p2s_mapper 2.0.0 → 2.1.0

package/dist/mappings.js.map

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

@@ -27,8 +27,10 @@ export declare function needlemanWunsch(seq1: string, seq2: string, gapOpen?: nu
 export declare function smithWaterman(seq1: string, seq2: string, gapOpen?: number, gapExtend?: number): AlignmentResult;
 /** The score of a sequence aligned to itself with no gaps. */
 export declare function selfScore(seq: string): number;
-export declare function scoredAlignment(seq1: string, seq2: string, algorithm: AlignmentAlgorithm): {
+export declare function scoredAlignment(transcript: string, structure: string, algorithm: AlignmentAlgorithm): {
     alignment: PairwiseAlignment;
     score: number;
 };
-export declare function runLocalAlignment(seq1: string, seq2: string, algorithm: AlignmentAlgorithm): PairwiseAlignment;
+export declare function alignSequences(transcript: string, structure: string, algorithm: AlignmentAlgorithm): PairwiseAlignment;
+/** @deprecated renamed to `alignSequences`, which runs either algorithm */
+export declare const runLocalAlignment: typeof alignSequences;

package/dist/pairwiseAlignment.js

@@ -1,12 +1,12 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.MAX_ALIGNMENT_CELLS = void 0;
+exports.runLocalAlignment = exports.MAX_ALIGNMENT_CELLS = void 0;
 exports.alignmentTooLarge = alignmentTooLarge;
 exports.needlemanWunsch = needlemanWunsch;
 exports.smithWaterman = smithWaterman;
 exports.selfScore = selfScore;
 exports.scoredAlignment = scoredAlignment;
-exports.runLocalAlignment = runLocalAlignment;
+exports.alignSequences = alignSequences;
 // BLOSUM62 scoring matrix — standard 20 amino acids + B, Z, X, *
 // prettier-ignore
 const AMINO_ACIDS = ['A', 'R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V', 'B', 'Z', 'X', '*'];
@@ -316,10 +316,10 @@ function selfScore(seq) {
     }
     return score;
 }
-function scoredAlignment(seq1, seq2, algorithm) {
+function scoredAlignment(transcript, structure, algorithm) {
     const { alignedSeq1, alignedSeq2, score } = algorithm === 'smith_waterman'
-        ? smithWaterman(seq1, seq2)
-        : needlemanWunsch(seq1, seq2);
+        ? smithWaterman(transcript, structure)
+        : needlemanWunsch(transcript, structure);
     return {
         alignment: {
             consensus: buildConsensus(alignedSeq1, alignedSeq2),
@@ -331,7 +331,9 @@ function scoredAlignment(seq1, seq2, algorithm) {
         score,
     };
 }
-function runLocalAlignment(seq1, seq2, algorithm) {
-    return scoredAlignment(seq1, seq2, algorithm).alignment;
+function alignSequences(transcript, structure, algorithm) {
+    return scoredAlignment(transcript, structure, algorithm).alignment;
 }
+/** @deprecated renamed to `alignSequences`, which runs either algorithm */
+exports.runLocalAlignment = alignSequences;
 //# sourceMappingURL=pairwiseAlignment.js.map

package/dist/pairwiseAlignment.js.map

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

@@ -29,12 +29,11 @@ export interface SegmentEntity {
     chains: readonly string[];
 }
 /**
- * Picks the UniProt entry that describes a given entity, with its segments
- * narrowed to that entity. Only the entity the plugin has mapped to the
- * transcript is relevant — a heteromer maps each of its chains to a different
- * accession, and using the wrong one would silently annotate the wrong protein.
- * When several accessions cover the same entity (a chimeric construct) the one
- * contributing the most residues wins.
+ * Picks the UniProt entry for a given entity, with its segments narrowed to
+ * that entity. Pass the entity mapped to the transcript: a heteromer's chains
+ * align to different accessions, and the wrong one would annotate the wrong
+ * protein. When several accessions cover one entity (a chimeric construct), the
+ * one covering the most residues wins.
  */
 export declare function chooseUniProtMappingForEntity(mappings: UniProtStructureMapping[], entity: SegmentEntity | undefined): UniProtStructureMapping | undefined;
 /**

package/dist/pdbUniProtMapping.js

@@ -32,12 +32,11 @@ function segmentsForEntity(mapping, entity) {
         : entity.chains.includes(s.chainId)));
 }
 /**
- * Picks the UniProt entry that describes a given entity, with its segments
- * narrowed to that entity. Only the entity the plugin has mapped to the
- * transcript is relevant — a heteromer maps each of its chains to a different
- * accession, and using the wrong one would silently annotate the wrong protein.
- * When several accessions cover the same entity (a chimeric construct) the one
- * contributing the most residues wins.
+ * Picks the UniProt entry for a given entity, with its segments narrowed to
+ * that entity. Pass the entity mapped to the transcript: a heteromer's chains
+ * align to different accessions, and the wrong one would annotate the wrong
+ * protein. When several accessions cover one entity (a chimeric construct), the
+ * one covering the most residues wins.
  */
 function chooseUniProtMappingForEntity(mappings, entity) {
     if (entity === undefined) {

package/dist/pdbUniProtMapping.js.map

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

@@ -1,19 +1,14 @@
 /**
  * Which molstar trajectory parser a structure needs.
  *
- * Getting this wrong is not a graceful failure in either direction: parsing a
- * PDB file as mmCIF throws ("Unexpected token. Expected data_, loop_, or data
- * name"), and — worse — parsing an mmCIF as PDB *succeeds* and yields a model
- * with zero polymer entities and thousands of misread atoms, so the view loads
- * with no sequence, no alignment and no genome mapping, and nothing reports an
- * error.
+ * A wrong choice fails either way. Parsing a PDB file as mmCIF throws
+ * ("Unexpected token. Expected data_, loop_, or data name"). Parsing an mmCIF
+ * as PDB succeeds and yields a model with zero polymer entities and thousands of
+ * misread atoms, so the structure loads with no sequence, no alignment and no
+ * genome mapping, and with no error.
  *
- * So detection lives here and is applied as the default at every entry point,
- * rather than at one of them.
- *
- * The two names are the subset of molstar's `BuiltInTrajectoryFormat` a
- * structure loaded from a file or a url can be, spelled out rather than
- * imported so nothing here depends on molstar.
+ * The two names are the subset of molstar's `BuiltInTrajectoryFormat` that a
+ * structure file or URL can be, written out so nothing here imports molstar.
  */
 export type StructureFormat = 'pdb' | 'mmcif';
 /** Trailing extension of a filename or URL, lowercased, ignoring any query or
@@ -21,18 +16,16 @@ export type StructureFormat = 'pdb' | 'mmcif';
 export declare function structureFileExtension(nameOrUrl: string): string;
 /**
  * Format for a filename or URL. Unknown extensions fall back to mmCIF, which is
- * what every URL this plugin generates itself serves (AlphaFold and RCSB both
- * hand out `.cif`).
+ * what AlphaFold and RCSB serve (`.cif`).
  */
 export declare function structureFormatFromName(nameOrUrl: string): StructureFormat;
 /** Whether a URL points at a binary-encoded structure, which molstar must be
  * told to download as bytes rather than text. */
 export declare function isBinaryStructureUrl(url: string): boolean;
 /**
- * Format for structure text that arrived without a filename — an inline `data`
- * snapshot, a pasted file, or the PDB the plugin synthesizes from Foldseek Cα
- * coordinates. Sniffs the content, which is strictly more reliable than a name
- * and is the only signal available here.
+ * Format for structure text with no filename, such as inline data, a pasted
+ * file, or a PDB built by `caCoordsToPdb`. The content is more reliable than a
+ * name, and here it is the only signal.
  *
  * mmCIF is line-oriented and its first meaningful line is a `data_` block
  * header (comments and blank lines may precede it); PDB has none.

package/dist/structureFormat.js

@@ -20,8 +20,7 @@ function structureFileExtension(nameOrUrl) {
 }
 /**
  * Format for a filename or URL. Unknown extensions fall back to mmCIF, which is
- * what every URL this plugin generates itself serves (AlphaFold and RCSB both
- * hand out `.cif`).
+ * what AlphaFold and RCSB serve (`.cif`).
  */
 function structureFormatFromName(nameOrUrl) {
     return PDB_EXTENSIONS.has(structureFileExtension(nameOrUrl)) ? 'pdb' : 'mmcif';
@@ -32,10 +31,9 @@ function isBinaryStructureUrl(url) {
     return structureFileExtension(url) === 'bcif';
 }
 /**
- * Format for structure text that arrived without a filename — an inline `data`
- * snapshot, a pasted file, or the PDB the plugin synthesizes from Foldseek Cα
- * coordinates. Sniffs the content, which is strictly more reliable than a name
- * and is the only signal available here.
+ * Format for structure text with no filename, such as inline data, a pasted
+ * file, or a PDB built by `caCoordsToPdb`. The content is more reliable than a
+ * name, and here it is the only signal.
  *
  * mmCIF is line-oriented and its first meaningful line is a `data_` block
  * header (comments and blank lines may precede it); PDB has none.

package/dist/structureFormat.js.map

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

@@ -11,7 +11,7 @@ export interface ExperimentalStructure {
     end: number;
     /** fraction of the UniProt sequence the entry covers, 0..1 */
     coverage: number;
-    /** author chain ids carrying the protein */
+    /** author chain ids of the protein */
     chains: string[];
 }
 /** One polymer entity aligned to the accession. */

package/dist/structureUrls.d.ts

@@ -12,20 +12,15 @@ export declare function getPdbStructureUrl(pdbId: string): string;
 export declare function isPdbId(value: string): boolean;
 export declare function rcsbEntryUrl(pdbId: string): string;
 /**
- * Resolve the `{ pdbId }` shorthand to a concrete structure URL, so a
- * hand-authored snapshot or a short launch URL doesn't have to know RCSB's
- * filename format. An explicit `url` (or inline `data`) always wins.
- * Idempotent: re-resolving an already-resolved spec returns the same url.
+ * Resolve the `{ pdbId }` shorthand to a structure URL, so a hand-written config
+ * or a short launch URL needs no RCSB filename. An explicit `url` (or inline
+ * `data`) always wins, and resolving an already-resolved spec returns the same
+ * url.
  *
- * `uniprotId` deliberately resolves to no url here, and still outranks a
- * `pdbId`. An accession's files are whatever AlphaFold DB currently holds — an
- * isoform model, several fragments, a new model version — so the structure
- * keeps the accession and the structure loader asks the prediction API which
- * file to open.
- *
- * Shared by the Structure model's snapshot preprocessor and the
- * LaunchView-ProteinView extension point, which would otherwise each carry
- * their own copy of the same precedence rule.
+ * `uniprotId` resolves to no url and still outranks a `pdbId`. AlphaFold DB's
+ * files for an accession change (an isoform model, several fragments, a new
+ * model version), so the caller keeps the accession and asks
+ * `fetchAlphaFoldModels` which file to open.
  */
 export declare function resolveStructureUrl({ url, data, uniprotId, pdbId, }: {
     url?: string;
@@ -45,9 +40,9 @@ export declare function getUniprotIdFromAlphaFoldTarget(target: string): string
 export declare function getStructureUrlFromTarget(target: string, db: string): string | undefined;
 export declare function getConfidenceUrlFromTarget(target: string): string | undefined;
 /**
- * What a structure is called in the UI: its PDB id, its AlphaFold accession,
- * else the file's name. Shared by the view title, the alignment panel heading
- * and the hover readout, so one structure reads the same everywhere.
+ * The name to show for a structure: its PDB id, its AlphaFold accession, else
+ * the file's name. Use it wherever a structure is named, so each place shows
+ * the same name.
  */
 export declare function structureDisplayLabel({ url, data, uniprotId, }: {
     url?: string;

package/dist/structureUrls.js

@@ -1,7 +1,5 @@
 "use strict";
-// Pure structure-URL builders and target parsers. Kept dependency-free so both
-// the launch flow and the ProteinView model (e.g. resolving a `uniprotId`/`pdbId`
-// shorthand at hydration) can import them without pulling in heavy launch code.
+// Structure URL builders and target parsers, with no dependencies.
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.uniprotGffUrl = uniprotGffUrl;
 exports.uniprotFastaUrl = uniprotFastaUrl;
@@ -17,10 +15,8 @@ exports.getStructureUrlFromTarget = getStructureUrlFromTarget;
 exports.getConfidenceUrlFromTarget = getConfidenceUrlFromTarget;
 exports.structureDisplayLabel = structureDisplayLabel;
 const ALPHAFOLD_VERSION = 'v6';
-// UniProt endpoints. rest.* is the machine API (the GFF the feature tracks and
-// the alignment's annotation rows both read, the FASTA the temporary protein
-// assembly is built from); www.*/entry is the human-facing entry page the UI
-// links to. Centralized so a path change is one edit rather than a grep.
+// UniProt endpoints. rest.* is the machine API, serving the features as GFF
+// and the sequence as FASTA; www.*/entry is the entry page for people.
 function uniprotGffUrl(uniprotId) {
     return `https://rest.uniprot.org/uniprotkb/${uniprotId}.gff`;
 }
@@ -52,20 +48,15 @@ function rcsbEntryUrl(pdbId) {
     return `https://www.rcsb.org/structure/${pdbId.toUpperCase()}`;
 }
 /**
- * Resolve the `{ pdbId }` shorthand to a concrete structure URL, so a
- * hand-authored snapshot or a short launch URL doesn't have to know RCSB's
- * filename format. An explicit `url` (or inline `data`) always wins.
- * Idempotent: re-resolving an already-resolved spec returns the same url.
+ * Resolve the `{ pdbId }` shorthand to a structure URL, so a hand-written config
+ * or a short launch URL needs no RCSB filename. An explicit `url` (or inline
+ * `data`) always wins, and resolving an already-resolved spec returns the same
+ * url.
  *
- * `uniprotId` deliberately resolves to no url here, and still outranks a
- * `pdbId`. An accession's files are whatever AlphaFold DB currently holds — an
- * isoform model, several fragments, a new model version — so the structure
- * keeps the accession and the structure loader asks the prediction API which
- * file to open.
- *
- * Shared by the Structure model's snapshot preprocessor and the
- * LaunchView-ProteinView extension point, which would otherwise each carry
- * their own copy of the same precedence rule.
+ * `uniprotId` resolves to no url and still outranks a `pdbId`. AlphaFold DB's
+ * files for an accession change (an isoform model, several fragments, a new
+ * model version), so the caller keeps the accession and asks
+ * `fetchAlphaFoldModels` which file to open.
  */
 function resolveStructureUrl({ url, data, uniprotId, pdbId, }) {
     if (url !== undefined || data !== undefined) {
@@ -132,9 +123,9 @@ function getConfidenceUrlFromTarget(target) {
     return undefined;
 }
 /**
- * What a structure is called in the UI: its PDB id, its AlphaFold accession,
- * else the file's name. Shared by the view title, the alignment panel heading
- * and the hover readout, so one structure reads the same everywhere.
+ * The name to show for a structure: its PDB id, its AlphaFold accession, else
+ * the file's name. Use it wherever a structure is named, so each place shows
+ * the same name.
  */
 function structureDisplayLabel({ url, data, uniprotId, }) {
     if (url === undefined) {

package/dist/structureUrls.js.map

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package/dist/types.d.ts

@@ -5,10 +5,7 @@ export declare const ALIGNMENT_ALGORITHMS: {
 };
 export declare const DEFAULT_ALIGNMENT_ALGORITHM: AlignmentAlgorithm;
 export declare const ALIGNMENT_ALGORITHM_VALUES: AlignmentAlgorithm[];
-/**
- * Parses an untrusted algorithm name (a URL session-spec param) into the union.
- * The only place a coercion is needed: the model property is an enumeration, so
- * everything downstream of hydration is already typed.
- */
+/** Parses an untrusted algorithm name, such as a URL parameter, falling back
+ * to Smith-Waterman. */
 export declare function coerceAlignmentAlgorithm(value: string): AlignmentAlgorithm;
 export declare const ALIGNMENT_ALGORITHM_LABELS: Record<AlignmentAlgorithm, string>;

package/dist/types.js

@@ -11,11 +11,8 @@ exports.ALIGNMENT_ALGORITHM_VALUES = [
     'needleman_wunsch',
     'smith_waterman',
 ];
-/**
- * Parses an untrusted algorithm name (a URL session-spec param) into the union.
- * The only place a coercion is needed: the model property is an enumeration, so
- * everything downstream of hydration is already typed.
- */
+/** Parses an untrusted algorithm name, such as a URL parameter, falling back
+ * to Smith-Waterman. */
 function coerceAlignmentAlgorithm(value) {
     return (exports.ALIGNMENT_ALGORITHM_VALUES.find(v => v === value) ??
         exports.DEFAULT_ALIGNMENT_ALGORITHM);

package/dist/types.js.map

@@ -1 +1 @@
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+{"version":3,"file":"types.js","sourceRoot":"","sources":["../src/types.ts"],"names":[],"mappings":";;;AAgBA,4DAKC;AAnBY,QAAA,oBAAoB,GAAG;IAClC,gBAAgB,EAAE,kBAAkB;IACpC,cAAc,EAAE,gBAAgB;CACxB,CAAA;AAEG,QAAA,2BAA2B,GAAuB,gBAAgB,CAAA;AAElE,QAAA,0BAA0B,GAAyB;IAC9D,kBAAkB;IAClB,gBAAgB;CACjB,CAAA;AAED;wBACwB;AACxB,SAAgB,wBAAwB,CAAC,KAAa;IACpD,OAAO,CACL,kCAA0B,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,KAAK,CAAC;QACjD,mCAA2B,CAC5B,CAAA;AACH,CAAC;AAEY,QAAA,0BAA0B,GAAuC;IAC5E,gBAAgB,EAAE,kBAAkB;IACpC,cAAc,EAAE,gBAAgB;CACjC,CAAA"}

package/dist/uniProtSearch.js

@@ -51,7 +51,6 @@ async function searchByXref(id, opts) {
         return { entries: await searchUniProt(query, 10, opts), error: undefined };
     }
     catch (e) {
-        console.error(`xref search failed for ${id}:`, e);
         return { entries: [], error: e };
     }
 }
@@ -63,18 +62,14 @@ async function searchByGeneName(geneName, organismId, opts) {
         // are 284812. The descendants are asked only on a miss, because for a
         // species with reviewed subspecies entries (human and Neanderthal) they
         // turn one answer into two.
-        // The taxon itself has answered, so the wider question failing leaves
-        // that answer standing rather than turning an empty result into an error.
+        // When the descendant search fails, the taxon's own empty result stands
+        // rather than becoming an error.
         const entries = exact.length === 0 && organismId
-            ? await searchUniProt(buildGeneNameQuery(geneName, organismId, 'taxonomy_id'), 5, opts).catch((e) => {
-                console.error(`descendant-taxon search failed for ${geneName}:`, e);
-                return exact;
-            })
+            ? await searchUniProt(buildGeneNameQuery(geneName, organismId, 'taxonomy_id'), 5, opts).catch(() => exact)
             : exact;
         return { entries, error: undefined };
     }
     catch (e) {
-        console.error(`gene name search failed for ${geneName}:`, e);
         return { entries: [], error: e };
     }
 }

package/dist/uniProtSearch.js.map

@@ -1 +1 @@
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package/esm/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;
 }