY,CAAA;AAC5C,OAAO,OAAO,MAAM,cAAc,CAAA;AAClC,OAAO,WAAW,MAAM,kBAAkB,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,sBAAsB,CAAA;AAK/C,MAAM,CAAC,OAAO,OAAO,YAAa,SAAQ,OAAO;IACvC,IAAI,CAAiB;IACrB,GAAG,CAAe;IAE1B,YAAY,IAAY,EAAE,gBAAwB;QAChD,KAAK,EAAE,CAAA;QACP,MAAM,GAAG,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;QAC1B,IAAI,CAAC,IAAI,GAAG,GAAG,CAAA;QACf,MAAM,GAAG,GAAG,GAAG,CAAC,gBAAgB,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,CAAA;QAC3C,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,MAAM,IAAI,KAAK,CAAC,uCAAuC,CAAC,CAAA;QAC1D,CAAC;QACD,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;IAChB,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;IACrC,CAAC;IAED,QAAQ;QACN,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAA;QAC7C,OAAO,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,CAAA;IAC1D,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,aAAa,GAAG,GAAG,CAAC,EAAE,CAAC,CAAA;IAC9E,CAAC;IAED,SAAS;QACP,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,CAAA;QACtC,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,CAAA;QACtC,OAAO;YACL,OAAO,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE;YACpB,UAAU,EAAE,MAAM,CAAC,WAAW,CAC5B,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CACrD;YACD,MAAM,EAAE,MAAM,CAAC,WAAW,CACxB,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAC7D;SACF,CAAA;IACH,CAAC;IAED,UAAU,CAAC,OAAe;QACxB,OAAO;YACL,IAAI,EAAE,OAAO;YACb,SAAS,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC;YACzC,MAAM,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC;SAC9C,CAAA;IACH,CAAC;IAED,QAAQ;QACN,OAAO,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IACtC,CAAC;IAED,aAAa;QACX,MAAM,QAAQ,GAAG,sCAAsC,CAAA;QACvD,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,CAAA;QACtC,MAAM,MAAM,GAGR,EAAE,CAAA;QACN,KAAK,MAAM,CAAC,EAAE,EAAE,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,EAAE,CAAC;YACrD,KAAK,MAAM,EAAE,IAAI,MAAM,EAAE,CAAC;gBACxB,MAAM,KAAK,GAAG,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;gBAC/B,IAAI,KAAK,EAAE,CAAC;oBACV,CAAC;oBAAA,CAAC,MAAM,CAAC,EAAE,CAAC,KAAK,EAAE,CAAC,CAAC,IAAI,CAAC;wBACxB,GAAG,EAAE,KAAK,CAAC,CAAC,CAAE,CAAC,WAAW,EAAE;wBAC5B,KAAK,EAAE,KAAK,CAAC,CAAC,CAAE;wBAChB,QAAQ,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE;wBACpB,MAAM,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE;qBACnB,CAAC,CAAA;gBACJ,CAAC;YACH,CAAC;QACH,CAAC;QACD,OAAO,MAAM,CAAA;IACf,CAAC;IAED,OAAO;QACL,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAA;QAChC,OAAO,IAAI,CAAC,CAAC,CAAC,eAAe,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,EAAE,CAAA;IACpE,CAAC;IAED,IAAI,YAAY;QACd,OAAO,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,QAAQ,CAAA;IAC7B,CAAC;IAED,IAAI,2BAA2B;QAC7B,OAAO,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,OAAO,CAAA;IAC5B,CAAC;IAED,IAAI,MAAM;QAMR,OAAO;YACL;gBACE,EAAE,EAAE,cAAc;gBAClB,IAAI,EAAE,oBAAoB;gBAC1B,IAAI,EAAE,IAAI,CAAC,YAAY;gBACvB,iBAAiB,EAAE,EAAE;aACtB;YACD;gBACE,EAAE,EAAE,iBAAiB;gBACrB,IAAI,EAAE,qBAAqB;gBAC3B,IAAI,EAAE,IAAI,CAAC,2BAA2B;gBACtC,oEAAoE;gBACpE,sEAAsE;gBACtE,sEAAsE;gBACtE,gEAAgE;gBAChE,iBAAiB,EAAE;oBACjB,GAAG,EAAE,WAAW;oBAChB,GAAG,EAAE,WAAW;oBAChB,GAAG,EAAE,WAAW;oBAChB,GAAG,EAAE,WAAW;oBAChB,GAAG,EAAE,MAAM;oBACX,GAAG,EAAE,MAAM;oBACX,GAAG,EAAE,MAAM;oBACX,GAAG,EAAE,MAAM;iBACZ;aACF;SACF,CAAA;IACH,CAAC;CACF;AAED,OAAO,EAAE,KAAK,IAAI,cAAc,EAAE,MAAM,sBAAsB,CAAA"}
+{"version":3,"file":"StockholmMSA.js","sourceRoot":"","sources":["../../src/msa/StockholmMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,eAAe,EAAE,MAAM,YAAY,CAAA;AAC5C,OAAO,OAAO,MAAM,cAAc,CAAA;AAClC,OAAO,WAAW,MAAM,kBAAkB,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,sBAAsB,CAAA;AAK/C,MAAM,CAAC,OAAO,OAAO,YAAa,SAAQ,OAAO;IACvC,IAAI,CAAiB;IACrB,GAAG,CAAe;IAE1B,YAAY,IAAY,EAAE,gBAAwB;QAChD,KAAK,EAAE,CAAA;QACP,MAAM,GAAG,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;QAC1B,IAAI,CAAC,IAAI,GAAG,GAAG,CAAA;QACf,MAAM,GAAG,GAAG,GAAG,CAAC,gBAAgB,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,CAAA;QAC3C,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,MAAM,IAAI,KAAK,CAAC,uCAAuC,CAAC,CAAA;QAC1D,CAAC;QACD,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;IAChB,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;IACrC,CAAC;IAED,QAAQ;QACN,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,CAAA;QAChC,OAAO,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,CAAA;IAC1D,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,aAAa,GAAG,GAAG,CAAC,EAAE,CAAC,CAAA;IAC9E,CAAC;IAED,SAAS;QACP,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,CAAA;QACtC,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,CAAA;QACtC,OAAO;YACL,OAAO,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE;YACpB,UAAU,EAAE,MAAM,CAAC,WAAW,CAC5B,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CACrD;YACD,MAAM,EAAE,MAAM,CAAC,WAAW,CACxB,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAC7D;SACF,CAAA;IACH,CAAC;IAED,UAAU,CAAC,OAAe;QACxB,OAAO;YACL,IAAI,EAAE,OAAO;YACb,SAAS,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC;YACzC,MAAM,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC;SAC9C,CAAA;IACH,CAAC;IAED,QAAQ;QACN,0EAA0E;QAC1E,oEAAoE;QACpE,OAAO,IAAI,CAAC,GAAG,CAAC,OAAO,CAAA;IACzB,CAAC;IAED,aAAa;QACX,MAAM,QAAQ,GAAG,sCAAsC,CAAA;QACvD,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,CAAA;QACtC,MAAM,MAAM,GAGR,EAAE,CAAA;QACN,KAAK,MAAM,CAAC,EAAE,EAAE,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,EAAE,CAAC;YACrD,KAAK,MAAM,EAAE,IAAI,MAAM,EAAE,CAAC;gBACxB,MAAM,KAAK,GAAG,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;gBAC/B,IAAI,KAAK,EAAE,CAAC;oBACV,CAAC;oBAAA,CAAC,MAAM,CAAC,EAAE,CAAC,KAAK,EAAE,CAAC,CAAC,IAAI,CAAC;wBACxB,GAAG,EAAE,KAAK,CAAC,CAAC,CAAE,CAAC,WAAW,EAAE;wBAC5B,KAAK,EAAE,KAAK,CAAC,CAAC,CAAE;wBAChB,QAAQ,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE;wBACpB,MAAM,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE;qBACnB,CAAC,CAAA;gBACJ,CAAC;YACH,CAAC;QACH,CAAC;QACD,OAAO,MAAM,CAAA;IACf,CAAC;IAED,OAAO;QACL,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAA;QAChC,OAAO,IAAI,CAAC,CAAC,CAAC,eAAe,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,EAAE,CAAA;IACpE,CAAC;IAED,IAAI,YAAY;QACd,OAAO,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,QAAQ,CAAA;IAC7B,CAAC;IAED,IAAI,2BAA2B;QAC7B,OAAO,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,OAAO,CAAA;IAC5B,CAAC;IAED,IAAI,MAAM;QAMR,OAAO;YACL;gBACE,EAAE,EAAE,cAAc;gBAClB,IAAI,EAAE,oBAAoB;gBAC1B,IAAI,EAAE,IAAI,CAAC,YAAY;gBACvB,iBAAiB,EAAE,EAAE;aACtB;YACD;gBACE,EAAE,EAAE,iBAAiB;gBACrB,IAAI,EAAE,qBAAqB;gBAC3B,IAAI,EAAE,IAAI,CAAC,2BAA2B;gBACtC,oEAAoE;gBACpE,sEAAsE;gBACtE,sEAAsE;gBACtE,gEAAgE;gBAChE,iBAAiB,EAAE;oBACjB,GAAG,EAAE,WAAW;oBAChB,GAAG,EAAE,WAAW;oBAChB,GAAG,EAAE,WAAW;oBAChB,GAAG,EAAE,WAAW;oBAChB,GAAG,EAAE,MAAM;oBACX,GAAG,EAAE,MAAM;oBACX,GAAG,EAAE,MAAM;oBACX,GAAG,EAAE,MAAM;iBACZ;aACF;SACF,CAAA;IACH,CAAC;CACF;AAED,OAAO,EAAE,KAAK,IAAI,cAAc,EAAE,MAAM,sBAAsB,CAAA"}

package/dist/msa/fastaRecords.d.ts

@@ -0,0 +1,11 @@
+export interface FastaRecord {
+    id: string;
+    seq: string;
+}
+/**
+ * Split FASTA-style text (shared by the FASTA and A3M parsers) into records.
+ * The id is the defline up to the first space. A repeated id keeps the first
+ * record: ids index the row data, so emitting the id twice would render a
+ * phantom duplicate row showing the last record's residues.
+ */
+export declare function splitFastaRecords(text: string): FastaRecord[];