p2s_mapper 1.0.0

package/dist/extractStructureSequences.js

@@ -0,0 +1,217 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.fillAuthSeqIds = fillAuthSeqIds;
+exports.residueNumber = residueNumber;
+exports.residueRangeToPositions = residueRangeToPositions;
+exports.oneLetterSequence = oneLetterSequence;
+exports.extractEntities = extractEntities;
+exports.entityLabel = entityLabel;
+exports.extractStructureSequences = extractStructureSequences;
+exports.toLabelSeqIds = toLabelSeqIds;
+exports.rangeToLabelSeqIds = rangeToLabelSeqIds;
+exports.makeLabelSeqIdIndex = makeLabelSeqIdIndex;
+/** Observed residues' label_seq_id -> auth_seq_id, per entity. The first chain
+ * carrying an entity wins, so a homodimer's copies agree. */
+function authSeqIdsByEntity(model) {
+    const hierarchy = model.obj?.data.atomicHierarchy;
+    const byEntity = new Map();
+    const { residues, residueAtomSegments, chainAtomSegments, chains } = hierarchy ?? {};
+    if (!residues || !residueAtomSegments || !chainAtomSegments || !chains) {
+        return undefined;
+    }
+    for (let residue = 0; residue < residueAtomSegments.count; residue++) {
+        const atom = residueAtomSegments.offsets[residue];
+        const entityId = chains.label_entity_id.value(chainAtomSegments.index[atom]);
+        let ids = byEntity.get(entityId);
+        if (!ids) {
+            ids = new Map();
+            byEntity.set(entityId, ids);
+        }
+        const labelSeqId = residues.label_seq_id.value(residue);
+        if (!ids.has(labelSeqId)) {
+            ids.set(labelSeqId, residues.auth_seq_id.value(residue));
+        }
+    }
+    return byEntity;
+}
+/**
+ * Author numbering for every SEQRES position, observed or not. A residue with
+ * no atoms has no auth_seq_id of its own, so it takes the offset of the nearest
+ * observed residue before it (after it, at an unobserved N-terminus): a
+ * disordered loop keeps counting the way the paper does. With nothing observed
+ * the label numbering stands.
+ */
+function fillAuthSeqIds(seqIds, observed) {
+    const out = [];
+    let offset;
+    const firstObserved = seqIds.find(id => observed?.has(id));
+    if (firstObserved !== undefined) {
+        offset = observed.get(firstObserved) - firstObserved;
+    }
+    for (const id of seqIds) {
+        const auth = observed?.get(id);
+        if (auth !== undefined) {
+            offset = auth - id;
+        }
+        out.push(id + (offset ?? 0));
+    }
+    return out;
+}
+/** The number a residue is called by: author numbering when the file carries
+ * it, else molstar's label_seq_id, which is the author numbering already for a
+ * SEQRES-less PDB and 1..N for everything else. */
+function residueNumber(entity, pos) {
+    return entity?.authSeqIds?.[pos] ?? entity?.seqIds[pos] ?? pos + 1;
+}
+/**
+ * The 0-based half-open position range covering an inclusive range of author
+ * residue numbers, the form a paper or a spec names a site by ("R248",
+ * "residues 102-292"). Undefined when no residue of the entity carries a number
+ * in the range, so a typo selects nothing rather than something else.
+ */
+function residueRangeToPositions(entity, range) {
+    if (!entity) {
+        return undefined;
+    }
+    let first;
+    let last;
+    for (let pos = 0; pos < entity.seq.length; pos++) {
+        const n = residueNumber(entity, pos);
+        if (n >= range.start && n <= range.end) {
+            first ??= pos;
+            last = pos;
+        }
+    }
+    return first === undefined || last === undefined
+        ? undefined
+        : { start: first, end: last + 1 };
+}
+function chainsByEntity(model) {
+    const chains = model.obj?.data.atomicHierarchy?.chains;
+    const byEntity = new Map();
+    if (chains) {
+        for (let i = 0; i < chains.label_entity_id.rowCount; i++) {
+            const entityId = chains.label_entity_id.value(i);
+            const chain = chains.auth_asym_id.value(i);
+            const list = byEntity.get(entityId) ?? [];
+            if (!list.includes(chain)) {
+                list.push(chain);
+            }
+            byEntity.set(entityId, list);
+        }
+    }
+    return byEntity;
+}
+// mmCIF entity_poly.type values for nucleic-acid polymers. Molstar derives the
+// subtype from residue components when a file (PDB format) carries no
+// entity_poly, so the flag is available for either format.
+const NUCLEIC_ACID_SUBTYPES = new Set([
+    'polydeoxyribonucleotide',
+    'polyribonucleotide',
+    'polydeoxyribonucleotide/polyribonucleotide hybrid',
+    'peptide nucleic acid',
+]);
+function isNucleicAcid(model, entityId) {
+    const entities = model.obj?.data.entities;
+    if (!entities) {
+        return false;
+    }
+    const index = entities.getEntityIndex(entityId);
+    return index >= 0 && NUCLEIC_ACID_SUBTYPES.has(entities.subtype.value(index));
+}
+function canonicalSequencesByEntity(model) {
+    const source = model.obj?.data.sourceData?.data;
+    const entityPoly = source?.db?.entity_poly;
+    const byEntity = new Map();
+    if (entityPoly) {
+        for (let i = 0; i < entityPoly.entity_id.rowCount; i++) {
+            byEntity.set(entityPoly.entity_id.value(i), entityPoly.pdbx_seq_one_letter_code_can.value(i).replaceAll(/\s/g, ''));
+        }
+    }
+    return byEntity;
+}
+/**
+ * One letter per position, so `seq[pos]` and `seqIds[pos]` name the same
+ * residue. Molstar's `label` column is not that: it spells a residue with no
+ * one-letter code by its component id (MSE, TPO, ACE) and an alternate site as
+ * "(S|P)", which shifted every later position. `code` writes X for those; the
+ * mmCIF canonical sequence then supplies the parent residue (MSE is M) when it
+ * has one letter per position, which a chromophore spelled "TYG" does not.
+ */
+function oneLetterSequence(codes, canonical) {
+    const letters = Array.from(codes);
+    return letters
+        .map((c, i) => c === 'X' && canonical?.length === letters.length ? canonical[i] : c)
+        .join('');
+}
+function extractEntities(model) {
+    const chains = chainsByEntity(model);
+    const authIds = authSeqIdsByEntity(model);
+    const canonical = canonicalSequencesByEntity(model);
+    return model.obj?.data.sequence.sequences.map(s => {
+        const seqIds = Array.from(s.sequence.seqId.toArray());
+        return {
+            entityId: s.entityId,
+            seq: oneLetterSequence(s.sequence.code.toArray(), canonical.get(s.entityId)),
+            seqIds,
+            chains: chains.get(s.entityId) ?? [],
+            ...(isNucleicAcid(model, s.entityId) ? { nucleicAcid: true } : {}),
+            ...(authIds
+                ? { authSeqIds: fillAuthSeqIds(seqIds, authIds.get(s.entityId)) }
+                : {}),
+        };
+    });
+}
+/** A user-facing name for an entity: its chains when known, else its id. */
+function entityLabel(entity) {
+    const chains = entity.chains.length > 0
+        ? `Chain ${entity.chains.join('/')}`
+        : `Entity ${entity.entityId}`;
+    return `${chains} (${entity.seq.length} ${entity.nucleicAcid ? 'nt' : 'aa'})`;
+}
+/** The protein chains' sequences, for the launch dialog's isoform matching,
+ * which has no use for a DNA strand that happens to align. */
+function extractStructureSequences(model) {
+    return extractEntities(model)
+        ?.filter(e => !e.nucleicAcid)
+        .map(e => e.seq);
+}
+/**
+ * The molstar `label_seq_id`s for a set of 0-based structure positions. Unknown
+ * positions are dropped rather than guessed, so an out-of-range position paints
+ * nothing instead of painting something wrong.
+ */
+function toLabelSeqIds(entity, positions) {
+    if (!entity) {
+        return [];
+    }
+    const out = [];
+    for (const pos of positions) {
+        const id = entity.seqIds[pos];
+        if (id !== undefined) {
+            out.push(id);
+        }
+    }
+    return out;
+}
+/** As toLabelSeqIds, for a half-open [start, end) structure-position range. */
+function rangeToLabelSeqIds(entity, range) {
+    if (!entity || !range) {
+        return [];
+    }
+    const start = Math.max(0, range.start);
+    const end = Math.min(entity.seqIds.length, range.end);
+    return end > start ? entity.seqIds.slice(start, end) : [];
+}
+/** Reverse of `seqIds`: molstar's label_seq_id -> 0-based structure position. */
+function makeLabelSeqIdIndex(entity) {
+    const index = new Map();
+    entity?.seqIds.forEach((id, pos) => {
+        // first wins: duplicate ids (micro-heterogeneity) collapse to one residue
+        if (!index.has(id)) {
+            index.set(id, pos);
+        }
+    });
+    return index;
+}
+//# sourceMappingURL=extractStructureSequences.js.map

package/dist/extractStructureSequences.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"extractStructureSequences.js","sourceRoot":"","sources":["../src/extractStructureSequences.ts"],"names":[],"mappings":";;AAuHA,wCAkBC;AAKD,sCAEC;AAQD,0DAmBC;AAwED,8CAUC;AAED,0CAoBC;AAGD,kCAMC;AAID,8DAMC;AAOD,sCAeC;AAGD,gDAUC;AAGD,kDASC;AAjQD;6DAC6D;AAC7D,SAAS,kBAAkB,CAAC,KAAqB;IAC/C,MAAM,SAAS,GAAG,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,eAAe,CAAA;IACjD,MAAM,QAAQ,GAAG,IAAI,GAAG,EAA+B,CAAA;IACvD,MAAM,EAAE,QAAQ,EAAE,mBAAmB,EAAE,iBAAiB,EAAE,MAAM,EAAE,GAChE,SAAS,IAAI,EAAE,CAAA;IACjB,IAAI,CAAC,QAAQ,IAAI,CAAC,mBAAmB,IAAI,CAAC,iBAAiB,IAAI,CAAC,MAAM,EAAE,CAAC;QACvE,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,KAAK,IAAI,OAAO,GAAG,CAAC,EAAE,OAAO,GAAG,mBAAmB,CAAC,KAAK,EAAE,OAAO,EAAE,EAAE,CAAC;QACrE,MAAM,IAAI,GAAG,mBAAmB,CAAC,OAAO,CAAC,OAAO,CAAE,CAAA;QAClD,MAAM,QAAQ,GAAG,MAAM,CAAC,eAAe,CAAC,KAAK,CAC3C,iBAAiB,CAAC,KAAK,CAAC,IAAI,CAAE,CAC/B,CAAA;QACD,IAAI,GAAG,GAAG,QAAQ,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAA;QAChC,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,GAAG,GAAG,IAAI,GAAG,EAAE,CAAA;YACf,QAAQ,CAAC,GAAG,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAA;QAC7B,CAAC;QACD,MAAM,UAAU,GAAG,QAAQ,CAAC,YAAY,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;QACvD,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,UAAU,CAAC,EAAE,CAAC;YACzB,GAAG,CAAC,GAAG,CAAC,UAAU,EAAE,QAAQ,CAAC,WAAW,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAA;QAC1D,CAAC;IACH,CAAC;IACD,OAAO,QAAQ,CAAA;AACjB,CAAC;AAED;;;;;;GAMG;AACH,SAAgB,cAAc,CAC5B,MAAgB,EAChB,QAAyC;IAEzC,MAAM,GAAG,GAAa,EAAE,CAAA;IACxB,IAAI,MAA0B,CAAA;IAC9B,MAAM,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,QAAQ,EAAE,GAAG,CAAC,EAAE,CAAC,CAAC,CAAA;IAC1D,IAAI,aAAa,KAAK,SAAS,EAAE,CAAC;QAChC,MAAM,GAAG,QAAS,CAAC,GAAG,CAAC,aAAa,CAAE,GAAG,aAAa,CAAA;IACxD,CAAC;IACD,KAAK,MAAM,EAAE,IAAI,MAAM,EAAE,CAAC;QACxB,MAAM,IAAI,GAAG,QAAQ,EAAE,GAAG,CAAC,EAAE,CAAC,CAAA;QAC9B,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;YACvB,MAAM,GAAG,IAAI,GAAG,EAAE,CAAA;QACpB,CAAC;QACD,GAAG,CAAC,IAAI,CAAC,EAAE,GAAG,CAAC,MAAM,IAAI,CAAC,CAAC,CAAC,CAAA;IAC9B,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AAED;;mDAEmD;AACnD,SAAgB,aAAa,CAAC,MAA0B,EAAE,GAAW;IACnE,OAAO,MAAM,EAAE,UAAU,EAAE,CAAC,GAAG,CAAC,IAAI,MAAM,EAAE,MAAM,CAAC,GAAG,CAAC,IAAI,GAAG,GAAG,CAAC,CAAA;AACpE,CAAC;AAED;;;;;GAKG;AACH,SAAgB,uBAAuB,CACrC,MAA0B,EAC1B,KAAqC;IAErC,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,IAAI,KAAyB,CAAA;IAC7B,IAAI,IAAwB,CAAA;IAC5B,KAAK,IAAI,GAAG,GAAG,CAAC,EAAE,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC,MAAM,EAAE,GAAG,EAAE,EAAE,CAAC;QACjD,MAAM,CAAC,GAAG,aAAa,CAAC,MAAM,EAAE,GAAG,CAAC,CAAA;QACpC,IAAI,CAAC,IAAI,KAAK,CAAC,KAAK,IAAI,CAAC,IAAI,KAAK,CAAC,GAAG,EAAE,CAAC;YACvC,KAAK,KAAK,GAAG,CAAA;YACb,IAAI,GAAG,GAAG,CAAA;QACZ,CAAC;IACH,CAAC;IACD,OAAO,KAAK,KAAK,SAAS,IAAI,IAAI,KAAK,SAAS;QAC9C,CAAC,CAAC,SAAS;QACX,CAAC,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE,GAAG,EAAE,IAAI,GAAG,CAAC,EAAE,CAAA;AACrC,CAAC;AAED,SAAS,cAAc,CAAC,KAAqB;IAC3C,MAAM,MAAM,GAAG,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,eAAe,EAAE,MAAM,CAAA;IACtD,MAAM,QAAQ,GAAG,IAAI,GAAG,EAAoB,CAAA;IAC5C,IAAI,MAAM,EAAE,CAAC;QACX,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,eAAe,CAAC,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;YACzD,MAAM,QAAQ,GAAG,MAAM,CAAC,eAAe,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YAChD,MAAM,KAAK,GAAG,MAAM,CAAC,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YAC1C,MAAM,IAAI,GAAG,QAAQ,CAAC,GAAG,CAAC,QAAQ,CAAC,IAAI,EAAE,CAAA;YACzC,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAC,KAAK,CAAC,EAAE,CAAC;gBAC1B,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YAClB,CAAC;YACD,QAAQ,CAAC,GAAG,CAAC,QAAQ,EAAE,IAAI,CAAC,CAAA;QAC9B,CAAC;IACH,CAAC;IACD,OAAO,QAAQ,CAAA;AACjB,CAAC;AAED,+EAA+E;AAC/E,sEAAsE;AACtE,2DAA2D;AAC3D,MAAM,qBAAqB,GAAG,IAAI,GAAG,CAAC;IACpC,yBAAyB;IACzB,oBAAoB;IACpB,mDAAmD;IACnD,sBAAsB;CACvB,CAAC,CAAA;AAEF,SAAS,aAAa,CAAC,KAAqB,EAAE,QAAgB;IAC5D,MAAM,QAAQ,GAAG,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,QAAQ,CAAA;IACzC,IAAI,CAAC,QAAQ,EAAE,CAAC;QACd,OAAO,KAAK,CAAA;IACd,CAAC;IACD,MAAM,KAAK,GAAG,QAAQ,CAAC,cAAc,CAAC,QAAQ,CAAC,CAAA;IAC/C,OAAO,KAAK,IAAI,CAAC,IAAI,qBAAqB,CAAC,GAAG,CAAC,QAAQ,CAAC,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAA;AAC/E,CAAC;AAaD,SAAS,0BAA0B,CAAC,KAAqB;IACvD,MAAM,MAAM,GAAG,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,UAAU,EAAE,IAAmC,CAAA;IAC9E,MAAM,UAAU,GAAG,MAAM,EAAE,EAAE,EAAE,WAAW,CAAA;IAC1C,MAAM,QAAQ,GAAG,IAAI,GAAG,EAAkB,CAAA;IAC1C,IAAI,UAAU,EAAE,CAAC;QACf,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,SAAS,CAAC,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;YACvD,QAAQ,CAAC,GAAG,CACV,UAAU,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC,EAC7B,UAAU,CAAC,4BAA4B,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,KAAK,EAAE,EAAE,CAAC,CACvE,CAAA;QACH,CAAC;IACH,CAAC;IACD,OAAO,QAAQ,CAAA;AACjB,CAAC;AAED;;;;;;;GAOG;AACH,SAAgB,iBAAiB,CAC/B,KAAwB,EACxB,SAA6B;IAE7B,MAAM,OAAO,GAAG,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;IACjC,OAAO,OAAO;SACX,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CACZ,CAAC,KAAK,GAAG,IAAI,SAAS,EAAE,MAAM,KAAK,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,CAAC,CAAC,CAAC,CAAC,CACtE;SACA,IAAI,CAAC,EAAE,CAAC,CAAA;AACb,CAAC;AAED,SAAgB,eAAe,CAAC,KAAqB;IACnD,MAAM,MAAM,GAAG,cAAc,CAAC,KAAK,CAAC,CAAA;IACpC,MAAM,OAAO,GAAG,kBAAkB,CAAC,KAAK,CAAC,CAAA;IACzC,MAAM,SAAS,GAAG,0BAA0B,CAAC,KAAK,CAAC,CAAA;IACnD,OAAO,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,QAAQ,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;QAChD,MAAM,MAAM,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,QAAQ,CAAC,KAAK,CAAC,OAAO,EAAE,CAAC,CAAA;QACrD,OAAO;YACL,QAAQ,EAAE,CAAC,CAAC,QAAQ;YACpB,GAAG,EAAE,iBAAiB,CACpB,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,OAAO,EAAE,EACzB,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,CAAC,CAC1B;YACD,MAAM;YACN,MAAM,EAAE,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,CAAC,IAAI,EAAE;YACpC,GAAG,CAAC,aAAa,CAAC,KAAK,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YAClE,GAAG,CAAC,OAAO;gBACT,CAAC,CAAC,EAAE,UAAU,EAAE,cAAc,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,EAAE;gBACjE,CAAC,CAAC,EAAE,CAAC;SACR,CAAA;IACH,CAAC,CAAC,CAAA;AACJ,CAAC;AAED,4EAA4E;AAC5E,SAAgB,WAAW,CAAC,MAAc;IACxC,MAAM,MAAM,GACV,MAAM,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC;QACtB,CAAC,CAAC,SAAS,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE;QACpC,CAAC,CAAC,UAAU,MAAM,CAAC,QAAQ,EAAE,CAAA;IACjC,OAAO,GAAG,MAAM,KAAK,MAAM,CAAC,GAAG,CAAC,MAAM,IAAI,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,GAAG,CAAA;AAC/E,CAAC;AAED;8DAC8D;AAC9D,SAAgB,yBAAyB,CACvC,KAAqB;IAErB,OAAO,eAAe,CAAC,KAAK,CAAC;QAC3B,EAAE,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC;SAC5B,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;AACpB,CAAC;AAED;;;;GAIG;AACH,SAAgB,aAAa,CAC3B,MAA0B,EAC1B,SAA2B;IAE3B,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,OAAO,EAAE,CAAA;IACX,CAAC;IACD,MAAM,GAAG,GAAa,EAAE,CAAA;IACxB,KAAK,MAAM,GAAG,IAAI,SAAS,EAAE,CAAC;QAC5B,MAAM,EAAE,GAAG,MAAM,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;QAC7B,IAAI,EAAE,KAAK,SAAS,EAAE,CAAC;YACrB,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;QACd,CAAC;IACH,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AAED,+EAA+E;AAC/E,SAAgB,kBAAkB,CAChC,MAA0B,EAC1B,KAAiD;IAEjD,IAAI,CAAC,MAAM,IAAI,CAAC,KAAK,EAAE,CAAC;QACtB,OAAO,EAAE,CAAA;IACX,CAAC;IACD,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,CAAC,KAAK,CAAC,CAAA;IACtC,MAAM,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,MAAM,EAAE,KAAK,CAAC,GAAG,CAAC,CAAA;IACrD,OAAO,GAAG,GAAG,KAAK,CAAC,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;AAC3D,CAAC;AAED,iFAAiF;AACjF,SAAgB,mBAAmB,CAAC,MAA0B;IAC5D,MAAM,KAAK,GAAG,IAAI,GAAG,EAAkB,CAAA;IACvC,MAAM,EAAE,MAAM,CAAC,OAAO,CAAC,CAAC,EAAE,EAAE,GAAG,EAAE,EAAE;QACjC,0EAA0E;QAC1E,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,CAAC;YACnB,KAAK,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,CAAC,CAAA;QACpB,CAAC;IACH,CAAC,CAAC,CAAA;IACF,OAAO,KAAK,CAAA;AACd,CAAC"}

package/dist/fetchUtils.d.ts

@@ -0,0 +1,34 @@
+/**
+ * The error a failed response deserves: status and host, plus at most the first
+ * line of the body. A whole body is an HTML error page or a megabyte of JSON,
+ * and pasting it into the dialog buries the one line that says what went wrong.
+ */
+export declare function httpError(response: Response, url: string): Promise<Error>;
+/**
+ * `fetch` rejects with a bare `TypeError: Failed to fetch` for a DNS failure,
+ * an offline browser and a refused cross-origin request alike, naming neither
+ * the host nor the cause. Anything else — an abort, most notably — passes
+ * through untouched.
+ */
+export declare function networkError(url: string, cause: unknown): unknown;
+/**
+ * Request options plus the `fetch` to make the request with. Every network
+ * function here takes them, so a caller can hand in a host's instrumented
+ * fetch, a test double, or nothing at all and get `globalThis.fetch`. Resolved
+ * per call rather than captured at import, so a page that installs its fetch
+ * late is still honored.
+ */
+export interface FetchOptions extends RequestInit {
+    fetch?: typeof globalThis.fetch;
+}
+export declare function rawfetch(url: string, args?: FetchOptions): Promise<Response>;
+export declare function myfetch(url: string, args?: FetchOptions): Promise<Response>;
+export declare function jsonfetch<T = unknown>(url: string, args?: FetchOptions): Promise<T>;
+/**
+ * An AbortSignal's reason as a real Error. `signal.reason` is `any` — usually a
+ * DOMException, but a caller can abort with anything at all — and throwing a
+ * non-Error loses the stack and breaks `instanceof Error` checks in the UI's
+ * error rendering. Normalize at every throw site.
+ */
+export declare function abortError(signal: AbortSignal): Error;
+export declare function timeout(time: number, signal?: AbortSignal): Promise<void>;

package/dist/fetchUtils.js

@@ -0,0 +1,91 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.httpError = httpError;
+exports.networkError = networkError;
+exports.rawfetch = rawfetch;
+exports.myfetch = myfetch;
+exports.jsonfetch = jsonfetch;
+exports.abortError = abortError;
+exports.timeout = timeout;
+function hostOf(url) {
+    try {
+        return new URL(url).host;
+    }
+    catch {
+        return url;
+    }
+}
+const MAX_DETAIL = 200;
+function firstLine(body) {
+    const line = body.split('\n', 1)[0]?.trim() ?? '';
+    return line.length > MAX_DETAIL ? `${line.slice(0, MAX_DETAIL)}…` : line;
+}
+/**
+ * The error a failed response deserves: status and host, plus at most the first
+ * line of the body. A whole body is an HTML error page or a megabyte of JSON,
+ * and pasting it into the dialog buries the one line that says what went wrong.
+ */
+async function httpError(response, url) {
+    const detail = firstLine(await response.text().catch(() => ''));
+    const status = `HTTP ${response.status}${response.statusText ? ` ${response.statusText}` : ''} from ${hostOf(url)}`;
+    return new Error(detail ? `${status}: ${detail}` : status);
+}
+/**
+ * `fetch` rejects with a bare `TypeError: Failed to fetch` for a DNS failure,
+ * an offline browser and a refused cross-origin request alike, naming neither
+ * the host nor the cause. Anything else — an abort, most notably — passes
+ * through untouched.
+ */
+function networkError(url, cause) {
+    return cause instanceof TypeError
+        ? new Error(`Could not reach ${hostOf(url)}. Check your network connection; the server may also be refusing cross-origin requests from this page.`, { cause })
+        : cause;
+}
+async function rawfetch(url, args) {
+    const { fetch: f = globalThis.fetch, ...init } = args ?? {};
+    try {
+        return await f(url, init);
+    }
+    catch (e) {
+        throw networkError(url, e);
+    }
+}
+async function myfetch(url, args) {
+    const response = await rawfetch(url, args);
+    if (!response.ok) {
+        throw await httpError(response, url);
+    }
+    return response;
+}
+async function jsonfetch(url, args) {
+    // The caller names the shape it expects; `Response.json` promises `any`, and
+    // narrowing it here rather than at the return keeps the body free of casts.
+    const response = await myfetch(url, args);
+    return response.json();
+}
+/**
+ * An AbortSignal's reason as a real Error. `signal.reason` is `any` — usually a
+ * DOMException, but a caller can abort with anything at all — and throwing a
+ * non-Error loses the stack and breaks `instanceof Error` checks in the UI's
+ * error rendering. Normalize at every throw site.
+ */
+function abortError(signal) {
+    return signal.reason instanceof Error
+        ? signal.reason
+        : new Error('Aborted', { cause: signal.reason });
+}
+function timeout(time, signal) {
+    return new Promise((resolve, reject) => {
+        if (signal?.aborted) {
+            reject(abortError(signal));
+        }
+        else {
+            const id = setTimeout(resolve, time);
+            signal?.addEventListener('abort', () => {
+                clearTimeout(id);
+                reject(abortError(signal));
+            }, { once: true });
+        }
+    });
+}
+//# sourceMappingURL=fetchUtils.js.map

package/dist/fetchUtils.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"fetchUtils.js","sourceRoot":"","sources":["../src/fetchUtils.ts"],"names":[],"mappings":";;AAoBA,8BAIC;AAQD,oCAOC;AAaD,4BAOC;AAED,0BAQC;AAED,8BAQC;AAQD,gCAIC;AAED,0BAgBC;AA7GD,SAAS,MAAM,CAAC,GAAW;IACzB,IAAI,CAAC;QACH,OAAO,IAAI,GAAG,CAAC,GAAG,CAAC,CAAC,IAAI,CAAA;IAC1B,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,GAAG,CAAA;IACZ,CAAC;AACH,CAAC;AAED,MAAM,UAAU,GAAG,GAAG,CAAA;AAEtB,SAAS,SAAS,CAAC,IAAY;IAC7B,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,CAAA;IACjD,OAAO,IAAI,CAAC,MAAM,GAAG,UAAU,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAA;AAC1E,CAAC;AAED;;;;GAIG;AACI,KAAK,UAAU,SAAS,CAAC,QAAkB,EAAE,GAAW;IAC7D,MAAM,MAAM,GAAG,SAAS,CAAC,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC,EAAE,CAAC,CAAC,CAAA;IAC/D,MAAM,MAAM,GAAG,QAAQ,QAAQ,CAAC,MAAM,GAAG,QAAQ,CAAC,UAAU,CAAC,CAAC,CAAC,IAAI,QAAQ,CAAC,UAAU,EAAE,CAAC,CAAC,CAAC,EAAE,SAAS,MAAM,CAAC,GAAG,CAAC,EAAE,CAAA;IACnH,OAAO,IAAI,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,GAAG,MAAM,KAAK,MAAM,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,CAAA;AAC5D,CAAC;AAED;;;;;GAKG;AACH,SAAgB,YAAY,CAAC,GAAW,EAAE,KAAc;IACtD,OAAO,KAAK,YAAY,SAAS;QAC/B,CAAC,CAAC,IAAI,KAAK,CACP,mBAAmB,MAAM,CAAC,GAAG,CAAC,wGAAwG,EACtI,EAAE,KAAK,EAAE,CACV;QACH,CAAC,CAAC,KAAK,CAAA;AACX,CAAC;AAaM,KAAK,UAAU,QAAQ,CAAC,GAAW,EAAE,IAAmB;IAC7D,MAAM,EAAE,KAAK,EAAE,CAAC,GAAG,UAAU,CAAC,KAAK,EAAE,GAAG,IAAI,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;IAC3D,IAAI,CAAC;QACH,OAAO,MAAM,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IAC3B,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,MAAM,YAAY,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;IAC5B,CAAC;AACH,CAAC;AAEM,KAAK,UAAU,OAAO,CAAC,GAAW,EAAE,IAAmB;IAC5D,MAAM,QAAQ,GAAG,MAAM,QAAQ,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IAE1C,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;QACjB,MAAM,MAAM,SAAS,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAA;IACtC,CAAC;IAED,OAAO,QAAQ,CAAA;AACjB,CAAC;AAEM,KAAK,UAAU,SAAS,CAC7B,GAAW,EACX,IAAmB;IAEnB,6EAA6E;IAC7E,4EAA4E;IAC5E,MAAM,QAAQ,GAA+B,MAAM,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IACrE,OAAO,QAAQ,CAAC,IAAI,EAAE,CAAA;AACxB,CAAC;AAED;;;;;GAKG;AACH,SAAgB,UAAU,CAAC,MAAmB;IAC5C,OAAO,MAAM,CAAC,MAAM,YAAY,KAAK;QACnC,CAAC,CAAC,MAAM,CAAC,MAAM;QACf,CAAC,CAAC,IAAI,KAAK,CAAC,SAAS,EAAE,EAAE,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,CAAC,CAAA;AACpD,CAAC;AAED,SAAgB,OAAO,CAAC,IAAY,EAAE,MAAoB;IACxD,OAAO,IAAI,OAAO,CAAO,CAAC,OAAO,EAAE,MAAM,EAAE,EAAE;QAC3C,IAAI,MAAM,EAAE,OAAO,EAAE,CAAC;YACpB,MAAM,CAAC,UAAU,CAAC,MAAM,CAAC,CAAC,CAAA;QAC5B,CAAC;aAAM,CAAC;YACN,MAAM,EAAE,GAAG,UAAU,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;YACpC,MAAM,EAAE,gBAAgB,CACtB,OAAO,EACP,GAAG,EAAE;gBACH,YAAY,CAAC,EAAE,CAAC,CAAA;gBAChB,MAAM,CAAC,UAAU,CAAC,MAAM,CAAC,CAAC,CAAA;YAC5B,CAAC,EACD,EAAE,IAAI,EAAE,IAAI,EAAE,CACf,CAAA;QACH,CAAC;IACH,CAAC,CAAC,CAAA;AACJ,CAAC"}

package/dist/index.d.ts

@@ -0,0 +1,23 @@
+export * from './types.ts';
+export * from './mappings.ts';
+export * from './pairwiseAlignment.ts';
+export * from './alignmentQuality.ts';
+export * from './coordinates.ts';
+export * from './invertMap.ts';
+export * from './stripStopCodon.ts';
+export * from './chooseMappedEntity.ts';
+export * from './extractStructureSequences.ts';
+export * from './extractPerResidueConfidence.ts';
+export * from './isoformRanking.ts';
+export * from './pdbUniProtMapping.ts';
+export * from './siftsNumbering.ts';
+export * from './alphaFoldModels.ts';
+export * from './pdbeBestStructures.ts';
+export * from './pdbeEntryMolecules.ts';
+export * from './structureSources.ts';
+export * from './uniProtSearch.ts';
+export * from './dbIds.ts';
+export * from './structureUrls.ts';
+export * from './structureFormat.ts';
+export * from './caCoordsToPdb.ts';
+export * from './fetchUtils.ts';

package/dist/index.js

@@ -0,0 +1,46 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __exportStar = (this && this.__exportStar) || function(m, exports) {
+    for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+// Alignment
+__exportStar(require("./types.js"), exports);
+__exportStar(require("./mappings.js"), exports);
+__exportStar(require("./pairwiseAlignment.js"), exports);
+__exportStar(require("./alignmentQuality.js"), exports);
+// Coordinates
+__exportStar(require("./coordinates.js"), exports);
+__exportStar(require("./invertMap.js"), exports);
+__exportStar(require("./stripStopCodon.js"), exports);
+// Chain choice
+__exportStar(require("./chooseMappedEntity.js"), exports);
+__exportStar(require("./extractStructureSequences.js"), exports);
+__exportStar(require("./extractPerResidueConfidence.js"), exports);
+__exportStar(require("./isoformRanking.js"), exports);
+// SIFTS
+__exportStar(require("./pdbUniProtMapping.js"), exports);
+__exportStar(require("./siftsNumbering.js"), exports);
+// Structure sources
+__exportStar(require("./alphaFoldModels.js"), exports);
+__exportStar(require("./pdbeBestStructures.js"), exports);
+__exportStar(require("./pdbeEntryMolecules.js"), exports);
+__exportStar(require("./structureSources.js"), exports);
+__exportStar(require("./uniProtSearch.js"), exports);
+__exportStar(require("./dbIds.js"), exports);
+// Urls and formats
+__exportStar(require("./structureUrls.js"), exports);
+__exportStar(require("./structureFormat.js"), exports);
+__exportStar(require("./caCoordsToPdb.js"), exports);
+__exportStar(require("./fetchUtils.js"), exports);
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;AAAA,YAAY;AACZ,6CAA0B;AAC1B,gDAA6B;AAC7B,yDAAsC;AACtC,wDAAqC;AAErC,cAAc;AACd,mDAAgC;AAChC,iDAA8B;AAC9B,sDAAmC;AAEnC,eAAe;AACf,0DAAuC;AACvC,iEAA8C;AAC9C,mEAAgD;AAChD,sDAAmC;AAEnC,QAAQ;AACR,yDAAsC;AACtC,sDAAmC;AAEnC,oBAAoB;AACpB,uDAAoC;AACpC,0DAAuC;AACvC,0DAAuC;AACvC,wDAAqC;AACrC,qDAAkC;AAClC,6CAA0B;AAE1B,mBAAmB;AACnB,qDAAkC;AAClC,uDAAoC;AACpC,qDAAkC;AAClC,kDAA+B"}

package/dist/invertMap.d.ts

@@ -0,0 +1,2 @@
+/** Swap keys and values of a numeric map, for reading a position map backwards. */
+export declare function invertMap(arg: Record<number, number>): Record<number, number>;

package/dist/invertMap.js

@@ -0,0 +1,8 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.invertMap = invertMap;
+/** Swap keys and values of a numeric map, for reading a position map backwards. */
+function invertMap(arg) {
+    return Object.fromEntries(Object.entries(arg).map(([a, b]) => [b, +a]));
+}
+//# sourceMappingURL=invertMap.js.map

package/dist/invertMap.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"invertMap.js","sourceRoot":"","sources":["../src/invertMap.ts"],"names":[],"mappings":";;AACA,8BAEC;AAHD,mFAAmF;AACnF,SAAgB,SAAS,CAAC,GAA2B;IACnD,OAAO,MAAM,CAAC,WAAW,CAAC,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AACzE,CAAC"}

package/dist/isoformRanking.d.ts

@@ -0,0 +1,47 @@
+/** A transcript isoform, named by whatever id the caller ranks by. `seq` is its
+ * translation, absent when none could be computed. */
+export interface Isoform {
+    id: string;
+    seq?: string;
+}
+export interface RankedIsoform {
+    id: string;
+    length: number;
+    /** identical residues against the structure, for an isoform that does not
+     * match it exactly; undefined with no structure to compare to */
+    identical?: number;
+    /** that alignment's score, which is what ranks non-matching isoforms */
+    score?: number;
+}
+export interface ClassifiedIsoforms {
+    matches: RankedIsoform[];
+    nonMatches: RankedIsoform[];
+    noData: string[];
+}
+/**
+ * The single rule for ranking transcript isoforms against a structure, shared
+ * by a picker UI and an auto-selection. An isoform whose translation is the
+ * structure's sequence wins outright. Among the rest, the best alignment score
+ * comes first, then the most identical residues, then length.
+ *
+ * The score has to lead: an isoform carrying an exon the structure lacks
+ * aligns every structure residue too, across a gap, so it ties on identical
+ * residues with the isoform the structure was made from (1MH1 against Rac1
+ * and Rac1b).
+ */
+export declare function classifyIsoforms({ isoforms, structureSequence, }: {
+    isoforms: readonly Isoform[];
+    structureSequence?: string;
+}): ClassifiedIsoforms;
+/** The id of the isoform to open, by the ranking above. */
+export declare function selectBestTranscript(args: {
+    isoforms: readonly Isoform[];
+    structureSequence?: string;
+}): string | undefined;
+/**
+ * Which of a structure's protein chains isoforms are compared against: one some
+ * isoform translates to exactly, else the chain `chooseMappedEntity` would map
+ * the longest isoform to, never simply the first (CDK2, on 1H26).
+ * `structureSequences` must hold protein chains only.
+ */
+export declare function pickStructureSequence(structureSequences: string[] | undefined, isoforms: readonly Isoform[] | undefined): string | undefined;

package/dist/isoformRanking.js

@@ -0,0 +1,91 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.classifyIsoforms = classifyIsoforms;
+exports.selectBestTranscript = selectBestTranscript;
+exports.pickStructureSequence = pickStructureSequence;
+const stripStopCodon_ts_1 = require("./stripStopCodon.js");
+const chooseMappedEntity_ts_1 = require("./chooseMappedEntity.js");
+// The picker re-ranks on every render and each non-exact isoform costs an
+// O(len²) alignment, so results are cached by sequence pair: a titin-sized
+// isoform against a long chain is a second of main-thread work each time.
+const alignmentCache = new Map();
+const ALIGNMENT_CACHE_LIMIT = 200;
+function alignToStructure(isoform, structure) {
+    const key = `${isoform}\n${structure}`;
+    let result = alignmentCache.get(key);
+    if (result === undefined) {
+        const scored = (0, chooseMappedEntity_ts_1.alignTranscriptToEntity)(isoform, structure, 'smith_waterman');
+        result = { identical: scored?.matches ?? 0, score: scored?.score ?? 0 };
+        if (alignmentCache.size >= ALIGNMENT_CACHE_LIMIT) {
+            alignmentCache.clear();
+        }
+        alignmentCache.set(key, result);
+    }
+    return result;
+}
+/**
+ * The single rule for ranking transcript isoforms against a structure, shared
+ * by a picker UI and an auto-selection. An isoform whose translation is the
+ * structure's sequence wins outright. Among the rest, the best alignment score
+ * comes first, then the most identical residues, then length.
+ *
+ * The score has to lead: an isoform carrying an exon the structure lacks
+ * aligns every structure residue too, across a gap, so it ties on identical
+ * residues with the isoform the structure was made from (1MH1 against Rac1
+ * and Rac1b).
+ */
+function classifyIsoforms({ isoforms, structureSequence, }) {
+    const matches = [];
+    const nonMatches = [];
+    const noData = [];
+    const structure = structureSequence
+        ? (0, stripStopCodon_ts_1.stripStopCodon)(structureSequence)
+        : undefined;
+    for (const { id, seq } of isoforms) {
+        if (seq === undefined) {
+            noData.push(id);
+        }
+        else if (structure && (0, stripStopCodon_ts_1.stripStopCodon)(seq) === structure) {
+            matches.push({ id, length: seq.length });
+        }
+        else {
+            nonMatches.push({
+                id,
+                length: seq.length,
+                ...(structure ? alignToStructure(seq, structure) : {}),
+            });
+        }
+    }
+    const byLengthDesc = (a, b) => b.length - a.length;
+    const byAlignmentThenLength = (a, b) => (b.score ?? 0) - (a.score ?? 0) ||
+        (b.identical ?? 0) - (a.identical ?? 0) ||
+        byLengthDesc(a, b);
+    return {
+        matches: matches.toSorted(byLengthDesc),
+        nonMatches: nonMatches.toSorted(byAlignmentThenLength),
+        noData,
+    };
+}
+/** The id of the isoform to open, by the ranking above. */
+function selectBestTranscript(args) {
+    const { matches, nonMatches } = classifyIsoforms(args);
+    return (matches[0] ?? nonMatches[0])?.id;
+}
+/**
+ * Which of a structure's protein chains isoforms are compared against: one some
+ * isoform translates to exactly, else the chain `chooseMappedEntity` would map
+ * the longest isoform to, never simply the first (CDK2, on 1H26).
+ * `structureSequences` must hold protein chains only.
+ */
+function pickStructureSequence(structureSequences, isoforms) {
+    const translations = (isoforms ?? []).flatMap(({ seq }) => seq === undefined ? [] : [(0, stripStopCodon_ts_1.stripStopCodon)(seq)]);
+    const translated = new Set(translations);
+    const exact = structureSequences?.find(s => translated.has((0, stripStopCodon_ts_1.stripStopCodon)(s)));
+    const longest = translations.reduce((a, b) => (a !== undefined && a.length >= b.length ? a : b), undefined);
+    const aligned = structureSequences && longest
+        ? (0, chooseMappedEntity_ts_1.chooseMappedEntity)(longest, structureSequences, 'smith_waterman')
+        : undefined;
+    return (exact ??
+        (aligned ? structureSequences?.[aligned.index] : structureSequences?.[0]));
+}
+//# sourceMappingURL=isoformRanking.js.map

package/dist/isoformRanking.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"isoformRanking.js","sourceRoot":"","sources":["../src/isoformRanking.ts"],"names":[],"mappings":";;AA+DA,4CAqCC;AAGD,oDAMC;AAQD,sDAqBC;AA1ID,2DAAoD;AACpD,mEAGgC;AA4BhC,0EAA0E;AAC1E,2EAA2E;AAC3E,0EAA0E;AAC1E,MAAM,cAAc,GAAG,IAAI,GAAG,EAAgD,CAAA;AAC9E,MAAM,qBAAqB,GAAG,GAAG,CAAA;AAEjC,SAAS,gBAAgB,CAAC,OAAe,EAAE,SAAiB;IAC1D,MAAM,GAAG,GAAG,GAAG,OAAO,KAAK,SAAS,EAAE,CAAA;IACtC,IAAI,MAAM,GAAG,cAAc,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;IACpC,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;QACzB,MAAM,MAAM,GAAG,IAAA,+CAAuB,EAAC,OAAO,EAAE,SAAS,EAAE,gBAAgB,CAAC,CAAA;QAC5E,MAAM,GAAG,EAAE,SAAS,EAAE,MAAM,EAAE,OAAO,IAAI,CAAC,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,IAAI,CAAC,EAAE,CAAA;QACvE,IAAI,cAAc,CAAC,IAAI,IAAI,qBAAqB,EAAE,CAAC;YACjD,cAAc,CAAC,KAAK,EAAE,CAAA;QACxB,CAAC;QACD,cAAc,CAAC,GAAG,CAAC,GAAG,EAAE,MAAM,CAAC,CAAA;IACjC,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAED;;;;;;;;;;GAUG;AACH,SAAgB,gBAAgB,CAAC,EAC/B,QAAQ,EACR,iBAAiB,GAIlB;IACC,MAAM,OAAO,GAAoB,EAAE,CAAA;IACnC,MAAM,UAAU,GAAoB,EAAE,CAAA;IACtC,MAAM,MAAM,GAAa,EAAE,CAAA;IAC3B,MAAM,SAAS,GAAG,iBAAiB;QACjC,CAAC,CAAC,IAAA,kCAAc,EAAC,iBAAiB,CAAC;QACnC,CAAC,CAAC,SAAS,CAAA;IACb,KAAK,MAAM,EAAE,EAAE,EAAE,GAAG,EAAE,IAAI,QAAQ,EAAE,CAAC;QACnC,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;YACtB,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;QACjB,CAAC;aAAM,IAAI,SAAS,IAAI,IAAA,kCAAc,EAAC,GAAG,CAAC,KAAK,SAAS,EAAE,CAAC;YAC1D,OAAO,CAAC,IAAI,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC,CAAA;QAC1C,CAAC;aAAM,CAAC;YACN,UAAU,CAAC,IAAI,CAAC;gBACd,EAAE;gBACF,MAAM,EAAE,GAAG,CAAC,MAAM;gBAClB,GAAG,CAAC,SAAS,CAAC,CAAC,CAAC,gBAAgB,CAAC,GAAG,EAAE,SAAS,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;aACvD,CAAC,CAAA;QACJ,CAAC;IACH,CAAC;IACD,MAAM,YAAY,GAAG,CAAC,CAAgB,EAAE,CAAgB,EAAE,EAAE,CAC1D,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,MAAM,CAAA;IACrB,MAAM,qBAAqB,GAAG,CAAC,CAAgB,EAAE,CAAgB,EAAE,EAAE,CACnE,CAAC,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC;QAC/B,CAAC,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC;QACvC,YAAY,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;IACpB,OAAO;QACL,OAAO,EAAE,OAAO,CAAC,QAAQ,CAAC,YAAY,CAAC;QACvC,UAAU,EAAE,UAAU,CAAC,QAAQ,CAAC,qBAAqB,CAAC;QACtD,MAAM;KACP,CAAA;AACH,CAAC;AAED,2DAA2D;AAC3D,SAAgB,oBAAoB,CAAC,IAGpC;IACC,MAAM,EAAE,OAAO,EAAE,UAAU,EAAE,GAAG,gBAAgB,CAAC,IAAI,CAAC,CAAA;IACtD,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC,IAAI,UAAU,CAAC,CAAC,CAAC,CAAC,EAAE,EAAE,CAAA;AAC1C,CAAC;AAED;;;;;GAKG;AACH,SAAgB,qBAAqB,CACnC,kBAAwC,EACxC,QAAwC;IAExC,MAAM,YAAY,GAAG,CAAC,QAAQ,IAAI,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE,EAAE,CACxD,GAAG,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAA,kCAAc,EAAC,GAAG,CAAC,CAAC,CAC/C,CAAA;IACD,MAAM,UAAU,GAAG,IAAI,GAAG,CAAC,YAAY,CAAC,CAAA;IACxC,MAAM,KAAK,GAAG,kBAAkB,EAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,UAAU,CAAC,GAAG,CAAC,IAAA,kCAAc,EAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC9E,MAAM,OAAO,GAAG,YAAY,CAAC,MAAM,CACjC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,SAAS,IAAI,CAAC,CAAC,MAAM,IAAI,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAC3D,SAAS,CACV,CAAA;IACD,MAAM,OAAO,GACX,kBAAkB,IAAI,OAAO;QAC3B,CAAC,CAAC,IAAA,0CAAkB,EAAC,OAAO,EAAE,kBAAkB,EAAE,gBAAgB,CAAC;QACnE,CAAC,CAAC,SAAS,CAAA;IACf,OAAO,CACL,KAAK;QACL,CAAC,OAAO,CAAC,CAAC,CAAC,kBAAkB,EAAE,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,kBAAkB,EAAE,CAAC,CAAC,CAAC,CAAC,CAC1E,CAAA;AACH,CAAC"}