--- before
+++ after
@@ -1,883 +0,0 @@
-import {
-  SEQUENCE_VIEWER_LIMITS,
-  SequenceViewerLimitError,
-} from "../../runtime-contract";
-import { enrichCdsFeature } from "../feature-translation";
-import type {
-  SequenceFeature,
-  SequenceFeatureSegment,
-  SequenceParseWarning,
-  SequenceRecord,
-} from "../types";
-
-// Compatibility is deliberately limited to revisions exercised by the primary
-// Biopython SnapGene fixtures, not inferred from a matching filename or cookie.
-// https://github.com/biopython/biopython/tree/master/Tests/SnapGene
-// Packet and coordinate reference:
-// https://github.com/biopython/biopython/blob/master/Bio/SeqIO/SnapGeneIO.py
-const SUPPORTED_REVISIONS = new Set([
-  "13:11",
-  "13:12",
-  "14:16",
-  "15:19",
-  "15:20",
-]);
-const MAX_XML_DEPTH = 32;
-const MAX_WARNING_KINDS = 64;
-const MAX_TRANSLATED_BASES = 1_000_000;
-const utf8 = new TextDecoder("utf-8", { fatal: true });
-
-type XmlElement = {
-  attributes: Map<string, string>;
-  children: Array<XmlElement>;
-  name: string;
-  text: string;
-};
-
-type Packet = { data: Uint8Array; type: number };
-type Qualifiers = SequenceFeature["qualifiers"];
-
-class Warnings {
-  private readonly entries = new Map<string, SequenceParseWarning>();
-  private omitted = 0;
-
-  add(code: string, message: string, detail = ""): void {
-    const key = `${code}:${detail}`;
-    if (this.entries.has(key)) return;
-    if (this.entries.size >= MAX_WARNING_KINDS) {
-      this.omitted += 1;
-      return;
-    }
-    this.entries.set(key, { code, message, severity: "warning" });
-  }
-
-  list(): Array<SequenceParseWarning> {
-    const warnings = [...this.entries.values()];
-    if (this.omitted > 0) {
-      warnings.push({
-        code: "snapgene-additional-warnings",
-        message:
-          "Additional unsupported SnapGene annotation properties were omitted from this bounded warning summary.",
-        severity: "warning",
-      });
-    }
-    return warnings;
-  }
-}
-
-export function parseSnapGeneRecord({
-  bytes,
-  fileName,
-}: {
-  bytes: Uint8Array;
-  fileName?: string;
-}): { record: SequenceRecord; warnings: Array<SequenceParseWarning> } {
-  if (bytes.byteLength > SEQUENCE_VIEWER_LIMITS.session.maxArtifactBytes) {
-    throw new SequenceViewerLimitError(
-      "snapgene-input-too-large",
-      "SnapGene import exceeds the bounded artifact byte limit.",
-    );
-  }
-  const packets = readPackets(bytes);
-  const cookie = packets.shift();
-  if (
-    cookie?.type !== 9 ||
-    cookie.data.length !== 14 ||
-    utf8.decode(cookie.data.subarray(0, 8)) !== "SnapGene"
-  ) {
-    throw new Error(
-      "The file does not start with a valid SnapGene cookie packet.",
-    );
-  }
-  const header = new DataView(
-    cookie.data.buffer,
-    cookie.data.byteOffset,
-    cookie.data.byteLength,
-  );
-  const sequenceType = header.getUint16(8);
-  const exportVersion = header.getUint16(10);
-  const importVersion = header.getUint16(12);
-  if (sequenceType !== 1) {
-    throw new Error("Only SnapGene DNA sequence containers are supported.");
-  }
-  if (!SUPPORTED_REVISIONS.has(`${exportVersion}:${importVersion}`)) {
-    throw new Error(
-      `Unsupported SnapGene revision ${exportVersion}:${importVersion}. Export this file to GenBank to view its sequence and annotations.`,
-    );
-  }
-
-  const warnings = new Warnings();
-  const singletonTypes = new Set<number>();
-  let dna: Uint8Array | undefined;
-  const xmlPackets: Array<{ root: XmlElement; type: number }> = [];
-  for (const packet of packets) {
-    if (packet.type === 9)
-      throw new Error("A SnapGene file cannot contain a second cookie packet.");
-    if ([0, 5, 6, 10].includes(packet.type)) {
-      if (singletonTypes.has(packet.type))
-        throw new Error(`Duplicate SnapGene packet type ${packet.type}.`);
-      singletonTypes.add(packet.type);
-      if (packet.type === 0) dna = packet.data;
-      else xmlPackets.push({ root: parseXml(packet.data), type: packet.type });
-    } else {
-      warnings.add(
-        "unsupported-snapgene-packet",
-        `SnapGene packet 0x${packet.type.toString(16).padStart(2, "0")} is not imported; its application settings, history, or other data remain only in the original file.`,
-        String(packet.type),
-      );
-    }
-  }
-  if (dna == null || dna.length < 2)
-    throw new Error("The SnapGene file has no nonempty DNA sequence packet.");
-  if (dna.length - 1 > SEQUENCE_VIEWER_LIMITS.input.maxTotalResidues) {
-    throw new SequenceViewerLimitError(
-      "snapgene-residue-limit",
-      "SnapGene sequence exceeds the total residue limit.",
-    );
-  }
-  const flags = dna[0] ?? 0;
-  const rawSequence = utf8.decode(dna.subarray(1));
-  if (!/^[ACGTRYSWKMBDHVNacgtryswkmbdhvn]+$/.test(rawSequence)) {
-    throw new Error(
-      "The SnapGene DNA packet contains invalid or unsupported sequence symbols.",
-    );
-  }
-  const sequence = rawSequence.toUpperCase();
-  if ((flags & ~1) !== 0) {
-    warnings.add(
-      "unsupported-snapgene-dna-flags",
-      "Only DNA topology is interpreted from the SnapGene sequence flags; strand chemistry and other flag properties are not reproduced.",
-    );
-  }
-  const sourceLabel =
-    fileName
-      ?.split(/[/\\]/)
-      .pop()
-      ?.replace(/\.dna$/i, "") || "SnapGene sequence";
-  const record: SequenceRecord = {
-    features: [],
-    id: sourceLabel,
-    length: sequence.length,
-    metadata: {
-      snapgeneDnaFlags: String(flags),
-      snapgeneExportVersion: String(exportVersion),
-      snapgeneImportVersion: String(importVersion),
-    },
-    molecule: "dna",
-    sequence,
-    sourceLabel,
-    topology: flags & 1 ? "circular" : "linear",
-  };
-  for (const { root, type } of xmlPackets) {
-    const expectedRoot =
-      type === 5 ? "Primers" : type === 6 ? "Notes" : "Features";
-    if (root.name !== expectedRoot)
-      throw new Error(`Expected a SnapGene ${expectedRoot} XML root.`);
-    if (type === 6) readNotes(root, record, warnings);
-    else if (type === 10) readFeatures(root, record, warnings);
-    else readPrimers(root, record, warnings);
-  }
-  const translationWarnings: Array<SequenceParseWarning> = [];
-  let translatedBases = 0;
-  record.features = record.features.map((feature) => {
-    if (feature.type.toLowerCase() !== "cds") return feature;
-    const length =
-      feature.segments?.reduce(
-        (sum, segment) => sum + segment.end - segment.start + 1,
-        0,
-      ) ?? 0;
-    if (length > MAX_TRANSLATED_BASES - translatedBases) {
-      warnings.add(
-        "snapgene-translation-budget",
-        "Some CDS coordinate maps exceed the bounded import translation budget; source translations are retained where available, but those maps are unavailable.",
-      );
-      return {
-        ...feature,
-        translationTrackReliable: false,
-        translationMappingUnavailableReason:
-          "bounded SnapGene import translation budget",
-      };
-    }
-    translatedBases += length;
-    return enrichCdsFeature({
-      feature,
-      sequence,
-      warnings: translationWarnings,
-    });
-  });
-  for (const warning of translationWarnings)
-    warnings.add(warning.code, warning.message);
-  return { record, warnings: warnings.list() };
-}
-
-function readPackets(bytes: Uint8Array): Array<Packet> {
-  const view = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);
-  const packets: Array<Packet> = [];
-  for (let offset = 0; offset < bytes.length;) {
-    if (bytes.length - offset < 5)
-      throw new Error("Truncated SnapGene packet header.");
-    const type = view.getUint8(offset);
-    const size = view.getUint32(offset + 1);
-    offset += 5;
-    if (size > bytes.length - offset)
-      throw new Error("SnapGene packet extends beyond the end of the file.");
-    if (packets.length >= SEQUENCE_VIEWER_LIMITS.input.maxTrackItems) {
-      throw new SequenceViewerLimitError(
-        "snapgene-packet-limit",
-        "SnapGene file contains too many packets.",
-      );
-    }
-    packets.push({ data: bytes.subarray(offset, offset + size), type });
-    offset += size;
-  }
-  return packets;
-}
-
-function readNotes(
-  root: XmlElement,
-  record: SequenceRecord,
-  warnings: Warnings,
-): void {
-  checkProperties(
-    root,
-    [],
-    root.children.map((child) => child.name),
-    warnings,
-  );
-  for (const child of root.children) {
-    checkProperties(child, [...child.attributes.keys()], [], warnings, true);
-    const value = plainText(child.text, warnings);
-    addValue(record.metadata, `snapgene.${child.name}`, value);
-    for (const [key, attribute] of child.attributes)
-      addValue(record.metadata, `snapgene.${child.name}.${key}`, attribute);
-    if (
-      child.name === "Description" ||
-      (child.name === "Comments" && !record.description)
-    )
-      record.description = value || undefined;
-  }
-}
-
-function readFeatures(
-  root: XmlElement,
-  record: SequenceRecord,
-  warnings: Warnings,
-): void {
-  checkProperties(root, ["nextValidID"], ["Feature"], warnings);
-  for (const node of root.children.filter(
-    (child) => child.name === "Feature",
-  )) {
-    checkProperties(
-      node,
-      ["name", "type", "directionality", "recentID"],
-      ["Segment", "Q"],
-      warnings,
-    );
-    const qualifiers: Qualifiers = {};
-    const name = plainText(node.attributes.get("name") ?? "", warnings);
-    const direction = node.attributes.get("directionality") ?? "0";
-    const strand =
-      direction === "1"
-        ? "+"
-        : direction === "2"
-          ? "-"
-          : direction === "0"
-            ? "."
-            : "?";
-    if (strand === "?")
-      warnings.add(
-        "unsupported-snapgene-directionality",
-        "Bidirectional or unknown SnapGene feature directionality is retained as unknown strand; its translation mapping is unavailable.",
-      );
-    addValue(qualifiers, "snapgene_directionality", direction);
-    const sourceId = node.attributes.get("recentID");
-    if (sourceId != null) addValue(qualifiers, "snapgene_id", sourceId);
-    let segments: Array<SequenceFeatureSegment> = [];
-    let mappingReason =
-      strand === "." || strand === "?"
-        ? "no single feature strand specified"
-        : undefined;
-    for (const segment of node.children.filter(
-      (child) => child.name === "Segment",
-    )) {
-      checkProperties(
-        segment,
-        ["range", "type", "name", "color", "translated"],
-        [],
-        warnings,
-      );
-      const range = requiredAttribute(segment, "range");
-      const parts = readRange(range, record, false);
-      const segmentType = segment.attributes.get("type") ?? "standard";
-      if (segmentType === "gap") {
-        addValue(qualifiers, "snapgene_gap_range", range);
-        warnings.add(
-          "snapgene-gap-segments",
-          "SnapGene gap segments are recorded as qualifiers and excluded from the biological feature path.",
-        );
-        continue;
-      }
-      if (
-        segmentType !== "standard" ||
-        (segment.attributes.has("translated") &&
-          segment.attributes.get("translated") !== "1")
-      ) {
-        mappingReason = "unsupported SnapGene segment translation semantics";
-        warnings.add(
-          "unsupported-snapgene-segment",
-          "A SnapGene segment has unsupported translation semantics; its coordinate bounds are retained, but translation mapping is unavailable.",
-        );
-      }
-      const segmentName = segment.attributes.get("name");
-      if (segmentName != null)
-        addValue(
-          qualifiers,
-          "snapgene_segment_name",
-          `${range}:${plainText(segmentName, warnings)}`,
-        );
-      const color = segment.attributes.get("color");
-      if (color != null) {
-        addValue(qualifiers, "snapgene_segment_color", `${range}:${color}`);
-        warnings.add(
-          "snapgene-display-properties",
-          "SnapGene segment colors are retained as coordinate-labelled qualifiers, but native map styling is not reproduced.",
-        );
-      }
-      segments.push(...parts);
-    }
-    if (segments.length === 0)
-      throw new Error("SnapGene feature has no supported non-gap location.");
-    if (strand === "-") segments = segments.reverse();
-    for (const qualifier of node.children.filter(
-      (child) => child.name === "Q",
-    )) {
-      checkProperties(qualifier, ["name"], ["V"], warnings);
-      const key = requiredAttribute(qualifier, "name");
-      if (qualifier.children.length === 0) addValue(qualifiers, key, "true");
-      for (const value of qualifier.children.filter(
-        (child) => child.name === "V",
-      )) {
-        checkProperties(value, ["text", "predef", "int"], [], warnings);
-        const values = ["text", "predef", "int"].filter((attribute) =>
-          value.attributes.has(attribute),
-        );
-        if (values.length !== 1) {
-          warnings.add(
-            "unsupported-snapgene-qualifier",
-            "A SnapGene qualifier value did not have exactly one supported text, predef, or int representation and was not imported.",
-          );
-          continue;
-        }
-        const attribute = values[0] ?? "text";
-        const rawValue = value.attributes.get(attribute) ?? "";
-        if (
-          attribute === "int" &&
-          (!/^-?\d+$/.test(rawValue) || !Number.isSafeInteger(Number(rawValue)))
-        )
-          throw new Error("Invalid SnapGene integer qualifier.");
-        addValue(
-          qualifiers,
-          key,
-          plainText(rawValue, warnings).replaceAll(/\r\n?|\n/g, " "),
-        );
-      }
-    }
-    if (name && !Object.hasOwn(qualifiers, "label"))
-      addValue(qualifiers, "label", name);
-    else if (name) addValue(qualifiers, "snapgene_name", name);
-    const type = node.attributes.get("type") || "misc_feature";
-    const translation = firstValue(qualifiers.translation)
-      ?.replaceAll(/\s+/g, "")
-      .toUpperCase();
-    if (type.toLowerCase() === "cds") {
-      const codonStart = firstValue(qualifiers.codon_start);
-      const geneticCode = firstValue(qualifiers.transl_table);
-      if (codonStart != null && !/^[123]$/.test(codonStart))
-        throw new Error("Invalid SnapGene CDS codon_start qualifier.");
-      if (
-        geneticCode != null &&
-        (!/^\d+$/.test(geneticCode) ||
-          !Number.isSafeInteger(Number(geneticCode)) ||
-          Number(geneticCode) < 1)
-      )
-        throw new Error("Invalid SnapGene CDS transl_table qualifier.");
-    }
-    appendFeature(record, {
-      ...featureLocation(segments, strand),
-      id: `snapgene-feature-${record.features.length + 1}`,
-      label: firstValue(qualifiers.label) || name || type,
-      qualifiers,
-      translation: translation || undefined,
-      translationMappingUnavailableReason: mappingReason,
-      translationSource: translation ? "qualifier" : undefined,
-      translationTrackReliable: mappingReason == null,
-      type,
-    });
-  }
-}
-
-function readPrimers(
-  root: XmlElement,
-  record: SequenceRecord,
-  warnings: Warnings,
-): void {
-  checkProperties(
-    root,
-    ["nextValidID"],
-    ["HybridizationParams", "Primer"],
-    warnings,
-  );
-  const params = root.children.filter(
-    (child) => child.name === "HybridizationParams",
-  );
-  if (params.length > 1)
-    throw new Error("Duplicate SnapGene primer hybridization parameters.");
-  const minLength = readOptionalNumber(params[0], "minContinuousMatchLen", 0);
-  const minTm = readOptionalNumber(params[0], "minMeltingTemperature", 0);
-  if (minLength != null && (!Number.isSafeInteger(minLength) || minLength < 0))
-    throw new Error("Invalid SnapGene minimum primer match length.");
-  if (params[0] != null)
-    checkProperties(
-      params[0],
-      ["minContinuousMatchLen", "minMeltingTemperature"],
-      [],
-      warnings,
-    );
-  for (const primer of root.children.filter(
-    (child) => child.name === "Primer",
-  )) {
-    checkProperties(
-      primer,
-      ["name", "sequence", "description", "recentID", "dateAdded"],
-      ["BindingSite"],
-      warnings,
-    );
-    const name = plainText(primer.attributes.get("name") ?? "Primer", warnings);
-    const sites = primer.children.filter(
-      (child) => child.name === "BindingSite",
-    );
-    const detailedSites = new Set<string>();
-    // Simplified sites can precede their detailed equivalents in the XML.
-    // Only suppress a duplicate when a detailed site survives visibility filters.
-    const orderedSites = [
-      ...sites.filter((site) => site.attributes.get("simplified") !== "1"),
-      ...sites.filter((site) => site.attributes.get("simplified") === "1"),
-    ];
-    if (sites.length === 0)
-      warnings.add(
-        "snapgene-unbound-primer",
-        "An unbound SnapGene primer has no genomic location and is not displayed as a feature.",
-      );
-    for (const site of orderedSites) {
-      checkProperties(
-        site,
-        [
-          "location",
-          "boundStrand",
-          "simplified",
-          "annealedBases",
-          "meltingTemperature",
-        ],
-        [],
-        warnings,
-      );
-      const rawRange = requiredAttribute(site, "location");
-      const boundStrand = site.attributes.get("boundStrand") ?? "0";
-      if (boundStrand !== "0" && boundStrand !== "1")
-        throw new Error("Unsupported SnapGene primer strand.");
-      const strand = boundStrand === "1" ? "-" : "+";
-      let segments = readRange(rawRange, record, true);
-      if (strand === "-") segments = segments.reverse();
-      if (
-        site.attributes.get("simplified") === "1" &&
-        detailedSites.has(`${rawRange}:${boundStrand}`)
-      ) {
-        warnings.add(
-          "snapgene-simplified-primer-sites",
-          "Duplicate simplified SnapGene primer sites are not shown twice.",
-        );
-        continue;
-      }
-      const annealed = site.attributes.get("annealedBases");
-      const tm = readOptionalNumber(site, "meltingTemperature", undefined);
-      if (
-        (annealed != null && annealed.length < (minLength ?? 0)) ||
-        (tm != null && tm < (minTm ?? 0))
-      ) {
-        warnings.add(
-          "snapgene-hidden-primer-sites",
-          "Primer sites below the file's hybridization length or melting-temperature threshold are not displayed, matching SnapGene's visible-site filtering.",
-        );
-        continue;
-      }
-      if (
-        (annealed == null && (minLength ?? 0) > 0) ||
-        (tm == null && (minTm ?? 0) > 0)
-      ) {
-        warnings.add(
-          "snapgene-primer-filter-unknown",
-          "Some primer sites lack the stored measurements needed to apply all hybridization thresholds; these imported sites may differ from SnapGene's visible sites.",
-        );
-      }
-      if (site.attributes.get("simplified") !== "1")
-        detailedSites.add(`${rawRange}:${boundStrand}`);
-      const qualifiers: Qualifiers = {
-        label: name,
-        snapgene_primer_location: rawRange,
-      };
-      for (const key of ["sequence", "description", "recentID", "dateAdded"]) {
-        const value = primer.attributes.get(key);
-        if (value != null)
-          addValue(qualifiers, `snapgene_${key}`, plainText(value, warnings));
-      }
-      if (annealed != null) addValue(qualifiers, "annealed_bases", annealed);
-      if (tm != null) addValue(qualifiers, "melting_temperature", String(tm));
-      appendFeature(record, {
-        ...featureLocation(segments, strand),
-        id: `snapgene-primer-${record.features.length + 1}`,
-        label: name,
-        qualifiers,
-        type: "primer_bind",
-      });
-    }
-  }
-}
-
-function readRange(
-  range: string,
-  record: SequenceRecord,
-  primer: boolean,
-): Array<SequenceFeatureSegment> {
-  const match = /^(\d+)-(\d+)$/.exec(range);
-  if (match == null) throw new Error("Invalid SnapGene annotation range.");
-  const start = Number(match[1]) + (primer ? 1 : 0);
-  const end = Number(match[2]) + (primer ? 1 : 0);
-  if (
-    !Number.isSafeInteger(start) ||
-    !Number.isSafeInteger(end) ||
-    start < 1 ||
-    end < 1 ||
-    start > record.length ||
-    end > record.length
-  )
-    throw new Error("SnapGene annotation range lies outside the sequence.");
-  if (start <= end) return [{ start, end }];
-  if (record.topology !== "circular")
-    throw new Error(
-      "An origin-spanning SnapGene annotation requires a circular sequence.",
-    );
-  return [
-    { start, end: record.length },
-    { start: 1, end },
-  ];
-}
-
-function featureLocation(
-  segments: Array<SequenceFeatureSegment>,
-  strand: SequenceFeature["strand"],
-): Pick<
-  SequenceFeature,
-  "start" | "end" | "segments" | "strand" | "sourceLocation"
-> {
-  let start = Infinity;
-  let end = 0;
-  for (const segment of segments) {
-    start = Math.min(start, segment.start);
-    end = Math.max(end, segment.end);
-  }
-  const forwardSegments = strand === "-" ? [...segments].reverse() : segments;
-  const ranges = forwardSegments.map(
-    (segment) => `${segment.start}..${segment.end}`,
-  );
-  const location =
-    ranges.length === 1 ? (ranges[0] ?? "") : `join(${ranges.join(",")})`;
-  return {
-    start,
-    end,
-    segments,
-    strand,
-    sourceLocation: strand === "-" ? `complement(${location})` : location,
-  };
-}
-
-function appendFeature(record: SequenceRecord, feature: SequenceFeature): void {
-  if (record.features.length >= SEQUENCE_VIEWER_LIMITS.input.maxTrackItems)
-    throw new SequenceViewerLimitError(
-      "snapgene-feature-limit",
-      "SnapGene file contains too many annotations.",
-    );
-  record.features.push(feature);
-}
-
-function requiredAttribute(node: XmlElement, name: string): string {
-  const value = node.attributes.get(name);
-  if (value == null || value.length === 0)
-    throw new Error(`Missing SnapGene ${node.name} ${name} attribute.`);
-  return value;
-}
-
-function readOptionalNumber(
-  node: XmlElement | undefined,
-  name: string,
-  fallback: number | undefined,
-): number | undefined {
-  const value = node?.attributes.get(name);
-  if (value == null) return fallback;
-  const parsed = Number(value);
-  if (!/^-?\d+(?:\.\d+)?$/.test(value) || !Number.isFinite(parsed))
-    throw new Error(`Invalid SnapGene ${name} value.`);
-  return parsed;
-}
-
-function addValue(target: Qualifiers, key: string, value: string): void {
-  const prior = Object.hasOwn(target, key) ? target[key] : undefined;
-  if (Array.isArray(prior)) {
-    prior.push(value);
-    return;
-  }
-  const next = prior == null ? value : [prior, value];
-  // Qualifier names are untrusted data, including __proto__ and constructor.
-  Object.defineProperty(target, key, {
-    configurable: true,
-    enumerable: true,
-    value: next,
-    writable: true,
-  });
-}
-
-function firstValue(
-  value: string | Array<string> | undefined,
-): string | undefined {
-  return Array.isArray(value) ? value[0] : value;
-}
-
-function plainText(value: string, warnings: Warnings): string {
-  const parts: Array<string> = [];
-  let offset = 0;
-  let hasMarkup = false;
-  while (offset < value.length) {
-    const start = value.indexOf("<", offset);
-    const end = start === -1 ? -1 : value.indexOf(">", start + 1);
-    if (start === -1 || end === -1) {
-      parts.push(value.slice(offset));
-      break;
-    }
-    parts.push(value.slice(offset, start));
-    const tag = /^\/?([A-Za-z][A-Za-z0-9-]*)(?:[ \t\r\n][^<>]*|\/)?$/.exec(
-      value.slice(start + 1, end),
-    );
-    if (tag == null) parts.push(value.slice(start, end + 1));
-    else {
-      hasMarkup = true;
-      if (["p", "br", "div"].includes(tag[1]?.toLowerCase() ?? ""))
-        parts.push(" ");
-    }
-    offset = end + 1;
-  }
-  if (hasMarkup) {
-    warnings.add(
-      "snapgene-rich-text",
-      "SnapGene rich-text markup is displayed as plain text; formatting is not reproduced.",
-    );
-  }
-  return parts.join("").trim();
-}
-
-function checkProperties(
-  node: XmlElement,
-  attributes: Array<string>,
-  children: Array<string>,
-  warnings: Warnings,
-  allowText = false,
-): void {
-  const allowedAttributes = new Set(attributes);
-  const allowedChildren = new Set(children);
-  if (
-    (!allowText && node.text.trim()) ||
-    [...node.attributes.keys()].some((key) => !allowedAttributes.has(key)) ||
-    node.children.some((child) => !allowedChildren.has(child.name))
-  ) {
-    warnings.add(
-      "unsupported-snapgene-xml-property",
-      `Some ${node.name} properties or child annotations are not represented by this viewer and remain in the original file.`,
-      node.name,
-    );
-  }
-}
-
-/** Small, bounded XML subset reader: no DOM, DTDs, entity expansion, or I/O. */
-function parseXml(bytes: Uint8Array): XmlElement {
-  const xml = utf8.decode(bytes);
-  if (/[\u0000-\u0008\u000b\u000c\u000e-\u001f\ufffe\uffff]/.test(xml))
-    throw new Error("Invalid control character in SnapGene XML.");
-  const stack: Array<XmlElement> = [];
-  let root: XmlElement | undefined;
-  let offset = 0;
-  let nodes = 0;
-  let declarationSeen = false;
-  const appendText = (text: string): void => {
-    const current = stack[stack.length - 1];
-    if (current != null) current.text += text;
-    else if (/[^ \t\r\n]/.test(text))
-      throw new Error("Unexpected text outside the SnapGene XML root.");
-  };
-  while (offset < xml.length) {
-    if (xml[offset] !== "<") {
-      const next = xml.indexOf("<", offset);
-      const end = next === -1 ? xml.length : next;
-      const value = xml.slice(offset, end);
-      if (value.includes("]]>")) throw new Error("Invalid SnapGene XML text.");
-      appendText(decodeEntities(value));
-      offset = end;
-      continue;
-    }
-    if (xml.startsWith("<!--", offset)) {
-      const end = xml.indexOf("-->", offset + 4);
-      if (end === -1 || xml.slice(offset + 4, end).includes("--"))
-        throw new Error("Malformed SnapGene XML comment.");
-      offset = end + 3;
-      continue;
-    }
-    if (xml.startsWith("<![CDATA[", offset)) {
-      const end = xml.indexOf("]]>", offset + 9);
-      if (end === -1 || stack.length === 0)
-        throw new Error("Malformed SnapGene XML CDATA.");
-      appendText(xml.slice(offset + 9, end));
-      offset = end + 3;
-      continue;
-    }
-    if (xml.startsWith("<?xml", offset)) {
-      const end = xml.indexOf("?>", offset + 5);
-      const declaration = xml.slice(offset, end + 2);
-      if (
-        end === -1 ||
-        offset !== 0 ||
-        declarationSeen ||
-        root != null ||
-        !/^<\?xml[ \t\r\n]+version[ \t\r\n]*=[ \t\r\n]*(["'])1\.0\1(?:[ \t\r\n]+encoding[ \t\r\n]*=[ \t\r\n]*(["'])UTF-8\2)?(?:[ \t\r\n]+standalone[ \t\r\n]*=[ \t\r\n]*(["'])(?:yes|no)\3)?[ \t\r\n]*\?>$/i.test(
-          declaration,
-        )
-      )
-        throw new Error("Unsupported SnapGene XML declaration.");
-      declarationSeen = true;
-      offset = end + 2;
-      continue;
-    }
-    if (xml.startsWith("<!", offset) || xml.startsWith("<?", offset))
-      throw new Error(
-        "DTD, entity declarations, and processing instructions are not supported in SnapGene XML.",
-      );
-    const close = xml.startsWith("</", offset);
-    offset += close ? 2 : 1;
-    const nameMatch = /^[A-Za-z_][A-Za-z0-9_.-]*/.exec(xml.slice(offset));
-    if (nameMatch == null)
-      throw new Error("Invalid SnapGene XML element name.");
-    const name = nameMatch[0];
-    offset += name.length;
-    if (close) {
-      while (/[ \t\r\n]/.test(xml[offset] ?? "") && offset < xml.length)
-        offset += 1;
-      if (xml[offset] !== ">" || stack.pop()?.name !== name)
-        throw new Error("Mismatched SnapGene XML closing element.");
-      offset += 1;
-      continue;
-    }
-    const element: XmlElement = {
-      attributes: new Map(),
-      children: [],
-      name,
-      text: "",
-    };
-    let selfClosing = false;
-    while (offset < xml.length) {
-      const beforeSpace = offset;
-      while (/[ \t\r\n]/.test(xml[offset] ?? "") && offset < xml.length)
-        offset += 1;
-      if (xml[offset] === ">") {
-        offset += 1;
-        break;
-      }
-      if (xml.startsWith("/>", offset)) {
-        selfClosing = true;
-        offset += 2;
-        break;
-      }
-      if (beforeSpace === offset)
-        throw new Error("Malformed SnapGene XML attribute separation.");
-      const attribute =
-        /^([A-Za-z_][A-Za-z0-9_.-]*)[ \t\r\n]*=[ \t\r\n]*(["'])/.exec(
-          xml.slice(offset),
-        );
-      if (attribute == null)
-        throw new Error("Malformed SnapGene XML attribute.");
-      const key = attribute[1] ?? "";
-      const quote = attribute[2] ?? '"';
-      offset += attribute[0].length;
-      const end = xml.indexOf(quote, offset);
-      if (
-        end === -1 ||
-        element.attributes.has(key) ||
-        xml.slice(offset, end).includes("<")
-      )
-        throw new Error("Invalid or duplicate SnapGene XML attribute.");
-      element.attributes.set(key, decodeEntities(xml.slice(offset, end)));
-      nodes += 1;
-      if (nodes > SEQUENCE_VIEWER_LIMITS.input.maxTrackItems)
-        throw new SequenceViewerLimitError(
-          "snapgene-xml-limit",
-          "SnapGene XML exceeds the bounded node or attribute limit.",
-        );
-      offset = end + 1;
-    }
-    if (xml[offset - 1] !== ">")
-      throw new Error("Unterminated SnapGene XML element.");
-    nodes += 1;
-    if (
-      nodes > SEQUENCE_VIEWER_LIMITS.input.maxTrackItems ||
-      stack.length >= MAX_XML_DEPTH
-    )
-      throw new SequenceViewerLimitError(
-        "snapgene-xml-limit",
-        "SnapGene XML exceeds the bounded node or nesting limit.",
-      );
-    const parent = stack[stack.length - 1];
-    if (parent != null) parent.children.push(element);
-    else if (root == null) root = element;
-    else throw new Error("SnapGene XML contains multiple roots.");
-    if (!selfClosing) stack.push(element);
-  }
-  if (root == null || stack.length > 0)
-    throw new Error("Incomplete SnapGene XML document.");
-  return root;
-}
-
-function decodeEntities(value: string): string {
-  return value.replaceAll(
-    /&([^;&\s]*);|&/g,
-    (entity: string, name: string | undefined) => {
-      if (name === "amp") return "&";
-      if (name === "lt") return "<";
-      if (name === "gt") return ">";
-      if (name === "quot") return '"';
-      if (name === "apos") return "'";
-      const numeric =
-        name != null && /^#(?:[0-9]+|x[0-9a-fA-F]+)$/.test(name)
-          ? name.startsWith("#x")
-            ? Number.parseInt(name.slice(2), 16)
-            : Number(name.slice(1))
-          : NaN;
-      if (
-        numeric === 9 ||
-        numeric === 10 ||
-        numeric === 13 ||
-        (numeric >= 0x20 &&
-          numeric <= 0x10ffff &&
-          !(numeric >= 0xd800 && numeric <= 0xdfff) &&
-          numeric !== 0xfffe &&
-          numeric !== 0xffff)
-      )
-        return String.fromCodePoint(numeric);
-      throw new Error("Unknown or invalid entity in SnapGene XML.");
-    },
-  );
-}

Full technical diff · 395 changed fields

changed `/files/.codex-plugin~1plugin.json/sha256`

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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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}

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{
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{
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{
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{
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{
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{
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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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SHA-256 of public snapshot: 3d0564840f9fe2a4607dcfa3ac18b6f38a1415ca67c6b3f49ff495736b42f386

Update to Biological Sequence & Alignment Viewer

Package or technical metadata updated

Package file

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Compare saved observations

Changed files

src/sequence/formats/snapgene.ts

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removed `/files/smoke-fixtures~1alignment.pir`

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removed `/files/smoke-fixtures~1equal-width-ungapped-ambiguous.fasta`

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