varri-js 1.0.0

package/dist/vaRRI.min.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../src/vaRRI.js"],
+  "sourcesContent": ["/**\n * vaRRI.js \u2014 Browser-only JavaScript port of the vaRRI RNA-RNA interaction \n * visualiser.\n *\n * This library translates the Python vaRRI source into pure browser JavaScript,\n * removing all command-line dependencies (RNAfold, RNAplfold, Playwright).\n * It relies on Fornac (https://github.com/ViennaRNA/fornac) and D3.js which\n * must be loaded before this script.\n *\n * @module vaRRI\n */\n\n(function (global) {\n    'use strict';\n\n    // -----------------------------------------------------------------------\n    // Constants\n    // -----------------------------------------------------------------------\n\n    /** Number of invisible gap nodes Fornac inserts between two molecules. */\n    const GAP = 3;\n\n    /** Metadata type for invisible linear-RRI span constraints. */\n    const LINEAR_RRI_LINK_TYPE = 'rri_linear';\n\n    /** Metadata type for invisible intramolecular span constraints. */\n    const LINEAR_STRUCTURE_LINK_TYPE = 'structure_linear';\n\n    /** Fractional per-tick correction used to guide index labels outside a helix rail. */\n    const LINEAR_HELIX_LABEL_BIAS_GAIN = 0.2;\n\n    /** Maximum label correction per tick, relative to its ordinary link length. */\n    const LINEAR_HELIX_LABEL_BIAS_MAX_STEP = 0.05;\n\n    /** Small positive half-plane target used only while a label is on the wrong side. */\n    const LINEAR_HELIX_LABEL_BIAS_TARGET = 0.1;\n\n    /** Active requestAnimationFrame ID for the background-highlight animation loop (null when idle). */\n    let _animFrameId = null;\n\n    /** Active timeout ID for delayed post-processing after a render (null when idle). */\n    let _renderTimeoutId = null;\n\n    /** Resolver for the render promise that is currently waiting for post-processing. */\n    let _pendingRenderResolve = null;\n\n    /** Live Fornac container used by the current render, if any. */\n    let _activeContainer = null;\n\n    /**\n     * Colours used by vaRRI rendering functions initialized to defaults.\n     * \n     *\n     * Change these at runtime with {@link setColors}; the new values take\n     * effect on the next call to any rendering function.\n     */\n    const COLORS = {\n        /** Fill colour for nucleotide circles of sequence 1 in strand-colouring mode. */\n        sequence1: 'lightblue',\n        /** Fill colour for nucleotide circles of sequence 2 in strand-colouring mode. */\n        sequence2: '#F4BB44',\n        /** Default fill colour for sequence-1 accessibility/profile overlays. */\n        seq1profileColor: 'purple',\n        /** Default fill colour for sequence-2 accessibility/profile overlays. */\n        seq2profileColor: 'red',\n        /** Default fill colour for point mutation overlays. */\n        mutationColor: 'Darkgreen',\n        /** Stroke colour used for intermolecular nucleotide and index-label highlighting. */\n        intermolecularHighlight: 'red',\n        /** Fill/stroke colour used for background (region / basepair-stack) highlighting. */\n        backgroundHighlight: 'red',\n        /** Stroke colour used for subsequence-highlighting polylines and circles. */\n        subsequenceHighlight: 'purple',\n        /** Stroke colour used for basepair links. */\n        basepair: 'red',\n    };\n\n    /** In-memory registries for user-defined annotations. */\n    const SUBSEQUENCE_REGISTRY = { items: [], nextId: 1, label: 'Highlight' };\n    const REGION_REGISTRY = { items: [], nextId: 1, label: 'Region highlight' };\n    const MUTATION_REGISTRY = { items: [], nextId: 1, label: 'Mutation' };\n\n    // Short aliases keep rendering code focused on domain objects.\n    const SUBSEQUENCE_HIGHLIGHTS = SUBSEQUENCE_REGISTRY.items;\n    const REGION_HIGHLIGHTS = REGION_REGISTRY.items;\n    const POINT_MUTATIONS = MUTATION_REGISTRY.items;\n\n    function clearRegistry(registry) {\n        registry.items.length = 0;\n        registry.nextId = 1;\n    }\n\n    function getRegistryItem(registry, id) {\n        const item = registry.items.find(candidate => candidate.id === id);\n        if (!item) throw new Error(registry.label + ' with id ' + id + ' not found.');\n        return item;\n    }\n\n    function listRegistryItems(registry, cloneItem) {\n        return registry.items.map(cloneItem);\n    }\n\n    function registerRegistryItem(registry, item, cloneItem) {\n        item.id = registry.nextId++;\n        registry.items.push(item);\n        return cloneItem(item);\n    }\n\n    function removeRegistryItem(registry, id) {\n        const index = registry.items.findIndex(item => item.id === id);\n        if (index === -1) return false;\n        registry.items.splice(index, 1);\n        return true;\n    }\n\n    /**\n     * Return a deep-enough clone of a highlight object for external consumers.\n     *\n     * @param {Object} highlight\n     * @returns {Object}\n     */\n    function cloneSubsequenceHighlight(highlight) {\n        return {\n            id: highlight.id,\n            sequence: highlight.sequence,\n            range: highlight.range.map(([start, end]) => [start, end]),\n            color: highlight.color,\n            alpha: highlight.alpha,\n            rangeText: highlight.rangeText,\n        };\n    }\n\n    /**\n     * Validate and normalize a sequence selector for subsequence highlighting.\n     *\n     * @param {string|number} sequence\n     * @returns {'1'|'2'}\n     */\n    function normaliseHighlightSequence(sequence) {\n        const seq = String(sequence);\n        if (seq !== '1' && seq !== '2') {\n            throw new Error('Highlight sequence must be \"1\" or \"2\".');\n        }\n        return seq;\n    }\n\n    /**\n     * Normalize and validate a highlight range input.\n     *\n     * @param {string|Array<[number, number]>} rangeInput\n     * @param {{id:string, offset:number, length:number}=} context\n     * @returns {{range:Array<[number, number]>, rangeText:string}}\n     */\n    function normaliseHighlightRanges(rangeInput, context) {\n        if (typeof rangeInput === 'string') {\n            const range = parseSubsequences(\n                rangeInput,\n                context ? context.offset : undefined,\n                context ? context.length : undefined,\n                context ? context.id : undefined\n            );\n            if (!range || range.length === 0) {\n                throw new Error('Highlight range must not be empty.');\n            }\n            return { range, rangeText: rangeInput.trim() };\n        }\n\n        if (!Array.isArray(rangeInput) || rangeInput.length === 0) {\n            throw new Error('Highlight range must not be empty.');\n        }\n\n        const range = rangeInput.map((pair, idx) => {\n            if (!Array.isArray(pair) || pair.length !== 2) {\n                throw new Error(`${context.id ? context.id+\": \": \"\"} Invalid subsequence range ${pair} at index ${idx}. Expected [start, end].`);\n            }\n            const start = Number(pair[0]);\n            const end = Number(pair[1]);\n            if (!Number.isInteger(start) || !Number.isInteger(end)) {\n                throw new Error(`${context.id ? context.id+\": \": \"\"}Invalid subsequence range at index ${idx}. Range bounds must be integers.`);\n            }\n            if (start === 0 || end === 0) {\n                throw new Error(`${context.id ? context.id+\": \": \"\"}Invalid subsequence range at index ${idx}. Index 0 is not valid.`);\n            }\n            if (start > end) {\n                throw new Error(`${context.id ? context.id+\": \": \"\"}Invalid subsequence range at index ${idx}. Start index must be <= end index.`);\n            }\n            return [start, end];\n        });\n\n        if (context) {\n            parseSubsequences(\n                range.map(([start, end]) => `${start}-${end}`).join(','),\n                context.offset,\n                context.length,\n                context.id\n            );\n        }\n\n        return {\n            range,\n            rangeText: range.map(([start, end]) => `${start}-${end}`).join(','),\n        };\n    }\n\n    /**\n     * Build a normalized subsequence-highlight object from user input.\n     *\n     * @param {{sequence:string|number, range:string|Array<[number, number]>, color?:string, alpha?:number, id?:number}} input\n     * @param {{'1'?:{offset:number, length:number}, '2'?:{offset:number, length:number}}=} sequenceContext\n     * @returns {{id:number, sequence:'1'|'2', range:Array<[number, number]>, color:string, rangeText:string}}\n     */\n    function createSubsequenceHighlight(input, sequenceContext = {}) {\n\n        const sequence = normaliseHighlightSequence(input.sequence);\n        const context = sequenceContext[sequence];\n        const normalizedRange = normaliseHighlightRanges(input.range, context);\n        const color = (input.color || '').trim() || COLORS.subsequenceHighlight;\n        const alpha = input.alpha !== undefined ? Number(input.alpha) : 0.3;\n\n        return {\n            id: Number.isInteger(input.id) ? input.id : 0,\n            sequence,\n            range: normalizedRange.range,\n            color,\n            alpha,\n            rangeText: normalizedRange.rangeText,\n        };\n    }\n\n    /**\n     * Register a new subsequence highlight object.\n     *\n     * @param {{sequence:string|number, range:string|Array<[number, number]>, color?:string, alpha?:number}} input\n     * @param {{'1'?:{offset:number, length:number}, '2'?:{offset:number, length:number}}=} sequenceContext\n     * @returns {Object}\n     */\n    function registerSubsequenceHighlight(input, sequenceContext = {}) {\n        return registerRegistryItem(\n            SUBSEQUENCE_REGISTRY,\n            createSubsequenceHighlight(input, sequenceContext),\n            cloneSubsequenceHighlight\n        );\n    }\n\n    /**\n     * Update an existing subsequence highlight object.\n     *\n     * @param {number} id\n     * @param {{sequence?:string|number, range?:string|Array<[number, number]>, color?:string}} patch\n     * @param {{'1'?:{offset:number, length:number}, '2'?:{offset:number, length:number}}=} sequenceContext\n     * @returns {Object}\n     */\n    function updateSubsequenceHighlight(id, patch, sequenceContext = {}) {\n        const target = getRegistryItem(SUBSEQUENCE_REGISTRY, id);\n\n        const normalized = createSubsequenceHighlight({\n            id,\n            sequence: patch.sequence !== undefined ? patch.sequence : target.sequence,\n            range: patch.range !== undefined ? patch.range : target.range,\n            color: patch.color !== undefined ? patch.color : target.color,\n            alpha: patch.alpha !== undefined ? patch.alpha : target.alpha,\n        }, sequenceContext);\n\n        Object.assign(target, normalized);\n\n        return cloneSubsequenceHighlight(target);\n    }\n\n    /**\n     * Remove a subsequence highlight object by id.\n     *\n     * @param {number} id\n     * @returns {boolean}\n     */\n    function removeSubsequenceHighlight(id) {\n        return removeRegistryItem(SUBSEQUENCE_REGISTRY, id);\n    }\n\n    /**\n     * Remove all registered subsequence highlights.\n     */\n    function clearSubsequenceHighlights() {\n        clearRegistry(SUBSEQUENCE_REGISTRY);\n    }\n\n    /**\n     * Read registered subsequence highlights.\n     *\n     * @returns {Array<Object>}\n     */\n    function getSubsequenceHighlights() {\n        return listRegistryItems(SUBSEQUENCE_REGISTRY, cloneSubsequenceHighlight);\n    }\n\n    /**\n     * Return a deep-enough clone of a region-highlight object for external consumers.\n     *\n     * @param {Object} highlight\n     * @returns {Object}\n     */\n    function cloneRegionHighlight(highlight) {\n        return {\n            id: highlight.id,\n            sequence1Range: [highlight.sequence1Range[0], highlight.sequence1Range[1]],\n            sequence2Range: [highlight.sequence2Range[0], highlight.sequence2Range[1]],\n            color: highlight.color,\n            alpha: highlight.alpha,\n            rangeText: highlight.rangeText,\n            generated: !!highlight.generated,\n        };\n    }\n\n    /**\n     * Normalize a range input for region highlighting.\n     *\n     * @param {string|Array<number|[number, number]>} rangeInput\n     * @param {{id: string, offset:number, length:number}=} context\n     * @returns {{range:[number, number], rangeText:string}}\n     */\n    function normaliseRegionRange(rangeInput, context = {}) {\n        if (typeof rangeInput === 'string') {\n            const ranges = parseSubsequences(rangeInput, context.offset, context.length, context.id);\n            if (!ranges || ranges.length === 0) {\n                throw new Error('Region range must not be empty.');\n            }\n            if (ranges.length > 1) {\n                throw new Error('Region highlighting supports a single range per sequence.');\n            }\n            const [start, end] = ranges[0];\n            return { range: [start, end], rangeText: rangeInput.trim() };\n        }\n\n        if (!Array.isArray(rangeInput) || rangeInput.length === 0) {\n            throw new Error('Region range must not be empty.');\n        }\n\n        const pair = rangeInput;\n        if (!Array.isArray(pair) || pair.length !== 2) {\n            throw new Error('Invalid region range. Expected [start, end].');\n        }\n\n        const start = Number(pair[0]);\n        const end = Number(pair[1]);\n        if (!Number.isInteger(start) || !Number.isInteger(end)) {\n            throw new Error('Invalid region range. Range bounds must be integers.');\n        }\n        if (start === 0 || end === 0) {\n            throw new Error('Invalid region range. Index 0 is not valid.');\n        }\n        if (start > end) {\n            throw new Error('Invalid region range. Start index must be <= end index.');\n        }\n\n        if (context) {\n            parseSubsequences(`${start}-${end}`, context.offset, context.length, context.id);\n        }\n\n        return {\n            range: [start, end],\n            rangeText: `${start}-${end}`,\n        };\n    }\n\n    /**\n     * Build a normalized region-highlight object from user input.\n     *\n     * @param {{sequence1Range:string|[number, number], sequence2Range:string|[number, number], color?:string, alpha?:number, generated?:boolean, id?:number}} input\n     * @param {{'1'?:{offset:number, length:number}, '2'?:{offset:number, length:number}}=} sequenceContext\n     * @returns {{id:number, sequence1Range:[number, number], sequence2Range:[number, number], color:string, rangeText:string, generated:boolean}}\n     */\n    function createRegionHighlight(input, sequenceContext = {}) {\n        const context1 = sequenceContext['1'];\n        const context2 = sequenceContext['2'];\n        const seq1Range = normaliseRegionRange(input.sequence1Range, context1);\n        const seq2Range = normaliseRegionRange(input.sequence2Range, context2);\n        const color = (input.color || '').trim() || COLORS.backgroundHighlight;\n        const alpha = input.alpha !== undefined ? Number(input.alpha) : 0.2;\n\n        return {\n            id: Number.isInteger(input.id) ? input.id : 0,\n            sequence1Range: seq1Range.range,\n            sequence2Range: seq2Range.range,\n            color,\n            alpha,\n            rangeText: `${seq1Range.rangeText}&${seq2Range.rangeText}`,\n            generated: !!input.generated,\n        };\n    }\n\n    /**\n     * Register a new region highlight object.\n     *\n     * @param {{sequence1Range:string|[number, number], sequence2Range:string|[number, number], color?:string, alpha?:number, generated?:boolean}} input\n     * @param {{'1'?:{offset:number, length:number}, '2'?:{offset:number, length:number}}=} sequenceContext\n     * @returns {Object}\n     */\n    function registerRegionHighlight(input, sequenceContext = {}) {\n        return registerRegistryItem(\n            REGION_REGISTRY,\n            createRegionHighlight(input, sequenceContext),\n            cloneRegionHighlight\n        );\n    }\n\n    /**\n     * Update an existing region highlight object.\n     *\n     * @param {number} id\n     * @param {{sequence1Range?:string|[number, number], sequence2Range?:string|[number, number], color?:string, generated?:boolean}} patch\n     * @param {{'1'?:{offset:number, length:number}, '2'?:{offset:number, length:number}}=} sequenceContext\n     * @returns {Object}\n     */\n    function updateRegionHighlight(id, patch, sequenceContext = {}) {\n        const target = getRegistryItem(REGION_REGISTRY, id);\n\n        const normalized = createRegionHighlight({\n            id,\n            sequence1Range: patch.sequence1Range !== undefined ? patch.sequence1Range : target.sequence1Range,\n            sequence2Range: patch.sequence2Range !== undefined ? patch.sequence2Range : target.sequence2Range,\n            color: patch.color !== undefined ? patch.color : target.color,\n            alpha: patch.alpha !== undefined ? patch.alpha : target.alpha,\n            generated: patch.generated !== undefined ? patch.generated : target.generated,\n        }, sequenceContext);\n\n        Object.assign(target, normalized);\n\n        return cloneRegionHighlight(target);\n    }\n\n    /**\n     * Remove a region highlight object by id.\n     *\n     * @param {number} id\n     * @returns {boolean}\n     */\n    function removeRegionHighlight(id) {\n        return removeRegistryItem(REGION_REGISTRY, id);\n    }\n\n    /**\n     * Remove all registered region highlights.\n     */\n    function clearRegionHighlights() {\n        clearRegistry(REGION_REGISTRY);\n    }\n\n    /**\n     * Read registered region highlights.\n     *\n     * @returns {Array<Object>}\n     */\n    function getRegionHighlights() {\n        return listRegistryItems(REGION_REGISTRY, cloneRegionHighlight);\n    }\n\n    /**\n     * Return a deep-enough clone of a point-mutation object for external consumers.\n     *\n     * @param {Object} mutation\n     * @returns {Object}\n     */\n    function clonePointMutation(mutation) {\n        return {\n            id: mutation.id,\n            sequence: mutation.sequence,\n            position: mutation.position,\n            replacement: mutation.replacement,\n            reference: mutation.reference,\n            nodeId: mutation.nodeId,\n            color: mutation.color,\n            labelText: mutation.labelText,\n        };\n    }\n\n    /**\n     * Validate and normalize a mutation sequence selector.\n     *\n     * @param {string|number} sequence\n     * @returns {'1'|'2'}\n     */\n    function normaliseMutationSequence(sequence) {\n        const seq = String(sequence);\n        if (seq !== '1' && seq !== '2') {\n            throw new Error('Mutation sequence must be \"1\" or \"2\".');\n        }\n        return seq;\n    }\n\n    /**\n     * Build a map of valid sequence positions to their bases.\n     *\n     * @param {{offset:number, sequence:string}|undefined} context\n     * @returns {Object.<number, string>}\n     */\n    function buildSequencePositionMap(context) {\n        const map = {};\n        if (!context || !Number.isInteger(context.offset) || typeof context.sequence !== 'string') {\n            return map;\n        }\n\n        getSequenceIndices('s', context.offset, context.sequence.length).forEach(([, position], index) => {\n            map[position] = context.sequence[index];\n        });\n        return map;\n    }\n\n    /**\n     * Normalize a mutation position and validate it against the current sequence context.\n     *\n     * @param {number|string} positionInput\n     * @param {{offset:number, sequence:string}|undefined} context\n     * @returns {number}\n     */\n    function normaliseMutationPosition(positionInput, context) {\n        if (positionInput === undefined || positionInput === null || positionInput === '') {\n             throw new Error('Mutation position must not be empty.');\n        }\n        const position = validateOffset(String(positionInput));\n\n        if (context) {\n            const sequencePositionMap = buildSequencePositionMap(context);\n            if (!(position in sequencePositionMap)) {\n                throw new Error('Mutation position must be a valid sequence index.');\n            }\n        }\n\n        return position;\n    }\n\n    /**\n     * Validate a point-mutation replacement base.\n     *\n     * @param {string} replacement\n     * @returns {string}\n     */\n    function normaliseMutationReplacement(replacement) {\n        const newLetter = String(replacement || '').trim();\n        if (newLetter.length !== 1) {\n            throw new Error('Mutation replacement must be a single letter.');\n        }\n        return newLetter;\n    }\n\n    /**\n     * Build a normalized point-mutation object from user input.\n     *\n     * @param {{sequence:string|number, position:number|string, replacement:string, color?:string, id?:number}} input\n     * @param {{'1'?:{offset:number, sequence:string}, '2'?:{offset:number, sequence:string}}=} sequenceContext\n     * @returns {{id:number, sequence:'1'|'2', position:number, replacement:string, reference:string, nodeId:number, color:string, labelText:string}}\n     */\n    function createPointMutation(input, sequenceContext = {}) {\n        const sequence = normaliseMutationSequence(input.sequence);\n        const context = sequenceContext[sequence];\n        const position = normaliseMutationPosition(input.position, context);\n        const replacement = normaliseMutationReplacement(input.replacement);\n        const color = (input.color || '').trim() || COLORS.intermolecularHighlight;\n\n        const referenceMap = context ? buildSequencePositionMap(context) : {};\n        const reference = referenceMap[position] || '';\n\n        return {\n            id: Number.isInteger(input.id) ? input.id : 0,\n            sequence,\n            position,\n            replacement,\n            reference,\n            nodeId: 0,\n            color,\n            labelText: `${reference || '?'}${position}${replacement}`,\n        };\n    }\n\n    /**\n     * Register a new point mutation.\n     *\n     * @param {{sequence:string|number, position:number|string, replacement:string, color?:string}} input\n     * @param {{'1'?:{offset:number, sequence:string}, '2'?:{offset:number, sequence:string}}=} sequenceContext\n     * @returns {Object}\n     */\n    function registerPointMutation(input, sequenceContext = {}) {\n        return registerRegistryItem(\n            MUTATION_REGISTRY,\n            createPointMutation(input, sequenceContext),\n            clonePointMutation\n        );\n    }\n\n    /**\n     * Update an existing point mutation.\n     *\n     * @param {number} id\n     * @param {{sequence?:string|number, position?:number|string, replacement?:string, color?:string}} patch\n     * @param {{'1'?:{offset:number, sequence:string}, '2'?:{offset:number, sequence:string}}=} sequenceContext\n     * @returns {Object}\n     */\n    function updatePointMutation(id, patch, sequenceContext = {}) {\n        const target = getRegistryItem(MUTATION_REGISTRY, id);\n\n        const normalized = createPointMutation({\n            id,\n            sequence: patch.sequence !== undefined ? patch.sequence : target.sequence,\n            position: patch.position !== undefined ? patch.position : target.position,\n            replacement: patch.replacement !== undefined ? patch.replacement : target.replacement,\n            color: patch.color !== undefined ? patch.color : target.color,\n        }, sequenceContext);\n\n        Object.assign(target, normalized);\n\n        return clonePointMutation(target);\n    }\n\n    /**\n     * Remove a point mutation by id.\n     *\n     * @param {number} id\n     * @returns {boolean}\n     */\n    function removePointMutation(id) {\n        return removeRegistryItem(MUTATION_REGISTRY, id);\n    }\n\n    /**\n     * Remove all registered point mutations.\n     */\n    function clearPointMutations() {\n        clearRegistry(MUTATION_REGISTRY);\n    }\n\n    /**\n     * Read registered point mutations.\n     *\n     * @returns {Array<Object>}\n     */\n    function getPointMutations() {\n        return listRegistryItems(MUTATION_REGISTRY, clonePointMutation);\n    }\n\n    /**\n     * Find the node ID that corresponds to a given sequence position.\n     *\n     * @param {Object} v\n     * @param {'1'|'2'} sequence\n     * @param {number} position\n     * @returns {number}\n     */\n    function getNodeIdForSequencePosition(v, sequence, position) {\n        for (const [nodeId, [seqName, seqPosition]] of Object.entries(getIndexDictionary(v))) {\n            if (seqName === `s${sequence}` && seqPosition === position) {\n                return parseInt(nodeId, 10);\n            }\n        }\n        return 0;\n    }\n\n    /**\n     * Override one or more default rendering colours.\n     *\n     * Only the keys present in `overrides` are changed; all others retain\n     * their current values.  The new colours take effect on the next call to\n     * any rendering function.\n     *\n    * Valid keys: `sequence1`, `sequence2`, `seq1profileColor`, `seq2profileColor`,\n    * `mutationColor`, `intermolecularHighlight`, `backgroundHighlight`, `subsequenceHighlight`, `basepair`.\n     *\n     * @param {Partial<typeof COLORS>} overrides  Key \u2192 CSS-colour-string map.\n     */\n    function setColors(overrides) {\n        Object.assign(COLORS, overrides);\n    }\n\n    /**\n     * Return a shallow copy of the current colour settings.\n     *\n     * @returns {typeof COLORS}\n     */\n    function getColors() {\n        return { ...COLORS };\n    }\n\n    // -----------------------------------------------------------------------\n    // Utilities  (ported from utils.py)\n    // -----------------------------------------------------------------------\n\n    /**\n     * Identify intermolecular basepair positions in a structure string.\n     *\n     * Analyses a dot-bracket structure and returns positions involved in\n     * intermolecular basepairs.  Unmatched opening or closing brackets are\n     * considered intermolecular.\n     *\n     * Supports `()`, `[]`, `{}`, `<>` bracket types independently.\n     *\n     * @param {string} struc  Structure string in dot-bracket notation.\n     * @param {number} [shift=0]  Offset added to every returned index.\n     * @returns {Array<[number, string]>}  Sorted list of [1-based index, bracket] pairs.\n     */\n    function listIntermolNodes(struc, shift = 0) {\n        const interBasepairs = [];\n        const openBasepairs = { '(': [], '<': [], '[': [], '{': [] };\n        const bracketPairs = [['(', ')'], ['[', ']'], ['{', '}'], ['<', '>']];\n\n        for (let i = 0; i < struc.length; i++) {\n            const char = struc[i];\n            const index = i + 1; // 1-based\n            for (const [open, close] of bracketPairs) {\n                if (char === open) {\n                    openBasepairs[open].push([index + shift, char]);\n                    break;\n                }\n                if (char === close) {\n                    if (openBasepairs[open].length > 0) {\n                        openBasepairs[open].pop();\n                    } else {\n                        interBasepairs.push([index + shift, char]);\n                    }\n                    break;\n                }\n            }\n        }\n\n        for (const pairs of Object.values(openBasepairs)) {\n            interBasepairs.push(...pairs);\n        }\n\n        interBasepairs.sort((a, b) => a[0] - b[0]);\n        return interBasepairs;\n    }\n\n    // -----------------------------------------------------------------------\n    // Input validation  (ported from input_validation.py)\n    // -----------------------------------------------------------------------\n\n    /**\n     * Split a string at the first `&` character.\n     *\n     * Always returns exactly two strings; the second is empty when `&` is absent.\n     *\n     * @param {string} str\n     * @returns {[string, string]}\n     */\n    function splitAtAmpersand(str) {\n        const idx = str.indexOf('&');\n        if (idx === -1) return [str, ''];\n        return [str.slice(0, idx), str.slice(idx + 1)];\n    }\n\n    /**\n     * Validate a structure string for correctly-paired brackets.\n     *\n     * Ensures `()`, `<>`, `[]`, `{}` are properly opened and closed.\n     *\n     * @param {string} structure  Dot-bracket structure, may contain `&`.\n     * @throws {Error} When bracket counts do not balance.\n     */\n    function checkStructureInputSimple(structure) {\n        const basepairs = { '(': 0, '<': 0, '[': 0, '{': 0 };\n        const closingBp = { ')': '(', '>': '<', ']': '[', '}': '{' };\n\n        for (const char of structure) {\n            if (char in basepairs) {\n                basepairs[char]++;\n            } else if (char in closingBp) {\n                const open = closingBp[char];\n                basepairs[open]--;\n                if (basepairs[open] < 0) {\n                    throw new Error(\n                        `The number of brackets does not line up. Too many closing ${char} brackets:\\n${structure}`\n                    );\n                }\n            }\n        }\n\n        for (const [bp, count] of Object.entries(basepairs)) {\n            if (count > 0) {\n                throw new Error(\n                    `The number of brackets does not line up. Too many opening ${bp} brackets:\\n${structure}`\n                );\n            }\n        }\n    }\n\n    /**\n     * Find base-pair indices in a dot-bracket structure string.\n     *\n     * @param {string} structure\n     * @returns {Array<[number, number]>}  List of [open, close] index pairs (0-based).\n     */\n    function findBasePairs(structure) {\n        const basepairList = [];\n        const openBasepairs = { '(': [], '<': [], '[': [], '{': [] };\n        const closingBp = { ')': '(', '>': '<', ']': '[', '}': '{' };\n\n        for (let i = 0; i < structure.length; i++) {\n            const char = structure[i];\n            if (char in openBasepairs) {\n                openBasepairs[char].push(i);\n            } else if (char in closingBp) {\n                const open = closingBp[char];\n                if (openBasepairs[open].length > 0) {\n                    const openIdx = openBasepairs[open].pop();\n                    basepairList.push([openIdx, i]);\n                }\n            }\n        }\n        return basepairList;\n    }\n\n    /**\n     * Validate a sequence string \u2014 must consist of IUPAC nucleotide characters,\n     * optionally separated by a single `&`.\n     *\n     * @param {string} sequence\n     * @returns {string}  The validated sequence.\n     * @throws {Error}\n     */\n    function validateSequenceInput(sequence) {\n        if (sequence === '') throw new Error('No sequence given');\n        if (/^([aAcCgGtTuUrRyYsSwWkKmMbBdDhHvVnN]+&)?[aAcCgGtTuUrRyYsSwWkKmMbBdDhHvVnN]+$/.test(sequence)) {\n            return sequence;\n        }\n        // find first invalid character for better error message\n        const invalidChars = sequence.replace(/[aAcCgGtTuUrRyYsSwWkKmMbBdDhHvVnN&]/g, '');\n        throw new Error(`The given sequence input has invalid none-IUPAC characters: ${invalidChars}`);\n    }\n\n    /**\n     * Validate cropping input.  Must be an integer string, and disallowed for\n     * @param {string} cropping (integer string to be validated)\n     * @param {string} structure Validated structure string, used to check for unpaired-only structures)\n     * @returns the validated cropping string\n     * @throws {Error}  When cropping is not a valid integer or when cropping is disallowed for unpaired-only structures.\n     */\n    function validateCroppingInput(structure, cropping) {\n        // check if cropping is not set, return default value\n        if (!cropping) return '-1';  // default value\n\n        // check if cropping is a valid integer string\n        if (!/^-?\\d+$/.test(cropping)) {\n            throw new Error(`The given cropping input is not an integer: ${cropping}`);\n        }\n        \n        // negative cropping is indicating no cropping, return -1\n        if (parseInt(cropping, 10) < 0) return -1;  \n\n        // check if structure is only composed of dots (unpaired) and if so, disallow cropping\n        if( structure ) {\n            if (!structure.match(/[^.&]/)) {\n                throw new Error('Cropping is not allowed for structures with only unpaired nucleotides.');\n            }\n            if (structure.includes('&')) {\n                // check structure of the first molecule (before &) if present\n                const [struc1, struc2] = splitAtAmpersand(structure);\n                if (!struc1.match(/[^.]/) || !struc2.match(/[^.]/)) {\n                    throw new Error('Cropping is not allowed for structures with only unpaired nucleotides in either molecule.');\n                }\n            }\n        }\n        return cropping;\n    }\n\n\n\n    /**\n     * Validate a structure string in dot-bracket notation.\n     *\n     * @param {string} structure\n     * @param {string} sequence  Used to check length parity when `&` is present.\n     * @returns {string}  The validated structure.\n     * @throws {Error}\n     */\n    function validateStructureInput(structure, sequence) {\n        if (structure === '') throw new Error('No structure given');\n\n        if (structure.includes('&')) {\n            const [struc1, struc2] = splitAtAmpersand(structure);\n            const [seq1, seq2] = splitAtAmpersand(sequence);\n            for (const [idx, struc, seq] of [[1, struc1, seq1], [2, struc2, seq2]]) {\n                if (struc.length !== seq.length) {\n                    throw new Error(\n                        `Structure length (${struc.length}) and Sequence length (${seq.length}) ` +\n                        `of molecule ${idx} do not match`\n                    );\n                }\n            }\n        } else {\n            if (structure.length !== sequence.length) {\n                throw new Error(\n                    `Structure length (${structure.length}) and Sequence length (${sequence.length}) do not match`\n                );\n            }\n        }\n\n        if (/^([\\.()<>\\[\\]{}]+&)?[\\.()<>\\[\\]{}]+$/.test(structure)) {\n            checkStructureInputSimple(structure);\n            return structure;\n        }\n        throw new Error(`The given structure input is not valid: ${structure}`);\n    }\n\n    /**\n     * Validate an offset value.\n     *\n     * @param {string} offsetStr  String representation of the offset.\n     * @returns {number}\n     * @throws {Error}\n     */\n    function validateOffset(offsetStr) {\n        if (offsetStr === '0') throw new Error('Index 0 is not valid; use a value of -1 or less, or 1 or greater');\n        if (/^-?\\d+$/.test(offsetStr)) return parseInt(offsetStr, 10);\n        throw new Error(`The given index input is not valid: ${offsetStr}`);\n    }\n\n    /**\n     * Validate the highlighting option.\n     *\n     * @param {string} highlighting\n     * @returns {string}\n     * @throws {Error}\n     */\n    function validateHighlighting(highlighting) {\n        const valid = ['nothing', 'basepairs', 'region'];\n        if (valid.includes(highlighting)) return highlighting;\n        throw new Error(\n            `The given highlighting input (${highlighting}) is not accepted [nothing, basepairs, region]`\n        );\n    }\n\n    /**\n     * Validate the backgroundhighlighting option.\n     *\n     * @param {string} bgHighlighting\n     * @returns {string}\n     * @throws {Error}\n     */\n    function validateBackgroundhighlighting(bgHighlighting) {\n        const valid = ['nothing', 'basepairs', 'region'];\n        if (valid.includes(bgHighlighting)) return bgHighlighting;\n        throw new Error(\n            `The given backgroundhighlighting input (${bgHighlighting}) is not accepted [nothing, basepairs, region]`\n        );\n    }\n\n    /**\n     * Split structure string and apply the Fornac `&...` fix.\n     *\n     * Fornac incorrectly cuts the first 2 nodes of the second sequence when\n     * the separator is exactly `&`.  Inserting `&...` compensates for this.\n     *\n     * @param {string} structure  Raw structure (may contain `&`).\n     * @returns {{structure1: string, structure2: string, structure: string, structure_dict: Object}}\n     */\n    function formatStructure(structure) {\n        const [first, second] = splitAtAmpersand(structure);\n\n        // Fix: Fornac incorrectly cuts the first 2 nodes of the second sequence\n        // when the separator is exactly `&`.  Inserting 3 gap dots compensates.\n        // Build strings explicitly from the already-split parts to avoid\n        // partial-replacement ambiguity on the `&` character.\n        const fixedStructure = second !== '' ? first + '&...' + second : first;\n        const bareStructure  = second !== '' ? first + '...'  + second : first;\n\n        const structureDict = {};\n        for (let i = 0; i < bareStructure.length; i++) {\n            structureDict[String(i + 1)] = bareStructure[i];\n        }\n\n        return { structure1: first, structure2: second, structure: fixedStructure, structure_dict: structureDict };\n    }\n\n    /**\n     * Split sequence string and apply the Fornac `&...` fix.\n     *\n     * @param {string} sequence  Raw sequence (may contain `&`).\n     * @returns {{sequence1: string, sequence2: string, sequence: string, sequence_dict: Object}}\n     */\n    function formatSequence(sequence) {\n        const [first, second] = splitAtAmpersand(sequence);\n\n        // Same Fornac fix as formatStructure \u2014 build from split parts explicitly.\n        const fixedSequence = second !== '' ? first + '&...' + second : first;\n        const bareSequence  = second !== '' ? first + '...'  + second : first;\n\n        const sequenceDict = {};\n        for (let i = 0; i < bareSequence.length; i++) {\n            sequenceDict[String(i + 1)] = bareSequence[i];\n        }\n\n        return { sequence1: first, sequence2: second, sequence: fixedSequence, sequence_dict: sequenceDict };\n    }\n\n    /**\n     * Determine how many molecules are given (`\"1\"` or `\"2\"`).\n     *\n     * @param {{sequence2: string}} validated\n     * @returns {\"1\"|\"2\"}\n     */\n    function getMolecules(validated) {\n        return validated.sequence2 !== '' ? '2' : '1';\n    }\n\n    /**\n     * Generate indexed sequence positions with RNA-style numbering (skipping 0).\n     *\n     * @param {string} seqId  Sequence identifier, e.g. `\"s1\"`.\n     * @param {number} offset  Starting index.\n     * @param {number} length  Length of the sequence.\n     * @returns {Array<[string, number]>}  Array of [seqId, index] pairs.\n     */\n    function getSequenceIndices(seqId, offset, length) {\n        const indices = [];\n        for (let i = offset; i < offset + length; i++) {\n            indices.push([seqId, i]);\n        }\n        // RNA-style: skip 0\n        const zeroIdx = indices.findIndex(([, n]) => n === 0);\n        if (zeroIdx !== -1) {\n            indices.splice(zeroIdx, 1);\n            const [seq, lastNum] = indices[indices.length - 1];\n            indices.push([seq, lastNum + 1]);\n        }\n        return indices;\n    }\n\n    /**\n     * Build a mapping from Fornac node ID (1-based) to [sequenceId, position].\n     *\n     * @param {{offset1: number, offset2: number, sequence1: string, sequence2: string}} v\n     * @returns {Object.<number, [string, number]>}\n     */\n    function getIndexDictionary(v) {\n        const { offset1, offset2, sequence1, sequence2 } = v;\n        const gapList = Array.from({ length: GAP }, () => ['e', 0]);\n\n        const indices = [\n            ...getSequenceIndices('s1', offset1, sequence1.length),\n            ...gapList,\n            ...getSequenceIndices('s2', offset2, sequence2.length),\n        ];\n\n        const dict = {};\n        indices.forEach(([seq, num], i) => {\n            dict[i + 1] = [seq, num];\n        });\n        return dict;\n    }\n\n    /**\n     * Crop leading and trailing unpaired nucleotides from sequences and structures.\n     * \n     * @param {string} rawSeq \n     * @param {string} validStruc \n     * @param {integer} offset1 \n     * @param {integer} offset2 \n     * @param {integer} cropping \n     * @returns Object with updated rawSeq, validStruc, offset1, offset2\n     */\n    function applyCropping(rawSeq, validStruc, offset1, offset2, cropping) {\n\n        // check if cropping is not set or is negative, return original values\n        if( !cropping || cropping < 0 ) {\n            return { rawSeq, validStruc, offset1, offset2 };\n        }\n\n        let seq = rawSeq.split('&');\n        let str = validStruc.split('&');\n        let off = [offset1, offset2];\n                \n        for (let i = 0; i < seq.length; i++) {\n            // leading cropping\n            let unpairedLeading = str[i].match(/^\\.+/);\n            if (unpairedLeading && unpairedLeading[0].length > cropping) {\n                seq[i] = seq[i].slice(unpairedLeading[0].length - cropping);\n                str[i] = str[i].slice(unpairedLeading[0].length - cropping);\n                const offOld = off[i];\n                off[i] += unpairedLeading[0].length - cropping;\n                if (off[i] >= 0 && offOld < 0) { off[i] += 1; } // skip 0\n            }\n            // trailing cropping\n            let trailing = str[i].match(/\\.+$/);\n            if (trailing && trailing[0].length > cropping) {\n                seq[i] = seq[i].slice(0, seq[i].length - (trailing[0].length - cropping));\n                str[i] = str[i].slice(0, str[i].length - (trailing[0].length - cropping));\n                }\n        }\n                    \n        // return updated values\n        return { rawSeq: seq.join(\"&\"), validStruc: str.join(\"&\"), offset1: off[0], offset2: off[1] };\n    }\n\n    /**\n     * Validate all inputs and return a `validated` parameter object ready for rendering.\n     *\n     * @param {Object} args  Raw input parameters.\n     * @param {string} args.structure    Dot-bracket structure, one or two molecules separated by `&`.\n     * @param {string} args.sequence     RNA sequence, one or two molecules separated by `&`.\n     * @param {string} [args.cropping=\"-1\"]  Cropping value (integer string).\n     * @param {string} [args.startIndex1=\"1\"]  Start index for sequence 1.\n     * @param {string} [args.startIndex2=\"1\"]  Start index for sequence 2.\n     * @param {string} [args.labelInterval=\"10\"]  Interval for index label display.\n     * @param {string} [args.coloring=\"strand\"]  Coloring option: `\"strand\"` or `\"loop\"`.\n     * @param {string} [args.highlighting=\"region\"]  Highlighting option: `\"nothing\"`, `\"basepairs\"`, `\"region\"`.\n     * @param {string} [args.backgroundhighlighting=\"basepairs\"]  Background-highlighting option.\n     * @param {boolean} [args.distinctBpTypes=true]  Whether to display G-U basepairs as dashed lines.\n    * @param {Array<{sequence:string|number, range:string|Array<[number, number]>, color?:string}>} [args.subsequenceHighlights=[]]\n    *     Generic subsequence-highlight definitions.\n     * @returns {Object}  Validated parameter dictionary.\n     * @throws {Error}  On invalid input.\n     */\n    function validate(args) {\n        const v = {};\n\n        // Sequence\n        const rawSeq = (args.sequence || '').trim();\n        validateSequenceInput(rawSeq);\n        \n        // Structure\n        const rawStruc = (args.structure || '').trim();\n        const validStruc = validateStructureInput(rawStruc, rawSeq);\n        \n        // Offsets\n        v.offset1 = validateOffset(String(args.startIndex1 || '1'));\n        v.offset2 = validateOffset(String(args.startIndex2 || '1'));\n        \n        // Cropping\n        const cropping = validateCroppingInput(validStruc, String(args.cropping || '-1'));\n\n        // update sequences, structures and offsets based on cropping\n        const cropped = applyCropping(rawSeq, validStruc, v.offset1, v.offset2, cropping);\n\n        // update offset information\n        v.offset1 = cropped.offset1;\n        v.offset2 = cropped.offset2;\n\n        // create the formatted sequence and structure objects\n        const seqFmt = formatSequence(cropped.rawSeq);\n        Object.assign(v, seqFmt);\n        const strucFmt = formatStructure(cropped.validStruc);\n        Object.assign(v, strucFmt);\n\n        // Molecules\n        v.molecules = getMolecules(v);\n\n        // Options\n        v.coloring = args.coloring || 'strand';\n        v.highlighting = validateHighlighting(args.highlighting || 'region');\n        v.backgroundhighlighting = validateBackgroundhighlighting(\n            args.backgroundhighlighting || 'basepairs'\n        );\n        v.distinctBpTypes = args.distinctBpTypes !== false; // default true\n        v.labelInterval = parseInt(String(args.labelInterval || '10'), 10) || 10;\n\n        // Subsequence highlights\n        const sequenceContext = {\n            '1': { offset: v.offset1, length: v.sequence1.length, sequence: v.sequence1 },\n            '2': { offset: v.offset2, length: v.sequence2.length, sequence: v.sequence2 },\n        };\n\n        if (Array.isArray(args.subsequenceHighlights)) {\n            v.subsequenceHighlights = args.subsequenceHighlights.map(h =>\n                createSubsequenceHighlight(h, sequenceContext)\n            );\n        } else {\n            v.subsequenceHighlights = [];\n        }\n\n        if (Array.isArray(args.regionHighlights)) {\n            v.regionHighlights = args.regionHighlights.map(highlight =>\n                createRegionHighlight(highlight, sequenceContext)\n            );\n        } else {\n            v.regionHighlights = [];\n        }\n\n        if (Array.isArray(args.pointMutations)) {\n            v.pointMutations = args.pointMutations.map(mutation =>\n                createPointMutation(mutation, sequenceContext)\n            );\n\n            const seenMutationPositions = new Set();\n            v.pointMutations.forEach(mutation => {\n                const key = `${mutation.sequence}:${mutation.position}`;\n                if (seenMutationPositions.has(key)) {\n                    throw new Error(`Duplicate point mutation at ${key}.`);\n                }\n                seenMutationPositions.add(key);\n\n                mutation.nodeId = getNodeIdForSequencePosition(v, mutation.sequence, mutation.position);\n                if (!mutation.nodeId) {\n                    throw new Error(`Mutation position ${mutation.position} is not visible in the current rendering.`);\n                }\n                mutation.labelText = `${mutation.reference || '?'}${mutation.position}${mutation.replacement}`;\n            });\n        } else {\n            v.pointMutations = [];\n        }\n\n        return v;\n    }\n\n    /**\n     * Parse a comma-separated list of `\"start-end\"` range strings.\n     *\n     * @param {string|null|undefined} input\n     * @param {number} [startIndex]\n     * @param {number} [sequenceLength]\n     * @param {string|null|undefined} [sequenceId]\n     * @returns {Array<[number,number]>|null}\n     */\n    function parseSubsequences(input, startIndex, sequenceLength, sequenceId) {\n        if (!input || input.trim() === '') return null;\n        let validIndices = null;\n        if (Number.isInteger(startIndex) && Number.isInteger(sequenceLength) && sequenceLength >= 0) {\n            validIndices = new Set(\n                getSequenceIndices('s', startIndex, sequenceLength).map(([, index]) => index)\n            );\n        }\n        const ranges = input.split(',').map(s => s.trim()).filter(Boolean);\n        return ranges.map(r => {\n            const match = r.match(/^(-?\\d+)-(-?\\d+)$/);\n            if (!match) {\n                throw new Error(`${sequenceId ? sequenceId+\": \" : \"\"}Invalid subsequence range: \"${r}\". Expected \"start-end\".`);\n            }\n            const start = parseInt(match[1], 10);\n            const end = parseInt(match[2], 10);\n\n            if (start === 0 || end === 0) {\n                throw new Error(`${sequenceId ? sequenceId+\": \" : \"\"}Invalid subsequence range: \"${r}\". Index 0 is not valid.`);\n            }\n            if (start > end) {\n                throw new Error(`${sequenceId ? sequenceId+\": \" : \"\"}Invalid subsequence range: \"${r}\". Start index must be <= end index.`);\n            }\n            if (validIndices && (!validIndices.has(start) || !validIndices.has(end))) {\n                throw new Error(\n                    `${sequenceId ? sequenceId+\": \" : \"\"}Invalid subsequence range: \"${r}\". Range endpoints must be valid sequence indices.`\n                );\n            }\n\n            return [start, end];\n        });\n    }\n\n    // -----------------------------------------------------------------------\n    // DOM modification helpers  (ported from modifications.py)\n    // -----------------------------------------------------------------------\n\n    /**\n     * Set an attribute on all elements that match `[targetAttr=\"targetValue\"]`.\n     *\n     * @param {string} targetAttr\n     * @param {string} targetValue\n     * @param {string} setAttr\n     * @param {string} setValue\n     */\n    function setAttributeForElements(targetAttr, targetValue, setAttr, setValue) {\n        document.querySelectorAll(`[${targetAttr}=\"${targetValue}\"]`).forEach(el => {\n            el.setAttribute(setAttr, setValue);\n        });\n    }\n\n    /**\n     * Generate a color list for two sequences.\n     *\n     * Each nucleotide in `seq1` maps to {@link COLORS.sequence1};\n     * each nucleotide in `seq2` maps to {@link COLORS.sequence2}.\n     *\n     * @param {string} seq1\n     * @param {string} seq2\n     * @returns {string[]}\n     */\n    function sequenceColoring(seq1, seq2) {\n        return [\n            ...Array.from(seq1, () => COLORS.sequence1),\n            ...Array.from(seq2, () => COLORS.sequence2),\n        ];\n    }\n\n    /**\n     * Apply strand-based coloring to all nucleotide circles in the Fornac plot.\n     *\n     * @param {{sequence1: string, sequence2: string}} v\n     */\n    function changeBackgroundColor(v) {\n        const coloring = sequenceColoring(v.sequence1, v.sequence2);\n        if (coloring.length === 0) return;\n        const nodes = document.querySelectorAll('[r=\"5\"]');\n        nodes.forEach((node, index) => {\n            node.setAttribute('style', `fill: ${coloring[index]};`);\n        });\n    }\n\n    /**\n     * Assign `start` and `end` attributes to every `<line>` link element.\n     *\n     * Fornac stores link identity in a tooltip text child; this function\n     * parses it and promotes the IDs to proper attributes.\n     */\n    function setLinksId() {\n        document.querySelectorAll('line').forEach(line => {\n            const textContent = line.children[0] && line.children[0].textContent;\n            if (!textContent) return;\n            const parts = textContent.split(':')[1];\n            if (!parts) return;\n            const ids = parts.split('-').filter(x => !isNaN(parseInt(x, 10)) && x !== '');\n            if (ids.length >= 2) {\n                line.setAttribute('start', ids[0].trim());\n                line.setAttribute('end', ids[1].trim());\n            }\n        });\n    }\n\n    /**\n     * Assign sequential `label_gnum` / `label_num` IDs to label elements.\n     */\n    function setLabelsId() {\n        document.querySelectorAll('g[num=\"n-1\"]').forEach((label, index) => {\n            label.setAttribute('label_gnum', String(index + 1));\n            if (label.firstChild) {\n                label.firstChild.setAttribute('label_num', String(index + 1));\n            }\n        });\n    }\n\n    /**\n     * Update node tooltip text to display correct sequence and index labels.\n     *\n     * @param {Object} v  Validated parameter dictionary.\n     */\n    function updateNodeToolTips(v) {\n        const indexDict = getIndexDictionary(v);\n        for (const [key, [seq, num]] of Object.entries(indexDict)) {\n            document.querySelectorAll(`circle[node_num=\"${key}\"]`).forEach(node => {\n                if (node.firstChild) {\n                    node.firstChild.innerHTML = `${seq}[${num}]`;\n                }\n            });\n        }\n    }\n\n    /**\n     * Validate whether a label marker should be placed at the given position.\n     *\n     * Prevents two adjacent markers from being displayed simultaneously.\n     *\n     * @param {number} pos\n     * @param {Object.<number, number>} indexing\n     * @param {number} number\n     * @returns {number}  The number to place, or 0 to suppress.\n     */\n    function validateLabelPos(pos, indexing, number) {\n        for (const neighbor of [pos - 1, pos + 1]) {\n            if (neighbor in indexing && indexing[neighbor] !== 0) {\n                return 0;\n            }\n        }\n        return number;\n    }\n\n    /**\n     * Apply the intermolecular-highlight stroke style to the label at the given index.\n     *\n     * @param {number} targetIndex\n     */\n    function highlightLabel(targetIndex) {\n        document.querySelectorAll(`[label_num=\"${targetIndex}\"]`).forEach(label => {\n            label.setAttribute('style', `stroke: ${COLORS.intermolecularHighlight};stroke-width: 0.8;`);\n        });\n    }\n\n    /**\n     * Set or update the SVG title used as a hover tooltip for a label.\n     *\n     * @param {SVGElement} label\n     * @param {string} text\n     */\n    function setLabelTooltip(label, text) {\n        const parent = label.parentElement;\n        if (!parent) return;\n\n        const existingTitleOnLabel = label.querySelector('title');\n        if (existingTitleOnLabel) existingTitleOnLabel.remove();\n\n        let title = parent.querySelector('title');\n        if (!title) {\n            title = document.createElementNS('http://www.w3.org/2000/svg', 'title');\n            parent.insertBefore(title, parent.firstChild);\n        }\n        title.textContent = text;\n    }\n\n    /**\n     * Remove label group elements at the given index.\n     *\n     * @param {number} index\n     */\n    function removeLabel(index) {\n        document.querySelectorAll(`[label_gnum=\"${index}\"]`).forEach(node => node.remove());\n    }\n\n    /**\n     * Remove label-link line elements at the given index.\n     *\n     * @param {number} index\n     */\n    function removeLabelLink(index) {\n        document.querySelectorAll(`line[start=\"${index}\"]`).forEach(line => {\n            if (line.getAttribute('link_type') === 'label_link') {\n                line.remove();\n            }\n        });\n    }\n\n    /** Return every combined nucleotide position and its selected index label. */\n    function getIndexLabelValues(v) {\n        const { structure1, structure2, sequence1, labelInterval, molecules, sequence_dict } = v;\n        const length1 = sequence1.length;\n        const lengthTotal = Object.keys(sequence_dict).length;\n        const indexDict = getIndexDictionary(v);\n        const indexLabels = {};\n        for (const key of Object.keys(indexDict)) {\n            indexLabels[parseInt(key, 10)] = 0;\n        }\n\n        // Priority 1 \u2014 sequence boundaries\n        for (const pos of [1, length1, length1 + GAP + 1, lengthTotal]) {\n            if (!(pos in indexDict)) break;\n            const [, number] = indexDict[pos];\n            indexLabels[pos] = validateLabelPos(pos, indexLabels, number);\n        }\n\n        // Priority 2 \u2014 intermolecular basepair region boundaries\n        if (molecules === '2') {\n            const basepairRegion = getIntermolBasepairRegion(structure1, structure2);\n            for (const region of basepairRegion) {\n                for (const pos of region) {\n                    if (!(pos in indexDict)) continue;\n                    const [, number] = indexDict[pos];\n                    indexLabels[pos] = validateLabelPos(pos, indexLabels, number);\n                }\n            }\n        }\n\n        // Priority 3 \u2014 every labelInterval\n        for (const [posStr, [, number]] of Object.entries(indexDict)) {\n            const pos = parseInt(posStr, 10);\n            if (number % labelInterval === 0 || number === 1) {\n                indexLabels[pos] = validateLabelPos(pos, indexLabels, number);\n            }\n        }\n\n        return indexLabels;\n    }\n\n    /**\n     * Set index labels on the Fornac plot using a priority system.\n     *\n     * Priority order (highest \u2192 lowest):\n     * 1. Start/end of each sequence.\n     * 2. Start/end of intermolecular basepair region.\n     * 3. Every `labelInterval`-th position.\n     *\n     * @param {Object} v  Validated parameter dictionary.\n     */\n    function setIndexLabels(v) {\n        const indexLabels = getIndexLabelValues(v);\n        const mutationByNodeId = {};\n        (Array.isArray(v.pointMutations) ? v.pointMutations : []).forEach(mutation => {\n            if (mutation.nodeId) mutationByNodeId[mutation.nodeId] = mutation;\n        });\n\n        if (v.molecules === '2') {\n            getIntermolBasepairRegion(v.structure1, v.structure2)\n                .flat()\n                .forEach(highlightLabel);\n        }\n\n        // Apply labels\n        const labelValues = Object.entries(indexLabels);\n        document.querySelectorAll('[label_type=\"label\"]').forEach((label, index) => {\n            const [posStr, value] = labelValues[index] || [];\n            const pos = posStr ? parseInt(posStr, 10) : 0;\n            const mutation = pos && mutationByNodeId[pos] ? mutationByNodeId[pos] : null;\n\n            if (mutation) {\n                label.innerHTML = mutation.replacement;\n                setLabelTooltip(label, `Mutation: ${mutation.labelText}`);\n                label.setAttribute('style', `fill: ${mutation.color}; stroke: ${mutation.color}; stroke-width: 0.2; font-weight: bolder;`);\n                addStyleToNodes([mutation.nodeId], `stroke: ${mutation.color}; stroke-width: 2px;`);\n                return;\n            }\n\n            label.removeAttribute('style');\n            const parent = label.parentElement;\n            const existingTitle = parent?.querySelector('title');\n            if (existingTitle) existingTitle.remove();\n            label.innerHTML = value !== undefined ? value : '';\n        });\n\n        // Remove suppressed labels\n        for (const [posStr, value] of Object.entries(indexLabels)) {\n            const pos = parseInt(posStr, 10);\n            if (value === 0 && !mutationByNodeId[pos]) {\n                removeLabel(pos);\n                removeLabelLink(pos);\n            }\n        }\n    }\n\n    /**\n     * Update tooltip text on link elements to display correct index values.\n     *\n     * @param {Object} v  Validated parameter dictionary.\n     */\n    function updateLinkTooltips(v) {\n        const updatedIndices = {};\n        for (const [key, [, index]] of Object.entries(getIndexDictionary(v))) {\n            updatedIndices[String(key)] = String(index);\n        }\n        document.querySelectorAll('line').forEach(line => {\n            const start = line.getAttribute('start');\n            const end = line.getAttribute('end');\n            if (!line.firstChild) return;\n            if (line.getAttribute('link_type') === 'label_link') {\n                line.firstChild.textContent = updatedIndices[start] || '';\n            } else {\n                line.firstChild.textContent =\n                    (updatedIndices[start] || '') + '-' + (updatedIndices[end] || '');\n            }\n        });\n    }\n\n    /**\n     * Apply a CSS style string to an array of nodes by `node_num`.\n     *\n     * @param {number[]} nodeIds\n     * @param {string} style\n     */\n    function addStyleToNodes(nodeIds, style) {\n        nodeIds.forEach(nodeId => {\n            document.querySelectorAll(`circle[node_num=\"${nodeId}\"]`).forEach(node => {\n                node.setAttribute('style', (node.getAttribute('style') || '') + style);\n            });\n        });\n    }\n\n    /**\n     * Retrieve the x,y position of a Fornac node from its `transform` attribute.\n     *\n     * @param {number} nodeId\n     * @returns {number[]}  [x, y] coordinates.\n     */\n    function getPositionOfNode(nodeId) {\n        const pos = [];\n        document.querySelectorAll(`g[num=\"n${nodeId}\"]`).forEach(node => {\n            const transform = node.getAttribute('transform') || '';\n            const matches = [...transform.matchAll(/-?\\d+(?:\\.\\d+)?/g)];\n            matches.forEach(([val]) => pos.push(parseFloat(val)));\n        });\n        return pos;\n    }\n\n    /**\n     * Resolve where new overlay elements should be inserted.\n     *\n     * If a vaRRI rotation layer exists, insert into that layer so newly added\n     * overlays follow the current rotation.\n     *\n     * @returns {SVGElement|null}\n     */\n    function getPlotInsertRoot() {\n        const plot = document.getElementsByClassName('fornac-plot')[0];\n        if (!plot) return null;\n\n        const rotationLayer = Array.from(plot.children).find(child =>\n            child.tagName && child.tagName.toLowerCase() === 'g' &&\n            child.getAttribute('data-varri-rotation-layer') === 'true'\n        );\n\n        return rotationLayer || plot;\n    }\n\n    /**\n     * Create and insert an SVG element at the beginning of the Fornac plot.\n     *\n     * @param {string} elementType  SVG tag name (e.g. `\"circle\"`, `\"polyline\"`).\n     * @param {Object.<string,string>} attr  Attribute key\u2192value map.\n     */\n    function addElement(elementType, attr) {\n        const el = document.createElementNS('http://www.w3.org/2000/svg', elementType);\n        for (const [key, value] of Object.entries(attr)) {\n            el.setAttribute(key, value);\n        }\n        const insertRoot = getPlotInsertRoot();\n        if (insertRoot) insertRoot.insertBefore(el, insertRoot.firstChild);\n    }\n\n    /**\n     * Resolve the x/y coordinates of a list of Fornac node IDs.\n     *\n     * @param {number[]} indices  Fornac node IDs to resolve.\n     * @returns {Array<[number, number]>}\n     */\n    function getNodePointPairs(indices) {\n        const points = [];\n        indices.forEach(index => {\n            document.querySelectorAll(`g[num=\"n${index}\"]`).forEach(node => {\n                const transform = node.getAttribute('transform') || '';\n                const match = [...transform.matchAll(/-?\\d+(?:\\.\\d+)?/g)];\n                if (match.length >= 2) {\n                    points.push([parseFloat(match[0][0]), parseFloat(match[1][0])]);\n                }\n            });\n        });\n        return points;\n    }\n\n    /**\n     * Close a polygon point list by appending the first point at the end.\n     *\n     * @param {Array<[number, number]>} points\n     * @returns {string[]}\n     */\n    function closePolygonPoints(points) {\n        if (!Array.isArray(points) || points.length === 0) return [];\n        const pointStrings = points.map(([x, y]) => `${x},${y}`);\n        if (pointStrings.length < 2) return pointStrings;\n        return [...pointStrings, pointStrings[0]];\n    }\n\n    function insertSvgShape(tagName, pointString, style, extraAttrs) {\n        const shape = document.createElementNS('http://www.w3.org/2000/svg', tagName);\n        shape.setAttribute('points', pointString);\n        shape.setAttribute('style', style);\n        for (const [name, value] of Object.entries(extraAttrs)) {\n            shape.setAttribute(name, value);\n        }\n        const insertRoot = getPlotInsertRoot();\n        if (insertRoot) insertRoot.insertBefore(shape, insertRoot.firstChild);\n    }\n\n    /**\n     * Draw a polyline connecting a list of Fornac node positions.\n     *\n     * @param {number[]} indices  Fornac node IDs to connect.\n     * @param {string} style  CSS style string for the polyline.\n     */\n    function polyline(indices, style, extraAttrs = {}) {\n        const points = getNodePointPairs(indices);\n        const pointString = points.map(([x, y]) => `${x},${y}`).join(' ');\n\n        insertSvgShape('polyline', pointString, style, extraAttrs);\n    }\n\n    /**\n     * Draw a closed polygon connecting a list of Fornac node positions.\n     *\n     * @param {number[]} indices  Fornac node IDs to connect.\n     * @param {string} style  CSS style string for the polygon.\n     */\n    function polygon(indices, style, extraAttrs = {}) {\n        const points = getNodePointPairs(indices);\n        const pointString = closePolygonPoints(points).join(' ');\n\n        insertSvgShape('polygon', pointString, style, extraAttrs);\n    }\n\n    /**\n     * Compute [start, end] ranges of intermolecular basepair regions.\n     *\n     * @param {string} structure1\n     * @param {string} structure2\n     * @returns {Array<[number, number]>}\n     */\n    function getIntermolBasepairRegion(structure1, structure2) {\n        const basepairRegion = [];\n        const offset = structure1.length + GAP;\n\n        for (const [structure, shift] of [[structure1, 0], [structure2, offset]]) {\n            const basepairList = listIntermolNodes(structure, shift).map(([idx]) => idx);\n            if (basepairList.length === 0) return [];\n            basepairRegion.push([basepairList[0], basepairList[basepairList.length - 1]]);\n        }\n        return basepairRegion;\n    }\n\n    /**\n     * Highlight nodes in the intermolecular basepair region with a stroke.\n     *\n     * @param {Object} v  Validated parameter dictionary.\n     */\n    function highlightRegion(v) {\n        const basepairRegion = getIntermolBasepairRegion(v.structure1, v.structure2);\n        const intermolNodes = [];\n        for (const [start, end] of basepairRegion) {\n            for (let i = start; i <= end; i++) intermolNodes.push(i);\n        }\n        addStyleToNodes(intermolNodes, `stroke: ${COLORS.intermolecularHighlight};`);\n    }\n\n    /**\n     * Highlight individual intermolecular basepair nodes with a stroke.\n     *\n     * @param {Object} v  Validated parameter dictionary.\n     */\n    function highlightBasepairs(v) {\n        const split = v.sequence1.length + 1;\n        // Highlight all nodes that are part of intermolecular basepairs of main layouting (basepair) or 2ndary layouting (pseudoknot)\n        for (const type of [\"basepair\", \"pseudoknot\"]) {\n            document.querySelectorAll(`[link_type=\"${type}\"]`).forEach(link => {\n                const nodes = [\n                    parseInt(link.getAttribute('start'), 10),\n                    parseInt(link.getAttribute('end'), 10),\n                ];\n                if (!(nodes[0] < split && nodes[1] > split)) return;\n                nodes.forEach(nodeNum => {\n                    const node = document.querySelector(`circle[node_num=\"${nodeNum}\"]`);\n                    if (node) {\n                        node.setAttribute('style', (node.getAttribute('style') || '') + `stroke: ${COLORS.intermolecularHighlight};`);\n                    }\n                });\n            });\n        }\n    }\n\n    /**\n     * Remove duplicate basepair links (keep only links where start < end).\n     */\n    function removeSecondLink() {\n        document.querySelectorAll('[link_type=\"basepair\"]').forEach(link => {\n            const start = parseInt(link.getAttribute('start'), 10);\n            const end = parseInt(link.getAttribute('end'), 10);\n            if (start > end) link.remove();\n        });\n    }\n\n    /**\n     * Remove a Fornac node group element by ID.\n     *\n     * @param {number} id\n     */\n    function removeNode(id) {\n        document.querySelectorAll(`[num=\"n${id}\"]`).forEach(node => node.remove());\n    }\n\n    /**\n     * Remove the directional arrow from a node.\n     *\n     * @param {number} id\n     */\n    function removeArrow(id) {\n        document.querySelectorAll(`[num=\"n${id}\"]`).forEach(node => {\n            if (node.firstChild) node.firstChild.remove();\n        });\n    }\n\n    /**\n     * Remove a backbone link between two nodes.\n     *\n     * @param {number} startId\n     * @param {number} endId\n     */\n    function removeLink(startId, endId) {\n        const targetIds = `${startId},${endId}`;\n        document.querySelectorAll('[link_type=\"backbone\"]').forEach(link => {\n            const ids = `${link.getAttribute('start')},${link.getAttribute('end')}`;\n            if (ids === targetIds) link.remove();\n        });\n    }\n\n    /**\n     * Remove dummy gap nodes that Fornac inserts between two molecules.\n     *\n     * @param {string} sequence  The combined sequence string (with `&` and fix dots).\n     */\n    function removeDummyNodes(sequence) {\n        for (let index = 0; index < sequence.length; index++) {\n            if (sequence[index] === '.') {\n                removeLink(index, index + 1);\n                removeArrow(index + 1);\n                removeNode(index);\n            }\n        }\n    }\n\n    /**\n     * Highlight subsequence ranges with polyline/circle overlays.\n     *\n     * @param {Object} v  Validated parameter dictionary.\n     * @param {\"1\"|\"2\"} seq  Which sequence to highlight.\n     * @param {Array<[number, number]>} range  Parsed index range.\n     * @param {string} color  Highlight color.\n     * @param {number} Highlight opacity.\n     */\n    function highlightSubsequence(v, seq, range, color, alpha) {\n        const highlightDiameter = 14;\n        const keyOffset = `offset${seq}`;\n\n        // Map RNA index \u2192 Fornac web node id for the relevant sequence\n        const indexDict = {};\n        for (const [web, [mol, index]] of Object.entries(getIndexDictionary(v))) {\n            if (mol === `s${seq}`) {\n                indexDict[index] = parseInt(web, 10);\n            }\n        }\n\n        const shift = seq === '2' ? v.sequence1.length + GAP : 0;\n\n        for (const [start, end] of (range || [])) {\n            const startIndex = v[keyOffset];\n\n            if (start === end) {\n                const webId = indexDict[start];\n                const [x, y] = getPositionOfNode(webId);\n                addElement('circle', {\n                    cx: String(x),\n                    cy: String(y),\n                    r: `${Math.ceil(highlightDiameter/2)}px`,\n                    style: `fill:${color};opacity:${alpha};`,\n                    'data-varri-subseq': 'true',\n                });\n                continue;\n            }\n\n            let distance1 = start - startIndex;\n            let distance2 = end - start;\n\n            if (startIndex < 0 && start > 0) distance1 -= 1;\n            if (start < 0 && end > 0) distance2 -= 1;\n\n            const startNode = distance1 + 1 + shift;\n            const endNode = distance1 + distance2 + 1 + shift;\n            const indices = [];\n            for (let i = startNode; i <= endNode; i++) indices.push(i);\n\n            polyline(indices,\n                `stroke:${color};stroke-width:14;opacity:${alpha};fill:None;` +\n                'stroke-linejoin:round;stroke-linecap:round',\n                { 'data-varri-subseq': 'true' }\n            );\n        }\n    }\n\n    /**\n     * Remove all generated region highlights from the active registry.\n     */\n    function clearGeneratedRegionHighlights() {\n        getRegionHighlights().filter(highlight => highlight.generated).forEach(highlight => {\n            removeRegionHighlight(highlight.id);\n        });\n    }\n\n    /**\n     * Register a generated region highlight from sequence ranges.\n     *\n     * @param {Object} v\n     * @param {{sequence1Range:[number, number], sequence2Range:[number, number], color?:string, alpha?:number}} spec\n     * @returns {Object}\n     */\n    function registerGeneratedRegionHighlight(v, spec) {\n        const sequenceContext = {\n            '1': { offset: v.offset1, length: v.sequence1 ? v.sequence1.length : 0, sequence: v.sequence1 },\n            '2': { offset: v.offset2, length: v.sequence2 ? v.sequence2.length : 0, sequence: v.sequence2 },\n        };\n\n        return registerRegionHighlight({\n            sequence1Range: spec.sequence1Range,\n            sequence2Range: spec.sequence2Range,\n            color: spec.color || COLORS.backgroundHighlight,\n            alpha: spec.alpha,\n            generated: true,\n        }, sequenceContext);\n    }\n\n    /**\n     * Derive a true sequence-position range (matching offset/skip-zero\n     * numbering) for a given sequence from a list of combined node/structure\n     * positions (as produced by {@link listIntermolPairs} or\n     * {@link getIntermolBasepairRegion}).\n     *\n     * @param {Object} v\n     * @param {number[]} positions  Combined node positions (1-based, gap-inclusive).\n     * @param {'1'|'2'} sequence\n     * @returns {[number, number]|null}\n     */\n    function getBackgroundRangeForPositions(v, positions, sequence) {\n        const indexDict = getIndexDictionary(v);\n        const values = positions\n            .map(position => indexDict[position])\n            .filter(entry => Array.isArray(entry) && entry[0] === `s${sequence}`)\n            .map(([, seqPosition]) => seqPosition)\n            .filter(Number.isFinite);\n\n        if (values.length === 0) return null;\n        return [Math.min(...values), Math.max(...values)];\n    }\n\n    /**\n     * Compute the generated region-highlight ranges for the \"entire\n     * intermolecular region\" background-highlighting mode, expressed as true\n     * sequence positions (matching offset/skip-zero numbering).\n     *\n     * @param {Object} v  Validated parameter dictionary.\n     * @returns {{sequence1Range:[number,number], sequence2Range:[number,number]}|null}\n     */\n    function computeBackgroundRegionRanges(v) {\n        const basepairRegion = getIntermolBasepairRegion(v.structure1, v.structure2);\n        if (!basepairRegion || basepairRegion.length < 2) return null;\n\n        const sequence1Range = getBackgroundRangeForPositions(v, basepairRegion[0], '1');\n        const sequence2Range = getBackgroundRangeForPositions(v, basepairRegion[1], '2');\n        if (!sequence1Range || !sequence2Range) return null;\n\n        return { sequence1Range, sequence2Range };\n    }\n\n    /**\n     * Build the node-ID path for a region highlight's filled polygon.\n     *\n     * @param {Object} v\n     * @param {Object} highlight\n     * @returns {number[]}\n     */\n    function getRegionHighlightNodePath(v, highlight) {\n        const nodeIds = [];\n        const seq1Range = Array.isArray(highlight.sequence1Range) ? highlight.sequence1Range : [];\n        const seq2Range = Array.isArray(highlight.sequence2Range) ? highlight.sequence2Range : [];\n\n        for (let position = seq1Range[0]; position <= seq1Range[1]; position++) {\n            const nodeId = getNodeIdForSequencePosition(v, '1', position);\n            if (nodeId) nodeIds.push(nodeId);\n        }\n\n        for (let position = seq2Range[0]; position <= seq2Range[1]; position++) {\n            const nodeId = getNodeIdForSequencePosition(v, '2', position);\n            if (nodeId) nodeIds.push(nodeId);\n        }\n\n        return nodeIds;\n    }\n\n    /**\n     * Apply all region highlights from the active registry.\n     *\n     * @param {Object} v\n     */\n    function applyRegionHighlights(v) {\n        const registryHighlights = getRegionHighlights();\n        const highlights = registryHighlights.length > 0\n            ? registryHighlights\n            : (Array.isArray(v.regionHighlights) ? v.regionHighlights : []);\n\n        highlights.forEach(highlight => {\n            const nodePath = getRegionHighlightNodePath(v, highlight);\n            if (nodePath.length >= 3) {\n                polygon(\n                    nodePath,\n                    `fill:${highlight.color || COLORS.backgroundHighlight};opacity:${highlight.alpha};stroke:${highlight.color || COLORS.backgroundHighlight};stroke-width:7`,\n                    { 'data-varri-region': 'true' }\n                );\n            } else if (nodePath.length === 2) {\n                polyline(\n                    nodePath,\n                    `stroke:${highlight.color || COLORS.backgroundHighlight};opacity:${highlight.alpha};stroke-width:7`,\n                    { 'data-varri-region': 'true' }\n                );\n            }\n        });\n    }\n\n    /**\n     * Apply all subsequence highlights from `v.subsequenceHighlights`.\n     *\n     * @param {Object} v\n     */\n    function applySubsequenceHighlights(v) {\n        const highlights = Array.isArray(v.subsequenceHighlights) ? v.subsequenceHighlights : [];\n        highlights.forEach(highlight => {\n            highlightSubsequence(\n                v,\n                highlight.sequence,\n                highlight.range,\n                highlight.color || COLORS.subsequenceHighlight,\n                highlight.alpha\n            );\n        });\n    }\n\n    /**\n     * Apply point-mutation styling to nucleotide nodes.\n     *\n     * @param {Object} v\n     */\n    function applyPointMutations(v) {\n        const mutations = Array.isArray(v.pointMutations) ? v.pointMutations : [];\n        mutations.forEach(mutation => {\n            if (!mutation.nodeId) return;\n            addStyleToNodes([mutation.nodeId], `stroke: ${mutation.color}; stroke-width: 2px;`);\n        });\n    }\n\n    /**\n     * Visualise basepairs: apply the basepair colour to all basepair links,\n     * and additionally mark G-U basepairs with a dashed line style.\n     *\n     * @param {Object} v  Validated parameter dictionary.\n     */\n    function styleBasepairs(v) {\n        // Apply basepair colour to all basepair links using inline style so it\n        // overrides the Fornac CSS rule `line.fornac-link[link_type=\"basepair\"]\n        // { stroke: red; }`, which takes precedence over SVG presentation\n        // attributes.\n        document.querySelectorAll('[link_type=\"basepair\"]').forEach(link => {\n            link.style.stroke = COLORS.basepair;\n        });\n\n        if (v.distinctBpTypes) {\n            // Build a 1-based sequence map including gap dots\n            const seq1 = v.sequence1;\n            const seq2 = v.sequence2;\n            const gapDots = '.'.repeat(GAP);\n            const combined = seq1 + gapDots + seq2;\n            const seqDict = {};\n            for (let i = 0; i < combined.length; i++) {\n                seqDict[String(i + 1)] = combined[i];\n            }\n\n            document.querySelectorAll('[link_type=\"basepair\"], [link_type=\"pseudoknot\"]').forEach(link => {\n                const l1 = seqDict[link.getAttribute('start')];\n                const l2 = seqDict[link.getAttribute('end')];\n                const bp = [l1, l2].sort().join('-').toLowerCase();\n                if (bp === 'g-u') {\n                    link.style.strokeLinecap = 'butt';\n                    link.style.strokeDasharray = '1 1';\n                } else if (bp === 'c-g' || bp === 'a-u') {\n                    link.style.strokeLinecap = 'butt';\n                    link.style.strokeDasharray = '';\n                } else {\n                    link.style.strokeLinecap = 'round';\n                    link.style.strokeDasharray = '0 3';\n                }\n            });\n        } else {\n            document.querySelectorAll('[link_type=\"basepair\"], [link_type=\"pseudoknot\"]').forEach(link => {\n                link.style.strokeLinecap = 'butt';\n                link.style.strokeDasharray = '';\n            });\n        }\n    }\n\n    /**\n     * Parse basepairs from a dot-bracket-like structure dictionary.\n     *\n     * @param {Object.<string, string>} struc  Position \u2192 bracket character map.\n     * @returns {Array<[number, number]>}  Sorted basepair index pairs.\n     */\n    function listBasepairs(struc) {\n        const basepairs = [];\n        const openBasepairs = { '(': [], '<': [], '[': [], '{': [] };\n        const brackets = [['(', ')'], ['[', ']'], ['{', '}'], ['<', '>']];\n\n        for (const [indexStr, char] of Object.entries(struc)) {\n            const index = parseInt(indexStr, 10);\n            for (const [open, close] of brackets) {\n                if (char === open) { openBasepairs[open].push(index); break; }\n                if (char === close) {\n                    if (openBasepairs[open].length > 0) {\n                        basepairs.push([openBasepairs[open].pop(), index]);\n                    }\n                    break;\n                }\n            }\n        }\n        basepairs.sort((a, b) => a[0] - b[0]);\n        return basepairs;\n    }\n\n    /**\n     * Extract intermolecular basepair pairs from the combined structure.\n     *\n     * @param {Object} v  Validated parameter dictionary.\n     * @returns {Array<[number, number]>}\n     */\n    function listIntermolPairs(v) {\n        const struc = v.structure_dict;\n        const struc1 = v.structure1;\n        const struc2 = v.structure2;\n        const shift = struc1.length + GAP;\n\n        const intermol = {};\n        for (const i of Object.keys(struc)) intermol[i] = '.';\n\n        for (const [index, bracket] of [\n            ...listIntermolNodes(struc1),\n            ...listIntermolNodes(struc2, shift),\n        ]) {\n            intermol[String(index)] = bracket;\n        }\n\n        return listBasepairs(intermol);\n    }\n\n    /**\n     * Normalize base-pair endpoints and return a deterministic, duplicate-free\n     * list ordered by the first and then the second nucleotide.\n     *\n     * @param {Array<[number, number]>} basepairs\n     * @returns {Array<[number, number]>}\n     */\n    function normaliseBasepairList(basepairs) {\n        const seen = new Set();\n        const pairs = [];\n\n        (Array.isArray(basepairs) ? basepairs : []).forEach(pair => {\n            if (!Array.isArray(pair) || pair.length < 2) return;\n            const first = Number(pair[0]);\n            const second = Number(pair[1]);\n            if (!Number.isInteger(first) || !Number.isInteger(second) || first === second) return;\n\n            const normalized = first < second ? [first, second] : [second, first];\n            const key = normalized[0] + ':' + normalized[1];\n            if (seen.has(key)) return;\n            seen.add(key);\n            pairs.push(normalized);\n        });\n\n        return pairs.sort((left, right) =>\n            left[0] - right[0] || left[1] - right[1]\n        );\n    }\n\n    /**\n     * Find the direct nested children of every base pair.\n     *\n     * For a fixed outer pair, candidates are visited by increasing opening\n     * endpoint. A candidate is covered by an earlier candidate exactly when\n     * that earlier candidate has the larger closing endpoint. Keeping the\n     * largest earlier closing endpoint therefore computes the cover relation\n     * in O(n^2), without joining an outer pair to a deeper pair through an\n     * intervening base-pair column.\n     *\n     * @param {Array<[number, number]>} basepairs\n     * @returns {Array<{outer:[number,number],children:Array<[number,number]>}>}\n     */\n    function listDirectNestedPairChildren(basepairs) {\n        const pairs = normaliseBasepairList(basepairs);\n\n        return pairs.map((outer, outerIndex) => {\n            const children = [];\n            let largestEarlierClose = -Infinity;\n\n            for (let innerIndex = outerIndex + 1; innerIndex < pairs.length; innerIndex++) {\n                const inner = pairs[innerIndex];\n                if (inner[0] >= outer[1]) break;\n                if (inner[1] >= outer[1]) continue;\n\n                if (largestEarlierClose <= inner[1]) children.push(inner);\n                largestEarlierClose = Math.max(largestEarlierClose, inner[1]);\n            }\n\n            return { outer, children };\n        });\n    }\n\n    function pairEquals(left, right) {\n        return left[0] === right[0] && left[1] === right[1];\n    }\n\n    function pairsCross(left, right) {\n        return (\n            left[0] < right[0] && right[0] < left[1] && left[1] < right[1]\n        ) || (\n            right[0] < left[0] && left[0] < right[1] && right[1] < left[1]\n        );\n    }\n\n    function createLoopBoundary(outer, inner, extra = {}) {\n        const firstGap = inner[0] - outer[0] - 1;\n        const secondGap = outer[1] - inner[1] - 1;\n        return {\n            outer: outer.slice(),\n            inner: inner.slice(),\n            gaps: [firstGap, secondGap],\n            loopType: firstGap > 0 && secondGap > 0 ? 'interior' : 'bulge',\n            ...extra,\n        };\n    }\n\n    /**\n     * Identify intermolecular base-pair columns that directly bound RRI\n     * bulges or interior loops.\n     *\n     * A result obeys the exact antiparallel cover relation from issue #59.\n     * Fully stacked columns are excluded. A candidate touched by a crossing\n     * RRI pair is also excluded because bulge/interior-loop decomposition is\n     * not defined for that pseudoknotted region.\n     *\n     * @param {Object} v  Validated parameter dictionary.\n     * @returns {Array<{outer:[number,number],inner:[number,number],gaps:[number,number],loopType:string}>}\n     */\n    function listRriLoopBoundaryPairs(v) {\n        const pairs = normaliseBasepairList(listIntermolPairs(v));\n        const boundaries = [];\n\n        listDirectNestedPairChildren(pairs).forEach(({ outer, children }) => {\n            children.forEach(inner => {\n                const firstGap = inner[0] - outer[0] - 1;\n                const secondGap = outer[1] - inner[1] - 1;\n                if (firstGap === 0 && secondGap === 0) return;\n\n                const crossesBoundary = pairs.some(pair => {\n                    if (pairEquals(pair, outer) || pairEquals(pair, inner)) return false;\n                    if (pairsCross(pair, outer) || pairsCross(pair, inner)) return true;\n                    const firstInside = outer[0] < pair[0] && pair[0] < inner[0];\n                    const secondInside = inner[1] < pair[1] && pair[1] < outer[1];\n                    return firstInside !== secondInside;\n                });\n                if (!crossesBoundary) boundaries.push(createLoopBoundary(outer, inner));\n            });\n        });\n\n        return boundaries;\n    }\n\n    /**\n     * Group intramolecular base pairs by strand using Fornac node numbers.\n     * Synthetic inter-molecule gap nodes are deliberately excluded.\n     *\n     * @param {Object} v  Validated parameter dictionary.\n     * @returns {{\"1\":Array<[number,number]>,\"2\":Array<[number,number]>}}\n     */\n    function listIntramolPairsBySequence(v) {\n        const sequence1End = v.sequence1.length;\n        const sequence2Start = sequence1End + GAP + 1;\n        const sequence2End = sequence1End + GAP + v.sequence2.length;\n        const grouped = { '1': [], '2': [] };\n\n        listBasepairs(v.structure_dict).forEach(pair => {\n            if (pair[0] >= 1 && pair[1] <= sequence1End) {\n                grouped['1'].push(pair);\n            } else if (pair[0] >= sequence2Start && pair[1] <= sequence2End) {\n                grouped['2'].push(pair);\n            }\n        });\n\n        return grouped;\n    }\n\n    /**\n     * Identify intramolecular bulges/interior loops independently per strand.\n     * A true bulge/interior loop has one direct child stem; hairpins (zero),\n     * multiloops (multiple), ordinary stacks, and crossing pairs are excluded.\n     *\n     * @param {Object} v  Validated parameter dictionary.\n     * @returns {Array<{sequence:\"1\"|\"2\",outer:[number,number],inner:[number,number],gaps:[number,number],loopType:string}>}\n     */\n    function listStructureLoopBoundaryPairs(v) {\n        const boundaries = [];\n        const grouped = listIntramolPairsBySequence(v);\n\n        for (const sequence of ['1', '2']) {\n            const pairs = normaliseBasepairList(grouped[sequence]);\n            listDirectNestedPairChildren(pairs).forEach(({ outer, children }) => {\n                if (children.length !== 1) return;\n                const inner = children[0];\n                const firstGap = inner[0] - outer[0] - 1;\n                const secondGap = outer[1] - inner[1] - 1;\n                if (firstGap === 0 && secondGap === 0) return;\n\n                const touchesCrossing = pairs.some(pair =>\n                    !pairEquals(pair, outer) && !pairEquals(pair, inner) &&\n                    (pairsCross(pair, outer) || pairsCross(pair, inner))\n                );\n                if (!touchesCrossing) {\n                    boundaries.push(createLoopBoundary(outer, inner, { sequence }));\n                }\n            });\n        }\n\n        return boundaries;\n    }\n\n    function loopBoundariesToConstraintSpecs(boundaries, kind) {\n        const constraints = [];\n\n        boundaries.forEach((boundary, index) => {\n            const loopId = boundary.sequence\n                ? kind + ':' + boundary.sequence + ':' + index\n                : kind + ':' + index;\n            const common = {\n                kind,\n                loopId,\n                loopType: boundary.loopType,\n            };\n\n            constraints.push({\n                ...common,\n                source: boundary.outer[0],\n                target: boundary.inner[0],\n                sequence: boundary.sequence || '1',\n            });\n            constraints.push({\n                ...common,\n                source: boundary.inner[1],\n                target: boundary.outer[1],\n                sequence: boundary.sequence || '2',\n            });\n        });\n\n        return constraints;\n    }\n\n    /**\n     * Build the two same-strand spring specifications for every RRI loop.\n     * Rest lengths are intentionally absent here: they are measured from the\n     * live Fornac coordinates when the springs are installed.\n     *\n     * @param {Object} v  Validated parameter dictionary.\n     * @returns {Array<{source:number,target:number,sequence:\"1\"|\"2\",kind:string,loopId:string,loopType:string}>}\n     */\n    function getLinearRriConstraintSpecs(v) {\n        return loopBoundariesToConstraintSpecs(listRriLoopBoundaryPairs(v), 'rri');\n    }\n\n    /**\n     * Build the two same-strand spring specifications for every intramolecular\n     * bulge/interior loop on either sequence.\n     *\n     * @param {Object} v  Validated parameter dictionary.\n     * @returns {Array<{source:number,target:number,sequence:\"1\"|\"2\",kind:string,loopId:string,loopType:string}>}\n     */\n    function getLinearStructureConstraintSpecs(v) {\n        return loopBoundariesToConstraintSpecs(\n            listStructureLoopBoundaryPairs(v),\n            'structure'\n        );\n    }\n\n    /** Resolve a nucleotide node by its 1-based Fornac node number. */\n    function getGraphNucleotideByNumber(graph, nodeNumber) {\n        if (!graph || !Array.isArray(graph.nodes)) return null;\n        return graph.nodes.find(node =>\n            node && node.nodeType === 'nucleotide' && node.num === nodeNumber\n        ) || null;\n    }\n\n    function getNodeDistance(first, second) {\n        const coordinates = [first?.x, first?.y, second?.x, second?.y];\n        if (!coordinates.every(value =>\n            typeof value === 'number' && Number.isFinite(value)\n        )) return null;\n        const [firstX, firstY, secondX, secondY] = coordinates;\n        return Math.hypot(secondX - firstX, secondY - firstY);\n    }\n\n    function pairKey(pair) {\n        return pair[0] + ':' + pair[1];\n    }\n\n    /**\n     * Return the one antiparallel RRI chain that can be represented by two\n     * ordered rails. Crossing RRI pairs are deliberately left to the ordinary\n     * force layout because a single two-rail ordering does not exist for them.\n     */\n    function listRriHelixPairGroups(v) {\n        const pairs = normaliseBasepairList(listIntermolPairs(v));\n        if (pairs.length < 2) return [];\n\n        for (let first = 0; first < pairs.length; first++) {\n            for (let second = first + 1; second < pairs.length; second++) {\n                if (pairsCross(pairs[first], pairs[second])) return [];\n            }\n        }\n        for (let index = 1; index < pairs.length; index++) {\n            if (pairs[index - 1][1] <= pairs[index][1]) return [];\n        }\n        return [{ kind: 'rri', sequence: null, pairs }];\n    }\n\n    /**\n     * Split intramolecular base pairs into maximal single-child stem paths.\n     * Paths stop at multiloops and only paths containing a bulge/interior loop\n     * need an additional linear constraint; uninterrupted stacks are already\n     * linear in Fornac's native layout.\n     */\n    function listStructureHelixPairGroups(v) {\n        const groups = [];\n        const grouped = listIntramolPairsBySequence(v);\n\n        for (const sequence of ['1', '2']) {\n            const pairs = normaliseBasepairList(grouped[sequence]);\n            const crossingPairKeys = new Set();\n            pairs.forEach((pair, index) => {\n                pairs.slice(index + 1).forEach(other => {\n                    if (!pairsCross(pair, other)) return;\n                    crossingPairKeys.add(pairKey(pair));\n                    crossingPairKeys.add(pairKey(other));\n                });\n            });\n\n            const nextPair = new Map();\n            const hasIncoming = new Set();\n            listDirectNestedPairChildren(pairs).forEach(({ outer, children }) => {\n                if (children.length !== 1) return;\n                const inner = children[0];\n                if (crossingPairKeys.has(pairKey(outer)) ||\n                    crossingPairKeys.has(pairKey(inner))) return;\n                nextPair.set(pairKey(outer), inner);\n                hasIncoming.add(pairKey(inner));\n            });\n\n            pairs.filter(pair =>\n                !crossingPairKeys.has(pairKey(pair)) &&\n                !hasIncoming.has(pairKey(pair))\n            ).forEach(root => {\n                const path = [];\n                const visited = new Set();\n                let pair = root;\n                while (pair && !visited.has(pairKey(pair))) {\n                    path.push(pair);\n                    visited.add(pairKey(pair));\n                    pair = nextPair.get(pairKey(pair));\n                }\n                const containsLoop = path.slice(1).some((inner, index) => {\n                    const outer = path[index];\n                    return inner[0] - outer[0] > 1 || outer[1] - inner[1] > 1;\n                });\n                if (path.length >= 2 && containsLoop) {\n                    groups.push({ kind: 'structure', sequence, pairs: path });\n                }\n            });\n        }\n        return groups;\n    }\n\n    /**\n     * Measure the two issue-59 loop spans without adding them to Fornac's\n     * render graph. Keeping constraint metadata outside graph.links makes the\n     * constraints unconditionally invisible, including after container.update().\n     */\n    function collectLinearHelixSpanConstraints(container, specs, linkType) {\n        const graph = container && container.graph;\n        if (!graph || !Array.isArray(graph.nodes)) return [];\n\n        const rawMultiplier = Number(container.options?.linkDistanceMultiplier);\n        const multiplier = Number.isFinite(rawMultiplier) && rawMultiplier > 0\n            ? rawMultiplier\n            : 15;\n        const byLoop = new Map();\n        specs.forEach(spec => {\n            if (!byLoop.has(spec.loopId)) byLoop.set(spec.loopId, []);\n            byLoop.get(spec.loopId).push(spec);\n        });\n\n        const constraints = [];\n        byLoop.forEach(loopSpecs => {\n            if (loopSpecs.length !== 2) return;\n            const resolved = loopSpecs.map(spec => ({\n                spec,\n                source: getGraphNucleotideByNumber(graph, spec.source),\n                target: getGraphNucleotideByNumber(graph, spec.target),\n            }));\n            if (resolved.some(link => !link.source || !link.target)) return;\n\n            const distances = resolved.map(link => getNodeDistance(link.source, link.target));\n            if (distances.some(distance => distance === null)) return;\n            const loopSpan = Math.max(...distances);\n            if (!Number.isFinite(loopSpan) || loopSpan <= 0) return;\n\n            resolved.forEach(({ spec, source, target }) => {\n                constraints.push({\n                    source,\n                    target,\n                    value: loopSpan / multiplier,\n                    linkType,\n                    extraLinkType: 'constraint',\n                    varriLinearHelix: true,\n                    varriLinearHelixKind: spec.kind,\n                    varriLinearHelixLoop: spec.loopId,\n                    varriTargetDistance: loopSpan,\n                });\n            });\n        });\n        return constraints;\n    }\n\n    /**\n     * Build a straight two-rail template from the current live geometry.\n     * Loop-to-loop increments use max(d1,d2), exactly as requested in issue\n     * #59; uninterrupted stack increments use Fornac's backbone rest length.\n     * The template itself is centered at the origin so it can subsequently be\n     * fitted to the freely translating and rotating force-layout component.\n     */\n    function createLinearHelixRailTemplate(container, group) {\n        const graph = container && container.graph;\n        if (!graph || !Array.isArray(graph.nodes) || !group?.pairs?.length) return null;\n\n        const rawMultiplier = Number(container.options?.linkDistanceMultiplier);\n        const multiplier = Number.isFinite(rawMultiplier) && rawMultiplier > 0\n            ? rawMultiplier\n            : 15;\n        const pairNodes = group.pairs.map(pair => ({\n            pair,\n            first: getGraphNucleotideByNumber(graph, pair[0]),\n            second: getGraphNucleotideByNumber(graph, pair[1]),\n        }));\n        if (pairNodes.some(column =>\n            !column.first || !column.second ||\n            column.first.fixed || column.second.fixed ||\n            getNodeDistance(column.first, column.second) === null\n        )) return null;\n\n        const offsets = [0];\n        const intervals = [];\n        for (let index = 1; index < pairNodes.length; index++) {\n            const previous = pairNodes[index - 1];\n            const current = pairNodes[index];\n            const firstGap = current.pair[0] - previous.pair[0] - 1;\n            const secondGap = previous.pair[1] - current.pair[1] - 1;\n            const isLoop = firstGap > 0 || secondGap > 0;\n            const measured = Math.max(\n                getNodeDistance(previous.first, current.first),\n                getNodeDistance(previous.second, current.second)\n            );\n            const span = isLoop && Number.isFinite(measured) && measured > 0\n                ? measured\n                : multiplier;\n            intervals.push({ span, isLoop, gaps: [firstGap, secondGap] });\n            offsets.push(offsets[offsets.length - 1] + span);\n        }\n\n        const meanOffset = offsets.reduce((sum, value) => sum + value, 0) /\n            offsets.length;\n        const points = [];\n        pairNodes.forEach((column, index) => {\n            const along = offsets[index] - meanOffset;\n            points.push({ node: column.first, x: along, y: -multiplier / 2 });\n            points.push({ node: column.second, x: along, y: multiplier / 2 });\n        });\n\n        const template = {\n            kind: group.kind,\n            sequence: group.sequence,\n            pairs: group.pairs.map(pair => pair.slice()),\n            points,\n            intervals,\n            railGap: multiplier,\n        };\n        const ordinaryFit = fitLinearHelixRailTemplate(template, 'x', 'y', 1);\n        const reflectedFit = fitLinearHelixRailTemplate(template, 'x', 'y', -1);\n        template.reflection = reflectedFit &&\n            (!ordinaryFit || reflectedFit.error < ordinaryFit.error)\n            ? -1\n            : 1;\n        return template;\n    }\n\n    /**\n     * Fit a translated/rotated copy of one possibly reflected rail template\n     * to a requested pair of live node-coordinate fields.\n     */\n    function fitLinearHelixRailTemplate(template, xField, yField, reflection) {\n        if (!template || !Array.isArray(template.points) || template.points.length < 4) {\n            return null;\n        }\n        const live = template.points.map(point => point.node);\n        if (live.some(node =>\n            !node || ![node[xField], node[yField]].every(Number.isFinite)\n        )) {\n            return null;\n        }\n\n        const center = live.reduce((sum, node) => ({\n            x: sum.x + node[xField],\n            y: sum.y + node[yField],\n        }), { x: 0, y: 0 });\n        center.x /= live.length;\n        center.y /= live.length;\n\n        let dot = 0;\n        let cross = 0;\n        template.points.forEach(point => {\n            const templateY = reflection * point.y;\n            const liveX = point.node[xField] - center.x;\n            const liveY = point.node[yField] - center.y;\n            dot += point.x * liveX + templateY * liveY;\n            cross += point.x * liveY - templateY * liveX;\n        });\n        const angle = Math.atan2(cross, dot);\n        const cosine = Math.cos(angle);\n        const sine = Math.sin(angle);\n        let error = 0;\n        const targets = template.points.map(point => {\n            const templateY = reflection * point.y;\n            const target = {\n                x: center.x + cosine * point.x - sine * templateY,\n                y: center.y + sine * point.x + cosine * templateY,\n            };\n            const deltaX = point.node[xField] - target.x;\n            const deltaY = point.node[yField] - target.y;\n            error += deltaX * deltaX + deltaY * deltaY;\n            return target;\n        });\n        return { angle, center, error, targets };\n    }\n\n    /**\n     * Project one live helix onto the closest translated/rotated copy of its\n     * straight template (2-D orthogonal Procrustes fit). Current and previous\n     * coordinate clouds are projected separately, preserving the rigid body's\n     * translational and rotational velocity instead of zeroing it each tick.\n     */\n    function projectLinearHelixRailTemplate(template) {\n        if (!template || !Array.isArray(template.points)) return false;\n        const live = template.points.map(point => point.node);\n        if (live.some(node => !node || node.fixed)) return false;\n\n        const reflection = template.reflection === -1 ? -1 : 1;\n        const currentFit = fitLinearHelixRailTemplate(template, 'x', 'y', reflection);\n        if (!currentFit) return false;\n        const previousFit = fitLinearHelixRailTemplate(template, 'px', 'py', reflection) ||\n            currentFit;\n\n        template.points.forEach((point, index) => {\n            point.node.x = currentFit.targets[index].x;\n            point.node.y = currentFit.targets[index].y;\n            point.node.px = previousFit.targets[index].x;\n            point.node.py = previousFit.targets[index].y;\n            point.node.varriLinearHelix = true;\n            point.node.varriLinearHelixKind = template.kind;\n        });\n        template.angle = currentFit.angle;\n        template.center = currentFit.center;\n        template.previousAngle = previousFit.angle;\n        template.previousCenter = previousFit.center;\n        return true;\n    }\n\n    function normaliseRotationRadians(radians) {\n        return Math.atan2(Math.sin(radians), Math.cos(radians));\n    }\n\n    function rotateCoordinateCloud(nodes, xField, yField, center, radians) {\n        if (!center || ![center.x, center.y, radians].every(Number.isFinite)) return false;\n        const cosine = Math.cos(radians);\n        const sine = Math.sin(radians);\n        nodes.forEach(node => {\n            const offsetX = node[xField] - center.x;\n            const offsetY = node[yField] - center.y;\n            node[xField] = center.x + cosine * offsetX - sine * offsetY;\n            node[yField] = center.y + sine * offsetX + cosine * offsetY;\n        });\n        return true;\n    }\n\n    function rotateTemplateFitState(template, centerField, angleField, pivot, radians) {\n        const center = template?.[centerField];\n        const angle = template?.[angleField];\n        if (!center || ![center.x, center.y, angle].every(Number.isFinite)) return;\n        const cosine = Math.cos(radians);\n        const sine = Math.sin(radians);\n        const offsetX = center.x - pivot.x;\n        const offsetY = center.y - pivot.y;\n        template[centerField] = {\n            x: pivot.x + cosine * offsetX - sine * offsetY,\n            y: pivot.y + sine * offsetX + cosine * offsetY,\n        };\n        template[angleField] = normaliseRotationRadians(angle + radians);\n    }\n\n    /**\n     * Remove the global angular degree of freedom from an RRI layout by\n     * rotating the complete graph until the paired-column centreline is\n     * horizontal. Current and previous coordinate clouds are rotated\n     * independently so translation is preserved without angular drift.\n     */\n    function orientLinearRriInteractionHorizontally(graph, rriTemplate, templates) {\n        if (!graph || !Array.isArray(graph.nodes) || !rriTemplate) return false;\n        const nodes = graph.nodes.filter(Boolean);\n        if (nodes.length === 0 || nodes.some(node =>\n            node.fixed || ![node.x, node.y, node.px, node.py].every(Number.isFinite)\n        )) return false;\n        if (![rriTemplate.angle, rriTemplate.previousAngle].every(Number.isFinite) ||\n            !rriTemplate.center || !rriTemplate.previousCenter) return false;\n\n        if (rriTemplate.horizontalDirection !== 1 &&\n            rriTemplate.horizontalDirection !== -1) {\n            rriTemplate.horizontalDirection = Math.cos(rriTemplate.angle) >= 0 ? 1 : -1;\n        }\n        const targetAngle = rriTemplate.horizontalDirection === 1 ? 0 : Math.PI;\n        const currentRotation = normaliseRotationRadians(\n            targetAngle - rriTemplate.angle\n        );\n        const previousRotation = normaliseRotationRadians(\n            targetAngle - rriTemplate.previousAngle\n        );\n        const currentPivot = { ...rriTemplate.center };\n        const previousPivot = { ...rriTemplate.previousCenter };\n\n        rotateCoordinateCloud(nodes, 'x', 'y', currentPivot, currentRotation);\n        rotateCoordinateCloud(nodes, 'px', 'py', previousPivot, previousRotation);\n        templates.forEach(template => {\n            rotateTemplateFitState(\n                template,\n                'center',\n                'angle',\n                currentPivot,\n                currentRotation\n            );\n            rotateTemplateFitState(\n                template,\n                'previousCenter',\n                'previousAngle',\n                previousPivot,\n                previousRotation\n            );\n        });\n        rriTemplate.lastHorizontalRotation = currentRotation;\n        return true;\n    }\n\n    function listVisibleIndexLabelPositions(v) {\n        const positions = new Set(\n            Object.entries(getIndexLabelValues(v))\n                .filter(([, value]) => value !== 0)\n                .map(([position]) => Number(position))\n        );\n        (Array.isArray(v.pointMutations) ? v.pointMutations : []).forEach(mutation => {\n            const nodeId = Number(mutation.nodeId);\n            if (Number.isInteger(nodeId)) positions.add(nodeId);\n        });\n        return positions;\n    }\n\n    function resolveGraphLinkNode(graph, endpoint) {\n        if (endpoint && typeof endpoint === 'object') return endpoint;\n        const index = Number(endpoint);\n        return Number.isInteger(index) ? graph.nodes[index] || null : null;\n    }\n\n    /**\n     * Match retained number labels to paired rail nodes and their mates.\n     * Fornac's label link fixes distance but not which side of the rail wins,\n     * so these records provide a transient, direction-only settling hint.\n     */\n    function collectLinearHelixIndexLabelBiases(container, v, templates) {\n        const graph = container && container.graph;\n        if (!graph || !Array.isArray(graph.nodes) || !Array.isArray(graph.links)) return [];\n\n        const visiblePositions = listVisibleIndexLabelPositions(v);\n        const partnerByNode = new Map();\n        templates.forEach(template => {\n            for (let index = 0; index + 1 < template.points.length; index += 2) {\n                const first = template.points[index].node;\n                const second = template.points[index + 1].node;\n                partnerByNode.set(first, second);\n                partnerByNode.set(second, first);\n            }\n        });\n\n        const rawMultiplier = Number(container.options?.linkDistanceMultiplier);\n        const multiplier = Number.isFinite(rawMultiplier) && rawMultiplier > 0\n            ? rawMultiplier\n            : 15;\n        const seenLabels = new Set();\n        const biases = [];\n\n        graph.links.forEach(link => {\n            if (link?.linkType !== 'label_link') return;\n            const source = resolveGraphLinkNode(graph, link.source);\n            const target = resolveGraphLinkNode(graph, link.target);\n            const label = source?.nodeType === 'label'\n                ? source\n                : target?.nodeType === 'label' ? target : null;\n            const anchor = source?.nodeType === 'nucleotide'\n                ? source\n                : target?.nodeType === 'nucleotide' ? target : null;\n            const partner = partnerByNode.get(anchor);\n            if (!label || !anchor || !partner || seenLabels.has(label) ||\n                !visiblePositions.has(Number(anchor.num))) return;\n\n            const rawValue = Number(link.value);\n            const linkDistance = multiplier * (\n                Number.isFinite(rawValue) && rawValue > 0 ? rawValue : 1\n            );\n            seenLabels.add(label);\n            biases.push({ label, anchor, partner, linkDistance });\n        });\n        return biases;\n    }\n\n    /**\n     * Gently move wrong-side number labels across the rail centreline.\n     * Once a label reaches its exterior half-plane this becomes a no-op and\n     * Fornac's native label link completes the ordinary spacing.\n     */\n    function nudgeLinearHelixIndexLabels(biases) {\n        let moved = 0;\n        biases.forEach(bias => {\n            const { label, anchor, partner, linkDistance } = bias;\n            if (!label || !anchor || !partner ||\n                label.fixed || anchor.fixed || partner.fixed) return;\n            if (![label.x, label.y, label.px, label.py,\n                anchor.x, anchor.y, partner.x, partner.y,\n                linkDistance].every(Number.isFinite)) return;\n\n            const outwardX = anchor.x - partner.x;\n            const outwardY = anchor.y - partner.y;\n            const outwardLength = Math.hypot(outwardX, outwardY);\n            if (!(outwardLength > 0)) return;\n            const unitX = outwardX / outwardLength;\n            const unitY = outwardY / outwardLength;\n            const side = (label.x - anchor.x) * unitX +\n                (label.y - anchor.y) * unitY;\n            const target = LINEAR_HELIX_LABEL_BIAS_TARGET * linkDistance;\n            if (!(side < target)) return;\n\n            // Use the same bounded correction on every lifecycle event. The\n            // end handler must never turn this settling hint into a late snap.\n            const distance = Math.min(\n                (target - side) * LINEAR_HELIX_LABEL_BIAS_GAIN,\n                LINEAR_HELIX_LABEL_BIAS_MAX_STEP * linkDistance\n            );\n            const deltaX = distance * unitX;\n            const deltaY = distance * unitY;\n            label.x += deltaX;\n            label.y += deltaY;\n            label.px += deltaX;\n            label.py += deltaY;\n            moved += 1;\n        });\n        return moved;\n    }\n\n    /** Cache projected nodes, gently biased labels, and their visible links. */\n    function createLinearHelixDomCache(\n        graph,\n        templates,\n        labelBiases = [],\n        syncWholeGraph = false\n    ) {\n        if (typeof document === 'undefined') return { nodes: [], links: [] };\n        const projectedNodes = syncWholeGraph\n            ? new Set(graph.nodes)\n            : new Set([\n                ...templates.flatMap(template => template.points.map(point => point.node)),\n                ...labelBiases.map(bias => bias.label),\n            ]);\n        const graphLinks = Array.isArray(graph.links) ? graph.links : [];\n        const incidentLinks = syncWholeGraph\n            ? new Set(graphLinks)\n            : new Set(graphLinks.filter(link =>\n                projectedNodes.has(link?.source) || projectedNodes.has(link?.target)\n            ));\n        return {\n            nodes: Array.from(document.querySelectorAll('g.gnode'))\n                .filter(element => projectedNodes.has(element.__data__)),\n            links: Array.from(document.querySelectorAll('line.link'))\n                .filter(element => incidentLinks.has(element.__data__)),\n        };\n    }\n\n    function syncFornacDirectionArrow(element, node) {\n        const arrow = element.querySelector?.('path.fornac-directionArrow');\n        const previous = node?.prevNode;\n        if (!arrow || !previous || !node.linked ||\n            ![node.x, node.y, previous.x, previous.y, node.radius].every(Number.isFinite)) {\n            return;\n        }\n        let directionX = previous.x - node.x;\n        let directionY = previous.y - node.y;\n        const length = Math.hypot(directionX, directionY);\n        if (!(length > 0)) return;\n        directionX /= length;\n        directionY /= length;\n        const normalX = -directionY;\n        const normalY = directionX;\n        const tipX = (node.radius + 0.4) * directionX;\n        const tipY = (node.radius + 0.4) * directionY;\n        const size = 6;\n        const width = 0.7;\n        arrow.setAttribute('d',\n            `M${tipX + size * (directionX / 2 + normalX * width / 2)},` +\n            `${tipY + size * (directionY / 2 + normalY * width / 2)}` +\n            `L${tipX},${tipY}` +\n            `L${tipX + size * (directionX / 2 - normalX * width / 2)},` +\n            `${tipY + size * (directionY / 2 - normalY * width / 2)}`\n        );\n    }\n\n    /** Keep Fornac's already-created SVG in sync with post-tick projection. */\n    function syncLinearHelixDom(cache) {\n        cache.nodes.forEach(element => {\n            const node = element.__data__;\n            if (!node || ![node.x, node.y].every(Number.isFinite)) return;\n            element.setAttribute('transform', `translate(${node.x},${node.y})`);\n            syncFornacDirectionArrow(element, node);\n        });\n        cache.links.forEach(element => {\n            const link = element.__data__;\n            if (!link?.source || !link?.target) return;\n            element.setAttribute('x1', String(link.source.x));\n            element.setAttribute('y1', String(link.source.y));\n            element.setAttribute('x2', String(link.target.x));\n            element.setAttribute('y2', String(link.target.y));\n        });\n    }\n\n    function clearLinearHelixConstraintState(container) {\n        const hadConstraintState = !!container && (\n            Object.prototype.hasOwnProperty.call(container, 'varriLinearHelixConstraints') ||\n            Object.prototype.hasOwnProperty.call(container, 'varriLinearHelixTemplates') ||\n            Object.prototype.hasOwnProperty.call(container, 'varriLinearHelixLabelBiases')\n        );\n        if (hadConstraintState && container.force && typeof container.force.on === 'function') {\n            container.force.on('tick.varriLinearHelix', null);\n            container.force.on('end.varriLinearHelix', null);\n        }\n        delete container?.varriLinearHelixConstraints;\n        delete container?.varriLinearHelixTemplates;\n        delete container?.varriLinearHelixLabelBiases;\n    }\n\n    /**\n     * Apply rigid, invisible two-rail constraints for the requested RRI and/or\n     * intramolecular helices, then restart the live D3 force once.\n     *\n     * @param {Object} container  Live Fornac container.\n     * @param {Object} v  Validated parameter dictionary.\n     * @param {{rri?:boolean,structure?:boolean}} [options]\n     * @returns {number} Number of measured same-strand loop-span constraints.\n     */\n    function applyLinearHelixSprings(container, v, options = {}) {\n        clearLinearHelixConstraintState(container);\n        const graph = container && container.graph;\n        if (!graph || !Array.isArray(graph.nodes) || !Array.isArray(graph.links)) return 0;\n\n        const constraints = [];\n        const groups = [];\n        if (options.rri && v.molecules === '2') {\n            constraints.push(...collectLinearHelixSpanConstraints(\n                container,\n                getLinearRriConstraintSpecs(v),\n                LINEAR_RRI_LINK_TYPE\n            ));\n            groups.push(...listRriHelixPairGroups(v));\n        }\n        if (options.structure) {\n            constraints.push(...collectLinearHelixSpanConstraints(\n                container,\n                getLinearStructureConstraintSpecs(v),\n                LINEAR_STRUCTURE_LINK_TYPE\n            ));\n            groups.push(...listStructureHelixPairGroups(v));\n        }\n\n        const templates = groups\n            .map(group => createLinearHelixRailTemplate(container, group))\n            .filter(Boolean);\n        if (templates.length === 0) return 0;\n\n        const constrainedNodes = new Set(\n            templates.flatMap(template => template.points.map(point => point.node))\n        );\n        const activeConstraints = constraints.filter(constraint =>\n            constrainedNodes.has(constraint.source) &&\n            constrainedNodes.has(constraint.target)\n        );\n        container.varriLinearHelixConstraints = activeConstraints;\n        container.varriLinearHelixTemplates = templates;\n        const labelBiases = collectLinearHelixIndexLabelBiases(container, v, templates);\n        container.varriLinearHelixLabelBiases = labelBiases;\n        const rriTemplate = options.rri\n            ? templates.find(template => template.kind === 'rri') || null\n            : null;\n        const domCache = createLinearHelixDomCache(\n            graph,\n            templates,\n            labelBiases,\n            !!rriTemplate\n        );\n        const enforceAndSync = () => {\n            templates.forEach(projectLinearHelixRailTemplate);\n            if (rriTemplate) {\n                orientLinearRriInteractionHorizontally(graph, rriTemplate, templates);\n            }\n            nudgeLinearHelixIndexLabels(labelBiases);\n            syncLinearHelixDom(domCache);\n        };\n        let hasRefittedAtRest = false;\n        const enforceSyncAndRefit = () => {\n            enforceAndSync();\n            if (!hasRefittedAtRest && typeof container.centerView === 'function') {\n                hasRefittedAtRest = true;\n                container.centerView();\n            }\n        };\n        enforceAndSync();\n\n        if (container.force) {\n            if (typeof container.force.on === 'function') {\n                container.force.on('tick.varriLinearHelix', () => enforceAndSync());\n                // The final projection can extend beyond the bounds measured by\n                // applyModifications while the force is still moving. Refit once\n                // at rest so asymmetric bulges are not clipped at the viewport.\n                container.force.on('end.varriLinearHelix', enforceSyncAndRefit);\n            }\n            if (typeof container.force.start === 'function') {\n                container.force.start();\n            }\n        }\n        return activeConstraints.length;\n    }\n\n    /**\n     * Add background highlighting for intermolecular basepair stacks.\n     *\n     * @param {Object} v  Validated parameter dictionary.\n     */\n    function backgroundhighlightBasepairs(v) {\n        const intermolPairs = listIntermolPairs(v);\n        if (intermolPairs.length === 0) {\n            clearGeneratedRegionHighlights();\n            return;\n        }\n\n        let stack = [intermolPairs.shift()];\n        const highlightAreas = [];\n\n        for (const [open, close] of intermolPairs) {\n            const [stackOpen, stackClose] = stack[stack.length - 1];\n            if (open - 1 === stackOpen && close + 1 === stackClose) {\n                stack.push([open, close]);\n                continue;\n            }\n            const area = stack.flatMap(([a, b]) => [a, b]).sort((a, b) => a - b);\n            highlightAreas.push(area);\n            stack = [[open, close]];\n        }\n        const area = stack.flatMap(([a, b]) => [a, b]).sort((a, b) => a - b);\n        highlightAreas.push(area);\n\n        clearGeneratedRegionHighlights();\n        highlightAreas.forEach(region => {\n            const seq1Range = getBackgroundRangeForPositions(v, region, '1');\n            const seq2Range = getBackgroundRangeForPositions(v, region, '2');\n            if (seq1Range && seq2Range) {\n                registerGeneratedRegionHighlight(v, {\n                    sequence1Range: seq1Range,\n                    sequence2Range: seq2Range,\n                    color: COLORS.backgroundHighlight,\n                });\n            }\n        });\n    }\n\n    /**\n     * Add background highlighting for the entire intermolecular region.\n     *\n     * @param {Object} v  Validated parameter dictionary.\n     */\n    function backgroundhighlightRegion(v) {\n        const ranges = computeBackgroundRegionRanges(v);\n        if (!ranges) {\n            return;\n        }\n\n        registerGeneratedRegionHighlight(v, {\n            sequence1Range: ranges.sequence1Range,\n            sequence2Range: ranges.sequence2Range,\n            color: COLORS.backgroundHighlight,\n        });\n    }\n\n    /**\n     * Add an accessibility-overlay circle on top of an existing node.\n     *\n     * @param {number} id   Node ID.\n     * @param {string} style  CSS style for the overlay.\n     * @param {string} tooltip  Extra tooltip text to append.\n     */\n    function addAccessibilityOverlay(id, style, tooltip) {\n        document.querySelectorAll(`circle[node_num=\"${id}\"]`).forEach(node => {\n            const overlay = node.cloneNode(true);\n            overlay.setAttribute('node_num', `o${id}`);\n            overlay.setAttribute('style', style);\n            if (overlay.firstChild) {\n                overlay.firstChild.innerHTML += tooltip;\n            }\n            node.after(overlay);\n        });\n    }\n\n    /**\n     * Map a probability value to an opacity (higher probability \u2192 lower opacity).\n     *\n     * @param {number} prb  Value in [0, 1].\n     * @returns {number}\n     */\n    function mapProbabilityToOpacity(prb, representsOne) {\n        return representsOne ? prb : (1 - prb);\n    }\n\n    /**\n     * Visualise nucleotide accessibility data as overlaid coloured circles.\n     *\n     * @param {Object.<number, number>} accessData  Map of node ID \u2192 accessibility probability.\n     * @param {number} lenSeq  Length of sequence 1 (used to distinguish colour by molecule).\n     * @param {{sequence1?: string, sequence2?: string}|null} accessColors  Optional colors for sequence 1/2 overlays.\n     * @param {{sequence1RepresentsOne?: boolean, sequence2RepresentsOne?: boolean}|null} accessColorMode\n     *     Optional per-sequence mapping flags. If true, probability 1 maps to full color.\n     */\n    function visualiseAccessibility(accessData, lenSeq, accessColors = null, accessColorMode = null) {\n        const seq1Color = accessColors?.sequence1 || COLORS.seq1profileColor;\n        const seq2Color = accessColors?.sequence2 || COLORS.seq2profileColor;\n        const seq1RepresentsOne = !!accessColorMode?.sequence1RepresentsOne;\n        const seq2RepresentsOne = !!accessColorMode?.sequence2RepresentsOne;\n        for (const [indexStr, prb] of Object.entries(accessData)) {\n            const index = parseInt(indexStr, 10);\n            const isSeq1 = index <= lenSeq;\n            const color = isSeq1 ? seq1Color : seq2Color;\n            const representsOne = isSeq1 ? seq1RepresentsOne : seq2RepresentsOne;\n            const style = `fill: ${color};opacity: ${mapProbabilityToOpacity(prb, representsOne)}; stroke-width: 0;`;\n            const prbTooltip = '\\n' + prb.toExponential(2);\n            addAccessibilityOverlay(index, style, prbTooltip);\n        }\n    }\n\n    /**\n     * Resolve a force-graph link endpoint to a node object when possible.\n     *\n     * @param {Object} graph\n     * @param {Object|number|string|null|undefined} endpoint\n     * @returns {Object|null}\n     */\n    function resolveGraphNodeFromEndpoint(graph, endpoint) {\n        if (endpoint && typeof endpoint === 'object') return endpoint;\n\n        const idx = parseInt(String(endpoint), 10);\n        if (!Number.isFinite(idx)) return null;\n\n        if (Array.isArray(graph?.nodes) && graph.nodes[idx]) return graph.nodes[idx];\n        if (Array.isArray(graph?.nodes)) {\n            const byNumber = graph.nodes.find(node => node && node.num === idx);\n            if (byNumber) return byNumber;\n        }\n\n        return null;\n    }\n\n    /**\n     * Identify the force-graph nodes that implement Fornac's \"free-form\"\n     * loop circularisation: the two synthetic closure nodes plus every hub\n     * whose loop is exterior-flavoured, along with the full member set of\n     * each such hub.\n     *\n     * Fornac's `reinforceLoops()` gives every loop of the structure (stems\n     * excluded) its own fake \"middle\" hub node via `addFakeNode()`, which\n     * pulls that loop's member nucleotides toward one shared point (keeping\n     * the loop visually rounded). For the true top-level external loop\n     * specifically \u2014 and only when Fornac's `circularizeExternal` option is\n     * enabled, which is the default \u2014 two extra synthetic \"closure\" middle\n     * nodes (`num: -2` and `num: -3`), positioned at the RNA's very first\n     * and very last nucleotide, are additionally appended to that loop's\n     * member list before its hub is created. This is exactly the\n     * constraint that pulls the two sequence ends together.\n     *\n     * That hub cannot be found reliably via link adjacency: `addFakeNode()`\n     * skips creating any link (hub spoke *and* the two \"chord\" links to\n     * nearby members \u2014 see below) for member-list entries whose index\n     * exceeds the sequence length, which is exactly what the closure nodes'\n     * synthetic indices are. So the closure nodes are never linked to the\n     * hub directly, only incidentally chord-linked to a couple of nearby\n     * real nucleotide members. Instead, each hub's own `nucs` array \u2014 a\n     * snapshot of the 1-based `graph.nodes` array indices of every member\n     * of that loop, recorded when the hub was created \u2014 is used: for the\n     * true external loop only, it includes the closure nodes' own array\n     * indices, which identifies that hub precisely.\n     *\n     * vaRRI additionally inserts extra unpaired \"gap\" characters between two\n     * molecules to work around a Fornac rendering bug. Fornac's own\n     * `breakNodesToFakeNodes()` marks every member of *any* loop that\n     * touches that gap as `elemType: \"e\"` (the same label used for the true\n     * exterior loop), regardless of that loop's real type \u2014 this is exactly\n     * the \"trailing ends around the & spacer\" that should also be freed.\n     * Any hub whose resolved members include an `elemType: \"e\"` nucleotide\n     * is therefore treated the same way as the true external-loop hub.\n     *\n     * Each qualifying hub's `nucs` array also lists every other member of\n     * its loop (real nucleotides, and closure nodes for the true external\n     * hub). Those member sets are returned too, because `addFakeNode()`\n     * additionally links members directly to each other with two kinds of\n     * \"chord\" links (skipping the hub entirely) to keep the loop's ring\n     * shape from collapsing \u2014 e.g. a member is linked straight to the\n     * member roughly opposite it in the loop. Those direct member-to-member\n     * links must also be removed to fully free the loop's nucleotides;\n     * removing only the hub and closure nodes leaves them in place, which\n     * still visibly pulls opposite sides of the loop together. Loops that\n     * don't qualify (i.e. every other stem/hairpin/interior/multi loop) are\n     * left completely untouched.\n     *\n     * @param {Object} graph\n     * @returns {{closureUids: Set<string>, hubUids: Set<string>, memberUids: Set<string>}|null}\n     */\n    function getFreeableLoopScaffoldUids(graph) {\n        if (!graph || !Array.isArray(graph.nodes)) return null;\n\n        const closureNodes = graph.nodes.filter(node =>\n            node && node.nodeType === 'middle' && (node.num === -2 || node.num === -3)\n        );\n        const closureUids = new Set(closureNodes.map(node => node.uid).filter(Boolean));\n        const closureIndices = new Set(closureNodes.map(node => graph.nodes.indexOf(node) + 1));\n\n        const hubs = graph.nodes.filter(node =>\n            node && node.nodeType === 'middle' && node.num === -1 && Array.isArray(node.nucs)\n        );\n\n        const hubUids = new Set();\n        const memberUids = new Set(closureUids);\n\n        hubs.forEach(hub => {\n            const members = hub.nucs.map(idx => graph.nodes[idx - 1]).filter(Boolean);\n            const touchesClosure = hub.nucs.some(idx => closureIndices.has(idx));\n            const touchesExternalElemType = members.some(member => member.elemType === 'e');\n\n            if (!touchesClosure && !touchesExternalElemType) return;\n\n            hubUids.add(hub.uid);\n            members.forEach(member => {\n                if (member.uid) memberUids.add(member.uid);\n            });\n        });\n\n        if (closureUids.size === 0 && hubUids.size === 0) return null;\n\n        return { closureUids, hubUids, memberUids };\n    }\n\n    /**\n     * Remove Fornac's exterior-flavoured loop circularisation scaffolds \u2014\n     * the closure nodes and every hub whose loop is exterior-flavoured\n     * (the true top-level external loop, plus any loop touching vaRRI's\n     * inter-molecule gap) \u2014 from the force graph and rerun the layout.\n     * Every other loop's own hub and circular constraint is left untouched.\n     *\n     * @param {Object} container\n     * @param {Object} v\n     * @returns {boolean}\n     */\n    function relaxForceGraphScaffold(container, v) {\n        const graph = container && container.graph;\n        const scaffold = getFreeableLoopScaffoldUids(graph);\n        if (!scaffold) return false;\n\n        const removableNodeUids = new Set(scaffold.closureUids);\n        scaffold.hubUids.forEach(uid => removableNodeUids.add(uid));\n\n        graph.links = graph.links.filter(link => {\n            const linkType = String(link && link.linkType);\n            if (linkType !== 'fake' && linkType !== 'fake_fake') return true;\n\n            const sourceNode = resolveGraphNodeFromEndpoint(graph, link.source);\n            const targetNode = resolveGraphNodeFromEndpoint(graph, link.target);\n            const sourceUid = sourceNode && sourceNode.uid;\n            const targetUid = targetNode && targetNode.uid;\n\n            // Drop anything touching a freed hub or the closure nodes themselves.\n            if ((sourceUid && removableNodeUids.has(sourceUid)) || (targetUid && removableNodeUids.has(targetUid))) {\n                return false;\n            }\n\n            // Drop direct member-to-member \"chord\" links that bypass the hub\n            // entirely but still connect two nucleotides of the external loop.\n            if (sourceUid && targetUid && scaffold.memberUids.has(sourceUid) && scaffold.memberUids.has(targetUid)) {\n                return false;\n            }\n\n            return true;\n        });\n\n        graph.nodes = graph.nodes.filter(node => !(node && node.uid && removableNodeUids.has(node.uid)));\n\n        if (typeof container.update === 'function') {\n            container.update();\n        }\n\n        if (container.force && typeof container.force.resume === 'function') {\n            container.force.resume();\n        } else if (container.force && typeof container.force.start === 'function') {\n            container.force.start();\n        }\n\n        return true;\n    }\n\n    /**\n     * Override Fornac's \"pseudoknot\" link force strength on a live container.\n     *\n     * Fornac's `FornaContainer` sets `container.linkStrengths.pseudoknot = 0`\n     * by default, meaning pseudoknot basepair links exert no pull in the\n     * force simulation. `container.linkStrengths` is read by the link-force\n     * accessor function on every `force.start()` call (which rebuilds the\n     * internal per-link strength array), but *not* by `force.resume()`\n     * (which only restarts ticking without rebuilding that array). So the\n     * new strength must be set before calling `force.start()` specifically.\n     *\n     * @param {Object} container\n     * @param {boolean} enabled  When true, sets pseudoknot strength to 10.\n     */\n    function applyPseudoknotLinkStrength(container, enabled) {\n        if (!container || !container.linkStrengths) return;\n\n        container.linkStrengths.pseudoknot = enabled ? 10 : 0;\n\n        if (container.force && typeof container.force.start === 'function') {\n            container.force.start();\n        }\n    }\n    \n\n    // -----------------------------------------------------------------------\n    // Main render function\n    // -----------------------------------------------------------------------\n\n    /**\n     * Stop the active Fornac force and cancel delayed/animation-frame work.\n     * Pending render promises resolve as cancelled.\n     */\n    function cancelActiveRender() {\n        if (_animFrameId !== null) {\n            cancelAnimationFrame(_animFrameId);\n            _animFrameId = null;\n        }\n\n        if (_renderTimeoutId !== null) {\n            clearTimeout(_renderTimeoutId);\n            _renderTimeoutId = null;\n            if (_pendingRenderResolve) {\n                const resolvePendingRender = _pendingRenderResolve;\n                queueMicrotask(() => resolvePendingRender({ cancelled: true }));\n                _pendingRenderResolve = null;\n            }\n        }\n\n        // D3 v3 dispatches `end` synchronously from force.stop(). Remove the\n        // helix lifecycle listeners first so a cancelled render cannot refit\n        // a detached/cleared SVG container.\n        if (_activeContainer) {\n            clearLinearHelixConstraintState(_activeContainer);\n        }\n        if (_activeContainer?.force && typeof _activeContainer.force.stop === 'function') {\n            _activeContainer.force.stop();\n        }\n        _activeContainer = null;\n    }\n\n    /**\n     * Build the Fornac RNA visualisation inside `containerId` and apply all\n     * vaRRI modifications.\n     *\n     * This is the main entry point.  Call `validate()` first to produce `v`.\n     *\n     * @param {string} containerId  CSS selector or element ID of the Fornac container.\n     * @param {Object} v  Validated parameter dictionary (from `validate()`).\n     * @param {Object} [options]\n     * @param {boolean} [options.forceLayout=false]  Enable Fornac force-layout animation.\n     * @param {boolean} [options.forceLayoutLinearRRI=false]  Enforce a rigid two-rail RRI layout and orient the complete interaction horizontally.\n     * @param {boolean} [options.forceLayoutLinearStructure=false]  Enforce the same two-rail geometry within intramolecular helices.\n     * @param {boolean} [options.freeTrailingEnds=false]  Remove Fornac's external-loop circularisation constraint (the \"closure\" scaffold linking the sequence ends) from the force graph, leaving all other loop constraints intact.\n     * @param {boolean} [options.pullPseudoknotBasepairs=false]  Set Fornac's pseudoknot link force strength to 10 (default 0), pulling pseudoknot basepairs together in the force layout.\n     * @param {Object.<number,number>|null} [options.accessData=null]  Accessibility data map.\n     * @param {{sequence1?: string, sequence2?: string}|null} [options.accessColors=null]  Optional accessibility-overlay colors.\n     * @param {{sequence1RepresentsOne?: boolean, sequence2RepresentsOne?: boolean}|null} [options.accessColorMode=null]\n     *     Optional per-sequence mapping flags; true means probability 1 maps to full color.\n     */\n    function render(containerId, v, options = {}) {\n        cancelActiveRender();\n\n        const {\n            forceLayout = false,\n            forceLayoutLinearRRI = false,\n            forceLayoutLinearStructure = false,\n            freeTrailingEnds = false,\n            pullPseudoknotBasepairs = false,\n            accessData = null,\n            accessColors = null,\n            accessColorMode = null,\n        } = options;\n\n        // Build molecules via Fornac\n        const container = new fornac.FornaContainer(\n            `#${containerId}`,\n            { \n                animation: forceLayout, \n                labelInterval: 1\n            }\n        );\n        _activeContainer = container;\n        container.addRNA(v.structure, { structure: v.structure, sequence: v.sequence });\n\n        if (forceLayout && freeTrailingEnds) {\n            relaxForceGraphScaffold(container, v);\n        }\n\n        if (forceLayout && pullPseudoknotBasepairs) {\n            applyPseudoknotLinkStrength(container, true);\n        }\n\n        if (forceLayout && (forceLayoutLinearRRI || forceLayoutLinearStructure)) {\n            applyLinearHelixSprings(container, v, {\n                rri: forceLayoutLinearRRI,\n                structure: forceLayoutLinearStructure,\n            });\n        }\n\n        function applyModifications() {\n            // Set IDs for DOM querying\n            setLinksId();\n            setLabelsId();\n\n            // Remove gap nodes\n            removeDummyNodes(v.sequence);\n\n            // Remove duplicate intermolecular links\n            if (v.molecules === '2') {\n                removeSecondLink();\n            }\n\n            // Strand coloring\n            if (v.coloring === 'strand') {\n                changeBackgroundColor(v);\n            }\n\n            // Tooltips and labels\n            updateNodeToolTips(v);\n            updateLinkTooltips(v);\n            setIndexLabels(v);\n\n            // Highlighting (only for 2-molecule input)\n            clearGeneratedRegionHighlights();\n            if (v.molecules === '2') {\n                if (v.highlighting === 'region') highlightRegion(v);\n                if (v.highlighting === 'basepairs') highlightBasepairs(v);\n                if (v.backgroundhighlighting === 'region') backgroundhighlightRegion(v);\n                if (v.backgroundhighlighting === 'basepairs') backgroundhighlightBasepairs(v);\n            }\n\n            // Basepair styling (colour + optional G-U dashing)\n            styleBasepairs(v);\n\n            // Region highlights\n            applyRegionHighlights(v);\n\n            // Subsequence highlights\n            applySubsequenceHighlights(v);\n\n            // Point mutations\n            applyPointMutations(v);\n\n            // Accessibility overlay\n            if (accessData) {\n                visualiseAccessibility(accessData, v.sequence1.length, accessColors, accessColorMode);\n            }\n\n            // Linear-helix constraints may extend the initial bounds. Refit\n            // after the first force ticks and all hidden nodes are removed.\n            if (forceLayout && (forceLayoutLinearRRI || forceLayoutLinearStructure) &&\n                typeof container.centerView === 'function') {\n                container.centerView();\n            }\n\n            // When animation is on, keep the background-highlight polygon in sync\n            // with the force-layout by redrawing it on every animation frame.\n            if (forceLayout) {\n                function highlightSyncLoop() {\n                    document.querySelectorAll('[data-varri-region]').forEach(el => el.remove());\n                    document.querySelectorAll('[data-varri-subseq]').forEach(el => el.remove());\n\n                    applyRegionHighlights(v);\n                    applySubsequenceHighlights(v);\n\n                    _animFrameId = requestAnimationFrame(highlightSyncLoop);\n                }\n                _animFrameId = requestAnimationFrame(highlightSyncLoop);\n            }\n        }\n\n        return new Promise((resolve, reject) => {\n            _pendingRenderResolve = resolve;\n            _renderTimeoutId = setTimeout(() => {\n                _renderTimeoutId = null;\n                _pendingRenderResolve = null;\n\n                try {\n                    applyModifications();\n                    resolve({ cancelled: false });\n                } catch (err) {\n                    reject(err);\n                }\n            }, 200);\n        });\n    }\n\n    // -----------------------------------------------------------------------\n    // Rotation helpers\n    // -----------------------------------------------------------------------\n\n    /**\n     * Normalise a rotation angle to the range [-180, 180].\n     *\n     * @param {number} degrees\n     * @returns {number}\n     */\n    function normaliseRotationDegrees(degrees) {\n        if (!Number.isFinite(degrees)) {\n            throw new Error('Rotation degrees must be a finite number');\n        }\n        let value = degrees % 360;\n        if (value > 180) value -= 360;\n        if (value < -180) value += 360;\n        return value;\n    }\n\n    /**\n     * Resolve the element that should host the rotation layer.\n     *\n     * If Fornac's plot group exists, rotate inside that group so that\n     * pan/zoom transforms stay in screen-space and dragging keeps expected\n     * directions after rotation.\n     *\n     * @param {SVGSVGElement} svgEl\n     * @returns {SVGElement}\n     */\n    function getRotationHost(svgEl) {\n        const fornacPlot = svgEl.querySelector('.fornac-plot');\n        return fornacPlot || svgEl;\n    }\n\n    /**\n     * Ensure a host element has a dedicated layer that can be rotated.\n     *\n     * @param {SVGElement} hostEl\n     * @returns {SVGGElement}\n     */\n    function ensureRotationLayer(hostEl) {\n        let layer = Array.from(hostEl.children).find(child =>\n            child.tagName && child.tagName.toLowerCase() === 'g' &&\n            child.getAttribute('data-varri-rotation-layer') === 'true'\n        );\n\n        if (!layer) {\n            layer = document.createElementNS('http://www.w3.org/2000/svg', 'g');\n            layer.setAttribute('data-varri-rotation-layer', 'true');\n            hostEl.appendChild(layer);\n        }\n\n        const nodesToMove = Array.from(hostEl.childNodes).filter(node => {\n            if (node === layer) return false;\n            if (hostEl.tagName && hostEl.tagName.toLowerCase() === 'svg' &&\n                    node.nodeType === Node.ELEMENT_NODE && node.tagName &&\n                    node.tagName.toLowerCase() === 'defs') {\n                return false;\n            }\n            return true;\n        });\n        nodesToMove.forEach(node => layer.appendChild(node));\n\n        return layer;\n    }\n\n    /**\n     * Compute the centre of an SVG element's bounding box.\n     *\n     * @param {SVGGraphicsElement} el\n     * @returns {{x:number, y:number}|null}\n     */\n    function getBBoxCenter(el) {\n        try {\n            const bbox = el.getBBox();\n            if (!Number.isFinite(bbox.x) || !Number.isFinite(bbox.y) ||\n                    !Number.isFinite(bbox.width) || !Number.isFinite(bbox.height)) {\n                return null;\n            }\n            return {\n                x: bbox.x + (bbox.width / 2),\n                y: bbox.y + (bbox.height / 2),\n            };\n        } catch (err) {\n            return null;\n        }\n    }\n\n    /**\n     * Rotate the current visualisation around its bounding-box centre while\n     * keeping text labels horizontally aligned.\n     *\n     * @param {string} containerId  ID of the container element.\n     * @param {number} degrees  Rotation amount.\n     * @param {Object} [options]\n     * @param {'delta'|'absolute'} [options.mode='delta']\n     * @returns {number}  Applied absolute angle in degrees (normalised).\n     */\n    function rotateVisualization(containerId, degrees, options = {}) {\n        const container = document.getElementById(containerId);\n        const svgEl = container && container.querySelector('svg');\n        if (!svgEl) throw new Error('No SVG found in container');\n\n        const amount = Number(degrees);\n        if (!Number.isFinite(amount)) {\n            throw new Error('Rotation degrees must be a finite number');\n        }\n\n        const mode = options.mode === 'absolute' ? 'absolute' : 'delta';\n        const current = Number(svgEl.getAttribute('data-varri-rotation') || 0);\n        const target = normaliseRotationDegrees(mode === 'absolute' ? amount : current + amount);\n\n        const hostEl = getRotationHost(svgEl);\n        const layer = ensureRotationLayer(hostEl);\n        const center = getBBoxCenter(layer);\n        if (!center) return current;\n\n        layer.setAttribute('transform', `rotate(${target} ${center.x} ${center.y})`);\n        svgEl.setAttribute('data-varri-rotation', String(target));\n\n        layer.querySelectorAll('text').forEach(textEl => {\n            if (!textEl.hasAttribute('data-varri-base-transform')) {\n                textEl.setAttribute('data-varri-base-transform', textEl.getAttribute('transform') || '');\n            }\n            const baseTransform = textEl.getAttribute('data-varri-base-transform') || '';\n            if (target === 0) {\n                if (baseTransform) {\n                    textEl.setAttribute('transform', baseTransform);\n                } else {\n                    textEl.removeAttribute('transform');\n                }\n                return;\n            }\n\n            const textCenter = getBBoxCenter(textEl) || center;\n            const transformParts = [];\n            if (baseTransform) transformParts.push(baseTransform);\n            transformParts.push(`rotate(${-target} ${textCenter.x} ${textCenter.y})`);\n            textEl.setAttribute('transform', transformParts.join(' '));\n        });\n\n        return target;\n    }\n\n    // -----------------------------------------------------------------------\n    // SVG / PNG export\n    // -----------------------------------------------------------------------\n\n    /**\n     * SVG presentation properties to inline when exporting.\n     *\n     * These cover every visual property used by Fornac and vaRRI: fill/stroke\n     * paint, font, text alignment, and element visibility.  Using this fixed\n     * list avoids dumping hundreds of irrelevant properties from\n     * `getComputedStyle` (e.g. layout-only CSS that SVG viewers ignore).\n     */\n    const SVG_STYLE_PROPS = [\n        'fill', 'fill-opacity', 'fill-rule',\n        'stroke', 'stroke-width', 'stroke-opacity',\n        'stroke-dasharray', 'stroke-linecap', 'stroke-linejoin', 'stroke-miterlimit',\n        'font-family', 'font-size', 'font-weight', 'font-style',\n        'text-anchor', 'dominant-baseline', 'alignment-baseline',\n        'opacity', 'visibility', 'display',\n        'marker-start', 'marker-end', 'marker-mid',\n        'color',\n    ];\n\n    /**\n     * Walk `originalEl` and `cloneEl` in parallel, reading computed styles\n     * from `originalEl` (which has all browser CSS applied) and writing them\n     * as an inline `style` attribute on `cloneEl`.\n     *\n     * This makes every element carry its own fully-resolved presentation\n     * values so the exported SVG is self-contained \u2014 no external stylesheet\n     * is required.  In particular:\n     *  - class-based rules (`.fornac-node`, `.fornac-link`, etc.) are baked in\n     *  - relative units (`0.4em` font-size) are resolved to absolute pixels\n     *  - inline `style` overrides from vaRRI (strand colours, highlights) are\n     *    already included in the computed value, so nothing is lost\n     *\n     * @param {Element} originalEl  Live DOM element (inside the visible SVG).\n     * @param {Element} cloneEl     Corresponding cloned element.\n     */\n    function inlineComputedStyles(originalEl, cloneEl) {\n        if (!originalEl || originalEl.nodeType !== Node.ELEMENT_NODE) return;\n\n        // Leave <style> and <defs> subtrees alone \u2014 they hold definitions, not\n        // rendered shapes, and rewriting their style attributes would break them.\n        const tag = (originalEl.tagName || '').toLowerCase();\n        if (tag === 'style' || tag === 'defs') return;\n\n        const computed = window.getComputedStyle(originalEl);\n        let inlined = '';\n        for (const prop of SVG_STYLE_PROPS) {\n            const val = computed.getPropertyValue(prop);\n            if (val) inlined += `${prop}:${val};`;\n        }\n        if (inlined) cloneEl.setAttribute('style', inlined);\n\n        // Recurse into child elements in lock-step.\n        const origKids  = originalEl.children;\n        const cloneKids = cloneEl.children;\n        for (let i = 0; i < origKids.length; i++) {\n            if (cloneKids[i]) inlineComputedStyles(origKids[i], cloneKids[i]);\n        }\n    }\n\n    /**\n     * Build a self-contained SVG string from the current Fornac visualisation.\n     *\n     * Strategy:\n     *  1. Clone the live SVG element (preserves all D3 transforms and vaRRI\n     *     DOM modifications).\n     *  2. Walk original + clone in parallel and inline every computed\n     *     presentation property so the file is fully self-contained.\n     *  3. Set explicit pixel width/height on the root so viewers render at\n     *     the same size as the browser display.\n     *  4. Prepend a white background rect to match the container's background.\n     *  5. Serialise with XMLSerializer (namespace-aware).\n     *\n     * @param {string} containerId  ID of the container element.\n     * @returns {string}  Full SVG markup.\n     */\n    function buildSVGString(containerId) {\n        const container = document.getElementById(containerId);\n        const svgEl = container && container.querySelector('svg');\n        if (!svgEl) throw new Error('No SVG found in container');\n\n        // Clone the live SVG so we can annotate it without touching the DOM.\n        const clone = svgEl.cloneNode(true);\n\n        // Inline all computed presentation styles before any other annotation\n        // so that class-based CSS rules, relative units, and inherited values\n        // are all baked into the clone as plain inline style attributes.\n        inlineComputedStyles(svgEl, clone);\n\n        // Required namespace declarations for a standalone SVG file.\n        clone.setAttribute('xmlns',       'http://www.w3.org/2000/svg');\n        clone.setAttribute('xmlns:xlink', 'http://www.w3.org/1999/xlink');\n\n        // Derive pixel dimensions from the rendered element so the exported\n        // file renders at the same size as what the user sees in the browser.\n        const w = svgEl.clientWidth  || container.clientWidth  || 800;\n        const h = svgEl.clientHeight || container.clientHeight || 600;\n        clone.setAttribute('width',  w);\n        clone.setAttribute('height', h);\n\n        // Keep (or synthesise) the viewBox so the internal coordinate space\n        // that Fornac uses maps 1:1 to the exported pixel dimensions.\n        if (!clone.getAttribute('viewBox')) {\n            clone.setAttribute('viewBox', `0 0 ${w} ${h}`);\n        }\n\n        // White background rect \u2014 matches the container's background: #fff\n        // so the exported image looks identical to the on-screen visualisation.\n        const bg = document.createElementNS('http://www.w3.org/2000/svg', 'rect');\n        bg.setAttribute('width',  '100%');\n        bg.setAttribute('height', '100%');\n        bg.setAttribute('fill',   'white');\n        clone.insertBefore(bg, clone.firstChild);\n\n        return new XMLSerializer().serializeToString(clone);\n    }\n\n    /**\n     * Trigger a browser download of the current visualisation as an SVG file.\n     *\n     * @param {string} containerId  ID of the container element.\n     * @param {string} [filename=\"vaRRI_output.svg\"]\n     */\n    function downloadSVG(containerId, filename = 'vaRRI_output.svg') {\n        const svgStr = buildSVGString(containerId);\n        const blob = new Blob([svgStr], { type: 'image/svg+xml' });\n        triggerDownload(URL.createObjectURL(blob), filename);\n    }\n\n    /**\n     * Trigger a browser download of the current visualisation as a PNG image.\n     *\n     * Rasterises the SVG to a canvas at `scale` \u00D7 the rendered size and\n     * converts it to a PNG data URL.  A white background is painted on the\n     * canvas before the image is drawn so the result matches the on-screen\n     * appearance.\n     *\n     * @param {string} containerId  ID of the container element.\n     * @param {string} [filename=\"vaRRI_output.png\"]\n     * @param {number} [scale=2]  Resolution multiplier (2 = retina quality).\n     */\n    function downloadPNG(containerId, filename = 'vaRRI_output.png', scale = 2) {\n        const svgStr = buildSVGString(containerId);\n        const blob = new Blob([svgStr], { type: 'image/svg+xml' });\n        const url = URL.createObjectURL(blob);\n\n        // Determine the rendered pixel size from the live container so that\n        // canvas dimensions are correct regardless of the SVG's naturalWidth.\n        const container = document.getElementById(containerId);\n        const svgEl = container && container.querySelector('svg');\n        const w = (svgEl && svgEl.clientWidth)  || (container && container.clientWidth)  || 800;\n        const h = (svgEl && svgEl.clientHeight) || (container && container.clientHeight) || 600;\n\n        function rasterise(imgEl, canvasW, canvasH) {\n            const canvas = document.createElement('canvas');\n            canvas.width  = canvasW;\n            canvas.height = canvasH;\n            const ctx = canvas.getContext('2d');\n            // White background to match the container's CSS background colour.\n            ctx.fillStyle = 'white';\n            ctx.fillRect(0, 0, canvasW, canvasH);\n            ctx.drawImage(imgEl, 0, 0, canvasW, canvasH);\n            return canvas.toDataURL('image/png');\n        }\n\n        const img = new Image();\n        img.onload = () => {\n            const dataUrl = rasterise(img, w * scale, h * scale);\n            URL.revokeObjectURL(url);\n            triggerDownload(dataUrl, filename);\n        };\n        img.onerror = () => {\n            // Fallback: load the SVG via a data URI instead of a blob URL.\n            URL.revokeObjectURL(url);\n            const dataUri = 'data:image/svg+xml;charset=utf-8,' + encodeURIComponent(svgStr);\n            const imgFallback = new Image();\n            imgFallback.onload = () => {\n                triggerDownload(rasterise(imgFallback, w * scale, h * scale), filename);\n            };\n            imgFallback.src = dataUri;\n        };\n        img.src = url;\n    }\n\n    /**\n     * Create a hidden `<a>` element and programmatically click it to download.\n     *\n     * @param {string} href  URL or data URI.\n     * @param {string} filename\n     */\n    function triggerDownload(href, filename) {\n        const a = document.createElement('a');\n        a.href = href;\n        a.download = filename;\n        a.style.display = 'none';\n        document.body.appendChild(a);\n        a.click();\n        document.body.removeChild(a);\n    }\n\n    // -----------------------------------------------------------------------\n    // Public API\n    // -----------------------------------------------------------------------\n\n    const vaRRI = {\n        // Core\n        cancelActiveRender,\n        normaliseRotationDegrees,\n        render,\n        rotateVisualization,\n        validate,\n\n        // Colors\n        getColors,\n        setColors,\n\n        // Annotation registries\n        clearPointMutations,\n        clearRegionHighlights,\n        clearSubsequenceHighlights,\n        computeBackgroundRegionRanges,\n        createPointMutation,\n        createRegionHighlight,\n        createSubsequenceHighlight,\n        getPointMutations,\n        getRegionHighlightNodePath,\n        getRegionHighlights,\n        getSubsequenceHighlights,\n        registerGeneratedRegionHighlight,\n        registerPointMutation,\n        registerRegionHighlight,\n        registerSubsequenceHighlight,\n        removePointMutation,\n        removeRegionHighlight,\n        removeSubsequenceHighlight,\n        updatePointMutation,\n        updateRegionHighlight,\n        updateSubsequenceHighlight,\n\n        // Validation and formatting\n        checkStructureInputSimple,\n        findBasePairs,\n        formatSequence,\n        formatStructure,\n        getIndexDictionary,\n        getMolecules,\n        getSequenceIndices,\n        parseSubsequences,\n        splitAtAmpersand,\n        validateBackgroundhighlighting,\n        validateCroppingInput,\n        validateHighlighting,\n        validateOffset,\n        normaliseMutationPosition,\n        validateSequenceInput,\n        validateStructureInput,\n\n        // Base-pair utilities\n        getIntermolBasepairRegion,\n        getLinearRriConstraintSpecs,\n        getLinearStructureConstraintSpecs,\n        listBasepairs,\n        listIntermolNodes,\n        listIntermolPairs,\n        listRriLoopBoundaryPairs,\n        listStructureLoopBoundaryPairs,\n        sequenceColoring,\n\n        // DOM modifications (advanced use)\n        addElement,\n        addStyleToNodes,\n        applyLinearHelixSprings,\n        applyPointMutations,\n        applyRegionHighlights,\n        applySubsequenceHighlights,\n        backgroundhighlightBasepairs,\n        backgroundhighlightRegion,\n        changeBackgroundColor,\n        closePolygonPoints,\n        getPositionOfNode,\n        highlightBasepairs,\n        highlightRegion,\n        highlightSubsequence,\n        polyline,\n        removeDummyNodes,\n        removeSecondLink,\n        setAttributeForElements,\n        setIndexLabels,\n        setLabelsId,\n        setLinksId,\n        styleBasepairs,\n        updateLinkTooltips,\n        updateNodeToolTips,\n        visualiseAccessibility,\n\n        // Export\n        buildSVGString,\n        downloadPNG,\n        downloadSVG,\n    };\n\n    // Export\n    global.vaRRI = vaRRI;\n    if (typeof module !== 'undefined' && module.exports) {\n        module.exports = vaRRI;\n    }\n\n}(typeof window !== 'undefined' ? window : this));\n"],
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"createLinearHelixRailTemplate", "group", "pairNodes", "column", "offsets", "intervals", "previous", "current", "isLoop", "measured", "span", "meanOffset", "sum", "along", "template", "ordinaryFit", "fitLinearHelixRailTemplate", "reflectedFit", "xField", "yField", "reflection", "live", "point", "center", "dot", "cross", "templateY", "liveX", "liveY", "angle", "cosine", "sine", "error", "targets", "deltaX", "deltaY", "projectLinearHelixRailTemplate", "currentFit", "previousFit", "normaliseRotationRadians", "radians", "rotateCoordinateCloud", "offsetX", "offsetY", "rotateTemplateFitState", "centerField", "angleField", "pivot", "orientLinearRriInteractionHorizontally", "rriTemplate", "templates", "targetAngle", "currentRotation", "previousRotation", "currentPivot", "previousPivot", "listVisibleIndexLabelPositions", "resolveGraphLinkNode", "endpoint", "collectLinearHelixIndexLabelBiases", "visiblePositions", "partnerByNode", "seenLabels", "biases", "anchor", "partner", "rawValue", "linkDistance", "nudgeLinearHelixIndexLabels", "moved", "bias", "outwardX", "outwardY", "outwardLength", "unitX", "unitY", "side", "createLinearHelixDomCache", "labelBiases", "syncWholeGraph", "projectedNodes", "graphLinks", "incidentLinks", "element", "syncFornacDirectionArrow", "arrow", "directionX", "directionY", "normalX", "normalY", "tipX", "tipY", "size", "width", "syncLinearHelixDom", "cache", "clearLinearHelixConstraintState", "applyLinearHelixSprings", "options", "constrainedNodes", "activeConstraints", "constraint", "domCache", "enforceAndSync", "hasRefittedAtRest", "enforceSyncAndRefit", "backgroundhighlightBasepairs", "intermolPairs", "stack", "highlightAreas", "stackOpen", "stackClose", "area", "backgroundhighlightRegion", "addAccessibilityOverlay", "tooltip", "overlay", "mapProbabilityToOpacity", "prb", "representsOne", "visualiseAccessibility", "accessData", "lenSeq", "accessColors", "accessColorMode", "seq1Color", "seq2Color", "seq1RepresentsOne", "seq2RepresentsOne", "isSeq1", "prbTooltip", "resolveGraphNodeFromEndpoint", "byNumber", "getFreeableLoopScaffoldUids", "closureNodes", "closureUids", "closureIndices", "hubs", "hubUids", "memberUids", "hub", "members", "touchesClosure", "touchesExternalElemType", "member", "relaxForceGraphScaffold", "scaffold", "removableNodeUids", "uid", "sourceNode", "targetNode", "sourceUid", "targetUid", "applyPseudoknotLinkStrength", "enabled", "cancelActiveRender", "resolvePendingRender", "render", "containerId", "forceLayout", "forceLayoutLinearRRI", "forceLayoutLinearStructure", "freeTrailingEnds", "pullPseudoknotBasepairs", "applyModifications", "highlightSyncLoop", "resolve", "reject", "err", "normaliseRotationDegrees", "degrees", "getRotationHost", "svgEl", "ensureRotationLayer", "hostEl", "layer", "getBBoxCenter", "bbox", "rotateVisualization", "amount", "mode", "textEl", "baseTransform", "textCenter", "transformParts", "SVG_STYLE_PROPS", "inlineComputedStyles", "originalEl", "cloneEl", "tag", "computed", "inlined", "prop", "origKids", "cloneKids", "buildSVGString", "clone", "w", "bg", "downloadSVG", "filename", "svgStr", "blob", "triggerDownload", "downloadPNG", "scale", "url", "rasterise", "imgEl", "canvasW", "canvasH", "canvas", "ctx", "img", "dataUrl", "dataUri", "imgFallback", "href", "vaRRI"]
+}

package/fornac/README.md

@@ -0,0 +1,10 @@
+
+## `fornac` - A JavaScript library for visualizing RNA secondary structures in the browser.
+
+- version v1.0.1 - download from [GitHub](https://github.com/ViennaRNA/fornac)
+- license: Apache License v2.0 (see [LICENSE](fornac.LICENSE.txt) file)
+
+## `d3` - A JavaScript library for manipulating documents based on data.
+
+- version 3.4.13 - download from [GitHub](https://github.com/d3/d3)
+- license: ISC License (see [LICENSE](d3.LICENSE.txt) file)