@datagrok/bio 2.11.7 → 2.11.10

package/dist/79.js.map

@@ -1 +1 @@
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const monomerWorksConsts = {\n    // constants for parsing molfile V2000\n    V2K_RGP_SHIFT: 8,\n    V2K_RGP_LINE: 'M  RGP',\n    V2K_A_LINE: 'A  ',\n    // constants for parsing/reconstruction of molfile V3000\n    V3K_COUNTS_SHIFT: 14,\n    V3K_IDX_SHIFT: 7,\n    V3K_HEADER_FIRST_LINE: '\\nDatagrok macromolecule handler\\n\\n',\n    V3K_HEADER_SECOND_LINE: '  0  0  0  0  0  0            999 V3000\\n',\n    V3K_BEGIN_CTAB_BLOCK: 'M  V30 BEGIN CTAB\\n',\n    V3K_END_CTAB_BLOCK: 'M  V30 END CTAB\\n',\n    V3K_BEGIN_COUNTS_LINE: 'M  V30 COUNTS ',\n    V3K_COUNTS_LINE_ENDING: ' 0 0 0\\n',\n    V3K_BEGIN_ATOM_BLOCK: 'M  V30 BEGIN ATOM\\n',\n    V3K_END_ATOM_BLOCK: 'M  V30 END ATOM\\n',\n    V3K_BEGIN_BOND_BLOCK: 'M  V30 BEGIN BOND\\n',\n    V3K_END_BOND_BLOCK: 'M  V30 END BOND\\n',\n    V3K_BOND_CONFIG: ' CFG:',\n    V3K_BEGIN_DATA_LINE: 'M  V30 ',\n    V3K_END: 'M  END',\n    PRECISION_FACTOR: 10000,\n    // symbols for the corresponding monomers in HELM library\n    DEOXYRIBOSE: 'd',\n    RIBOSE: 'r',\n    PHOSPHATE: 'p',\n    OXYGEN: 'O',\n    HYDROGEN: 'H',\n};\n//# sourceMappingURL=consts.js.map","import { monomerWorksConsts as C } from './consts';\nimport { HELM_CORE_FIELDS, } from '../utils/const';\n/** Get a mapping of peptide symbols to HELM monomer library objects with selected fields.\n * @param {IMonomerLib} monomerLib - Monomer library\n * @param {HELM_POLYMER_TYPE} polymerType - Polymer type\n * @param {ALPHABET} alphabet - Alphabet of the column\n * @return {Map<string, any>} - Mapping of peptide symbols to HELM monomer library objects with selected fields*/\nexport function getFormattedMonomerLib(monomerLib, polymerType, alphabet) {\n    const map = new Map();\n    for (const monomerSymbol of monomerLib.getMonomerSymbolsByType(polymerType)) {\n        const it = monomerLib.getMonomer(polymerType, monomerSymbol);\n        if (polymerType === \"RNA\" /* HELM_POLYMER_TYPE.RNA */ &&\n            (it[\"monomerType\" /* HELM_FIELDS.MONOMER_TYPE */] === \"Branch\" /* HELM_MONOMER_TYPE.BRANCH */ ||\n                alphabet === \"DNA\" /* ALPHABET.DNA */ && it[\"symbol\" /* HELM_FIELDS.SYMBOL */] === C.DEOXYRIBOSE ||\n                alphabet === \"RNA\" /* ALPHABET.RNA */ && it[\"symbol\" /* HELM_FIELDS.SYMBOL */] === C.RIBOSE ||\n                it[\"symbol\" /* HELM_FIELDS.SYMBOL */] === C.PHOSPHATE) ||\n            polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */ &&\n                it[\"monomerType\" /* HELM_FIELDS.MONOMER_TYPE */] !== \"Branch\" /* HELM_MONOMER_TYPE.BRANCH */) {\n            const monomerObject = {};\n            HELM_CORE_FIELDS.forEach((field) => {\n                //@ts-ignore\n                monomerObject[field] = it[field];\n            });\n            map.set(it[\"symbol\" /* HELM_FIELDS.SYMBOL */], monomerObject);\n        }\n    }\n    return map;\n}\n/** Translate a sequence of monomer symbols into Molfile V3000\n * @param {string[]} monomerSeq - Sequence of monomer symbols\n * @param {Map<string, MolGraph>} monomersDict - Mapping of monomer symbols to MolGraph objects\n * @param {ALPHABET} alphabet - Alphabet of the column\n * @param {HELM_POLYMER_TYPE} polymerType - Polymer type\n * @return {string} - Molfile V3000*/\nexport function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerType) {\n    if (monomerSeq.length === 0) {\n        // throw new Error('monomerSeq is empty');\n        return '';\n    }\n    // define atom and bond counts, taking into account the bond type\n    const getAtomAndBondCounts = getResultingAtomBondCounts;\n    const { atomCount, bondCount } = getAtomAndBondCounts(monomerSeq, monomersDict, alphabet, polymerType);\n    // create arrays to store lines of the resulting molfile\n    const molfileAtomBlock = new Array(atomCount);\n    const molfileBondBlock = new Array(bondCount);\n    let addMonomerToMolblock; // todo: types?\n    let sugar = null;\n    let phosphate = null;\n    if (polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */) {\n        addMonomerToMolblock = addAminoAcidToMolblock;\n    }\n    else { // nucleotides\n        addMonomerToMolblock = addNucleotideToMolblock;\n        sugar = (alphabet === \"DNA\" /* ALPHABET.DNA */) ? monomersDict.get(C.DEOXYRIBOSE) : monomersDict.get(C.RIBOSE);\n        phosphate = monomersDict.get(C.PHOSPHATE);\n    }\n    const v = {\n        i: 0,\n        nodeShift: 0,\n        bondShift: 0,\n        backbonePositionShift: new Array(2).fill(0),\n        branchPositionShift: new Array(2).fill(0),\n        backboneAttachNode: 0,\n        branchAttachNode: 0,\n        flipFactor: 1,\n    };\n    const LC = {\n        sugar: sugar,\n        phosphate: phosphate,\n        seqLength: monomerSeq.length,\n        atomCount: atomCount,\n        bondCount: bondCount,\n    };\n    for (v.i = 0; v.i < LC.seqLength; ++v.i) {\n        const monomer = monomersDict.get(monomerSeq[v.i]);\n        addMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v, LC);\n    }\n    capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC);\n    const molfileCountsLine = C.V3K_BEGIN_COUNTS_LINE + atomCount + ' ' + bondCount + C.V3K_COUNTS_LINE_ENDING;\n    // todo: possible optimization may be achieved by replacing .join('') with +=\n    // since counterintuitively joining an array into a new string is reportedly\n    // slower than using += as below\n    let result = '';\n    result += C.V3K_HEADER_FIRST_LINE;\n    result += C.V3K_HEADER_SECOND_LINE;\n    result += C.V3K_BEGIN_CTAB_BLOCK;\n    result += molfileCountsLine;\n    result += C.V3K_BEGIN_ATOM_BLOCK;\n    result += molfileAtomBlock.join('');\n    result += C.V3K_END_ATOM_BLOCK;\n    result += C.V3K_BEGIN_BOND_BLOCK;\n    result += molfileBondBlock.join('');\n    result += C.V3K_END_BOND_BLOCK;\n    result += C.V3K_END_CTAB_BLOCK;\n    result += C.V3K_END;\n    // return molfileParts.join('');\n    return result;\n}\n/** Cap the resulting (after sewing up all the monomers) molfile with 'O'\n * @param {string[]} molfileAtomBlock - Array of lines of the resulting molfile atom block\n * @param {string[]} molfileBondBlock - Array of lines of the resulting molfile bond block\n * @param {LoopVariables} v - Loop variables\n * @param {LoopConstants} LC - Loop constants*/\nfunction capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC) {\n    // add terminal oxygen\n    const atomIdx = v.nodeShift + 1;\n    molfileAtomBlock[LC.atomCount] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n        C.OXYGEN + ' ' + keepPrecision(v.backbonePositionShift[0]) + ' ' +\n        v.flipFactor * keepPrecision(v.backbonePositionShift[1]) + ' ' + '0.000000 0' + '\\n';\n    // add terminal bond\n    const firstAtom = v.backboneAttachNode;\n    const secondAtom = atomIdx;\n    molfileBondBlock[LC.bondCount] = C.V3K_BEGIN_DATA_LINE + v.bondShift + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n}\nfunction addAminoAcidToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    v.flipFactor = (-1) ** (v.i % 2); // to flip every even monomer over OX\n    addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v);\n}\nfunction addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    // todo: remove these comments to the docstrings of the corr. functions\n    // construnct the lines of V3K molfile atom block\n    fillAtomLines(monomer, molfileAtomBlock, v);\n    // construct the lines of V3K molfile bond block\n    fillBondLines(monomer, molfileBondBlock, v);\n    // peptide bond\n    fillChainExtendingBond(monomer, molfileBondBlock, v);\n    // update branch variables if necessary\n    if (monomer.meta.branchShift !== null && monomer.meta.terminalNodes.length > 2)\n        updateBranchVariables(monomer, v);\n    // update loop variables\n    updateChainExtendingVariables(monomer, v);\n}\nfunction addNucleotideToMolblock(nucleobase, molfileAtomBlock, molfileBondBlock, v, LC) {\n    // construnct the lines of V3K molfile atom block corresponding to phosphate\n    // and sugar\n    if (v.i === 0) {\n        addBackboneMonomerToMolblock(LC.sugar, molfileAtomBlock, molfileBondBlock, v);\n    }\n    else {\n        for (const monomer of [LC.phosphate, LC.sugar])\n            addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v);\n    }\n    addBranchMonomerToMolblock(nucleobase, molfileAtomBlock, molfileBondBlock, v);\n}\nfunction addBranchMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    fillBranchAtomLines(monomer, molfileAtomBlock, v);\n    fillBondLines(monomer, molfileBondBlock, v);\n    fillBackboneToBranchBond(monomer, molfileBondBlock, v);\n    // C-N bond\n    const bondIdx = v.bondShift;\n    const firstAtom = v.branchAttachNode;\n    const secondAtom = monomer.meta.terminalNodes[0] + v.nodeShift;\n    molfileBondBlock[bondIdx - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n    // update loop variables\n    v.bondShift += monomer.bonds.atomPairs.length + 1;\n    v.nodeShift += monomer.atoms.atomTypes.length;\n}\nfunction updateChainExtendingVariables(monomer, v) {\n    v.backboneAttachNode = v.nodeShift + monomer.meta.terminalNodes[1];\n    v.bondShift += monomer.bonds.atomPairs.length + 1;\n    v.nodeShift += monomer.atoms.atomTypes.length;\n    v.backbonePositionShift[0] += monomer.meta.backboneShift[0]; // todo: non-null check\n    v.backbonePositionShift[1] += v.flipFactor * monomer.meta.backboneShift[1];\n}\nfunction updateBranchVariables(monomer, v) {\n    v.branchAttachNode = v.nodeShift + monomer.meta.terminalNodes[2];\n    for (let i = 0; i < 2; ++i)\n        v.branchPositionShift[i] = v.backbonePositionShift[i] + monomer.meta.branchShift[i];\n}\nfunction fillAtomLines(monomer, molfileAtomBlock, v) {\n    for (let j = 0; j < monomer.atoms.atomTypes.length; ++j) {\n        const atomIdx = v.nodeShift + j + 1;\n        molfileAtomBlock[v.nodeShift + j] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n            monomer.atoms.atomTypes[j] + ' ' +\n            keepPrecision(v.backbonePositionShift[0] + monomer.atoms.x[j]) + ' ' +\n            keepPrecision(v.backbonePositionShift[1] + v.flipFactor * monomer.atoms.y[j]) +\n            ' ' + monomer.atoms.kwargs[j];\n    }\n}\n// todo: remove as quickfix\nfunction fillBranchAtomLines(monomer, molfileAtomBlock, v) {\n    for (let j = 0; j < monomer.atoms.atomTypes.length; ++j) {\n        const atomIdx = v.nodeShift + j + 1;\n        molfileAtomBlock[v.nodeShift + j] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n            monomer.atoms.atomTypes[j] + ' ' +\n            keepPrecision(v.branchPositionShift[0] + monomer.atoms.x[j]) + ' ' +\n            keepPrecision(v.branchPositionShift[1] + v.flipFactor * monomer.atoms.y[j]) +\n            ' ' + monomer.atoms.kwargs[j];\n    }\n}\nfunction fillBondLines(monomer, molfileBondBlock, v) {\n    // construct the lines of V3K molfile bond block\n    for (let j = 0; j < monomer.bonds.atomPairs.length; ++j) {\n        const bondIdx = v.bondShift + j + 1;\n        const firstAtom = monomer.bonds.atomPairs[j][0] + v.nodeShift;\n        const secondAtom = monomer.bonds.atomPairs[j][1] + v.nodeShift;\n        let bondCfg = '';\n        if (monomer.bonds.bondConfiguration.has(j)) {\n            // flip orientation when necessary\n            let orientation = monomer.bonds.bondConfiguration.get(j);\n            if (v.flipFactor < 0)\n                orientation = (orientation === 1) ? 3 : 1;\n            bondCfg = ' CFG=' + orientation;\n        }\n        const kwargs = monomer.bonds.kwargs.has(j) ?\n            ' ' + monomer.bonds.kwargs.get(j) : '';\n        molfileBondBlock[v.bondShift + j] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n            monomer.bonds.bondTypes[j] + ' ' +\n            firstAtom + ' ' + secondAtom + bondCfg + kwargs + '\\n';\n    }\n}\nfunction fillChainExtendingBond(monomer, molfileBondBlock, v) {\n    if (v.backboneAttachNode !== 0) {\n        const bondIdx = v.bondShift;\n        const firstAtom = v.backboneAttachNode;\n        const secondAtom = monomer.meta.terminalNodes[0] + v.nodeShift;\n        molfileBondBlock[v.bondShift - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n            1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n    }\n}\n// todo: remove\nfunction fillBackboneToBranchBond(branchMonomer, molfileBondBlock, v) {\n    const bondIdx = v.bondShift;\n    const firstAtom = v.branchAttachNode;\n    const secondAtom = branchMonomer.meta.terminalNodes[0] + v.nodeShift;\n    molfileBondBlock[bondIdx - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n}\n/** Compute the atom/bond counts for the resulting molfile, depending on the\n    * type of polymer (peptide/nucleotide)\n    * @param {string[]}monomerSeq - the sequence of monomers\n    * @param {Map<string, MolGraph>}monomersDict - the dictionary of monomers\n    * @param {ALPHABET}alphabet - the alphabet of the monomers\n    * @param {HELM_POLYMER_TYPE}polymerType - the type of polymer\n    * @return {{atomCount: number, bondCount: number}} - the atom/bond counts*/\nfunction getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerType) {\n    let atomCount = 0;\n    let bondCount = 0;\n    // sum up all the atoms/nodes provided by the sequence\n    for (const monomerSymbol of monomerSeq) {\n        if (monomerSymbol === '')\n            continue; // Skip for gap/empty monomer in MSA\n        const monomer = monomersDict.get(monomerSymbol);\n        atomCount += monomer.atoms.x.length;\n        bondCount += monomer.bonds.bondTypes.length;\n    }\n    // add extra values depending on the polymer type\n    if (polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */) {\n        // add the rightmost/terminating cap group 'OH' (i.e. 'O')\n        atomCount += 1;\n        // add chain-extending bonds (C-NH per each monomer pair and terminal C-OH)\n        bondCount += monomerSeq.length;\n    }\n    else { // nucleotides\n        const sugar = (alphabet === \"DNA\" /* ALPHABET.DNA */) ?\n            monomersDict.get(C.DEOXYRIBOSE) : monomersDict.get(C.RIBOSE);\n        const phosphate = monomersDict.get(C.PHOSPHATE);\n        // add phosphate per each pair of nucleobase symbols\n        atomCount += (monomerSeq.length - 1) * phosphate.atoms.x.length;\n        // add sugar per each nucleobase symbol\n        atomCount += monomerSeq.length * sugar.atoms.x.length;\n        // add the leftmost cap group 'OH' (i.e. 'O')\n        atomCount += 1;\n        // add bonds from phosphate monomers\n        bondCount += (monomerSeq.length - 1) * phosphate.bonds.bondTypes.length;\n        // add bonds from sugar monomers\n        bondCount += monomerSeq.length * sugar.bonds.bondTypes.length;\n        // exclude the first chain-extending bond O-P (absent, no 'leftmost' phosphate)\n        bondCount -= 1;\n        // add chain-extending and branch bonds (O-P, C-O and C-N per each nucleotide)\n        bondCount += monomerSeq.length * 3;\n    }\n    return { atomCount, bondCount };\n}\n/** Keep precision upon floating point operations over atom coordinates\n * @param {number}x - the floating point number\n * @return {number} - the floating point number with the same precision\n*/\nexport function keepPrecision(x) {\n    return Math.round(C.PRECISION_FACTOR * x) / C.PRECISION_FACTOR;\n}\n//# sourceMappingURL=to-atomic-level-utils.js.map","export const HELM_CORE_LIB_FILENAME = '/data/HELMCoreLibrary.json';\n// core fields of HELM library object used in toAtomicLevel function\nexport const HELM_CORE_FIELDS = [\n    \"symbol\" /* HELM_FIELDS.SYMBOL */,\n    \"molfile\" /* HELM_FIELDS.MOLFILE */,\n    \"rgroups\" /* HELM_FIELDS.RGROUPS */,\n    \"name\" /* HELM_FIELDS.NAME */,\n    // HELM_FIELDS.MONOMER_TYPE, // add if terminal monomers for PEPTIDEs to be\n    // supported\n];\nexport const SDF_MONOMER_NAME = 'MonomerName';\n/** For PolyTool  */\nexport const helmFieldsToPolyToolInputFields = {\n    [\"symbol\" /* HELM_REQUIRED_FIELDS.SYMBOL */]: 'Short Name',\n    [\"name\" /* HELM_REQUIRED_FIELDS.NAME */]: 'Medium Name',\n    [\"smiles\" /* HELM_REQUIRED_FIELDS.SMILES */]: 'SMILES',\n};\n/** For PolyTool  */\nexport const R_GROUP_BLOCK_DUMMY = [\n    {\n        'capGroupSmiles': '[*:1][H]',\n        'alternateId': 'R1-H',\n        'capGroupName': 'H',\n        'label': 'R1'\n    },\n    {\n        'capGroupSmiles': 'O[*:2]',\n        'alternateId': 'R2-OH',\n        'capGroupName': 'OH',\n        'label': 'R2'\n    },\n    {\n        'capGroupSmiles': '[*:3][H]',\n        'alternateId': 'R3-H',\n        'capGroupName': 'H',\n        'label': 'R3'\n    }\n];\n// todo: ideally, keys should be expressed via constants\nexport const jsonSdfMonomerLibDict = {\n    'monomerType': null,\n    'smiles': null,\n    'name': 'MonomerName',\n    'author': null,\n    'molfile': 'molecule',\n    'naturalAnalog': 'MonomerNaturalAnalogCode',\n    'rgroups': 'MonomerCaps',\n    'createDate': null,\n    'id': null,\n    'polymerType': 'MonomerType',\n    'symbol': 'MonomerCode'\n};\nexport const DUMMY_MONOMER = {\n    'monomerType': 'Backbone',\n    'smiles': '',\n    'name': '',\n    'author': 'Datagrok',\n    'molfile': '',\n    'naturalAnalog': '',\n    'rgroups': [],\n    'createDate': null,\n    'id': 0,\n    'polymerType': 'PEPTIDE',\n    'symbol': ''\n};\n// range of hex nubers used in PepSea library to endode monomers\nexport const MONOMER_ENCODE_MIN = 0x100;\nexport const MONOMER_ENCODE_MAX = 0x40A;\nexport const RIBOSE_SYMBOL = 'r';\nexport const DEOXYRIBOSE_SYMBOL = 'd';\nexport const PHOSPHATE_SYMBOL = 'p';\nexport const HELM_WRAPPERS_REGEXP = new RegExp(`[${RIBOSE_SYMBOL}${DEOXYRIBOSE_SYMBOL}]\\\\((\\\\w)\\\\)${PHOSPHATE_SYMBOL}?`, 'g');\n//# sourceMappingURL=const.js.map","import { monomerSeqToMolfile } from './to-atomic-level-utils';\nonmessage = 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const monomerWorksConsts = {\n    // constants for parsing molfile V2000\n    V2K_RGP_SHIFT: 8,\n    V2K_RGP_LINE: 'M  RGP',\n    V2K_A_LINE: 'A  ',\n    // constants for parsing/reconstruction of molfile V3000\n    V3K_COUNTS_SHIFT: 14,\n    V3K_IDX_SHIFT: 7,\n    V3K_HEADER_FIRST_LINE: '\\nDatagrok macromolecule handler\\n\\n',\n    V3K_HEADER_SECOND_LINE: '  0  0  0  0  0  0            999 V3000\\n',\n    V3K_BEGIN_CTAB_BLOCK: 'M  V30 BEGIN CTAB\\n',\n    V3K_END_CTAB_BLOCK: 'M  V30 END CTAB\\n',\n    V3K_BEGIN_COUNTS_LINE: 'M  V30 COUNTS ',\n    V3K_COUNTS_LINE_ENDING: ' 0 0 0\\n',\n    V3K_BEGIN_ATOM_BLOCK: 'M  V30 BEGIN ATOM\\n',\n    V3K_END_ATOM_BLOCK: 'M  V30 END ATOM\\n',\n    V3K_BEGIN_BOND_BLOCK: 'M  V30 BEGIN BOND\\n',\n    V3K_END_BOND_BLOCK: 'M  V30 END BOND\\n',\n    V3K_BOND_CONFIG: ' CFG=',\n    V3K_BEGIN_DATA_LINE: 'M  V30 ',\n    V3K_END: 'M  END',\n    PRECISION_FACTOR: 10000,\n    // symbols for the corresponding monomers in HELM library\n    DEOXYRIBOSE: 'd',\n    RIBOSE: 'r',\n    PHOSPHATE: 'p',\n    OXYGEN: 'O',\n    HYDROGEN: 'H',\n};\n//# sourceMappingURL=consts.js.map","import { monomerWorksConsts as C } from './consts';\nimport { HELM_CORE_FIELDS, } from '../utils/const';\n/** Get a mapping of peptide symbols to HELM monomer library objects with selected fields.\n * @param {IMonomerLib} monomerLib - Monomer library\n * @param {HELM_POLYMER_TYPE} polymerType - Polymer type\n * @param {ALPHABET} alphabet - Alphabet of the column\n * @return {Map<string, any>} - Mapping of peptide symbols to HELM monomer library objects with selected fields*/\nexport function getFormattedMonomerLib(monomerLib, polymerType, alphabet) {\n    const map = new Map();\n    for (const monomerSymbol of monomerLib.getMonomerSymbolsByType(polymerType)) {\n        const it = monomerLib.getMonomer(polymerType, monomerSymbol);\n        if (polymerType === \"RNA\" /* HELM_POLYMER_TYPE.RNA */ &&\n            (it[\"monomerType\" /* HELM_FIELDS.MONOMER_TYPE */] === \"Branch\" /* HELM_MONOMER_TYPE.BRANCH */ ||\n                alphabet === \"DNA\" /* ALPHABET.DNA */ && it[\"symbol\" /* HELM_FIELDS.SYMBOL */] === C.DEOXYRIBOSE ||\n                alphabet === \"RNA\" /* ALPHABET.RNA */ && it[\"symbol\" /* HELM_FIELDS.SYMBOL */] === C.RIBOSE ||\n                it[\"symbol\" /* HELM_FIELDS.SYMBOL */] === C.PHOSPHATE) ||\n            polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */ &&\n                it[\"monomerType\" /* HELM_FIELDS.MONOMER_TYPE */] !== \"Branch\" /* HELM_MONOMER_TYPE.BRANCH */) {\n            const monomerObject = {};\n            HELM_CORE_FIELDS.forEach((field) => {\n                //@ts-ignore\n                monomerObject[field] = it[field];\n            });\n            map.set(it[\"symbol\" /* HELM_FIELDS.SYMBOL */], monomerObject);\n        }\n    }\n    return map;\n}\n/** Translate a sequence of monomer symbols into Molfile V3000\n * @param {string[]} monomerSeq - Sequence of monomer symbols\n * @param {Map<string, MolGraph>} monomersDict - Mapping of monomer symbols to MolGraph objects\n * @param {ALPHABET} alphabet - Alphabet of the column\n * @param {HELM_POLYMER_TYPE} polymerType - Polymer type\n * @return {string} - Molfile V3000*/\nexport function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerType) {\n    if (monomerSeq.length === 0) {\n        // throw new Error('monomerSeq is empty');\n        return '';\n    }\n    // define atom and bond counts, taking into account the bond type\n    const getAtomAndBondCounts = getResultingAtomBondCounts;\n    const { atomCount, bondCount } = getAtomAndBondCounts(monomerSeq, monomersDict, alphabet, polymerType);\n    // create arrays to store lines of the resulting molfile\n    const molfileAtomBlock = new Array(atomCount);\n    const molfileBondBlock = new Array(bondCount);\n    let addMonomerToMolblock; // todo: types?\n    let sugar = null;\n    let phosphate = null;\n    if (polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */) {\n        addMonomerToMolblock = addAminoAcidToMolblock;\n    }\n    else { // nucleotides\n        addMonomerToMolblock = addNucleotideToMolblock;\n        sugar = (alphabet === \"DNA\" /* ALPHABET.DNA */) ? monomersDict.get(C.DEOXYRIBOSE) : monomersDict.get(C.RIBOSE);\n        phosphate = monomersDict.get(C.PHOSPHATE);\n    }\n    const v = {\n        i: 0,\n        nodeShift: 0,\n        bondShift: 0,\n        backbonePositionShift: new Array(2).fill(0),\n        branchPositionShift: new Array(2).fill(0),\n        backboneAttachNode: 0,\n        branchAttachNode: 0,\n        flipFactor: 1,\n    };\n    const LC = {\n        sugar: sugar,\n        phosphate: phosphate,\n        seqLength: monomerSeq.length,\n        atomCount: atomCount,\n        bondCount: bondCount,\n    };\n    for (v.i = 0; v.i < LC.seqLength; ++v.i) {\n        const monomer = monomersDict.get(monomerSeq[v.i]);\n        addMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v, LC);\n    }\n    capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC);\n    const molfileCountsLine = C.V3K_BEGIN_COUNTS_LINE + atomCount + ' ' + bondCount + C.V3K_COUNTS_LINE_ENDING;\n    // todo: possible optimization may be achieved by replacing .join('') with +=\n    // since counterintuitively joining an array into a new string is reportedly\n    // slower than using += as below\n    let result = '';\n    result += C.V3K_HEADER_FIRST_LINE;\n    result += C.V3K_HEADER_SECOND_LINE;\n    result += C.V3K_BEGIN_CTAB_BLOCK;\n    result += molfileCountsLine;\n    result += C.V3K_BEGIN_ATOM_BLOCK;\n    result += molfileAtomBlock.join('');\n    result += C.V3K_END_ATOM_BLOCK;\n    result += C.V3K_BEGIN_BOND_BLOCK;\n    result += molfileBondBlock.join('');\n    result += C.V3K_END_BOND_BLOCK;\n    result += C.V3K_END_CTAB_BLOCK;\n    result += C.V3K_END;\n    // return molfileParts.join('');\n    return result;\n}\n/** Cap the resulting (after sewing up all the monomers) molfile with 'O'\n * @param {string[]} molfileAtomBlock - Array of lines of the resulting molfile atom block\n * @param {string[]} molfileBondBlock - Array of lines of the resulting molfile bond block\n * @param {LoopVariables} v - Loop variables\n * @param {LoopConstants} LC - Loop constants*/\nfunction capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC) {\n    // add terminal oxygen\n    const atomIdx = v.nodeShift + 1;\n    molfileAtomBlock[LC.atomCount] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n        C.OXYGEN + ' ' + keepPrecision(v.backbonePositionShift[0]) + ' ' +\n        v.flipFactor * keepPrecision(v.backbonePositionShift[1]) + ' ' + '0.000000 0' + '\\n';\n    // add terminal bond\n    const firstAtom = v.backboneAttachNode;\n    const secondAtom = atomIdx;\n    molfileBondBlock[LC.bondCount] = C.V3K_BEGIN_DATA_LINE + v.bondShift + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n}\nfunction addAminoAcidToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    v.flipFactor = (-1) ** (v.i % 2); // to flip every even monomer over OX\n    addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v);\n}\nfunction addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    // todo: remove these comments to the docstrings of the corr. functions\n    // construnct the lines of V3K molfile atom block\n    fillAtomLines(monomer, molfileAtomBlock, v);\n    // construct the lines of V3K molfile bond block\n    fillBondLines(monomer, molfileBondBlock, v);\n    // peptide bond\n    fillChainExtendingBond(monomer, molfileBondBlock, v);\n    // update branch variables if necessary\n    if (monomer.meta.branchShift !== null && monomer.meta.terminalNodes.length > 2)\n        updateBranchVariables(monomer, v);\n    // update loop variables\n    updateChainExtendingVariables(monomer, v);\n}\nfunction addNucleotideToMolblock(nucleobase, molfileAtomBlock, molfileBondBlock, v, LC) {\n    // construnct the lines of V3K molfile atom block corresponding to phosphate\n    // and sugar\n    if (v.i === 0) {\n        addBackboneMonomerToMolblock(LC.sugar, molfileAtomBlock, molfileBondBlock, v);\n    }\n    else {\n        for (const monomer of [LC.phosphate, LC.sugar])\n            addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v);\n    }\n    addBranchMonomerToMolblock(nucleobase, molfileAtomBlock, molfileBondBlock, v);\n}\nfunction addBranchMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    fillBranchAtomLines(monomer, molfileAtomBlock, v);\n    fillBondLines(monomer, molfileBondBlock, v);\n    fillBackboneToBranchBond(monomer, molfileBondBlock, v);\n    // C-N bond\n    const bondIdx = v.bondShift;\n    const firstAtom = v.branchAttachNode;\n    const secondAtom = monomer.meta.terminalNodes[0] + v.nodeShift;\n    molfileBondBlock[bondIdx - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n    // update loop variables\n    v.bondShift += monomer.bonds.atomPairs.length + 1;\n    v.nodeShift += monomer.atoms.atomTypes.length;\n}\nfunction updateChainExtendingVariables(monomer, v) {\n    v.backboneAttachNode = v.nodeShift + monomer.meta.terminalNodes[1];\n    v.bondShift += monomer.bonds.atomPairs.length + 1;\n    v.nodeShift += monomer.atoms.atomTypes.length;\n    v.backbonePositionShift[0] += monomer.meta.backboneShift[0]; // todo: non-null check\n    v.backbonePositionShift[1] += v.flipFactor * monomer.meta.backboneShift[1];\n}\nfunction updateBranchVariables(monomer, v) {\n    v.branchAttachNode = v.nodeShift + monomer.meta.terminalNodes[2];\n    for (let i = 0; i < 2; ++i)\n        v.branchPositionShift[i] = v.backbonePositionShift[i] + monomer.meta.branchShift[i];\n}\nfunction fillAtomLines(monomer, molfileAtomBlock, v) {\n    for (let j = 0; j < monomer.atoms.atomTypes.length; ++j) {\n        const atomIdx = v.nodeShift + j + 1;\n        molfileAtomBlock[v.nodeShift + j] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n            monomer.atoms.atomTypes[j] + ' ' +\n            keepPrecision(v.backbonePositionShift[0] + monomer.atoms.x[j]) + ' ' +\n            keepPrecision(v.backbonePositionShift[1] + v.flipFactor * monomer.atoms.y[j]) +\n            ' ' + monomer.atoms.kwargs[j];\n    }\n}\n// todo: remove as quickfix\nfunction fillBranchAtomLines(monomer, molfileAtomBlock, v) {\n    for (let j = 0; j < monomer.atoms.atomTypes.length; ++j) {\n        const atomIdx = v.nodeShift + j + 1;\n        molfileAtomBlock[v.nodeShift + j] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n            monomer.atoms.atomTypes[j] + ' ' +\n            keepPrecision(v.branchPositionShift[0] + monomer.atoms.x[j]) + ' ' +\n            keepPrecision(v.branchPositionShift[1] + v.flipFactor * monomer.atoms.y[j]) +\n            ' ' + monomer.atoms.kwargs[j];\n    }\n}\nfunction fillBondLines(monomer, molfileBondBlock, v) {\n    // construct the lines of V3K molfile bond block\n    for (let j = 0; j < monomer.bonds.atomPairs.length; ++j) {\n        const bondIdx = v.bondShift + j + 1;\n        const firstAtom = monomer.bonds.atomPairs[j][0] + v.nodeShift;\n        const secondAtom = monomer.bonds.atomPairs[j][1] + v.nodeShift;\n        let bondCfg = '';\n        if (monomer.bonds.bondConfiguration.has(j)) {\n            // flip orientation when necessary\n            let orientation = monomer.bonds.bondConfiguration.get(j);\n            if (v.flipFactor < 0)\n                orientation = (orientation === 1) ? 3 : 1;\n            bondCfg = ' CFG=' + orientation;\n        }\n        const kwargs = monomer.bonds.kwargs.has(j) ?\n            ' ' + monomer.bonds.kwargs.get(j) : '';\n        molfileBondBlock[v.bondShift + j] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n            monomer.bonds.bondTypes[j] + ' ' +\n            firstAtom + ' ' + secondAtom + bondCfg + kwargs + '\\n';\n    }\n}\nfunction fillChainExtendingBond(monomer, molfileBondBlock, v) {\n    if (v.backboneAttachNode !== 0) {\n        const bondIdx = v.bondShift;\n        const firstAtom = v.backboneAttachNode;\n        const secondAtom = monomer.meta.terminalNodes[0] + v.nodeShift;\n        molfileBondBlock[v.bondShift - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n            1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n    }\n}\n// todo: remove\nfunction fillBackboneToBranchBond(branchMonomer, molfileBondBlock, v) {\n    const bondIdx = v.bondShift;\n    const firstAtom = v.branchAttachNode;\n    const secondAtom = branchMonomer.meta.terminalNodes[0] + v.nodeShift;\n    molfileBondBlock[bondIdx - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n}\n/** Compute the atom/bond counts for the resulting molfile, depending on the\n    * type of polymer (peptide/nucleotide)\n    * @param {string[]}monomerSeq - the sequence of monomers\n    * @param {Map<string, MolGraph>}monomersDict - the dictionary of monomers\n    * @param {ALPHABET}alphabet - the alphabet of the monomers\n    * @param {HELM_POLYMER_TYPE}polymerType - the type of polymer\n    * @return {{atomCount: number, bondCount: number}} - the atom/bond counts*/\nfunction getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerType) {\n    let atomCount = 0;\n    let bondCount = 0;\n    // sum up all the atoms/nodes provided by the sequence\n    for (const monomerSymbol of monomerSeq) {\n        if (monomerSymbol === '')\n            continue; // Skip for gap/empty monomer in MSA\n        const monomer = monomersDict.get(monomerSymbol);\n        atomCount += monomer.atoms.x.length;\n        bondCount += monomer.bonds.bondTypes.length;\n    }\n    // add extra values depending on the polymer type\n    if (polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */) {\n        // add the rightmost/terminating cap group 'OH' (i.e. 'O')\n        atomCount += 1;\n        // add chain-extending bonds (C-NH per each monomer pair and terminal C-OH)\n        bondCount += monomerSeq.length;\n    }\n    else { // nucleotides\n        const sugar = (alphabet === \"DNA\" /* ALPHABET.DNA */) ?\n            monomersDict.get(C.DEOXYRIBOSE) : monomersDict.get(C.RIBOSE);\n        const phosphate = monomersDict.get(C.PHOSPHATE);\n        // add phosphate per each pair of nucleobase symbols\n        atomCount += (monomerSeq.length - 1) * phosphate.atoms.x.length;\n        // add sugar per each nucleobase symbol\n        atomCount += monomerSeq.length * sugar.atoms.x.length;\n        // add the leftmost cap group 'OH' (i.e. 'O')\n        atomCount += 1;\n        // add bonds from phosphate monomers\n        bondCount += (monomerSeq.length - 1) * phosphate.bonds.bondTypes.length;\n        // add bonds from sugar monomers\n        bondCount += monomerSeq.length * sugar.bonds.bondTypes.length;\n        // exclude the first chain-extending bond O-P (absent, no 'leftmost' phosphate)\n        bondCount -= 1;\n        // add chain-extending and branch bonds (O-P, C-O and C-N per each nucleotide)\n        bondCount += monomerSeq.length * 3;\n    }\n    return { atomCount, bondCount };\n}\n/** Keep precision upon floating point operations over atom coordinates\n * @param {number}x - the floating point number\n * @return {number} - the floating point number with the same precision\n*/\nexport function keepPrecision(x) {\n    return Math.round(C.PRECISION_FACTOR * x) / C.PRECISION_FACTOR;\n}\n//# sourceMappingURL=to-atomic-level-utils.js.map","export const HELM_CORE_LIB_FILENAME = '/data/HELMCoreLibrary.json';\n// core fields of HELM library object used in toAtomicLevel function\nexport const HELM_CORE_FIELDS = [\n    \"symbol\" /* HELM_FIELDS.SYMBOL */,\n    \"molfile\" /* HELM_FIELDS.MOLFILE */,\n    \"rgroups\" /* HELM_FIELDS.RGROUPS */,\n    \"name\" /* HELM_FIELDS.NAME */,\n    // HELM_FIELDS.MONOMER_TYPE, // add if terminal monomers for PEPTIDEs to be\n    // supported\n];\nexport const SDF_MONOMER_NAME = 'MonomerName';\n/** For PolyTool  */\nexport const helmFieldsToPolyToolInputFields = {\n    [\"symbol\" /* HELM_REQUIRED_FIELDS.SYMBOL */]: 'Short Name',\n    [\"name\" /* HELM_REQUIRED_FIELDS.NAME */]: 'Medium Name',\n    [\"smiles\" /* HELM_REQUIRED_FIELDS.SMILES */]: 'SMILES',\n};\n/** For PolyTool  */\nexport const R_GROUP_BLOCK_DUMMY = [\n    {\n        'capGroupSmiles': '[*:1][H]',\n        'alternateId': 'R1-H',\n        'capGroupName': 'H',\n        'label': 'R1'\n    },\n    {\n        'capGroupSmiles': 'O[*:2]',\n        'alternateId': 'R2-OH',\n        'capGroupName': 'OH',\n        'label': 'R2'\n    },\n    {\n        'capGroupSmiles': '[*:3][H]',\n        'alternateId': 'R3-H',\n        'capGroupName': 'H',\n        'label': 'R3'\n    }\n];\n// todo: ideally, keys should be expressed via constants\nexport const jsonSdfMonomerLibDict = {\n    'monomerType': null,\n    'smiles': null,\n    'name': 'MonomerName',\n    'author': null,\n    'molfile': 'molecule',\n    'naturalAnalog': 'MonomerNaturalAnalogCode',\n    'rgroups': 'MonomerCaps',\n    'createDate': null,\n    'id': null,\n    'polymerType': 'MonomerType',\n    'symbol': 'MonomerCode'\n};\nexport const DUMMY_MONOMER = {\n    'monomerType': 'Backbone',\n    'smiles': '',\n    'name': '',\n    'author': 'Datagrok',\n    'molfile': '',\n    'naturalAnalog': '',\n    'rgroups': [],\n    'createDate': null,\n    'id': 0,\n    'polymerType': 'PEPTIDE',\n    'symbol': ''\n};\n// range of hex nubers used in PepSea library to endode monomers\nexport const MONOMER_ENCODE_MIN = 0x100;\nexport const MONOMER_ENCODE_MAX = 0x40A;\nexport const RIBOSE_SYMBOL = 'r';\nexport const DEOXYRIBOSE_SYMBOL = 'd';\nexport const PHOSPHATE_SYMBOL = 'p';\nexport const HELM_WRAPPERS_REGEXP = new RegExp(`[${RIBOSE_SYMBOL}${DEOXYRIBOSE_SYMBOL}]\\\\((\\\\w)\\\\)${PHOSPHATE_SYMBOL}?`, 'g');\n//# sourceMappingURL=const.js.map","import { monomerSeqToMolfile } from './to-atomic-level-utils';\nonmessage = (event) => {\n    const { monomerSequencesArray, monomersDict, alphabet, polymerType, start, end } = event.data;\n    const molfileList = new Array(end - start);\n    const molfileWarningList = new Array(0);\n    for (let rowI = start; rowI < end; ++rowI) {\n        try {\n            const monomerSeq = monomerSequencesArray[rowI];\n            molfileList[rowI - start] = monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerType);\n        }\n        catch (err) {\n            const errMsg = err instanceof Error ? err.message : err.toString();\n            const msg = `Cannot get molfile of row #${rowI}: ${errMsg}.`;\n            molfileWarningList.push(msg);\n        }\n    }\n    postMessage({ molfileList, molfileWarningList });\n};\n//# sourceMappingURL=seq-to-molfile-worker.js.map"],"names":["monomerWorksConsts","V2K_RGP_SHIFT","V2K_RGP_LINE","V2K_A_LINE","V3K_COUNTS_SHIFT","V3K_IDX_SHIFT","V3K_HEADER_FIRST_LINE","V3K_HEADER_SECOND_LINE","V3K_BEGIN_CTAB_BLOCK","V3K_END_CTAB_BLOCK","V3K_BEGIN_COUNTS_LINE","V3K_COUNTS_LINE_ENDING","V3K_BEGIN_ATOM_BLOCK","V3K_END_ATOM_BLOCK","V3K_BEGIN_BOND_BLOCK","V3K_END_BOND_BLOCK","V3K_BOND_CONFIG","V3K_BEGIN_DATA_LINE","V3K_END","PRECISION_FACTOR","DEOXYRIBOSE","RIBOSE","PHOSPHATE","OXYGEN","HYDROGEN","monomerSeqToMolfile","monomerSeq","monomersDict","alphabet","polymerType","length","getAtomAndBondCounts","getResultingAtomBondCounts","atomCount","bondCount","molfileAtomBlock","Array","molfileBondBlock","addMonomerToMolblock","sugar","phosphate","addAminoAcidToMolblock","addNucleotideToMolblock","get","v","i","nodeShift","bondShift","backbonePositionShift","fill","branchPositionShift","backboneAttachNode","branchAttachNode","flipFactor","LC","seqLength","atomIdx","keepPrecision","firstAtom","secondAtom","capResultingMolblock","molfileCountsLine","result","join","monomer","addBackboneMonomerToMolblock","j","atoms","atomTypes","x","y","kwargs","fillAtomLines","fillBondLines","bondIdx","meta","terminalNodes","fillChainExtendingBond","branchShift","updateBranchVariables","bonds","atomPairs","backboneShift","updateChainExtendingVariables","nucleobase","fillBranchAtomLines","branchMonomer","fillBackboneToBranchBond","addBranchMonomerToMolblock","bondCfg","bondConfiguration","has","orientation","bondTypes","monomerSymbol","Math","round","RegExp","onmessage","event","monomerSequencesArray","start","end","data","molfileList","molfileWarningList","rowI","err","msg","Error","message","toString","push","postMessage"],"sourceRoot":""}

package/dist/868.js

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n=s.get(e)||[];n.push(r),s.set(e,n)}));const n=new et([],[],[],t.getDims());for(let e of s.keys()){const o=s.get(e).sort(),i=r(o.map((r=>t.get(e,r))));for(let t=0;t<i.length;t++)n.set(e,o[t],i[t])}return n}const lt={max:t=>{let e=-1/0;for(let r=0;r<t.length;r++)e=t[r]>e?t[r]:e;return t.map((t=>t/e))},l1:t=>{let e=0;for(let r=0;r<t.length;r++)e+=t[r];return t.map((t=>t/e))},l2:t=>{let e=0;for(let r=0;r<t.length;r++)e+=t[r]**2;return t.map((t=>Math.sqrt(t**2/e)))}};function ut(t,e,r){const s=new Set,n=[],o=[],i=[],h=(s,h)=>{n.push(s),o.push(h);const a=r(t.get(s,h),e.get(s,h));i.push(a)},a=t.getValues(),l=t.getRows(),u=t.getCols();for(let t=0;t<a.length;t++){const e=l[t],r=u[t],n=`${e}:${r}`;s.add(n),h(e,r)}const c=e.getValues(),f=e.getRows(),m=e.getCols();for(let t=0;t<c.length;t++){const e=f[t],r=m[t],n=`${e}:${r}`;s.has(n)||h(e,r)}const g=[t.nRows,t.nCols];return new et(n,o,i,g)}function ct(t){const e=[];t.forEach(((t,r,s)=>{e.push({value:t,row:r,col:s})})),e.sort(((t,e)=>t.row===e.row?t.col-e.col:t.row-e.row));const r=[],s=[],n=[];let o=-1;for(let t=0;t<e.length;t++){const{row:i,col:h,value:a}=e[t];i!==o&&(o=i,n.push(t)),r.push(h),s.push(a)}return{indices:r,values:s,indptr:n}}class ft{constructor(t,e,r,s){this.hyperplanes=t,this.offsets=e,this.children=r,this.indices=s}}function mt(t,e,r,s){const n=Math.max(10,e),o=q(r).map(((e,r)=>function(t,e=30,r,s){return gt(t,q(t.length),e,r,s)}(t,n,r,s))),i=o.map((t=>function(t,e){const r=dt(t),s=wt(t),n=q(r).map((()=>t.hyperplane?1:0)),o=$(r),i=q(r).map((()=>[-1,-1])),h=q(s).map((()=>q(e).map((()=>-1))));return pt(t,n,o,i,h,0,0),new ft(n,o,i,h)}(t,n)));return i}function gt(t,e,r=30,s,n){if(e.length>r){const o=function(t,e,r){let s=V(e.length,r),n=V(e.length,r);n+=s===n?1:0,n%=e.length;const o=e[s],i=e[n];let h=0,a=0;a=t[o]-t[i],h-=a*(t[o]+t[i])/2;let l=0,u=0;const c=$(e.length);for(let s=0;s<e.length;s++){let 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r=t.toString();if(r.length<=e)return r;let s=t.toFixed(e);if(s.length>e&&(s=t.toFixed(Math.max(0,e-(s.length-e)))),s.length<=e&&!s.startsWith("0.000")&&!s.startsWith("-0.000"))return s;let n=t.toExponential(e);return n.length>e&&(n=t.toExponential(Math.max(0,e-(n.length-e)))),n.slice(0)}function Dt(t,e,r){let s=r?t.rows:t.rows-1;if(e<0||e>s)throw new RangeError("Row index out of range")}function Pt(t,e,r){let s=r?t.columns:t.columns-1;if(e<0||e>s)throw new RangeError("Column index out of range")}function Vt(t,e){if(e.to1DArray&&(e=e.to1DArray()),e.length!==t.columns)throw new RangeError("vector size must be the same as the number of columns");return e}function Ot(t,e){if(e.to1DArray&&(e=e.to1DArray()),e.length!==t.rows)throw new RangeError("vector size must be the same as the number of rows");return e}function jt(t,e,r,s,n){if(5!==arguments.length)throw new RangeError("expected 4 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Ut(r,s);for(let o=0;o<r;o++)for(let r=0;r<s;r++)n.set(o,r,Math.min(t.get(o,r),e.get(o,r)));return n}static max(t,e){t=this.checkMatrix(t),e=this.checkMatrix(e);let r=t.rows,s=t.columns,n=new this(r,s);for(let o=0;o<r;o++)for(let r=0;r<s;r++)n.set(o,r,Math.max(t.get(o,r),e.get(o,r)));return n}static checkMatrix(t){return Bt.isMatrix(t)?t:new Ut(t)}static isMatrix(t){return null!=t&&"Matrix"===t.klass}get size(){return this.rows*this.columns}apply(t){if("function"!=typeof t)throw new TypeError("callback must be a function");for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)t.call(this,e,r);return this}to1DArray(){let t=[];for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)t.push(this.get(e,r));return t}to2DArray(){let t=[];for(let e=0;e<this.rows;e++){t.push([]);for(let r=0;r<this.columns;r++)t[e].push(this.get(e,r))}return t}toJSON(){return this.to2DArray()}isRowVector(){return 1===this.rows}isColumnVector(){return 1===this.columns}isVector(){return 1===this.rows||1===this.columns}isSquare(){return this.rows===this.columns}isEmpty(){return 0===this.rows||0===this.columns}isSymmetric(){if(this.isSquare()){for(let t=0;t<this.rows;t++)for(let e=0;e<=t;e++)if(this.get(t,e)!==this.get(e,t))return!1;return!0}return!1}isEchelonForm(){let t=0,e=0,r=-1,s=!0,n=!1;for(;t<this.rows&&s;){for(e=0,n=!1;e<this.columns&&!1===n;)0===this.get(t,e)?e++:1===this.get(t,e)&&e>r?(n=!0,r=e):(s=!1,n=!0);t++}return s}isReducedEchelonForm(){let t=0,e=0,r=-1,s=!0,n=!1;for(;t<this.rows&&s;){for(e=0,n=!1;e<this.columns&&!1===n;)0===this.get(t,e)?e++:1===this.get(t,e)&&e>r?(n=!0,r=e):(s=!1,n=!0);for(let r=e+1;r<this.rows;r++)0!==this.get(t,r)&&(s=!1);t++}return s}echelonForm(){let t=this.clone(),e=0,r=0;for(;e<t.rows&&r<t.columns;){let s=e;for(let n=e;n<t.rows;n++)t.get(n,r)>t.get(s,r)&&(s=n);if(0===t.get(s,r))r++;else{t.swapRows(e,s);let n=t.get(e,r);for(let s=r;s<t.columns;s++)t.set(e,s,t.get(e,s)/n);for(let s=e+1;s<t.rows;s++){let n=t.get(s,r)/t.get(e,r);t.set(s,r,0);for(let o=r+1;o<t.columns;o++)t.set(s,o,t.get(s,o)-t.get(e,o)*n)}e++,r++}}return t}reducedEchelonForm(){let t=this.echelonForm(),e=t.columns,r=t.rows,s=r-1;for(;s>=0;)if(0===t.maxRow(s))s--;else{let n=0,o=!1;for(;n<r&&!1===o;)1===t.get(s,n)?o=!0:n++;for(let r=0;r<s;r++){let o=t.get(r,n);for(let i=n;i<e;i++){let e=t.get(r,i)-o*t.get(s,i);t.set(r,i,e)}}s--}return t}set(){throw new Error("set method is unimplemented")}get(){throw new Error("get method is unimplemented")}repeat(t={}){if("object"!=typeof t)throw new TypeError("options must be an object");const{rows:e=1,columns:r=1}=t;if(!Number.isInteger(e)||e<=0)throw new TypeError("rows must be a positive integer");if(!Number.isInteger(r)||r<=0)throw new TypeError("columns must be a positive integer");let s=new Ut(this.rows*e,this.columns*r);for(let t=0;t<e;t++)for(let e=0;e<r;e++)s.setSubMatrix(this,this.rows*t,this.columns*e);return s}fill(t){for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,t);return this}neg(){return this.mulS(-1)}getRow(t){Dt(this,t);let e=[];for(let r=0;r<this.columns;r++)e.push(this.get(t,r));return e}getRowVector(t){return Ut.rowVector(this.getRow(t))}setRow(t,e){Dt(this,t),e=Vt(this,e);for(let r=0;r<this.columns;r++)this.set(t,r,e[r]);return this}swapRows(t,e){Dt(this,t),Dt(this,e);for(let r=0;r<this.columns;r++){let s=this.get(t,r);this.set(t,r,this.get(e,r)),this.set(e,r,s)}return this}getColumn(t){Pt(this,t);let e=[];for(let r=0;r<this.rows;r++)e.push(this.get(r,t));return e}getColumnVector(t){return Ut.columnVector(this.getColumn(t))}setColumn(t,e){Pt(this,t),e=Ot(this,e);for(let r=0;r<this.rows;r++)this.set(r,t,e[r]);return this}swapColumns(t,e){Pt(this,t),Pt(this,e);for(let r=0;r<this.rows;r++){let s=this.get(r,t);this.set(r,t,this.get(r,e)),this.set(r,e,s)}return this}addRowVector(t){t=Vt(this,t);for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)+t[r]);return this}subRowVector(t){t=Vt(this,t);for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)-t[r]);return this}mulRowVector(t){t=Vt(this,t);for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)*t[r]);return this}divRowVector(t){t=Vt(this,t);for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)/t[r]);return this}addColumnVector(t){t=Ot(this,t);for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)+t[e]);return this}subColumnVector(t){t=Ot(this,t);for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)-t[e]);return this}mulColumnVector(t){t=Ot(this,t);for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)*t[e]);return this}divColumnVector(t){t=Ot(this,t);for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)/t[e]);return this}mulRow(t,e){Dt(this,t);for(let r=0;r<this.columns;r++)this.set(t,r,this.get(t,r)*e);return this}mulColumn(t,e){Pt(this,t);for(let r=0;r<this.rows;r++)this.set(r,t,this.get(r,t)*e);return this}max(t){if(this.isEmpty())return NaN;switch(t){case"row":{const t=new Array(this.rows).fill(Number.NEGATIVE_INFINITY);for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.get(e,r)>t[e]&&(t[e]=this.get(e,r));return t}case"column":{const t=new Array(this.columns).fill(Number.NEGATIVE_INFINITY);for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.get(e,r)>t[r]&&(t[r]=this.get(e,r));return t}case void 0:{let t=this.get(0,0);for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.get(e,r)>t&&(t=this.get(e,r));return t}default:throw new Error(`invalid option: ${t}`)}}maxIndex(){$t(this);let t=this.get(0,0),e=[0,0];for(let r=0;r<this.rows;r++)for(let s=0;s<this.columns;s++)this.get(r,s)>t&&(t=this.get(r,s),e[0]=r,e[1]=s);return e}min(t){if(this.isEmpty())return NaN;switch(t){case"row":{const t=new Array(this.rows).fill(Number.POSITIVE_INFINITY);for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.get(e,r)<t[e]&&(t[e]=this.get(e,r));return t}case"column":{const t=new Array(this.columns).fill(Number.POSITIVE_INFINITY);for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.get(e,r)<t[r]&&(t[r]=this.get(e,r));return t}case void 0:{let t=this.get(0,0);for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.get(e,r)<t&&(t=this.get(e,r));return t}default:throw new Error(`invalid option: ${t}`)}}minIndex(){$t(this);let t=this.get(0,0),e=[0,0];for(let r=0;r<this.rows;r++)for(let s=0;s<this.columns;s++)this.get(r,s)<t&&(t=this.get(r,s),e[0]=r,e[1]=s);return e}maxRow(t){if(Dt(this,t),this.isEmpty())return NaN;let e=this.get(t,0);for(let r=1;r<this.columns;r++)this.get(t,r)>e&&(e=this.get(t,r));return e}maxRowIndex(t){Dt(this,t),$t(this);let e=this.get(t,0),r=[t,0];for(let s=1;s<this.columns;s++)this.get(t,s)>e&&(e=this.get(t,s),r[1]=s);return r}minRow(t){if(Dt(this,t),this.isEmpty())return NaN;let e=this.get(t,0);for(let r=1;r<this.columns;r++)this.get(t,r)<e&&(e=this.get(t,r));return e}minRowIndex(t){Dt(this,t),$t(this);let e=this.get(t,0),r=[t,0];for(let s=1;s<this.columns;s++)this.get(t,s)<e&&(e=this.get(t,s),r[1]=s);return r}maxColumn(t){if(Pt(this,t),this.isEmpty())return NaN;let e=this.get(0,t);for(let r=1;r<this.rows;r++)this.get(r,t)>e&&(e=this.get(r,t));return e}maxColumnIndex(t){Pt(this,t),$t(this);let e=this.get(0,t),r=[0,t];for(let s=1;s<this.rows;s++)this.get(s,t)>e&&(e=this.get(s,t),r[0]=s);return r}minColumn(t){if(Pt(this,t),this.isEmpty())return NaN;let e=this.get(0,t);for(let r=1;r<this.rows;r++)this.get(r,t)<e&&(e=this.get(r,t));return e}minColumnIndex(t){Pt(this,t),$t(this);let e=this.get(0,t),r=[0,t];for(let s=1;s<this.rows;s++)this.get(s,t)<e&&(e=this.get(s,t),r[0]=s);return r}diag(){let t=Math.min(this.rows,this.columns),e=[];for(let r=0;r<t;r++)e.push(this.get(r,r));return e}norm(t="frobenius"){let e=0;if("max"===t)return this.max();if("frobenius"===t){for(let t=0;t<this.rows;t++)for(let r=0;r<this.columns;r++)e+=this.get(t,r)*this.get(t,r);return Math.sqrt(e)}throw new RangeError(`unknown norm type: ${t}`)}cumulativeSum(){let t=0;for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)t+=this.get(e,r),this.set(e,r,t);return this}dot(t){Bt.isMatrix(t)&&(t=t.to1DArray());let e=this.to1DArray();if(e.length!==t.length)throw new RangeError("vectors do not have the same size");let r=0;for(let s=0;s<e.length;s++)r+=e[s]*t[s];return r}mmul(t){t=Ut.checkMatrix(t);let e=this.rows,r=this.columns,s=t.columns,n=new Ut(e,s),o=new Float64Array(r);for(let i=0;i<s;i++){for(let e=0;e<r;e++)o[e]=t.get(e,i);for(let t=0;t<e;t++){let e=0;for(let s=0;s<r;s++)e+=this.get(t,s)*o[s];n.set(t,i,e)}}return n}strassen2x2(t){t=Ut.checkMatrix(t);let e=new Ut(2,2);const r=this.get(0,0),s=t.get(0,0),n=this.get(0,1),o=t.get(0,1),i=this.get(1,0),h=t.get(1,0),a=this.get(1,1),l=t.get(1,1),u=(r+a)*(s+l),c=(i+a)*s,f=r*(o-l),m=a*(h-s),g=(r+n)*l,p=u+m-g+(n-a)*(h+l),d=f+g,w=c+m,y=u-c+f+(i-r)*(s+o);return e.set(0,0,p),e.set(0,1,d),e.set(1,0,w),e.set(1,1,y),e}strassen3x3(t){t=Ut.checkMatrix(t);let e=new Ut(3,3);const r=this.get(0,0),s=this.get(0,1),n=this.get(0,2),o=this.get(1,0),i=this.get(1,1),h=this.get(1,2),a=this.get(2,0),l=this.get(2,1),u=this.get(2,2),c=t.get(0,0),f=t.get(0,1),m=t.get(0,2),g=t.get(1,0),p=t.get(1,1),d=t.get(1,2),w=t.get(2,0),y=t.get(2,1),b=t.get(2,2),M=(r-o)*(-f+p),x=(-r+o+i)*(c-f+p),E=(o+i)*(-c+f),S=r*c,v=(-r+a+l)*(c-m+d),N=(-r+a)*(m-d),k=(a+l)*(-c+m),C=(-n+l+u)*(p+w-y),A=(n-u)*(p-y),R=n*w,F=(l+u)*(-w+y),I=(-n+i+h)*(d+w-b),z=(n-h)*(d-b),T=(i+h)*(-w+b),_=S+R+s*g,D=(r+s+n-o-i-l-u)*p+x+E+S+C+R+F,P=S+v+k+(r+s+n-i-h-a-l)*d+R+I+T,V=M+i*(-c+f+g-p-d-w+b)+x+S+R+I+z,O=M+x+E+S+h*y,j=R+I+z+T+o*m,q=S+v+N+l*(-c+m+g-p-d-w+y)+C+A+R,L=C+A+R+F+a*f,$=S+v+N+k+u*b;return e.set(0,0,_),e.set(0,1,D),e.set(0,2,P),e.set(1,0,V),e.set(1,1,O),e.set(1,2,j),e.set(2,0,q),e.set(2,1,L),e.set(2,2,$),e}mmulStrassen(t){t=Ut.checkMatrix(t);let e=this.clone(),r=e.rows,s=e.columns,n=t.rows,o=t.columns;function i(t,e,r){let s=t.rows,n=t.columns;if(s===e&&n===r)return t;{let s=Bt.zeros(e,r);return s=s.setSubMatrix(t,0,0),s}}s!==n&&console.warn(`Multiplying ${r} x ${s} and ${n} x ${o} matrix: dimensions do not match.`);let h=Math.max(r,n),a=Math.max(s,o);return e=i(e,h,a),function t(e,r,s,n){if(s<=512||n<=512)return e.mmul(r);s%2==1&&n%2==1?(e=i(e,s+1,n+1),r=i(r,s+1,n+1)):s%2==1?(e=i(e,s+1,n),r=i(r,s+1,n)):n%2==1&&(e=i(e,s,n+1),r=i(r,s,n+1));let o=parseInt(e.rows/2,10),h=parseInt(e.columns/2,10),a=e.subMatrix(0,o-1,0,h-1),l=r.subMatrix(0,o-1,0,h-1),u=e.subMatrix(0,o-1,h,e.columns-1),c=r.subMatrix(0,o-1,h,r.columns-1),f=e.subMatrix(o,e.rows-1,0,h-1),m=r.subMatrix(o,r.rows-1,0,h-1),g=e.subMatrix(o,e.rows-1,h,e.columns-1),p=r.subMatrix(o,r.rows-1,h,r.columns-1),d=t(Bt.add(a,g),Bt.add(l,p),o,h),w=t(Bt.add(f,g),l,o,h),y=t(a,Bt.sub(c,p),o,h),b=t(g,Bt.sub(m,l),o,h),M=t(Bt.add(a,u),p,o,h),x=t(Bt.sub(f,a),Bt.add(l,c),o,h),E=t(Bt.sub(u,g),Bt.add(m,p),o,h),S=Bt.add(d,b);S.sub(M),S.add(E);let v=Bt.add(y,M),N=Bt.add(w,b),k=Bt.sub(d,w);k.add(y),k.add(x);let C=Bt.zeros(2*S.rows,2*S.columns);return C=C.setSubMatrix(S,0,0),C=C.setSubMatrix(v,S.rows,0),C=C.setSubMatrix(N,0,S.columns),C=C.setSubMatrix(k,S.rows,S.columns),C.subMatrix(0,s-1,0,n-1)}(e,t=i(t,h,a),h,a)}scaleRows(t={}){if("object"!=typeof t)throw new TypeError("options must be an object");const{min:e=0,max:r=1}=t;if(!Number.isFinite(e))throw new TypeError("min must be a number");if(!Number.isFinite(r))throw new TypeError("max must be a number");if(e>=r)throw new RangeError("min must be smaller than max");let s=new Ut(this.rows,this.columns);for(let t=0;t<this.rows;t++){const n=this.getRow(t);n.length>0&&Rt(n,{min:e,max:r,output:n}),s.setRow(t,n)}return s}scaleColumns(t={}){if("object"!=typeof t)throw new TypeError("options must be an object");const{min:e=0,max:r=1}=t;if(!Number.isFinite(e))throw new TypeError("min must be a number");if(!Number.isFinite(r))throw new TypeError("max must be a number");if(e>=r)throw new RangeError("min must be smaller than max");let s=new Ut(this.rows,this.columns);for(let t=0;t<this.columns;t++){const n=this.getColumn(t);n.length&&Rt(n,{min:e,max:r,output:n}),s.setColumn(t,n)}return s}flipRows(){const t=Math.ceil(this.columns/2);for(let e=0;e<this.rows;e++)for(let r=0;r<t;r++){let t=this.get(e,r),s=this.get(e,this.columns-1-r);this.set(e,r,s),this.set(e,this.columns-1-r,t)}return this}flipColumns(){const t=Math.ceil(this.rows/2);for(let e=0;e<this.columns;e++)for(let r=0;r<t;r++){let t=this.get(r,e),s=this.get(this.rows-1-r,e);this.set(r,e,s),this.set(this.rows-1-r,e,t)}return this}kroneckerProduct(t){t=Ut.checkMatrix(t);let e=this.rows,r=this.columns,s=t.rows,n=t.columns,o=new Ut(e*s,r*n);for(let i=0;i<e;i++)for(let e=0;e<r;e++)for(let r=0;r<s;r++)for(let h=0;h<n;h++)o.set(s*i+r,n*e+h,this.get(i,e)*t.get(r,h));return o}kroneckerSum(t){if(t=Ut.checkMatrix(t),!this.isSquare()||!t.isSquare())throw new Error("Kronecker Sum needs two Square Matrices");let e=this.rows,r=t.rows,s=this.kroneckerProduct(Ut.eye(r,r)),n=Ut.eye(e,e).kroneckerProduct(t);return s.add(n)}transpose(){let t=new Ut(this.columns,this.rows);for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)t.set(r,e,this.get(e,r));return t}sortRows(t=Wt){for(let e=0;e<this.rows;e++)this.setRow(e,this.getRow(e).sort(t));return this}sortColumns(t=Wt){for(let e=0;e<this.columns;e++)this.setColumn(e,this.getColumn(e).sort(t));return this}subMatrix(t,e,r,s){jt(this,t,e,r,s);let n=new Ut(e-t+1,s-r+1);for(let o=t;o<=e;o++)for(let e=r;e<=s;e++)n.set(o-t,e-r,this.get(o,e));return n}subMatrixRow(t,e,r){if(void 0===e&&(e=0),void 0===r&&(r=this.columns-1),e>r||e<0||e>=this.columns||r<0||r>=this.columns)throw new RangeError("Argument out of range");let s=new Ut(t.length,r-e+1);for(let n=0;n<t.length;n++)for(let o=e;o<=r;o++){if(t[n]<0||t[n]>=this.rows)throw new RangeError(`Row index out of range: ${t[n]}`);s.set(n,o-e,this.get(t[n],o))}return s}subMatrixColumn(t,e,r){if(void 0===e&&(e=0),void 0===r&&(r=this.rows-1),e>r||e<0||e>=this.rows||r<0||r>=this.rows)throw new RangeError("Argument out of range");let s=new Ut(r-e+1,t.length);for(let n=0;n<t.length;n++)for(let o=e;o<=r;o++){if(t[n]<0||t[n]>=this.columns)throw new RangeError(`Column index out of range: ${t[n]}`);s.set(o-e,n,this.get(o,t[n]))}return s}setSubMatrix(t,e,r){if((t=Ut.checkMatrix(t)).isEmpty())return this;jt(this,e,e+t.rows-1,r,r+t.columns-1);for(let s=0;s<t.rows;s++)for(let n=0;n<t.columns;n++)this.set(e+s,r+n,t.get(s,n));return this}selection(t,e){!function(t,e){if(!vt(e))throw new TypeError("row indices must be an array");for(let r=0;r<e.length;r++)if(e[r]<0||e[r]>=t.rows)throw new RangeError("row indices are out of range")}(this,t),function(t,e){if(!vt(e))throw new TypeError("column indices must be an array");for(let r=0;r<e.length;r++)if(e[r]<0||e[r]>=t.columns)throw new RangeError("column indices are out of range")}(this,e);let r=new Ut(t.length,e.length);for(let s=0;s<t.length;s++){let n=t[s];for(let t=0;t<e.length;t++){let o=e[t];r.set(s,t,this.get(n,o))}}return r}trace(){let t=Math.min(this.rows,this.columns),e=0;for(let r=0;r<t;r++)e+=this.get(r,r);return e}clone(){let t=new Ut(this.rows,this.columns);for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)t.set(e,r,this.get(e,r));return t}sum(t){switch(t){case"row":return function(t){let e=qt(t.rows);for(let r=0;r<t.rows;++r)for(let s=0;s<t.columns;++s)e[r]+=t.get(r,s);return e}(this);case"column":return function(t){let e=qt(t.columns);for(let r=0;r<t.rows;++r)for(let s=0;s<t.columns;++s)e[s]+=t.get(r,s);return e}(this);case void 0:return function(t){let e=0;for(let r=0;r<t.rows;r++)for(let s=0;s<t.columns;s++)e+=t.get(r,s);return e}(this);default:throw new Error(`invalid option: ${t}`)}}product(t){switch(t){case"row":return function(t){let e=qt(t.rows,1);for(let r=0;r<t.rows;++r)for(let s=0;s<t.columns;++s)e[r]*=t.get(r,s);return e}(this);case"column":return function(t){let e=qt(t.columns,1);for(let r=0;r<t.rows;++r)for(let s=0;s<t.columns;++s)e[s]*=t.get(r,s);return e}(this);case void 0:return function(t){let e=1;for(let r=0;r<t.rows;r++)for(let s=0;s<t.columns;s++)e*=t.get(r,s);return e}(this);default:throw new Error(`invalid option: ${t}`)}}mean(t){const e=this.sum(t);switch(t){case"row":for(let t=0;t<this.rows;t++)e[t]/=this.columns;return e;case"column":for(let t=0;t<this.columns;t++)e[t]/=this.rows;return e;case void 0:return e/this.size;default:throw new Error(`invalid option: ${t}`)}}variance(t,e={}){if("object"==typeof t&&(e=t,t=void 0),"object"!=typeof e)throw new TypeError("options must be an object");const{unbiased:r=!0,mean:s=this.mean(t)}=e;if("boolean"!=typeof r)throw new TypeError("unbiased must be a boolean");switch(t){case"row":if(!vt(s))throw new TypeError("mean must be an array");return function(t,e,r){const s=t.rows,n=t.columns,o=[];for(let i=0;i<s;i++){let s=0,h=0,a=0;for(let e=0;e<n;e++)a=t.get(i,e)-r[i],s+=a,h+=a*a;e?o.push((h-s*s/n)/(n-1)):o.push((h-s*s/n)/n)}return o}(this,r,s);case"column":if(!vt(s))throw new TypeError("mean must be an array");return function(t,e,r){const s=t.rows,n=t.columns,o=[];for(let i=0;i<n;i++){let n=0,h=0,a=0;for(let e=0;e<s;e++)a=t.get(e,i)-r[i],n+=a,h+=a*a;e?o.push((h-n*n/s)/(s-1)):o.push((h-n*n/s)/s)}return o}(this,r,s);case void 0:if("number"!=typeof s)throw new TypeError("mean must be a number");return function(t,e,r){const s=t.rows,n=t.columns,o=s*n;let i=0,h=0,a=0;for(let e=0;e<s;e++)for(let s=0;s<n;s++)a=t.get(e,s)-r,i+=a,h+=a*a;return e?(h-i*i/o)/(o-1):(h-i*i/o)/o}(this,r,s);default:throw new Error(`invalid option: ${t}`)}}standardDeviation(t,e){"object"==typeof t&&(e=t,t=void 0);const r=this.variance(t,e);if(void 0===t)return Math.sqrt(r);for(let t=0;t<r.length;t++)r[t]=Math.sqrt(r[t]);return r}center(t,e={}){if("object"==typeof t&&(e=t,t=void 0),"object"!=typeof e)throw new TypeError("options must be an object");const{center:r=this.mean(t)}=e;switch(t){case"row":if(!vt(r))throw new TypeError("center must be an array");return function(t,e){for(let r=0;r<t.rows;r++)for(let s=0;s<t.columns;s++)t.set(r,s,t.get(r,s)-e[r])}(this,r),this;case"column":if(!vt(r))throw new TypeError("center must be an array");return function(t,e){for(let r=0;r<t.rows;r++)for(let s=0;s<t.columns;s++)t.set(r,s,t.get(r,s)-e[s])}(this,r),this;case void 0:if("number"!=typeof r)throw new TypeError("center must be a number");return function(t,e){for(let r=0;r<t.rows;r++)for(let s=0;s<t.columns;s++)t.set(r,s,t.get(r,s)-e)}(this,r),this;default:throw new Error(`invalid option: ${t}`)}}scale(t,e={}){if("object"==typeof t&&(e=t,t=void 0),"object"!=typeof e)throw new TypeError("options must be an object");let r=e.scale;switch(t){case"row":if(void 0===r)r=function(t){const e=[];for(let r=0;r<t.rows;r++){let s=0;for(let e=0;e<t.columns;e++)s+=Math.pow(t.get(r,e),2)/(t.columns-1);e.push(Math.sqrt(s))}return e}(this);else if(!vt(r))throw new TypeError("scale must be an array");return function(t,e){for(let r=0;r<t.rows;r++)for(let s=0;s<t.columns;s++)t.set(r,s,t.get(r,s)/e[r])}(this,r),this;case"column":if(void 0===r)r=function(t){const e=[];for(let r=0;r<t.columns;r++){let s=0;for(let e=0;e<t.rows;e++)s+=Math.pow(t.get(e,r),2)/(t.rows-1);e.push(Math.sqrt(s))}return e}(this);else if(!vt(r))throw new TypeError("scale must be an array");return function(t,e){for(let r=0;r<t.rows;r++)for(let s=0;s<t.columns;s++)t.set(r,s,t.get(r,s)/e[s])}(this,r),this;case void 0:if(void 0===r)r=function(t){const e=t.size-1;let r=0;for(let s=0;s<t.columns;s++)for(let n=0;n<t.rows;n++)r+=Math.pow(t.get(n,s),2)/e;return Math.sqrt(r)}(this);else if("number"!=typeof r)throw new TypeError("scale must be a number");return function(t,e){for(let r=0;r<t.rows;r++)for(let s=0;s<t.columns;s++)t.set(r,s,t.get(r,s)/e)}(this,r),this;default:throw new Error(`invalid option: ${t}`)}}toString(t){return zt(this,t)}}function Wt(t,e){return t-e}Bt.prototype.klass="Matrix","undefined"!=typeof Symbol&&(Bt.prototype[Symbol.for("nodejs.util.inspect.custom")]=function(){return zt(this)}),Bt.random=Bt.rand,Bt.randomInt=Bt.randInt,Bt.diagonal=Bt.diag,Bt.prototype.diagonal=Bt.prototype.diag,Bt.identity=Bt.eye,Bt.prototype.negate=Bt.prototype.neg,Bt.prototype.tensorProduct=Bt.prototype.kroneckerProduct;class Ut extends Bt{constructor(t,e){if(super(),Ut.isMatrix(t))return t.clone();if(Number.isInteger(t)&&t>=0){if(this.data=[],!(Number.isInteger(e)&&e>=0))throw new TypeError("nColumns must be a positive integer");for(let r=0;r<t;r++)this.data.push(new Float64Array(e))}else{if(!vt(t))throw new TypeError("First argument must be a positive number or an array");{const r=t;if("number"!=typeof(e=(t=r.length)?r[0].length:0))throw new TypeError("Data must be a 2D array with at least one element");this.data=[];for(let s=0;s<t;s++){if(r[s].length!==e)throw new RangeError("Inconsistent array dimensions");if(!r[s].every((t=>"number"==typeof t)))throw new TypeError("Input data contains non-numeric values");this.data.push(Float64Array.from(r[s]))}}}this.rows=t,this.columns=e}set(t,e,r){return this.data[t][e]=r,this}get(t,e){return this.data[t][e]}removeRow(t){return Dt(this,t),this.data.splice(t,1),this.rows-=1,this}addRow(t,e){return void 0===e&&(e=t,t=this.rows),Dt(this,t,!0),e=Float64Array.from(Vt(this,e)),this.data.splice(t,0,e),this.rows+=1,this}removeColumn(t){Pt(this,t);for(let e=0;e<this.rows;e++){const r=new Float64Array(this.columns-1);for(let s=0;s<t;s++)r[s]=this.data[e][s];for(let s=t+1;s<this.columns;s++)r[s-1]=this.data[e][s];this.data[e]=r}return this.columns-=1,this}addColumn(t,e){void 0===e&&(e=t,t=this.columns),Pt(this,t,!0),e=Ot(this,e);for(let r=0;r<this.rows;r++){const s=new Float64Array(this.columns+1);let n=0;for(;n<t;n++)s[n]=this.data[r][n];for(s[n++]=e[r];n<this.columns+1;n++)s[n]=this.data[r][n-1];this.data[r]=s}return this.columns+=1,this}}!function(t,e){t.prototype.add=function(t){return"number"==typeof t?this.addS(t):this.addM(t)},t.prototype.addS=function(t){for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)+t);return this},t.prototype.addM=function(t){if(t=e.checkMatrix(t),this.rows!==t.rows||this.columns!==t.columns)throw new RangeError("Matrices dimensions must be equal");for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)+t.get(e,r));return this},t.add=function(t,r){return new e(t).add(r)},t.prototype.sub=function(t){return"number"==typeof t?this.subS(t):this.subM(t)},t.prototype.subS=function(t){for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)-t);return this},t.prototype.subM=function(t){if(t=e.checkMatrix(t),this.rows!==t.rows||this.columns!==t.columns)throw new RangeError("Matrices dimensions must be equal");for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)-t.get(e,r));return this},t.sub=function(t,r){return new e(t).sub(r)},t.prototype.subtract=t.prototype.sub,t.prototype.subtractS=t.prototype.subS,t.prototype.subtractM=t.prototype.subM,t.subtract=t.sub,t.prototype.mul=function(t){return"number"==typeof t?this.mulS(t):this.mulM(t)},t.prototype.mulS=function(t){for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)*t);return this},t.prototype.mulM=function(t){if(t=e.checkMatrix(t),this.rows!==t.rows||this.columns!==t.columns)throw new RangeError("Matrices dimensions must be equal");for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)*t.get(e,r));return this},t.mul=function(t,r){return new e(t).mul(r)},t.prototype.multiply=t.prototype.mul,t.prototype.multiplyS=t.prototype.mulS,t.prototype.multiplyM=t.prototype.mulM,t.multiply=t.mul,t.prototype.div=function(t){return"number"==typeof t?this.divS(t):this.divM(t)},t.prototype.divS=function(t){for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)/t);return this},t.prototype.divM=function(t){if(t=e.checkMatrix(t),this.rows!==t.rows||this.columns!==t.columns)throw new RangeError("Matrices dimensions must be equal");for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)/t.get(e,r));return this},t.div=function(t,r){return new e(t).div(r)},t.prototype.divide=t.prototype.div,t.prototype.divideS=t.prototype.divS,t.prototype.divideM=t.prototype.divM,t.divide=t.div,t.prototype.mod=function(t){return"number"==typeof t?this.modS(t):this.modM(t)},t.prototype.modS=function(t){for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)%t);return this},t.prototype.modM=function(t){if(t=e.checkMatrix(t),this.rows!==t.rows||this.columns!==t.columns)throw new RangeError("Matrices dimensions must be equal");for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)%t.get(e,r));return this},t.mod=function(t,r){return new e(t).mod(r)},t.prototype.modulus=t.prototype.mod,t.prototype.modulusS=t.prototype.modS,t.prototype.modulusM=t.prototype.modM,t.modulus=t.mod,t.prototype.and=function(t){return"number"==typeof t?this.andS(t):this.andM(t)},t.prototype.andS=function(t){for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)&t);return this},t.prototype.andM=function(t){if(t=e.checkMatrix(t),this.rows!==t.rows||this.columns!==t.columns)throw new RangeError("Matrices dimensions must be equal");for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)&t.get(e,r));return this},t.and=function(t,r){return new e(t).and(r)},t.prototype.or=function(t){return"number"==typeof t?this.orS(t):this.orM(t)},t.prototype.orS=function(t){for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)|t);return this},t.prototype.orM=function(t){if(t=e.checkMatrix(t),this.rows!==t.rows||this.columns!==t.columns)throw new RangeError("Matrices dimensions must be equal");for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)|t.get(e,r));return this},t.or=function(t,r){return new e(t).or(r)},t.prototype.xor=function(t){return"number"==typeof t?this.xorS(t):this.xorM(t)},t.prototype.xorS=function(t){for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)^t);return this},t.prototype.xorM=function(t){if(t=e.checkMatrix(t),this.rows!==t.rows||this.columns!==t.columns)throw new RangeError("Matrices dimensions must be equal");for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)^t.get(e,r));return this},t.xor=function(t,r){return new e(t).xor(r)},t.prototype.leftShift=function(t){return"number"==typeof t?this.leftShiftS(t):this.leftShiftM(t)},t.prototype.leftShiftS=function(t){for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)<<t);return this},t.prototype.leftShiftM=function(t){if(t=e.checkMatrix(t),this.rows!==t.rows||this.columns!==t.columns)throw new RangeError("Matrices dimensions must be equal");for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)<<t.get(e,r));return this},t.leftShift=function(t,r){return new e(t).leftShift(r)},t.prototype.signPropagatingRightShift=function(t){return"number"==typeof t?this.signPropagatingRightShiftS(t):this.signPropagatingRightShiftM(t)},t.prototype.signPropagatingRightShiftS=function(t){for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)>>t);return this},t.prototype.signPropagatingRightShiftM=function(t){if(t=e.checkMatrix(t),this.rows!==t.rows||this.columns!==t.columns)throw new RangeError("Matrices dimensions must be equal");for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)>>t.get(e,r));return this},t.signPropagatingRightShift=function(t,r){return new e(t).signPropagatingRightShift(r)},t.prototype.rightShift=function(t){return"number"==typeof t?this.rightShiftS(t):this.rightShiftM(t)},t.prototype.rightShiftS=function(t){for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)>>>t);return this},t.prototype.rightShiftM=function(t){if(t=e.checkMatrix(t),this.rows!==t.rows||this.columns!==t.columns)throw new RangeError("Matrices dimensions must be equal");for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,this.get(e,r)>>>t.get(e,r));return this},t.rightShift=function(t,r){return new e(t).rightShift(r)},t.prototype.zeroFillRightShift=t.prototype.rightShift,t.prototype.zeroFillRightShiftS=t.prototype.rightShiftS,t.prototype.zeroFillRightShiftM=t.prototype.rightShiftM,t.zeroFillRightShift=t.rightShift,t.prototype.not=function(){for(let t=0;t<this.rows;t++)for(let e=0;e<this.columns;e++)this.set(t,e,~this.get(t,e));return this},t.not=function(t){return new e(t).not()},t.prototype.abs=function(){for(let t=0;t<this.rows;t++)for(let e=0;e<this.columns;e++)this.set(t,e,Math.abs(this.get(t,e)));return this},t.abs=function(t){return new e(t).abs()},t.prototype.acos=function(){for(let t=0;t<this.rows;t++)for(let e=0;e<this.columns;e++)this.set(t,e,Math.acos(this.get(t,e)));return this},t.acos=function(t){return new e(t).acos()},t.prototype.acosh=function(){for(let t=0;t<this.rows;t++)for(let e=0;e<this.columns;e++)this.set(t,e,Math.acosh(this.get(t,e)));return this},t.acosh=function(t){return new e(t).acosh()},t.prototype.asin=function(){for(let t=0;t<this.rows;t++)for(let e=0;e<this.columns;e++)this.set(t,e,Math.asin(this.get(t,e)));return this},t.asin=function(t){return new e(t).asin()},t.prototype.asinh=function(){for(let t=0;t<this.rows;t++)for(let e=0;e<this.columns;e++)this.set(t,e,Math.asinh(this.get(t,e)));return this},t.asinh=function(t){return new e(t).asinh()},t.prototype.atan=function(){for(let t=0;t<this.rows;t++)for(let e=0;e<this.columns;e++)this.set(t,e,Math.atan(this.get(t,e)));return this},t.atan=function(t){return new e(t).atan()},t.prototype.atanh=function(){for(let t=0;t<this.rows;t++)for(let e=0;e<this.columns;e++)this.set(t,e,Math.atanh(this.get(t,e)));return this},t.atanh=function(t){return new e(t).atanh()},t.prototype.cbrt=function(){for(let t=0;t<this.rows;t++)for(let e=0;e<this.columns;e++)this.set(t,e,Math.cbrt(this.get(t,e)));return this},t.cbrt=function(t){return new e(t).cbrt()},t.prototype.ceil=function(){for(let t=0;t<this.rows;t++)for(let e=0;e<this.columns;e++)this.set(t,e,Math.ceil(this.get(t,e)));return this},t.ceil=function(t){return new e(t).ceil()},t.prototype.clz32=function(){for(let t=0;t<this.rows;t++)for(let e=0;e<this.columns;e++)this.set(t,e,Math.clz32(this.get(t,e)));return this},t.clz32=function(t){return new e(t).clz32()},t.prototype.cos=function(){for(let t=0;t<this.rows;t++)for(let e=0;e<this.columns;e++)this.set(t,e,Math.cos(this.get(t,e)));return this},t.cos=function(t){return new e(t).cos()},t.prototype.cosh=function(){for(let t=0;t<this.rows;t++)for(let e=0;e<this.columns;e++)this.set(t,e,Math.cosh(this.get(t,e)));return this},t.cosh=function(t){return new e(t).cosh()},t.prototype.exp=function(){for(let t=0;t<this.rows;t++)for(let e=0;e<this.columns;e++)this.set(t,e,Math.exp(this.get(t,e)));return this},t.exp=function(t){return new e(t).exp()},t.prototype.expm1=function(){for(let t=0;t<this.rows;t++)for(let e=0;e<this.columns;e++)this.set(t,e,Math.expm1(this.get(t,e)));return this},t.expm1=function(t){return new e(t).expm1()},t.prototype.floor=function(){for(let t=0;t<this.rows;t++)for(let e=0;e<this.columns;e++)this.set(t,e,Math.floor(this.get(t,e)));return this},t.floor=function(t){return new e(t).floor()},t.prototype.fround=function(){for(let t=0;t<this.rows;t++)for(let e=0;e<this.columns;e++)this.set(t,e,Math.fround(this.get(t,e)));return this},t.fround=function(t){return new e(t).fround()},t.prototype.log=function(){for(let t=0;t<this.rows;t++)for(let e=0;e<this.columns;e++)this.set(t,e,Math.log(this.get(t,e)));return this},t.log=function(t){return new e(t).log()},t.prototype.log1p=function(){for(let t=0;t<this.rows;t++)for(let e=0;e<this.columns;e++)this.set(t,e,Math.log1p(this.get(t,e)));return this},t.log1p=function(t){return new e(t).log1p()},t.prototype.log10=function(){for(let t=0;t<this.rows;t++)for(let e=0;e<this.columns;e++)this.set(t,e,Math.log10(this.get(t,e)));return this},t.log10=function(t){return new e(t).log10()},t.prototype.log2=function(){for(let t=0;t<this.rows;t++)for(let e=0;e<this.columns;e++)this.set(t,e,Math.log2(this.get(t,e)));return this},t.log2=function(t){return new e(t).log2()},t.prototype.round=function(){for(let t=0;t<this.rows;t++)for(let e=0;e<this.columns;e++)this.set(t,e,Math.round(this.get(t,e)));return this},t.round=function(t){return new e(t).round()},t.prototype.sign=function(){for(let t=0;t<this.rows;t++)for(let e=0;e<this.columns;e++)this.set(t,e,Math.sign(this.get(t,e)));return this},t.sign=function(t){return new e(t).sign()},t.prototype.sin=function(){for(let t=0;t<this.rows;t++)for(let e=0;e<this.columns;e++)this.set(t,e,Math.sin(this.get(t,e)));return this},t.sin=function(t){return new e(t).sin()},t.prototype.sinh=function(){for(let t=0;t<this.rows;t++)for(let e=0;e<this.columns;e++)this.set(t,e,Math.sinh(this.get(t,e)));return this},t.sinh=function(t){return new e(t).sinh()},t.prototype.sqrt=function(){for(let t=0;t<this.rows;t++)for(let e=0;e<this.columns;e++)this.set(t,e,Math.sqrt(this.get(t,e)));return this},t.sqrt=function(t){return new e(t).sqrt()},t.prototype.tan=function(){for(let t=0;t<this.rows;t++)for(let e=0;e<this.columns;e++)this.set(t,e,Math.tan(this.get(t,e)));return this},t.tan=function(t){return new e(t).tan()},t.prototype.tanh=function(){for(let t=0;t<this.rows;t++)for(let e=0;e<this.columns;e++)this.set(t,e,Math.tanh(this.get(t,e)));return this},t.tanh=function(t){return new e(t).tanh()},t.prototype.trunc=function(){for(let t=0;t<this.rows;t++)for(let e=0;e<this.columns;e++)this.set(t,e,Math.trunc(this.get(t,e)));return this},t.trunc=function(t){return new e(t).trunc()},t.pow=function(t,r){return new e(t).pow(r)},t.prototype.pow=function(t){return"number"==typeof t?this.powS(t):this.powM(t)},t.prototype.powS=function(t){for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,Math.pow(this.get(e,r),t));return this},t.prototype.powM=function(t){if(t=e.checkMatrix(t),this.rows!==t.rows||this.columns!==t.columns)throw new RangeError("Matrices dimensions must be equal");for(let e=0;e<this.rows;e++)for(let r=0;r<this.columns;r++)this.set(e,r,Math.pow(this.get(e,r),t.get(e,r)));return this}}(Bt,Ut);class Gt extends Bt{constructor(t){super(),this.data=t,this.rows=t.length,this.columns=t[0].length}set(t,e,r){return this.data[t][e]=r,this}get(t,e){return this.data[t][e]}}class Yt{constructor(t){let e,r,s,n,o,i,h,a,l,u=(t=Gt.checkMatrix(t)).clone(),c=u.rows,f=u.columns,m=new Float64Array(c),g=1;for(e=0;e<c;e++)m[e]=e;for(a=new Float64Array(c),r=0;r<f;r++){for(e=0;e<c;e++)a[e]=u.get(e,r);for(e=0;e<c;e++){for(l=Math.min(e,r),o=0,s=0;s<l;s++)o+=u.get(e,s)*a[s];a[e]-=o,u.set(e,r,a[e])}for(n=r,e=r+1;e<c;e++)Math.abs(a[e])>Math.abs(a[n])&&(n=e);if(n!==r){for(s=0;s<f;s++)i=u.get(n,s),u.set(n,s,u.get(r,s)),u.set(r,s,i);h=m[n],m[n]=m[r],m[r]=h,g=-g}if(r<c&&0!==u.get(r,r))for(e=r+1;e<c;e++)u.set(e,r,u.get(e,r)/u.get(r,r))}this.LU=u,this.pivotVector=m,this.pivotSign=g}isSingular(){let t=this.LU,e=t.columns;for(let r=0;r<e;r++)if(0===t.get(r,r))return!0;return!1}solve(t){t=Ut.checkMatrix(t);let e=this.LU;if(e.rows!==t.rows)throw new Error("Invalid matrix dimensions");if(this.isSingular())throw new Error("LU matrix is singular");let r,s,n,o=t.columns,i=t.subMatrixRow(this.pivotVector,0,o-1),h=e.columns;for(n=0;n<h;n++)for(r=n+1;r<h;r++)for(s=0;s<o;s++)i.set(r,s,i.get(r,s)-i.get(n,s)*e.get(r,n));for(n=h-1;n>=0;n--){for(s=0;s<o;s++)i.set(n,s,i.get(n,s)/e.get(n,n));for(r=0;r<n;r++)for(s=0;s<o;s++)i.set(r,s,i.get(r,s)-i.get(n,s)*e.get(r,n))}return i}get determinant(){let t=this.LU;if(!t.isSquare())throw new Error("Matrix must be square");let e=this.pivotSign,r=t.columns;for(let s=0;s<r;s++)e*=t.get(s,s);return e}get lowerTriangularMatrix(){let t=this.LU,e=t.rows,r=t.columns,s=new Ut(e,r);for(let n=0;n<e;n++)for(let e=0;e<r;e++)n>e?s.set(n,e,t.get(n,e)):n===e?s.set(n,e,1):s.set(n,e,0);return s}get upperTriangularMatrix(){let t=this.LU,e=t.rows,r=t.columns,s=new Ut(e,r);for(let n=0;n<e;n++)for(let e=0;e<r;e++)n<=e?s.set(n,e,t.get(n,e)):s.set(n,e,0);return s}get pivotPermutationVector(){return Array.from(this.pivotVector)}}function Kt(t,e){let r=0;return Math.abs(t)>Math.abs(e)?(r=e/t,Math.abs(t)*Math.sqrt(1+r*r)):0!==e?(r=t/e,Math.abs(e)*Math.sqrt(1+r*r)):0}class Ht{constructor(t){let e,r,s,n,o=(t=Gt.checkMatrix(t)).clone(),i=t.rows,h=t.columns,a=new Float64Array(h);for(s=0;s<h;s++){let t=0;for(e=s;e<i;e++)t=Kt(t,o.get(e,s));if(0!==t){for(o.get(s,s)<0&&(t=-t),e=s;e<i;e++)o.set(e,s,o.get(e,s)/t);for(o.set(s,s,o.get(s,s)+1),r=s+1;r<h;r++){for(n=0,e=s;e<i;e++)n+=o.get(e,s)*o.get(e,r);for(n=-n/o.get(s,s),e=s;e<i;e++)o.set(e,r,o.get(e,r)+n*o.get(e,s))}}a[s]=-t}this.QR=o,this.Rdiag=a}solve(t){t=Ut.checkMatrix(t);let e=this.QR,r=e.rows;if(t.rows!==r)throw new Error("Matrix row dimensions must agree");if(!this.isFullRank())throw new Error("Matrix is rank deficient");let s,n,o,i,h=t.columns,a=t.clone(),l=e.columns;for(o=0;o<l;o++)for(n=0;n<h;n++){for(i=0,s=o;s<r;s++)i+=e.get(s,o)*a.get(s,n);for(i=-i/e.get(o,o),s=o;s<r;s++)a.set(s,n,a.get(s,n)+i*e.get(s,o))}for(o=l-1;o>=0;o--){for(n=0;n<h;n++)a.set(o,n,a.get(o,n)/this.Rdiag[o]);for(s=0;s<o;s++)for(n=0;n<h;n++)a.set(s,n,a.get(s,n)-a.get(o,n)*e.get(s,o))}return a.subMatrix(0,l-1,0,h-1)}isFullRank(){let t=this.QR.columns;for(let e=0;e<t;e++)if(0===this.Rdiag[e])return!1;return!0}get upperTriangularMatrix(){let t,e,r=this.QR,s=r.columns,n=new Ut(s,s);for(t=0;t<s;t++)for(e=0;e<s;e++)t<e?n.set(t,e,r.get(t,e)):t===e?n.set(t,e,this.Rdiag[t]):n.set(t,e,0);return n}get orthogonalMatrix(){let t,e,r,s,n=this.QR,o=n.rows,i=n.columns,h=new Ut(o,i);for(r=i-1;r>=0;r--){for(t=0;t<o;t++)h.set(t,r,0);for(h.set(r,r,1),e=r;e<i;e++)if(0!==n.get(r,r)){for(s=0,t=r;t<o;t++)s+=n.get(t,r)*h.get(t,e);for(s=-s/n.get(r,r),t=r;t<o;t++)h.set(t,e,h.get(t,e)+s*n.get(t,r))}}return h}}class Jt{constructor(t,e={}){if((t=Gt.checkMatrix(t)).isEmpty())throw new Error("Matrix must be non-empty");let r=t.rows,s=t.columns;const{computeLeftSingularVectors:n=!0,computeRightSingularVectors:o=!0,autoTranspose:i=!1}=e;let h,a=Boolean(n),l=Boolean(o),u=!1;if(r<s)if(i){h=t.transpose(),r=h.rows,s=h.columns,u=!0;let e=a;a=l,l=e}else h=t.clone(),console.warn("Computing SVD on a matrix with more columns than rows. Consider enabling autoTranspose");else h=t.clone();let c=Math.min(r,s),f=Math.min(r+1,s),m=new Float64Array(f),g=new Ut(r,c),p=new Ut(s,s),d=new Float64Array(s),w=new Float64Array(r),y=new Float64Array(f);for(let t=0;t<f;t++)y[t]=t;let b=Math.min(r-1,s),M=Math.max(0,Math.min(s-2,r)),x=Math.max(b,M);for(let t=0;t<x;t++){if(t<b){m[t]=0;for(let e=t;e<r;e++)m[t]=Kt(m[t],h.get(e,t));if(0!==m[t]){h.get(t,t)<0&&(m[t]=-m[t]);for(let e=t;e<r;e++)h.set(e,t,h.get(e,t)/m[t]);h.set(t,t,h.get(t,t)+1)}m[t]=-m[t]}for(let e=t+1;e<s;e++){if(t<b&&0!==m[t]){let s=0;for(let n=t;n<r;n++)s+=h.get(n,t)*h.get(n,e);s=-s/h.get(t,t);for(let n=t;n<r;n++)h.set(n,e,h.get(n,e)+s*h.get(n,t))}d[e]=h.get(t,e)}if(a&&t<b)for(let e=t;e<r;e++)g.set(e,t,h.get(e,t));if(t<M){d[t]=0;for(let e=t+1;e<s;e++)d[t]=Kt(d[t],d[e]);if(0!==d[t]){d[t+1]<0&&(d[t]=0-d[t]);for(let e=t+1;e<s;e++)d[e]/=d[t];d[t+1]+=1}if(d[t]=-d[t],t+1<r&&0!==d[t]){for(let e=t+1;e<r;e++)w[e]=0;for(let e=t+1;e<r;e++)for(let r=t+1;r<s;r++)w[e]+=d[r]*h.get(e,r);for(let e=t+1;e<s;e++){let s=-d[e]/d[t+1];for(let n=t+1;n<r;n++)h.set(n,e,h.get(n,e)+s*w[n])}}if(l)for(let e=t+1;e<s;e++)p.set(e,t,d[e])}}let E=Math.min(s,r+1);if(b<s&&(m[b]=h.get(b,b)),r<E&&(m[E-1]=0),M+1<E&&(d[M]=h.get(M,E-1)),d[E-1]=0,a){for(let t=b;t<c;t++){for(let e=0;e<r;e++)g.set(e,t,0);g.set(t,t,1)}for(let t=b-1;t>=0;t--)if(0!==m[t]){for(let e=t+1;e<c;e++){let s=0;for(let n=t;n<r;n++)s+=g.get(n,t)*g.get(n,e);s=-s/g.get(t,t);for(let n=t;n<r;n++)g.set(n,e,g.get(n,e)+s*g.get(n,t))}for(let e=t;e<r;e++)g.set(e,t,-g.get(e,t));g.set(t,t,1+g.get(t,t));for(let e=0;e<t-1;e++)g.set(e,t,0)}else{for(let e=0;e<r;e++)g.set(e,t,0);g.set(t,t,1)}}if(l)for(let t=s-1;t>=0;t--){if(t<M&&0!==d[t])for(let e=t+1;e<s;e++){let r=0;for(let n=t+1;n<s;n++)r+=p.get(n,t)*p.get(n,e);r=-r/p.get(t+1,t);for(let n=t+1;n<s;n++)p.set(n,e,p.get(n,e)+r*p.get(n,t))}for(let e=0;e<s;e++)p.set(e,t,0);p.set(t,t,1)}let S=E-1,v=0,N=Number.EPSILON;for(;E>0;){let t,e;for(t=E-2;t>=-1&&-1!==t;t--){const e=Number.MIN_VALUE+N*Math.abs(m[t]+Math.abs(m[t+1]));if(Math.abs(d[t])<=e||Number.isNaN(d[t])){d[t]=0;break}}if(t===E-2)e=4;else{let r;for(r=E-1;r>=t&&r!==t;r--){let e=(r!==E?Math.abs(d[r]):0)+(r!==t+1?Math.abs(d[r-1]):0);if(Math.abs(m[r])<=N*e){m[r]=0;break}}r===t?e=3:r===E-1?e=1:(e=2,t=r)}switch(t++,e){case 1:{let e=d[E-2];d[E-2]=0;for(let r=E-2;r>=t;r--){let n=Kt(m[r],e),o=m[r]/n,i=e/n;if(m[r]=n,r!==t&&(e=-i*d[r-1],d[r-1]=o*d[r-1]),l)for(let t=0;t<s;t++)n=o*p.get(t,r)+i*p.get(t,E-1),p.set(t,E-1,-i*p.get(t,r)+o*p.get(t,E-1)),p.set(t,r,n)}break}case 2:{let e=d[t-1];d[t-1]=0;for(let s=t;s<E;s++){let n=Kt(m[s],e),o=m[s]/n,i=e/n;if(m[s]=n,e=-i*d[s],d[s]=o*d[s],a)for(let e=0;e<r;e++)n=o*g.get(e,s)+i*g.get(e,t-1),g.set(e,t-1,-i*g.get(e,s)+o*g.get(e,t-1)),g.set(e,s,n)}break}case 3:{const e=Math.max(Math.abs(m[E-1]),Math.abs(m[E-2]),Math.abs(d[E-2]),Math.abs(m[t]),Math.abs(d[t])),n=m[E-1]/e,o=m[E-2]/e,i=d[E-2]/e,h=m[t]/e,u=d[t]/e,c=((o+n)*(o-n)+i*i)/2,f=n*i*(n*i);let w=0;0===c&&0===f||(w=c<0?0-Math.sqrt(c*c+f):Math.sqrt(c*c+f),w=f/(c+w));let y=(h+n)*(h-n)+w,b=h*u;for(let e=t;e<E-1;e++){let n=Kt(y,b);0===n&&(n=Number.MIN_VALUE);let o=y/n,i=b/n;if(e!==t&&(d[e-1]=n),y=o*m[e]+i*d[e],d[e]=o*d[e]-i*m[e],b=i*m[e+1],m[e+1]=o*m[e+1],l)for(let t=0;t<s;t++)n=o*p.get(t,e)+i*p.get(t,e+1),p.set(t,e+1,-i*p.get(t,e)+o*p.get(t,e+1)),p.set(t,e,n);if(n=Kt(y,b),0===n&&(n=Number.MIN_VALUE),o=y/n,i=b/n,m[e]=n,y=o*d[e]+i*m[e+1],m[e+1]=-i*d[e]+o*m[e+1],b=i*d[e+1],d[e+1]=o*d[e+1],a&&e<r-1)for(let t=0;t<r;t++)n=o*g.get(t,e)+i*g.get(t,e+1),g.set(t,e+1,-i*g.get(t,e)+o*g.get(t,e+1)),g.set(t,e,n)}d[E-2]=y,v+=1;break}case 4:if(m[t]<=0&&(m[t]=m[t]<0?-m[t]:0,l))for(let e=0;e<=S;e++)p.set(e,t,-p.get(e,t));for(;t<S&&!(m[t]>=m[t+1]);){let e=m[t];if(m[t]=m[t+1],m[t+1]=e,l&&t<s-1)for(let r=0;r<s;r++)e=p.get(r,t+1),p.set(r,t+1,p.get(r,t)),p.set(r,t,e);if(a&&t<r-1)for(let s=0;s<r;s++)e=g.get(s,t+1),g.set(s,t+1,g.get(s,t)),g.set(s,t,e);t++}v=0,E--}}if(u){let t=p;p=g,g=t}this.m=r,this.n=s,this.s=m,this.U=g,this.V=p}solve(t){let e=t,r=this.threshold,s=this.s.length,n=Ut.zeros(s,s);for(let t=0;t<s;t++)Math.abs(this.s[t])<=r?n.set(t,t,0):n.set(t,t,1/this.s[t]);let o=this.U,i=this.rightSingularVectors,h=i.mmul(n),a=i.rows,l=o.rows,u=Ut.zeros(a,l);for(let t=0;t<a;t++)for(let e=0;e<l;e++){let r=0;for(let n=0;n<s;n++)r+=h.get(t,n)*o.get(e,n);u.set(t,e,r)}return u.mmul(e)}solveForDiagonal(t){return this.solve(Ut.diag(t))}inverse(){let t=this.V,e=this.threshold,r=t.rows,s=t.columns,n=new Ut(r,this.s.length);for(let o=0;o<r;o++)for(let r=0;r<s;r++)Math.abs(this.s[r])>e&&n.set(o,r,t.get(o,r)/this.s[r]);let o=this.U,i=o.rows,h=o.columns,a=new Ut(r,i);for(let t=0;t<r;t++)for(let e=0;e<i;e++){let r=0;for(let s=0;s<h;s++)r+=n.get(t,s)*o.get(e,s);a.set(t,e,r)}return a}get condition(){return this.s[0]/this.s[Math.min(this.m,this.n)-1]}get norm2(){return this.s[0]}get rank(){let t=Math.max(this.m,this.n)*this.s[0]*Number.EPSILON,e=0,r=this.s;for(let s=0,n=r.length;s<n;s++)r[s]>t&&e++;return e}get diagonal(){return Array.from(this.s)}get threshold(){return Number.EPSILON/2*Math.max(this.m,this.n)*this.s[0]}get leftSingularVectors(){return this.U}get rightSingularVectors(){return this.V}get diagonalMatrix(){return Ut.diag(this.s)}}function Xt(t,e,r,s,n){let o=r*s*s,i=Ut.eye(e.length,e.length,o);const h=n(e);let a=new Float64Array(t.x.length);for(let e=0;e<t.x.length;e++)a[e]=h(t.x[e]);let l=function(t,e,r,s,n){const o=r.length,i=t.x.length;let h=new Array(o);for(let a=0;a<o;a++){h[a]=new Array(i);let o=r.slice();o[a]+=s;let l=n(o);for(let r=0;r<i;r++)h[a][r]=e[r]-l(t.x[r])}return new Ut(h)}(t,a,e,s,n),u=function(t,e){const r=t.x.length;let s=new Array(r);for(let n=0;n<r;n++)s[n]=[t.y[n]-e[n]];return new Ut(s)}(t,a),c=function(t,e=!1){return t=Gt.checkMatrix(t),e?new Jt(t).inverse():function(t,e,r=!1){return t=Gt.checkMatrix(t),e=Gt.checkMatrix(e),r?new Jt(t).solve(e):t.isSquare()?new Yt(t).solve(e):new Ht(t).solve(e)}(t,Ut.eye(t.rows))}(i.add(l.mmul(l.transpose())));return(e=(e=new Ut([e])).sub(c.mmul(l).mmul(u).mul(s).transpose())).to1DArray()}const Qt=1e-5,Zt=.001;class te{get neighbors(){return this.nNeighbors}constructor(t={}){this.learningRate=1,this.localConnectivity=1,this.minDist=.1,this.nComponents=2,this.nEpochs=0,this.nNeighbors=15,this.negativeSampleRate=5,this.random=Math.random,this.repulsionStrength=1,this.setOpMixRatio=1,this.spread=1,this.transformQueueSize=4,this.targetMetric="categorical",this.targetWeight=.5,this.targetNNeighbors=this.nNeighbors,this.distanceFn=ee,this.isInitialized=!1,this.rpForest=[],this.embedding=[],this.optimizationState=new re;const e=e=>{void 0!==t[e]&&(this[e]=t[e])};e("distanceFn"),e("learningRate"),e("localConnectivity"),e("minDist"),e("nComponents"),e("nEpochs"),e("nNeighbors"),e("negativeSampleRate"),e("random"),e("repulsionStrength"),e("setOpMixRatio"),e("spread"),e("transformQueueSize")}fit(t){return this.initializeFit(t),this.optimizeLayout(),this.embedding}async fitAsync(t,e=(()=>!0)){return this.initializeFit(t),await this.optimizeLayoutAsync(e),this.embedding}setSupervisedProjection(t,e={}){this.Y=t,this.targetMetric=e.targetMetric||this.targetMetric,this.targetWeight=e.targetWeight||this.targetWeight,this.targetNNeighbors=e.targetNNeighbors||this.targetNNeighbors}setPrecomputedKNN(t,e){this.knnIndices=t,this.knnDistances=e}initializeFit(t){if(t.length<=this.nNeighbors)throw new Error(`Not enough data points (${t.length}) to create nNeighbors: ${this.nNeighbors}.  Add more data points or adjust the configuration.`);if(this.X===t&&this.isInitialized)return this.getNEpochs();if(this.X=t,!this.knnIndices&&!this.knnDistances){const e=this.nearestNeighbors(t);this.knnIndices=e.knnIndices,this.knnDistances=e.knnDistances}this.graph=this.fuzzySimplicialSet(t,this.nNeighbors,this.setOpMixRatio),this.makeSearchFns(),this.searchGraph=this.makeSearchGraph(t),this.processGraphForSupervisedProjection();const{head:e,tail:r,epochsPerSample:s}=this.initializeSimplicialSetEmbedding();return this.optimizationState.head=e,this.optimizationState.tail=r,this.optimizationState.epochsPerSample=s,this.initializeOptimization(),this.prepareForOptimizationLoop(),this.isInitialized=!0,this.getNEpochs()}makeSearchFns(){const{initFromTree:t,initFromRandom:e}=(r=this.distanceFn,{initFromRandom:function(t,e,s,n,o){for(let i=0;i<s.length;i++){const h=U(t,e.length,o);for(let t=0;t<h.length;t++)h[t]<0||H(n,i,r(e[h[t]],s[i]),h[t],1)}},initFromTree:function(t,e,s,n,o){for(let i=0;i<s.length;i++){const h=bt(s[i],t,o);for(let t=0;t<h.length;t++){if(h[t]<0)return;H(n,i,r(e[h[t]],s[i]),h[t],1)}}}});var r;this.initFromTree=t,this.initFromRandom=e,this.search=function(t){return function(e,r,s,n){const{indices:o,indptr:i}=ct(r);for(let r=0;r<n.length;r++){const h=new Set(s[0][r]);for(;;){const a=tt(s,r);if(-1===a)break;const l=o.slice(i[a],i[a+1]);for(const o of l)o===a||-1===o||h.has(o)||(J(s,r,t(e[o],n[r]),o,1),h.add(o))}}return s}}(this.distanceFn)}makeSearchGraph(t){const e=this.knnIndices,r=this.knnDistances,s=[t.length,t.length],n=new et([],[],[],s);for(let t=0;t<e.length;t++){const s=e[t],o=r[t];for(let e=0;e<s.length;e++){const r=s[e],i=o[e];i>0&&n.set(t,r,i)}}return ut(n,rt(n),((t,e)=>t>e?t:e))}transform(t){const e=this.X;if(void 0===e||0===e.length)throw new Error("No data has been fit.");let r=Math.floor(this.nNeighbors*this.transformQueueSize);r=Math.min(e.length,r);const s=function(t,e,r,s,n,o,i){const h=Y(r.length,s);if(n(s,e,r,h,i),t)for(let s of t)o(s,e,r,h,i);return h}(this.rpForest,e,t,r,this.initFromRandom,this.initFromTree,this.random),n=this.search(e,this.searchGraph,s,t);let{indices:o,weights:i}=Q(n);o=o.map((t=>t.slice(0,this.nNeighbors))),i=i.map((t=>t.slice(0,this.nNeighbors)));const h=Math.max(0,this.localConnectivity-1),{sigmas:a,rhos:l}=this.smoothKNNDistance(i,this.nNeighbors,h),{rows:u,cols:c,vals:f}=this.computeMembershipStrengths(o,i,a,l),m=[t.length,e.length];let g=new et(u,c,f,m);const p=ct(at(g,"l1")),d=t.length,w=function(t,e,r){const s=$(t.length).map((t=>$(r[0].length)));for(let n=0;n<t.length;n++)for(let o=0;o<t[0].length;o++)for(let i=0;i<r[0].length;i++){const h=t[n][o];s[n][i]+=e[n][o]*r[h][i]}return s}(G(p.indices,d,this.nNeighbors),G(p.values,d,this.nNeighbors),this.embedding),y=this.nEpochs?this.nEpochs/3:g.nRows<=1e4?100:30,b=g.getValues().reduce(((t,e)=>e>t?e:t),0);g=g.map((t=>t<b/y?0:t)),g=ht(g);const M=this.makeEpochsPerSample(g.getValues(),y),x=g.getRows(),E=g.getCols();return this.assignOptimizationStateParameters({headEmbedding:w,tailEmbedding:this.embedding,head:x,tail:E,currentEpoch:0,nEpochs:y,nVertices:g.getDims()[1],epochsPerSample:M}),this.prepareForOptimizationLoop(),this.optimizeLayout()}processGraphForSupervisedProjection(){const{Y:t,X:e}=this;if(t){if(t.length!==e.length)throw new Error("Length of X and y must be equal");if("categorical"===this.targetMetric){const e=this.targetWeight<1?1/(1-this.targetWeight)*2.5:1e12;this.graph=this.categoricalSimplicialSetIntersection(this.graph,t,e)}}}step(){const{currentEpoch:t}=this.optimizationState;return t<this.getNEpochs()&&this.optimizeLayoutStep(t),this.optimizationState.currentEpoch}getEmbedding(){return this.embedding}nearestNeighbors(t){const{distanceFn:e,nNeighbors:r}=this,s=function(t,e){return function(r,s,n,o=10,i=50,h=.001,a=.5,l=!0){const u=r.length,c=Y(r.length,n);for(let s=0;s<r.length;s++){const o=K(n,r.length,e);for(let e=0;e<o.length;e++){const n=t(r[s],r[o[e]]);H(c,s,n,o[e],1),H(c,o[e],n,s,1)}}if(l)for(let e=0;e<s.length;e++)for(let n=0;n<s[e].length&&!(s[e][n]<0);n++)for(let o=n+1;o<s[e].length&&!(s[e][o]<0);o++){const i=t(r[s[e][n]],r[s[e][o]]);H(c,s[e][n],i,s[e][o],1),H(c,s[e][o],i,s[e][n],1)}for(let s=0;s<o;s++){const s=X(c,u,n,i,e);let o=0;for(let n=0;n<u;n++)for(let h=0;h<i;h++){let l=Math.floor(s[0][n][h]);if(!(l<0||O(e)<a))for(let e=0;e<i;e++){const i=Math.floor(s[0][n][e]),a=s[2][n][h],u=s[2][n][e];if(i<0||!a&&!u)continue;const f=t(r[l],r[i]);o+=H(c,l,f,i,1),o+=H(c,i,f,l,1)}}if(o<=h*n*r.length)break}return Q(c)}}(e,this.random),n=5+Math.floor(.5==(o=t.length**.5/20)?0:Math.round(o));var o;const i=Math.max(5,Math.floor(Math.round((t=>Math.log(t)/Math.log(2))(t.length))));this.rpForest=mt(t,r,n,this.random);const h=function(t){if(t.length>0){const e=[];for(let r of t)e.push(...r.indices);return e}return[[-1]]}(this.rpForest),{indices:a,weights:l}=s(t,h,r,i);return{knnIndices:a,knnDistances:l}}fuzzySimplicialSet(t,e,r=1){const{knnIndices:s=[],knnDistances:n=[],localConnectivity:o}=this,{sigmas:i,rhos:h}=this.smoothKNNDistance(n,e,o),{rows:a,cols:l,vals:u}=this.computeMembershipStrengths(s,n,i,h),c=[t.length,t.length],f=new et(a,l,u,c),m=rt(f),g=st(f,m),p=ot(nt(f,m),g);return nt(it(p,r),it(g,1-r))}categoricalSimplicialSetIntersection(t,e,r,s=1){let n=function(t,e,r=1,s=5){return t.map(((t,n,o)=>-1===e[n]||-1===e[o]?t*Math.exp(-r):e[n]!==e[o]?t*Math.exp(-s):t))}(t,e,s,r);return n=ht(n),function(t){const e=rt(t=at(t,"max"));return ht(t=nt(t,ot(e,st(e,t))))}(n)}smoothKNNDistance(t,e,r=1,s=64,n=1){const o=Math.log(e)/Math.log(2)*n,i=$(t.length),h=$(t.length);for(let e=0;e<t.length;e++){let n=0,a=1/0,l=1;const u=t[e],c=u.filter((t=>t>0));if(c.length>=r){let t=Math.floor(r),s=r-t;t>0?(i[e]=c[t-1],s>Qt&&(i[e]+=s*(c[t]-c[t-1]))):i[e]=s*c[0]}else c.length>0&&(i[e]=W(c));for(let r=0;r<s;r++){let r=0;for(let s=1;s<t[e].length;s++){const n=t[e][s]-i[e];r+=n>0?Math.exp(-n/l):1}if(Math.abs(r-o)<Qt)break;r>o?(a=l,l=(n+a)/2):(n=l,a===1/0?l*=2:l=(n+a)/2)}if(h[e]=l,i[e]>0){const t=B(u);h[e]<Zt*t&&(h[e]=Zt*t)}else{const r=B(t.map(B));h[e]<Zt*r&&(h[e]=Zt*r)}}return{sigmas:h,rhos:i}}computeMembershipStrengths(t,e,r,s){const n=t.length,o=t[0].length,i=$(n*o),h=$(n*o),a=$(n*o);for(let l=0;l<n;l++)for(let n=0;n<o;n++){let u=0;-1!==t[l][n]&&(u=t[l][n]===l?0:e[l][n]-s[l]<=0?1:Math.exp(-(e[l][n]-s[l])/r[l]),i[l*o+n]=l,h[l*o+n]=t[l][n],a[l*o+n]=u)}return{rows:i,cols:h,vals:a}}initializeSimplicialSetEmbedding(){const t=this.getNEpochs(),{nComponents:e}=this,r=this.graph.getValues();let s=0;for(let t=0;t<r.length;t++){const e=r[t];s<r[t]&&(s=e)}const n=this.graph.map((e=>e<s/t?0:e));this.embedding=$(n.nRows).map((()=>$(e).map((()=>20*O(this.random)-10))));const o=[],i=[],h=[],a=n.getAll();for(let t=0;t<a.length;t++){const e=a[t];e.value&&(o.push(e.value),h.push(e.row),i.push(e.col))}return{head:i,tail:h,epochsPerSample:this.makeEpochsPerSample(o,t)}}makeEpochsPerSample(t,e){const r=L(t.length,-1),s=W(t),n=t.map((t=>t/s*e));return n.forEach(((t,s)=>{t>0&&(r[s]=e/n[s])})),r}assignOptimizationStateParameters(t){Object.assign(this.optimizationState,t)}prepareForOptimizationLoop(){const{repulsionStrength:t,learningRate:e,negativeSampleRate:r}=this,{epochsPerSample:s,headEmbedding:n,tailEmbedding:o}=this.optimizationState,i=n[0].length,h=n.length===o.length,a=s.map((t=>t/r)),l=[...a],u=[...s];this.assignOptimizationStateParameters({epochOfNextSample:u,epochOfNextNegativeSample:l,epochsPerNegativeSample:a,moveOther:h,initialAlpha:e,alpha:e,gamma:t,dim:i})}initializeOptimization(){const t=this.embedding,e=this.embedding,{head:r,tail:s,epochsPerSample:n}=this.optimizationState,o=this.getNEpochs(),i=this.graph.nCols,{a:h,b:a}=function(t,e){const r=function(t,e,r){return j(300).map(((t,r)=>0+r*((e-0)/299)))}(0,3*t).map((t=>t<e?1:t)),s=$(r.length).map(((s,n)=>r[n]>=e?Math.exp(-(r[n]-e)/t):s)),n={x:r,y:s},{parameterValues:o}=function(t,e,r={}){let{maxIterations:s=100,gradientDifference:n=.1,damping:o=0,errorTolerance:i=.01,minValues:h,maxValues:a,initialValues:l}=r;if(o<=0)throw new Error("The damping option must be a positive number");if(!t.x||!t.y)throw new Error("The data parameter must have x and y elements");if(!xt(t.x)||t.x.length<2||!xt(t.y)||t.y.length<2)throw new Error("The data parameter elements must be an array with more than 2 points");if(t.x.length!==t.y.length)throw new Error("The data parameter elements must have the same size");let u=l||new Array(e.length).fill(1),c=u.length;if(a=a||new Array(c).fill(Number.MAX_SAFE_INTEGER),h=h||new Array(c).fill(Number.MIN_SAFE_INTEGER),a.length!==h.length)throw new Error("minValues and maxValues must be the same size");if(!xt(u))throw new Error("initialValues must be an array");let f,m=Et(t,u,e),g=m<=i;for(f=0;f<s&&!g;f++){u=Xt(t,u,o,n,e);for(let t=0;t<c;t++)u[t]=Math.min(Math.max(h[t],u[t]),a[t]);if(m=Et(t,u,e),isNaN(m))break;g=m<=i}return{parameterValues:u,parameterError:m,iterations:f}}(n,(([t,e])=>r=>1/(1+t*r**(2*e))),{damping:1.5,initialValues:[.5,.5],gradientDifference:.1,maxIterations:100,errorTolerance:.01}),[i,h]=o;return{a:i,b:h}}(this.spread,this.minDist);this.assignOptimizationStateParameters({headEmbedding:t,tailEmbedding:e,head:r,tail:s,epochsPerSample:n,a:h,b:a,nEpochs:o,nVertices:i})}optimizeLayoutStep(t){const{optimizationState:e}=this,{head:r,tail:s,headEmbedding:n,tailEmbedding:o,epochsPerSample:i,epochOfNextSample:h,epochOfNextNegativeSample:a,epochsPerNegativeSample:l,moveOther:u,initialAlpha:c,alpha:f,gamma:m,a:g,b:p,dim:d,nEpochs:w,nVertices:y}=e;for(let e=0;e<i.length;e++){if(h[e]>t)continue;const c=r[e],w=s[e],b=n[c],M=o[w],x=ne(b,M);let E=0;x>0&&(E=-2*g*p*Math.pow(x,p-1),E/=g*Math.pow(x,p)+1);for(let t=0;t<d;t++){const e=se(E*(b[t]-M[t]),4);b[t]+=e*f,u&&(M[t]+=-e*f)}h[e]+=i[e];const S=Math.floor((t-a[e])/l[e]);for(let t=0;t<S;t++){const t=V(y,this.random),e=o[t],r=ne(b,e);let s=0;if(r>0)s=2*m*p,s/=(.001+r)*(g*Math.pow(r,p)+1);else if(c===t)continue;for(let t=0;t<d;t++){let r=4;s>0&&(r=se(s*(b[t]-e[t]),4)),b[t]+=r*f}}a[e]+=S*l[e]}return e.alpha=c*(1-t/w),e.currentEpoch+=1,n}optimizeLayoutAsync(t=(()=>!0)){return new Promise(((e,r)=>{const s=async()=>{try{const{nEpochs:r,currentEpoch:n}=this.optimizationState;this.embedding=this.optimizeLayoutStep(n);const o=this.optimizationState.currentEpoch,i=!1===t(o),h=o===r;if(i||h)return e(h);setTimeout((()=>s()),0)}catch(t){r(t)}};setTimeout((()=>s()),0)}))}optimizeLayout(t=(()=>!0)){let e=!1,r=[];for(;!e;){const{nEpochs:s,currentEpoch:n}=this.optimizationState;r=this.optimizeLayoutStep(n);const o=this.optimizationState.currentEpoch,i=!1===t(o);e=o===s||i}return r}getNEpochs(){const t=this.graph;if(this.nEpochs>0)return this.nEpochs;if(!t)return 200;const e=t.nRows;return e<=2500?500:e<=5e3?400:e<=7500?300:200}}function ee(t,e){return Math.abs(t-e)}class re{constructor(){this.currentEpoch=0,this.headEmbedding=[],this.tailEmbedding=[],this.head=[],this.tail=[],this.epochsPerSample=[],this.epochOfNextSample=[],this.epochOfNextNegativeSample=[],this.epochsPerNegativeSample=[],this.moveOther=!0,this.initialAlpha=1,this.alpha=1,this.gamma=1,this.a=1.5769434603113077,this.b=.8950608779109733,this.dim=2,this.nEpochs=500,this.nVertices=0}}function se(t,e){return t>e?e:t<-e?-e:t}function ne(t,e){let r=0;for(let s=0;s<t.length;s++)r+=Math.pow(t[s]-e[s],2);return r}var oe,ie=r(6814);class he{get data(){return this._data}get size(){return this._size}constructor(t,e){if(null==e){if(null==t)throw new Error("Arguments error: data or size is required.");if(this._data=t,this._size=(1+Math.sqrt(1+8*this._data.length))/2,this._size!=Math.floor(this._size))throw new Error(`Invalid data length ${this._data.length} leads to non integer size ${this._size}`)}else{this._size=e;const r=e*(e-1)/2;if(t){if(t.length!=r)throw new Error(`Invalid data length. Observations size ${e} requires data length ${r}.`);this._data=t}else this._data=new Float32Array(r)}}_linearizeIJ(t,e){if(!(t<e))throw new Error("i must be less than j");return this._size*t+e-Math.floor((t+2)*(t+1)/2)}get(t,e){return t==e?0:t<e?this._data[this._linearizeIJ(t,e)]:this._data[this._linearizeIJ(e,t)]}set(t,e,r){this._data[this._linearizeIJ(t,e)]=r}static calc(t,e){const r=t.length,s=new he(void 0,r);for(let n=0;n<r;n++)for(let o=n+1;o<r;o++)s.set(n,o,(0,ie.k)(t[n])||(0,ie.k)(t[o])?1:e(t[n],t[o]));return s}square(){for(let t=0;t<this._data.length;t++)this._data[t]=this._data[t]**2}add(t){if(this._size!==t._size)throw new Error(`Matrices must have the same size. This size: ${this._size}, other size: ${t._size}`);for(let e=0;e<this._data.length;e++)this._data[e]+=t._data[e]}sqrt(){for(let t=0;t<this._data.length;t++)this._data[t]=Math.sqrt(this._data[t])}normalize(){let t=0,e=this._data[0];for(let r=0;r<this._data.length;r++)this._data[r]<t&&(t=this._data[r]),this._data[r]>e&&(e=this._data[r]);const r=e-t;for(let s=0;s<this._data.length;s++)this._data[s]=0===r?this._data[s]-t:(this._data[s]-t)/(e-t)}}class ae{constructor(){this._workerCount=Math.max(navigator.hardwareConcurrency-2,1)}async calc(t,e,s,n={}){const o=t.length*(t.length-1)/2,i=Math.floor(o/this._workerCount),h=t.length>2e4?await this.getMinimalThreshold(t,e,n):0;s<h&&(console.log(`using threshold ${h}`),s=h),n.threshold=s;const a=new Array(this._workerCount),l=new Array(this._workerCount).fill(null).map((()=>new Worker(new URL(r.p+r.u(381),r.b))));for(let r=0;r<this._workerCount;r++)a[r]=new Promise(((h,a)=>{const u=r*i,c=r===this._workerCount-1?o:(r+1)*i;c<=u&&h({i:new Int32Array(0),j:new Int32Array(0),distance:new Float32Array(0),idx:r}),l[r].postMessage({values:t,startIdx:u,endIdx:c,threshold:s,fnName:e,opts:n}),l[r].onmessage=({data:{error:t,i:e,j:s,distance:n}})=>{t?(l[r].terminate(),a(t)):(l[r].terminate(),h({i:e,j:s,distance:n,idx:r}))}}));const u=await Promise.all(a),c=u.reduce(((t,e)=>t+e.i.length),0),f=new Int32Array(c),m=new Int32Array(c),g=new Float32Array(c);let p=0;for(const t of u)f.set(t.i,p),m.set(t.j,p),g.set(t.distance,p),p+=t.i.length;return{i:f,j:m,distance:g}}async getMinimalThreshold(t,e,s={}){const n=new Array(this._workerCount).fill(null).map((()=>new Worker(new URL(r.p+r.u(770),r.b)))),o=t.slice();for(let t=o.length-1;t>0;t--){const e=Math.floor(Math.random()*(t+1));[o[t],o[e]]=[o[e],o[t]]}try{const r=t.length*(t.length-1)/2,i=Math.floor(r/this._workerCount),h=Math.floor(Math.min(r/1e3,1e6)/this._workerCount),a=new Array(this._workerCount);for(let t=0;t<this._workerCount;t++)a[t]=new Promise(((a,l)=>{const u=t*i,c=t===this._workerCount-1?r:(t+1)*i;n[t].postMessage({values:o,startIdx:u,endIdx:c,sampleLength:h,fnName:e,opts:s}),n[t].onmessage=({data:{error:e,distance:r}})=>{n[t].terminate(),e?l(e):a({distance:r})}}));const l=await Promise.all(a),u=l.reduce(((t,e)=>t+e.distance.length),0),c=new Float32Array(u);let f=0;for(const t of l)c.set(t.distance,f),f+=t.distance.length;c.sort();let m=1-c[Math.floor(7e7/r*c.length)];return m=Math.max(m,.3),m}catch(t){return n?.forEach((t=>t?.terminate())),console.error(t),.5}}static calcSync(t,e,r,s){const n=[],o=[],i=[];let h=0,a=0,l=0;const u=t.length*(t.length-1)/2;for(;h<u;){const u=(0,ie.k)(t[a])||(0,ie.k)(t[l])?1:r(t[a],t[l]);(Object.values(y).some((t=>t===e))?1/(1+u):1-u)>=s&&(n.push(a),o.push(l),i.push(u)),h++,l++,l===t.length&&(a++,l=a+1)}return{i:new Int32Array(n),j:new Int32Array(o),distance:new Float32Array(i)}}}!function(t){t.UMAP="UMAP",t.T_SNE="t-SNE"}(oe||(oe={}));class le{constructor(t){this.data=t.data}}const ue={UMAP:class extends le{constructor(t){super(t),h("distanceFname"in t),h("distanceFn"in t),this.distanceFnArgs=t?.distanceFnArgs,this.distanceFn=t.distanceFn,this.usingSparseMatrix=!!t.usingSparseMatrix||!!t.sparseMatrix,this.sparseMatrixThreshold=t.sparseMatrixThreshold??.8,this.transferedSparseMatrix=t.sparseMatrix,this.progressFunc=t.progressFunc,this.distanceFname=t.distanceFname,this.dmIndexFunc=c(this.data.length),this.vectors=new Array(this.data.length).fill(0).map(((t,e)=>e)),this.usingDistanceMatrix=!(!t.preCalculateDistanceMatrix&&this.data.length>2e4||this.usingSparseMatrix),this.usingDistanceMatrix?t.distanceFn=this._encodedDistanceMatrix.bind(this):this.usingSparseMatrix?t.distanceFn=this._encodedSparseMatrix.bind(this):t.distanceFn=this._encodedDistance.bind(this),this.data.length<15&&(t.nNeighbors=this.data.length-1),this.reducer=new te(t)}_encodedDistanceMatrix(t,e){return t===e?0:t>e?this.distanceMatrix[this.dmIndexFunc(e,t)]:this.distanceMatrix[this.dmIndexFunc(t,e)]}_encodedSparseMatrix(t,e){return this.sparseMatrix.get(t)?.get(e)??this.sparseMatrix.get(e)?.get(t)??1}_encodedDistance(t,e){return this.distanceFn(this.data[t],this.data[e])}async transform(t){if(this.usingDistanceMatrix){if(this.distanceMatrix=t?await(async()=>{const t=new f(!0,!1);try{const e=await t.calc(this.data,this.distanceFname,!1,this.distanceFnArgs);return t.terminate(),e}catch(e){throw t.terminate(),e}})():(()=>he.calc(this.data,((t,e)=>this.distanceFn(t,e))).data)(),this.distanceMatrix&&!D(this.distanceFname)){const t=function(t,e,r){function s(t,e,r,s){if(r>t[t.length-1])return;let n=t.length-2;for(n=t.length-2;n>=0&&!(r>t[n]);n--);t.splice(t.length-1,1),t.splice(n+1,0,r),e.splice(e.length-1,1),e.splice(n+1,0,s)}console.time("knnGraph");const n=new Array(r).fill(null).map((()=>new Array(e).fill(1))),o=new Array(r).fill(null).map((()=>new Array(e).fill(1)));let i=0,h=1;for(let e=0;e<t.length;e++)s(o[i],n[i],t[e],h),s(o[h],n[h],t[e],i),h++,h>=r&&(i++,h=i+1);return console.timeEnd("knnGraph"),{knnIndexes:n,knnDistances:o}}(this.distanceMatrix,this.reducer.neighbors,this.data.length);this.reducer.setPrecomputedKNN(t.knnIndexes,t.knnDistances)}}else if(this.usingSparseMatrix){console.time("sparse matrix");let t=this.transferedSparseMatrix??await(new ae).calc(this.data,this.distanceFname,this.sparseMatrixThreshold,this.distanceFnArgs);if(console.timeEnd("sparse matrix"),!D(this.distanceFname)){const e=function(t,e,r,s,n){function o(t,e,r,s){if(r>t[t.length-1])return;let n=t.length-2;for(n=t.length-2;n>=0&&!(r>t[n]);n--);t.splice(t.length-1,1),t.splice(n+1,0,r),e.splice(e.length-1,1),e.splice(n+1,0,s)}console.time("knnGraph");const i=new Array(n).fill(null).map((()=>new Array(s).fill(1))),h=new Array(n).fill(null).map((()=>new Array(s).fill(1)));for(let s=0;s<t.length;s++)o(h[t[s]],i[t[s]],r[s],e[s]),o(h[e[s]],i[e[s]],r[s],t[s]);return console.timeEnd("knnGraph"),{knnIndexes:i,knnDistances:h}}(t.i,t.j,t.distance,this.reducer.neighbors,this.data.length);this.reducer.setPrecomputedKNN(e.knnIndexes,e.knnDistances)}console.time("sparse matrix to map"),this.sparseMatrix=new Map;for(let e=0;e<t.i.length;++e){const r=t.i[e],s=t.j[e],n=t.distance[e];this.sparseMatrix.has(r)||this.sparseMatrix.set(r,new Map),this.sparseMatrix.get(r).set(s,n)}console.timeEnd("sparse matrix to map"),t.distance=null,t.i=null,t.j=null,t=null,await new Promise((t=>{setTimeout((()=>{t()}),500)}))}const e=await this.reducer.fitAsync(this.vectors,(t=>{this.progressFunc&&this.progressFunc(t,this.reducer.getNEpochs(),this.reducer.getEmbedding())}));return{embedding:(r=e,new Array(r.length).fill(0).map(((t,e)=>n.from(r[e])))),...this.distanceMatrix?{distance:this.distanceMatrix}:{}};var r}},"t-SNE":class extends le{constructor(t){super(t),this.reducer=new s.Z(t),this.iterations=t?.iterations??100,this.distanceFname=t.distanceFname,this.distanceFn=t.distanceFn}async transform(t){const e=t?await(async()=>{const t=new f(!0,!1);try{const e=await t.calc(this.data,this.distanceFname);return t.terminate(),e}catch(e){throw t.terminate(),e}})():(()=>{const t=he.calc(this.data,((t,e)=>this.distanceFn(t,e)));return t.normalize(),t.data})(),r=function(t,e){const r=c(e);function s(t,e){const s=Number(t),n=Number(e);return r(s,n)}const n={get:(t,r,n)=>"length"===r?e:new Proxy(t,function(t){return{get:(e,r,n)=>t===r?0:e[Number(t)>Number(r)?s(r,t):s(t,r)]}}(r))};return new Proxy(t,n)}(e,this.data.length);this.reducer.initDataDist(r);for(let t=0;t<this.iterations;++t)this.reducer.step();return{distance:e,embedding:this.reducer.getSolution()}}},SPE:class extends le{constructor(t){super(t),this.reducer=new m(t)}async transform(){const t=await this.reducer.embed(this.data);return{distance:this.reducer.distance,embedding:t}}},pSPE:class extends le{constructor(t){super(t),this.reducer=new g(t)}async transform(){const t=await this.reducer.embed(this.data);return{distance:this.reducer.distance,embedding:t}}},OriginalSPE:class extends le{constructor(t){super(t),this.reducer=new p(t)}async transform(){const t=await this.reducer.embed(this.data);return{distance:this.reducer.distance,embedding:t}}}};class ce{constructor(t,e,r,s){const n=new P(r).getMeasure(s?.distanceFnArgs);let o={};if(D(r))for(let e=0;e<t.length;++e)t[e]=new v.Z(t[e]._data,t[e]._length);o="UMAP"==e?{data:t,distanceFn:n,distanceFname:r,nEpochs:s?.cycles,...s}:"t-SNE"==e?{data:t,distanceFn:n,distanceFname:r,iterations:s?.cycles??void 0,...s}:{data:t,distance:n,distanceFunctionName:r,...s},this.reducer=new ue[e](o)}async transform(t=!1,e){if(void 0===this.reducer)throw new Error("Reducer was not defined.");let{embedding:r,distance:s}=await this.reducer.transform(e);var o;return t&&(o=r,r=new Array(o[0].length).fill(0).map(((t,e)=>new n(o.length).fill(0).map(((t,r)=>o[r][e]))))),{distance:s,embedding:r}}static availableMetricsByType(t){return Object.keys(T[t])}static get availableMethods(){return Object.keys(ue)}static get availableMetrics(){let t=[];return Object.values(T).forEach((e=>{const r=Object.values(e);t=[...t,...r]})),t}}async function fe(t,e,r){t%5==0&&self.postMessage({epochNum:t,epochsLength:e,embedding:r})}self.onmessage=async({data:{columnData:t,method:e,measure:r,options:s,parallelDistanceWorkers:n}})=>{let o;try{o=await async function(t,e,r,s,n){const o=new ce(t,e,r,{...s,progressFunc:fe});return await o.transform(!0,n)}(t,e,r,s,n)}catch(t){o={error:t}}self.postMessage({error:o.error,distance:o.distance,embedding:o.embedding})}},7659:(t,e,r)=>{e.Z=void 0;var s=r(6215);Object.defineProperty(e,"Z",{enumerable:!0,get:function(){return s.TSNE}})},6215:(t,e)=>{Object.defineProperty(e,"__esModule",{value:!0}),e.TSNE=void 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You must have some data!"),this.assert(r>0," X[0] is empty? Where is the data?");const s=this.xtod(t);this.P=this.d2p(s,this.perplexity,1e-4),this.N=e,this.initSolution()}initDataDist(t){const e=t.length;this.assert(e>0," X is empty? 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