p2s_mapper 2.0.0 → 2.1.0

package/README.md

@@ -1,19 +1,17 @@
 # p2s_mapper
 
-Find which residue of a 3D protein structure each amino acid of a transcript
-lands on, and back.
-
-Give it a transcript's translation and a structure, an AlphaFold model or a PDB
-entry. p2s_mapper picks the chain that is the gene's protein, aligns the two,
-and builds the lookups between transcript positions, structure positions and the
-residue ids a viewer such as Mol\* uses. It also finds structures for a gene,
-judges whether a match is real, and uses a PDB entry's UniProt alignment to
-place UniProt annotations and drop the residues of a fusion partner.
-
-Pair it with [g2p_mapper](https://github.com/GMOD/g2p_mapper), which maps genome
-positions to protein positions, to go from a genome coordinate to a residue in
-3D. The package has no React, JBrowse or Mol\* dependency; it came out of
-[jbrowse-plugin-protein3d](https://github.com/GMOD/jbrowse-plugin-protein3d).
+Lines up a protein sequence with its 3D structure, residue by residue.
+
+- **In:** a protein sequence, and an AlphaFold or PDB structure
+- **Out:** which 3D residue each amino acid is, and back
+- Picks the right chain and flags a poor match
+- Finds structures for a gene
+- Places UniProt annotations on a PDB entry
+- With [g2p_mapper](https://github.com/GMOD/g2p_mapper): genome position ↔ 3D
+  residue
+- No React, JBrowse or Mol\* dependency
+- Used by
+  [jbrowse-plugin-protein3d](https://github.com/GMOD/jbrowse-plugin-protein3d)
 
 ## Install
 
@@ -63,14 +61,14 @@ if (picked) {
 }
 ```
 
-Every position is 0-based. The two kinds are separate branded types, so passing
-a structure position where a transcript position belongs is a compile error.
+Every position is 0-based. Structure and transcript positions are separate
+types, so passing one where the other belongs is a compile error.
 
 ### From a genome position to a residue, and back
 
-g2p_mapper turns the transcript's CDS into genome ↔ protein tables; p2s_mapper
-carries a protein position on to the structure and to the `label_seq_id` Mol\*
-addresses residues by.
+g2p_mapper maps genome positions to protein positions. p2s_mapper maps a protein
+position to a structure position, and that to the `label_seq_id` Mol\* uses to
+select a residue.
 
 ```ts
 import { genomeToTranscriptSeqMapping } from 'g2p_mapper'
@@ -131,8 +129,9 @@ if (hovered !== undefined) {
 
 ### With a structure loaded in Mol\*
 
-`extractEntities` reads each chain's sequence, ids and numbering from a loaded
-Mol\* model, through a narrow structural type rather than a Mol\* import.
+`extractEntities` reads each chain's sequence, residue ids and numbering from a
+loaded Mol\* model. `StructureModel` lists the fields it reads, so the package
+needs no Mol\* import.
 
 ```ts
 import {
@@ -186,12 +185,13 @@ if (accession) {
 ```
 
 Every network function takes `{ fetch?, signal? }` last, defaulting to
-`globalThis.fetch`, so a host can pass its own fetch and abort a stale request.
+`globalThis.fetch`, so the caller can pass a custom fetch and an `AbortSignal`.
 
 ### Place UniProt annotations on a PDB entry
 
-A PDB construct is usually a fragment, numbered differently from UniProt. The
-entry's UniProt alignment, read from RCSB, says how the two line up.
+A PDB construct is usually a fragment, numbered differently from UniProt.
+`fetchUniProtStructureMappings` reads the entry's alignment to UniProt from
+RCSB.
 
 ```ts
 import {
@@ -209,7 +209,7 @@ const toStructure = makeUniProtPositionMap(mapping?.segments ?? [])
 toStructure(248) // 154: UniProt residue 248 is structure position 154
 ```
 
-## How it fits together
+## Pipeline
 
 ![From a gene on the genome to a residue in 3D, and back](docs/img/pipeline.svg)
 
@@ -218,22 +218,21 @@ toStructure(248) // 154: UniProt residue 248 is structure position 154
 - [api.md](docs/api.md): every export, with its signature, types and an example
 - [pipeline.md](docs/pipeline.md): the flow above, step by step, and why chain
   choice divides by the shorter sequence
-- [coordinates.md](docs/coordinates.md): the four numberings of a residue and
-  the one route between each
+- [coordinates.md](docs/coordinates.md): the four ways a residue is numbered,
+  and which function converts between them
 - [faq.md](docs/faq.md): can I trust the mapping? What the package checks, and
   what it leaves to you
 
-## Things to know first
-
-- Every coordinate is **0-based** and branded by space, so the compiler rejects
-  mixing them. UniProt positions and author residue numbers are 1-based. See
-  [coordinates.md](docs/coordinates.md).
-- A `PairwiseAlignment` has **row 0 = transcript, row 1 = structure**. Use the
-  accessors, not indexes.
-- The best-matching chain always wins, even a poor match. Check it with
-  `isLowSimilarity` before trusting the mapping.
-- Cross into Mol\* only through `Entity.seqIds`: `label_seq_id` is not always
-  position + 1.
+## Pitfalls
+
+- Positions are **0-based**, except UniProt positions and author residue
+  numbers, which are 1-based. See [coordinates.md](docs/coordinates.md).
+- A `PairwiseAlignment` has **row 0 = transcript, row 1 = structure**. Read the
+  rows with `transcriptAlignedSeq` and `structureAlignedSeq`.
+- `chooseMappedEntity` returns the best-matching chain even when the match is
+  poor. Check it with `isLowSimilarity` before trusting the mapping.
+- Get Mol\*'s `label_seq_id` from `toLabelSeqIds`, which reads `Entity.seqIds`.
+  Adding 1 to the position gives the wrong residue in a PDB file without SEQRES.
 
 ## License
 

package/dist/alignmentQuality.d.ts

@@ -1,20 +1,20 @@
 import type { PairwiseAlignment } from './mappings.ts';
 export interface AlignmentQuality {
-    /** columns carrying a residue on both rows, i.e. mapped positions */
+    /** columns with a residue in both rows, i.e. mapped positions */
     aligned: number;
     identical: number;
     transcriptLength: number;
     structureLength: number;
     /** identical over aligned; 0 when nothing aligned */
     identity: number;
-    /** identical over the shorter of the two sequences: the statistic that
-     * separates a real match from a chance local alignment, see below */
+    /** identical over the shorter of the two sequences, which separates a
+     * real match from a chance local alignment (see LOW_IDENTITY_OVER_SHORTER) */
     identityOverShorter: number;
     /** aligned over the structure's length */
     structureCoverage: number;
     /** first and last transcript residue the alignment covers, 1-based
-     * inclusive; 0 when nothing aligned. A structure is usually a fragment, and
-     * which part of the protein it holds is the reader's first question. */
+     * inclusive; 0 when nothing aligned. A structure is usually a fragment, so
+     * these show which part of the protein it contains. */
     transcriptStart: number;
     transcriptEnd: number;
 }

package/dist/alphaFoldModels.d.ts

@@ -22,11 +22,11 @@ export declare function parseAlphaFoldModels(json: unknown): AlphaFoldModel[];
 export declare function fetchAlphaFoldModels(uniprotId: string, opts?: FetchOptions): Promise<AlphaFoldModel[]>;
 /**
  * The model to open for a gene's transcripts: one folded from exactly a
- * transcript's translation, canonical first, so the view maps it as an
- * identity; else the canonical model; else the longest isoform model.
+ * transcript's translation, canonical first, so every residue maps to itself;
+ * else the canonical model; else the longest isoform model.
  *
- * Takes any record of sequences, since the structure loader knows one
- * translation rather than a gene's isoforms.
+ * Takes any record of sequences, since a caller may know one translation rather
+ * than a gene's isoforms.
  */
 export declare function pickAlphaFoldModel(models: AlphaFoldModel[], isoformSequences: Record<string, {
     seq: string;

package/dist/alphaFoldModels.js

@@ -48,11 +48,11 @@ async function fetchAlphaFoldModels(uniprotId, opts) {
 }
 /**
  * The model to open for a gene's transcripts: one folded from exactly a
- * transcript's translation, canonical first, so the view maps it as an
- * identity; else the canonical model; else the longest isoform model.
+ * transcript's translation, canonical first, so every residue maps to itself;
+ * else the canonical model; else the longest isoform model.
  *
- * Takes any record of sequences, since the structure loader knows one
- * translation rather than a gene's isoforms.
+ * Takes any record of sequences, since a caller may know one translation rather
+ * than a gene's isoforms.
  */
 function pickAlphaFoldModel(models, isoformSequences) {
     const translations = new Set(Object.values(isoformSequences ?? {}).map(v => (0, stripStopCodon_ts_1.stripStopCodon)(v.seq)));

package/dist/chooseMappedEntity.d.ts

@@ -9,12 +9,12 @@ import type { AlignmentAlgorithm } from './types.ts';
  */
 export declare function interactionMatchesMappedEntity(entityId: string, mappedEntityId: string | undefined): boolean;
 export interface EntitySelection extends ScoredAlignment {
-    /** index into the candidate array of the entity that is the transcript's */
+    /** index of the chosen entity in the candidate array */
     index: number;
 }
 export interface ScoredAlignment {
-    /** alignment of the transcript against the entity (stop codons stripped on
-     * both sides, matching the rest of the mapping pipeline) */
+    /** alignment of the transcript against the entity, with stop codons
+     * stripped from both */
     alignment: PairwiseAlignment;
     /** identical aligned residues */
     matches: number;
@@ -39,17 +39,15 @@ export declare function explainedFraction(matches: number, transcriptLength: num
  */
 export declare function alignTranscriptToEntity(transcript: string, entitySeq: string, algorithm: AlignmentAlgorithm): ScoredAlignment | undefined;
 /**
- * Pick which polymer entity of a structure corresponds to the transcript.
+ * Pick the polymer entity of a structure that is the transcript's protein.
  *
- * The plugin historically hardcoded entity `[0]`, which silently mis-maps every
- * heteromeric / protein-DNA / processed-peptide structure where the protein of
- * interest is some other chain. Selecting by alignment makes the structure self-
- * describe which entity is the gene's protein: an exact sequence match wins
- * outright, otherwise the entity with the highest identity over the shorter
- * sequence (see `explainedFraction`). Nucleic-acid entities are never
- * candidates.
+ * Taking entity `[0]` mis-maps every heteromeric, protein-DNA or
+ * processed-peptide structure where the protein is another chain. An exact
+ * sequence match wins outright; otherwise the entity with the highest identity
+ * over the shorter sequence wins (see `explainedFraction`). Nucleic-acid
+ * entities are never candidates.
  *
- * Returns `undefined` only when there is nothing to map (no transcript or no
- * protein entities) — never a silent fallback to the wrong entity.
+ * Returns `undefined` only when there is nothing to map: no transcript, or no
+ * protein entity. It never falls back to another entity.
  */
 export declare function chooseMappedEntity(transcript: string, entities: readonly (string | EntityCandidate)[], algorithm: AlignmentAlgorithm): EntitySelection | undefined;

package/dist/chooseMappedEntity.js

@@ -25,8 +25,7 @@ function interactionMatchesMappedEntity(entityId, mappedEntityId) {
  * usually is: on 1H26 the 11-residue p53 peptide matches 11 while CDK2 accrues
  * 58 scattered identities, and on 4ZZJ SIRT1 beats the 7-residue p53 peptide
  * 63 to 6. The Smith-Waterman score is no better there (56 vs 58). Dividing
- * by length asks the question the picker actually has, which chain *is* this
- * gene's product: the peptide scores 0.69 and 0.50, the partners 0.19 and
+ * by the shorter length identifies the chain that *is* this gene's product: the peptide scores 0.69 and 0.50, the partners 0.19 and
  * 0.17, and across a ribosome's 55 chains no decoy passes 0.29.
  *
  * Dividing by the *entity's* length alone penalised a fusion construct: a
@@ -91,18 +90,16 @@ function alignTranscriptToEntity(transcript, entitySeq, algorithm) {
     };
 }
 /**
- * Pick which polymer entity of a structure corresponds to the transcript.
+ * Pick the polymer entity of a structure that is the transcript's protein.
  *
- * The plugin historically hardcoded entity `[0]`, which silently mis-maps every
- * heteromeric / protein-DNA / processed-peptide structure where the protein of
- * interest is some other chain. Selecting by alignment makes the structure self-
- * describe which entity is the gene's protein: an exact sequence match wins
- * outright, otherwise the entity with the highest identity over the shorter
- * sequence (see `explainedFraction`). Nucleic-acid entities are never
- * candidates.
+ * Taking entity `[0]` mis-maps every heteromeric, protein-DNA or
+ * processed-peptide structure where the protein is another chain. An exact
+ * sequence match wins outright; otherwise the entity with the highest identity
+ * over the shorter sequence wins (see `explainedFraction`). Nucleic-acid
+ * entities are never candidates.
  *
- * Returns `undefined` only when there is nothing to map (no transcript or no
- * protein entities) — never a silent fallback to the wrong entity.
+ * Returns `undefined` only when there is nothing to map: no transcript, or no
+ * protein entity. It never falls back to another entity.
  */
 function chooseMappedEntity(transcript, entities, algorithm) {
     const t = (0, stripStopCodon_ts_1.stripStopCodon)(transcript);

package/dist/chooseMappedEntity.js.map

@@ -1 +1 @@
-{"version":3,"file":"chooseMappedEntity.js","sourceRoot":"","sources":["../src/chooseMappedEntity.ts"],"names":[],"mappings":";;AAkBA,wEAKC;AAkDD,8CAQC;AAsBD,0DAgCC;AAgBD,gDA8CC;AArMD,iEAI+B;AAC/B,2DAAoD;AACpD,+CAAyE;AAKzE;;;;;;GAMG;AACH,SAAgB,8BAA8B,CAC5C,QAAgB,EAChB,cAAkC;IAElC,OAAO,cAAc,KAAK,SAAS,IAAI,QAAQ,KAAK,cAAc,CAAA;AACpE,CAAC;AA2BD;;;;;;;;;;;;;;;;;;;;GAoBG;AACH,MAAM,qBAAqB,GAAG,CAAC,CAAA;AAE/B,SAAgB,iBAAiB,CAC/B,OAAe,EACf,gBAAwB,EACxB,YAAoB;IAEpB,OAAO,CACL,OAAO,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,gBAAgB,EAAE,YAAY,CAAC,GAAG,qBAAqB,CAAC,CAC7E,CAAA;AACH,CAAC;AAED,SAAS,YAAY,CAAC,EAAqB;IACzC,MAAM,CAAC,GAAG,IAAA,kCAAoB,EAAC,EAAE,CAAC,CAAA;IAClC,MAAM,CAAC,GAAG,IAAA,iCAAmB,EAAC,EAAE,CAAC,CAAA;IACjC,IAAI,OAAO,GAAG,CAAC,CAAA;IACf,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QAClC,MAAM,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;QACf,MAAM,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;QACf,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,EAAE,WAAW,EAAE,KAAK,EAAE,EAAE,WAAW,EAAE,EAAE,CAAC;YACxE,OAAO,EAAE,CAAA;QACX,CAAC;IACH,CAAC;IACD,OAAO,OAAO,CAAA;AAChB,CAAC;AAED;;;;;GAKG;AACH,SAAgB,uBAAuB,CACrC,UAAkB,EAClB,SAAiB,EACjB,SAA6B;IAE7B,MAAM,CAAC,GAAG,IAAA,kCAAc,EAAC,UAAU,CAAC,CAAA;IACpC,MAAM,CAAC,GAAG,IAAA,kCAAc,EAAC,SAAS,CAAC,CAAA;IACnC,IAAI,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,IAAA,wCAAiB,EAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC,EAAE,CAAC;QACtD,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;QACZ,OAAO;YACL,SAAS,EAAE;gBACT,SAAS,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC;gBAC/B,IAAI,EAAE;oBACJ,EAAE,EAAE,EAAE,MAAM,EAAE,GAAG,EAAE,CAAC,EAAE;oBACtB,EAAE,EAAE,EAAE,MAAM,EAAE,GAAG,EAAE,CAAC,EAAE;iBACvB;aACF;YACD,OAAO,EAAE,CAAC,CAAC,MAAM;YACjB,SAAS,EAAE,iBAAiB,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;YAC1D,KAAK,EAAE,IAAA,gCAAS,EAAC,CAAC,CAAC;SACpB,CAAA;IACH,CAAC;IACD,MAAM,EAAE,SAAS,EAAE,KAAK,EAAE,GAAG,IAAA,sCAAe,EAAC,CAAC,EAAE,CAAC,EAAE,SAAS,CAAC,CAAA;IAC7D,MAAM,OAAO,GAAG,YAAY,CAAC,SAAS,CAAC,CAAA;IACvC,OAAO;QACL,SAAS;QACT,OAAO;QACP,SAAS,EAAE,iBAAiB,CAAC,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACzD,KAAK;KACN,CAAA;AACH,CAAC;AAED;;;;;;;;;;;;;GAaG;AACH,SAAgB,kBAAkB,CAChC,UAAkB,EAClB,QAA+C,EAC/C,SAA6B;IAE7B,MAAM,CAAC,GAAG,IAAA,kCAAc,EAAC,UAAU,CAAC,CAAA;IACpC,IAAI,CAAC,CAAC,EAAE,CAAC;QACP,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,MAAM,UAAU,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAClC,OAAO,CAAC,KAAK,QAAQ;QACnB,CAAC,CAAC,EAAE,GAAG,EAAE,IAAA,kCAAc,EAAC,CAAC,CAAC,EAAE;QAC5B,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,GAAG,EAAE,IAAA,kCAAc,EAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CACzC,CAAA;IACD,MAAM,UAAU,GAAG,UAAU,CAAC,SAAS,CACrC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,WAAW,IAAI,CAAC,CAAC,GAAG,CAAC,MAAM,GAAG,CAAC,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,CACvD,CAAA;IACD,IAAI,UAAU,KAAK,CAAC,CAAC,EAAE,CAAC;QACtB,MAAM,KAAK,GAAG,uBAAuB,CACnC,CAAC,EACD,UAAU,CAAC,UAAU,CAAE,CAAC,GAAG,EAC3B,SAAS,CACT,CAAA;QACF,OAAO,EAAE,KAAK,EAAE,UAAU,EAAE,GAAG,KAAK,EAAE,CAAA;IACxC,CAAC;IAED,4EAA4E;IAC5E,2EAA2E;IAC3E,kEAAkE;IAClE,MAAM,KAAK,GAAG,IAAI,GAAG,EAAuC,CAAA;IAC5D,IAAI,IAAiC,CAAA;IACrC,KAAK,IAAI,KAAK,GAAG,CAAC,EAAE,KAAK,GAAG,UAAU,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE,CAAC;QACvD,MAAM,EAAE,GAAG,EAAE,WAAW,EAAE,GAAG,UAAU,CAAC,KAAK,CAAE,CAAA;QAC/C,IAAI,WAAW,EAAE,CAAC;YAChB,SAAQ;QACV,CAAC;QACD,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;YACpB,KAAK,CAAC,GAAG,CAAC,GAAG,EAAE,uBAAuB,CAAC,CAAC,EAAE,GAAG,EAAE,SAAS,CAAC,CAAC,CAAA;QAC5D,CAAC;QACD,MAAM,MAAM,GAAG,KAAK,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;QAC7B,IAAI,MAAM,IAAI,CAAC,CAAC,IAAI,IAAI,MAAM,CAAC,SAAS,GAAG,IAAI,CAAC,SAAS,CAAC,EAAE,CAAC;YAC3D,IAAI,GAAG,EAAE,KAAK,EAAE,GAAG,MAAM,EAAE,CAAA;QAC7B,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}
+{"version":3,"file":"chooseMappedEntity.js","sourceRoot":"","sources":["../src/chooseMappedEntity.ts"],"names":[],"mappings":";;AAkBA,wEAKC;AAiDD,8CAQC;AAsBD,0DAgCC;AAcD,gDA8CC;AAlMD,iEAI+B;AAC/B,2DAAoD;AACpD,+CAAyE;AAKzE;;;;;;GAMG;AACH,SAAgB,8BAA8B,CAC5C,QAAgB,EAChB,cAAkC;IAElC,OAAO,cAAc,KAAK,SAAS,IAAI,QAAQ,KAAK,cAAc,CAAA;AACpE,CAAC;AA2BD;;;;;;;;;;;;;;;;;;;GAmBG;AACH,MAAM,qBAAqB,GAAG,CAAC,CAAA;AAE/B,SAAgB,iBAAiB,CAC/B,OAAe,EACf,gBAAwB,EACxB,YAAoB;IAEpB,OAAO,CACL,OAAO,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,gBAAgB,EAAE,YAAY,CAAC,GAAG,qBAAqB,CAAC,CAC7E,CAAA;AACH,CAAC;AAED,SAAS,YAAY,CAAC,EAAqB;IACzC,MAAM,CAAC,GAAG,IAAA,kCAAoB,EAAC,EAAE,CAAC,CAAA;IAClC,MAAM,CAAC,GAAG,IAAA,iCAAmB,EAAC,EAAE,CAAC,CAAA;IACjC,IAAI,OAAO,GAAG,CAAC,CAAA;IACf,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QAClC,MAAM,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;QACf,MAAM,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;QACf,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,EAAE,WAAW,EAAE,KAAK,EAAE,EAAE,WAAW,EAAE,EAAE,CAAC;YACxE,OAAO,EAAE,CAAA;QACX,CAAC;IACH,CAAC;IACD,OAAO,OAAO,CAAA;AAChB,CAAC;AAED;;;;;GAKG;AACH,SAAgB,uBAAuB,CACrC,UAAkB,EAClB,SAAiB,EACjB,SAA6B;IAE7B,MAAM,CAAC,GAAG,IAAA,kCAAc,EAAC,UAAU,CAAC,CAAA;IACpC,MAAM,CAAC,GAAG,IAAA,kCAAc,EAAC,SAAS,CAAC,CAAA;IACnC,IAAI,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,IAAA,wCAAiB,EAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC,EAAE,CAAC;QACtD,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;QACZ,OAAO;YACL,SAAS,EAAE;gBACT,SAAS,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC;gBAC/B,IAAI,EAAE;oBACJ,EAAE,EAAE,EAAE,MAAM,EAAE,GAAG,EAAE,CAAC,EAAE;oBACtB,EAAE,EAAE,EAAE,MAAM,EAAE,GAAG,EAAE,CAAC,EAAE;iBACvB;aACF;YACD,OAAO,EAAE,CAAC,CAAC,MAAM;YACjB,SAAS,EAAE,iBAAiB,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;YAC1D,KAAK,EAAE,IAAA,gCAAS,EAAC,CAAC,CAAC;SACpB,CAAA;IACH,CAAC;IACD,MAAM,EAAE,SAAS,EAAE,KAAK,EAAE,GAAG,IAAA,sCAAe,EAAC,CAAC,EAAE,CAAC,EAAE,SAAS,CAAC,CAAA;IAC7D,MAAM,OAAO,GAAG,YAAY,CAAC,SAAS,CAAC,CAAA;IACvC,OAAO;QACL,SAAS;QACT,OAAO;QACP,SAAS,EAAE,iBAAiB,CAAC,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACzD,KAAK;KACN,CAAA;AACH,CAAC;AAED;;;;;;;;;;;GAWG;AACH,SAAgB,kBAAkB,CAChC,UAAkB,EAClB,QAA+C,EAC/C,SAA6B;IAE7B,MAAM,CAAC,GAAG,IAAA,kCAAc,EAAC,UAAU,CAAC,CAAA;IACpC,IAAI,CAAC,CAAC,EAAE,CAAC;QACP,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,MAAM,UAAU,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAClC,OAAO,CAAC,KAAK,QAAQ;QACnB,CAAC,CAAC,EAAE,GAAG,EAAE,IAAA,kCAAc,EAAC,CAAC,CAAC,EAAE;QAC5B,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,GAAG,EAAE,IAAA,kCAAc,EAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CACzC,CAAA;IACD,MAAM,UAAU,GAAG,UAAU,CAAC,SAAS,CACrC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,WAAW,IAAI,CAAC,CAAC,GAAG,CAAC,MAAM,GAAG,CAAC,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,CACvD,CAAA;IACD,IAAI,UAAU,KAAK,CAAC,CAAC,EAAE,CAAC;QACtB,MAAM,KAAK,GAAG,uBAAuB,CACnC,CAAC,EACD,UAAU,CAAC,UAAU,CAAE,CAAC,GAAG,EAC3B,SAAS,CACT,CAAA;QACF,OAAO,EAAE,KAAK,EAAE,UAAU,EAAE,GAAG,KAAK,EAAE,CAAA;IACxC,CAAC;IAED,4EAA4E;IAC5E,2EAA2E;IAC3E,kEAAkE;IAClE,MAAM,KAAK,GAAG,IAAI,GAAG,EAAuC,CAAA;IAC5D,IAAI,IAAiC,CAAA;IACrC,KAAK,IAAI,KAAK,GAAG,CAAC,EAAE,KAAK,GAAG,UAAU,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE,CAAC;QACvD,MAAM,EAAE,GAAG,EAAE,WAAW,EAAE,GAAG,UAAU,CAAC,KAAK,CAAE,CAAA;QAC/C,IAAI,WAAW,EAAE,CAAC;YAChB,SAAQ;QACV,CAAC;QACD,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;YACpB,KAAK,CAAC,GAAG,CAAC,GAAG,EAAE,uBAAuB,CAAC,CAAC,EAAE,GAAG,EAAE,SAAS,CAAC,CAAC,CAAA;QAC5D,CAAC;QACD,MAAM,MAAM,GAAG,KAAK,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;QAC7B,IAAI,MAAM,IAAI,CAAC,CAAC,IAAI,IAAI,MAAM,CAAC,SAAS,GAAG,IAAI,CAAC,SAAS,CAAC,EAAE,CAAC;YAC3D,IAAI,GAAG,EAAE,KAAK,EAAE,GAAG,MAAM,EAAE,CAAA;QAC7B,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}

package/dist/coordinates.d.ts

@@ -1,15 +1,14 @@
 import type { PairwiseAlignment } from './mappings.ts';
 /**
- * Branded coordinate spaces. Every position in this plugin is a bare `number`,
- * but the *meaning* differs: a structure residue index is not interchangeable
- * with a transcript residue index or an alignment column, and mixing them is
- * the root cause of the off-by-one class of bugs. Branding makes the compiler
- * reject cross-space mixing; construct values with the helpers below at the
- * boundaries where raw numbers enter (molstar picks, hover events, features).
+ * Branded coordinate spaces. Every position is a plain `number` at runtime, but
+ * a structure residue index, a transcript residue index and an alignment column
+ * mean different things, and mixing them causes off-by-one bugs. The brands
+ * make the compiler reject mixing; wrap a raw number with the helpers below
+ * where it enters, such as a molstar pick, a hover event or a feature.
  *
- * Conventions: all are 0-based. StructurePos indexes the ungapped structure
- * sequence; TranscriptPos the ungapped transcript sequence; AlignmentCol a
- * column of the pairwise alignment (gaps included).
+ * All are 0-based. StructurePos indexes the ungapped structure sequence,
+ * TranscriptPos the ungapped transcript sequence, and AlignmentCol a column of
+ * the pairwise alignment, gaps included.
  */
 export type StructurePos = number & {
     readonly __brand: 'StructurePos';
@@ -39,10 +38,9 @@ export interface CoordinateMapper {
     transcriptToAlignment: (p: TranscriptPos) => AlignmentCol | undefined;
     alignmentToTranscript: (c: AlignmentCol) => TranscriptPos | undefined;
     /**
-     * Raw lookup tables, for consumers that iterate the whole map rather than
-     * convert a single position (e.g. per-residue track rendering, selection of
-     * all aligned residues). Plain numbers — prefer the typed methods above for
-     * point conversions.
+     * The lookup tables as plain numbers, for code that iterates a whole map,
+     * such as drawing a per-residue track or selecting every aligned residue.
+     * Use the typed methods above to convert one position.
      */
     readonly maps: CoordinateMaps;
 }

package/dist/coordinates.js.map

@@ -1 +1 @@
-{"version":3,"file":"coordinates.js","sourceRoot":"","sources":["../src/coordinates.ts"],"names":[],"mappings":";;;AA2DA,oDAiCC;AASD,0EAgBC;AArHD,+CAIsB;AACtB,iDAA0C;AAoBnC,MAAM,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAiB,CAAA;AAA/C,QAAA,YAAY,gBAAmC;AACrD,MAAM,aAAa,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAkB,CAAA;AAAjD,QAAA,aAAa,iBAAoC;AACvD,MAAM,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAiB,CAAA;AAA/C,QAAA,YAAY,gBAAmC;AA2B5D;;;;GAIG;AACH,SAAgB,oBAAoB,CAClC,iBAAoC;IAEpC,MAAM,EACJ,mCAAmC,EACnC,mCAAmC,GACpC,GAAG,IAAA,4CAA8B,EAAC,iBAAiB,CAAC,CAAA;IACrD,MAAM,KAAK,GAAG,IAAA,6CAA+B,EAAC,iBAAiB,CAAC,CAAA;IAChE,MAAM,KAAK,GAAG,IAAA,8CAAgC,EAAC,iBAAiB,CAAC,CAAA;IACjE,MAAM,KAAK,GAAG,IAAA,wBAAS,EAAC,KAAK,CAAC,CAAA;IAC9B,MAAM,KAAK,GAAG,IAAA,wBAAS,EAAC,KAAK,CAAC,CAAA;IAE9B,uEAAuE;IACvE,6EAA6E;IAC7E,sEAAsE;IACtE,OAAO;QACL,qBAAqB,EAAE,CAAC,CAAC,EAAE,CACzB,mCAAmC,CAAC,CAAC,CAA8B;QACrE,qBAAqB,EAAE,CAAC,CAAC,EAAE,CACzB,mCAAmC,CAAC,CAAC,CAA6B;QACpE,oBAAoB,EAAE,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAA6B;QAC/D,oBAAoB,EAAE,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAA6B;QAC/D,qBAAqB,EAAE,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAA6B;QAChE,qBAAqB,EAAE,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAA8B;QACjE,IAAI,EAAE;YACJ,mCAAmC;YACnC,mCAAmC;YACnC,+BAA+B,EAAE,KAAK;YACtC,gCAAgC,EAAE,KAAK;YACvC,4BAA4B,EAAE,KAAK;YACnC,6BAA6B,EAAE,KAAK;SACrC;KACF,CAAA;AACH,CAAC;AAED;;;;;;GAMG;AACH,SAAgB,+BAA+B,CAC7C,MAAwB,EACxB,KAAqC;IAErC,IAAI,KAAyB,CAAA;IAC7B,IAAI,IAAwB,CAAA;IAC5B,KAAK,IAAI,OAAO,GAAG,KAAK,CAAC,KAAK,EAAE,OAAO,IAAI,KAAK,CAAC,GAAG,EAAE,OAAO,EAAE,EAAE,CAAC;QAChE,MAAM,GAAG,GAAG,MAAM,CAAC,qBAAqB,CAAC,IAAA,qBAAa,EAAC,OAAO,GAAG,CAAC,CAAC,CAAC,CAAA;QACpE,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;YACtB,KAAK,GAAG,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;YACxD,IAAI,GAAG,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,CAAA;QACvD,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"}
+{"version":3,"file":"coordinates.js","sourceRoot":"","sources":["../src/coordinates.ts"],"names":[],"mappings":";;;AAyDA,oDAiCC;AASD,0EAgBC;AAnHD,+CAIsB;AACtB,iDAA0C;AAmBnC,MAAM,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAiB,CAAA;AAA/C,QAAA,YAAY,gBAAmC;AACrD,MAAM,aAAa,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAkB,CAAA;AAAjD,QAAA,aAAa,iBAAoC;AACvD,MAAM,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAiB,CAAA;AAA/C,QAAA,YAAY,gBAAmC;AA0B5D;;;;GAIG;AACH,SAAgB,oBAAoB,CAClC,iBAAoC;IAEpC,MAAM,EACJ,mCAAmC,EACnC,mCAAmC,GACpC,GAAG,IAAA,4CAA8B,EAAC,iBAAiB,CAAC,CAAA;IACrD,MAAM,KAAK,GAAG,IAAA,6CAA+B,EAAC,iBAAiB,CAAC,CAAA;IAChE,MAAM,KAAK,GAAG,IAAA,8CAAgC,EAAC,iBAAiB,CAAC,CAAA;IACjE,MAAM,KAAK,GAAG,IAAA,wBAAS,EAAC,KAAK,CAAC,CAAA;IAC9B,MAAM,KAAK,GAAG,IAAA,wBAAS,EAAC,KAAK,CAAC,CAAA;IAE9B,uEAAuE;IACvE,6EAA6E;IAC7E,sEAAsE;IACtE,OAAO;QACL,qBAAqB,EAAE,CAAC,CAAC,EAAE,CACzB,mCAAmC,CAAC,CAAC,CAA8B;QACrE,qBAAqB,EAAE,CAAC,CAAC,EAAE,CACzB,mCAAmC,CAAC,CAAC,CAA6B;QACpE,oBAAoB,EAAE,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAA6B;QAC/D,oBAAoB,EAAE,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAA6B;QAC/D,qBAAqB,EAAE,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAA6B;QAChE,qBAAqB,EAAE,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAA8B;QACjE,IAAI,EAAE;YACJ,mCAAmC;YACnC,mCAAmC;YACnC,+BAA+B,EAAE,KAAK;YACtC,gCAAgC,EAAE,KAAK;YACvC,4BAA4B,EAAE,KAAK;YACnC,6BAA6B,EAAE,KAAK;SACrC;KACF,CAAA;AACH,CAAC;AAED;;;;;;GAMG;AACH,SAAgB,+BAA+B,CAC7C,MAAwB,EACxB,KAAqC;IAErC,IAAI,KAAyB,CAAA;IAC7B,IAAI,IAAwB,CAAA;IAC5B,KAAK,IAAI,OAAO,GAAG,KAAK,CAAC,KAAK,EAAE,OAAO,IAAI,KAAK,CAAC,GAAG,EAAE,OAAO,EAAE,EAAE,CAAC;QAChE,MAAM,GAAG,GAAG,MAAM,CAAC,qBAAqB,CAAC,IAAA,qBAAa,EAAC,OAAO,GAAG,CAAC,CAAC,CAAC,CAAA;QACpE,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;YACtB,KAAK,GAAG,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;YACxD,IAAI,GAAG,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,CAAA;QACvD,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"}

package/dist/extractStructureSequences.d.ts

@@ -1,42 +1,35 @@
 /** A polymer entity of a loaded structure: its mmCIF entity id, its one-letter
- * sequence, and the molstar `label_seq_id` of each of those residues.
+ * sequence, and the molstar `label_seq_id` of each residue.
  *
- * The entity id is what lets every downstream step talk about "the gene's
- * protein" by identity instead of by the fragile entity-[0] position.
+ * Structure positions are 0-based indices into `seq`, and molstar selects
+ * residues by `label_seq_id`. The two differ by 1 only when the entity's
+ * sequence covers every residue from 1, which holds for any mmCIF with an
+ * `entity_poly_seq` category (all of RCSB and AlphaFold) and for a PDB file
+ * with SEQRES records, from which molstar builds that category.
  *
- * `seqIds` is what lets it talk about a *residue* by identity. Structure
- * positions in this plugin are 0-based indices into `seq`; molstar addresses
- * residues by `label_seq_id`. Those are related by `+1` only when the entity's
- * sequence covers every residue from 1 — true for any mmCIF with an
- * `entity_poly_seq` category (all of RCSB and AlphaFold) and for PDB files
- * carrying SEQRES records, because molstar synthesizes the category from them.
- *
- * A PDB-format file with no SEQRES has no such category, so molstar falls back
- * to `StructureSequence.fromHierarchy` and takes `label_seq_id` straight from
- * the observed residues' author numbering: a chain whose coordinates start at
- * residue 94 yields seqIds 94.., and an unobserved loop leaves a hole. Deriving
- * the id arithmetically there is off by the whole offset, in both directions —
- * every hover reads the wrong residue and every highlight paints the wrong one.
- * So carry the real ids and convert through them.
+ * For a PDB file without SEQRES, molstar falls back to
+ * `StructureSequence.fromHierarchy` and takes `label_seq_id` from the observed
+ * residues' author numbering: a chain whose coordinates start at residue 94 has
+ * seqIds 94.., and an unobserved loop leaves a gap. Adding 1 there is off by the
+ * whole offset, in both directions, so convert through `seqIds`.
  */
 export interface Entity {
-    /** mmCIF entity id, molstar's own bookkeeping */
+    /** mmCIF entity id */
     entityId: string;
     /** one letter per residue, observed or not */
     seq: string;
     /** molstar `label_seq_id` per position of `seq` */
     seqIds: number[];
-    /** author chain ids carrying this entity, e.g. ['A', 'B'] for a homodimer:
-     * what a user recognises from the PDB entry page */
+    /** author chain ids of this entity, e.g. ['A', 'B'] for a homodimer, as
+     * the PDB entry page lists them */
     chains: string[];
-    /** DNA, RNA or a hybrid, by molstar's entity subtype. Its letters spell
-     * amino acids too (A, C, G, T, U), so it is kept out of the alignment
-     * rather than left to score low. */
+    /** DNA, RNA or a hybrid, by molstar's entity subtype. A, C, G, T and U
+     * are amino-acid letters too, so chooseMappedEntity skips these. */
     nucleicAcid?: boolean;
     /** `auth_seq_id` per position: the depositors' numbering, which papers cite
-     * (1TUP's position 154 is R248) and Mol*'s hover shows. Display only;
-     * address Mol* through `seqIds`. Absent when the model has no atomic
-     * hierarchy. See `residueNumber`. */
+     * (1TUP's position 154 is R248) and Mol*'s hover shows. For display only;
+     * use `seqIds` to select residues in Mol*. Absent when the model has no
+     * atomic hierarchy. See `residueNumber`. */
     authSeqIds?: number[];
 }
 export interface Column<T> {
@@ -123,8 +116,8 @@ export declare function oneLetterSequence(codes: ArrayLike<string>, canonical: s
 export declare function extractEntities(model: StructureModel): Entity[] | undefined;
 /** A user-facing name for an entity: its chains when known, else its id. */
 export declare function entityLabel(entity: Entity): string;
-/** The protein chains' sequences, for the launch dialog's isoform matching,
- * which has no use for a DNA strand that happens to align. */
+/** The protein chains' sequences, for ranking isoforms against a structure.
+ * DNA chains are left out, because their letters align as amino acids. */
 export declare function extractStructureSequences(model: StructureModel): string[] | undefined;
 /**
  * The molstar `label_seq_id`s for a set of 0-based structure positions. Unknown

package/dist/extractStructureSequences.js

@@ -169,8 +169,8 @@ function entityLabel(entity) {
         : `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. */
+/** The protein chains' sequences, for ranking isoforms against a structure.
+ * DNA chains are left out, because their letters align as amino acids. */
 function extractStructureSequences(model) {
     return extractEntities(model)
         ?.filter(e => !e.nucleicAcid)

package/dist/extractStructureSequences.js.map

@@ -1 +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"}
+{"version":3,"file":"extractStructureSequences.js","sourceRoot":"","sources":["../src/extractStructureSequences.ts"],"names":[],"mappings":";;AAgHA,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;0EAC0E;AAC1E,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

@@ -12,9 +12,9 @@ export declare class HttpError extends Error {
  * not. */
 export declare function isDefinitiveFailure(e: unknown): boolean;
 /**
- * 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.
+ * The error for a failed response: 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, which
+ * hides the line that says what went wrong.
  */
 export declare function httpError(response: Response, url: string): Promise<HttpError>;
 /**
@@ -38,10 +38,10 @@ export declare function rawfetch(url: string, args?: FetchOptions): Promise<Resp
 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.
+ * An AbortSignal's reason as a real Error. `signal.reason` is `any`, usually a
+ * DOMException, but a caller can abort with any value, and throwing a non-Error
+ * loses the stack and breaks `instanceof Error` checks. Use it 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

@@ -43,9 +43,9 @@ function isDefinitiveFailure(e) {
     return e instanceof HttpError && e.status >= 400 && e.status < 500;
 }
 /**
- * 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.
+ * The error for a failed response: 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, which
+ * hides the line that says what went wrong.
  */
 async function httpError(response, url) {
     const detail = firstLine(await response.text().catch(() => ''));
@@ -104,10 +104,10 @@ async function jsonfetch(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.
+ * An AbortSignal's reason as a real Error. `signal.reason` is `any`, usually a
+ * DOMException, but a caller can abort with any value, and throwing a non-Error
+ * loses the stack and breaks `instanceof Error` checks. Use it at every throw
+ * site.
  */
 function abortError(signal) {
     return signal.reason instanceof Error

package/dist/isoformRanking.d.ts

@@ -10,7 +10,7 @@ export interface RankedIsoform {
     /** 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 */
+    /** that alignment's score, which ranks the non-matching isoforms */
     score?: number;
 }
 export interface ClassifiedIsoforms {

package/dist/mappings.d.ts

@@ -3,13 +3,11 @@ export interface AlignmentRow {
     seq: string;
 }
 /**
- * A two-row alignment whose ROW ORDER IS A CONTRACT: row 0 is the transcript,
- * row 1 is the structure. Every producer honors it — runLocalAlignment is
- * always called as (transcript, structure), and the manual-import dialog tells
- * the user to paste them in that order — and every consumer depends on it, but
- * nothing in the type can enforce it, and swapping the two silently inverts
- * every coordinate map. Read the rows through the accessors below rather than
- * indexing, so a call site states which sequence it means.
+ * A two-row alignment: row 0 is the transcript and row 1 is the structure.
+ * alignSequences takes them in that order and every consumer depends on it,
+ * but the type cannot enforce it, and swapped rows invert every coordinate map
+ * without an error. Read the rows with the accessors below, so a call site
+ * names the sequence it means.
  */
 export interface PairwiseAlignment {
     consensus: string;
@@ -21,11 +19,10 @@ export declare const structureAlignedSeq: (pa: PairwiseAlignment) => string;
  * `pairwiseAlignmentProblem` is what guarantees it. */
 export declare const alignmentLength: (pa: PairwiseAlignment) => number;
 /**
- * Why a pairwise alignment can't be used, or undefined if it's usable. The two
- * rows must be the same non-zero length — every coordinate map walks them in
- * lockstep, so a ragged pair would map positions to nonsense. Callers that
- * accept alignments from outside (the manual-import dialog) check this and
- * report it; the internal map builders assert on it.
+ * Why a pairwise alignment can't be used, or undefined if it's usable. Both
+ * rows must have the same non-zero length, because every coordinate map walks
+ * them in step. Check an alignment from outside the package with this; the
+ * internal map builders throw on it.
  */
 export declare function pairwiseAlignmentProblem(pa: PairwiseAlignment): string | undefined;
 /**

package/dist/mappings.js

@@ -19,11 +19,10 @@ exports.structureAlignedSeq = structureAlignedSeq;
 const alignmentLength = (pa) => (0, exports.transcriptAlignedSeq)(pa).length;
 exports.alignmentLength = alignmentLength;
 /**
- * Why a pairwise alignment can't be used, or undefined if it's usable. The two
- * rows must be the same non-zero length — every coordinate map walks them in
- * lockstep, so a ragged pair would map positions to nonsense. Callers that
- * accept alignments from outside (the manual-import dialog) check this and
- * report it; the internal map builders assert on it.
+ * Why a pairwise alignment can't be used, or undefined if it's usable. Both
+ * rows must have the same non-zero length, because every coordinate map walks
+ * them in step. Check an alignment from outside the package with this; the
+ * internal map builders throw on it.
  */
 function pairwiseAlignmentProblem(pa) {
     const transcript = (0, exports.transcriptAlignedSeq)(pa);