Added monadic parser to mol-util

src/mol-script/core-symbols.ts → src/mol-script/symbol-table/core.ts

-/*
+/**
  * Copyright (c) 2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import Type from './type'
-import Symbol, { Arguments, Argument } from './symbol'
-import { symbol, normalizeTable, symbolList } from './helpers'
+import Type from '../type'
+import Symbol, { Arguments, Argument } from '../symbol'
+import { symbol, normalizeTable, symbolList } from '../helpers'
 
 export namespace Types {
     export type List<T = any> = ArrayLike<T>

src/mol-script/symbol-table/structure-query.ts

+/**
+ * Copyright (c) 2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import Type from '../type'
+import * as Core from './core'
+import { Arguments, Argument } from '../symbol'
+import { symbol } from '../helpers'
+
+export namespace Types {
+    export const ElementSymbol = Type.Value('Structure', 'ElementSymbol');
+    export const AtomName = Type.Value('Structure', 'AtomName');
+
+    export const BondFlag = Type.OneOf('Structure', 'BondFlag', Type.Str, ['covalent', 'metallic', 'ion', 'hydrogen', 'sulfide', 'computed', 'aromatic']);
+    export const BondFlags = Core.Types.Flags(BondFlag, 'BondFlags');
+
+    export const SecondaryStructureFlag = Type.OneOf('Structure', 'SecondaryStructureFlag', Type.Str, ['alpha', 'beta', '3-10', 'pi', 'sheet', 'strand', 'helix', 'turn', 'none']);
+    export const SecondaryStructureFlags = Core.Types.Flags(SecondaryStructureFlag, 'SecondaryStructureFlag');
+
+    export const RingFingerprint = Type.Value('Structure', 'RingFingerprint');
+    export const EntityType = Type.OneOf('Structure', 'EntityType', Type.Str, ['polymer', 'non-polymer', 'water', 'unknown']);
+    export const ResidueId = Type.Value('Structure', 'ResidueId');
+
+    export const ElementSet = Type.Value('Structure', 'ElementSet');
+    export const ElementSelection = Type.Value('Structure', 'ElementSelection');
+    export const ElementReference = Type.Value('Structure', 'ElementReference');
+
+    export const ElementSelectionQuery = Core.Types.Fn(ElementSelection, 'ElementSelectionQuery');
+}
+
+const type = {
+    '@header': 'Types',
+    elementSymbol: symbol(
+        Arguments.Dictionary({ 0: Argument(Type.Str) }),
+        Types.ElementSymbol, 'Create element symbol representation from a string value.'),
+
+    atomName: symbol(
+        Arguments.Dictionary({ 0: Argument(Type.AnyValue) }), Types.AtomName, 'Convert a value to an atom name.'),
+
+    entityType: symbol(
+        Arguments.Dictionary({ 0: Argument(Types.EntityType) }),
+        Types.EntityType,
+        `Create normalized representation of entity type: ${Type.oneOfValues(Types.EntityType).join(', ')}.`),
+
+    bondFlags: symbol(
+        Arguments.List(Types.BondFlag),
+        Types.BondFlags,
+        `Create bond flags representation from a list of strings. Allowed flags: ${Type.oneOfValues(Types.BondFlag).join(', ')}.`),
+
+    ringFingerprint: symbol(
+        Arguments.List(Types.ElementSymbol, { nonEmpty: true }),
+        Types.RingFingerprint,
+        'Create ring fingerprint from the supplied atom element list.'),
+
+    secondaryStructureFlags: symbol(
+        Arguments.List(Types.SecondaryStructureFlag),
+        Types.SecondaryStructureFlags,
+        `Create secondary structure flags representation from a list of strings. Allowed flags: ${Type.oneOfValues(Types.SecondaryStructureFlag).join(', ')}.`),
+
+    authResidueId: symbol(Arguments.Dictionary({
+        0: Argument(Type.Str, { description: 'auth_asym_id' }),
+        1: Argument(Type.Num, { description: 'auth_seq_id' }),
+        2: Argument(Type.Str, { description: 'pdbx_PDB_ins_code', isOptional: true })
+    }), Types.ResidueId, `Residue identifier based on "auth_" annotation.`),
+    labelResidueId: symbol(Arguments.Dictionary({
+        0: Argument(Type.Str, { description: 'label_entity_id' }),
+        1: Argument(Type.Str, { description: 'label_asym_id' }),
+        2: Argument(Type.Num, { description: 'label_seq_id' }),
+        3: Argument(Type.Str, { description: 'pdbx_PDB_ins_code', isOptional: true })
+    }), Types.ResidueId, `Residue identifier based on mmCIF's "label_" annotation.`)
+};
+
+const slot = {
+    '@header': 'Iteration Slots',
+    element: symbol(Arguments.None, Types.ElementReference, 'A reference to the current element.'),
+    elementSetReduce: symbol(Arguments.None, Type.Variable('a', Type.AnyValue, true), 'Current value of the element set reducer.')
+}
+
+const generator = {
+    '@header': 'Generators',
+    all: symbol(Arguments.None, Types.ElementSelectionQuery, 'The entire structure.'),
+
+    atomGroups: symbol(Arguments.Dictionary({
+        'entity-test': Argument(Type.Bool, { isOptional: true, defaultValue: true, description: 'Test for the 1st atom of every entity' }),
+        'chain-test': Argument(Type.Bool, { isOptional: true, defaultValue: true, description: 'Test for the 1st atom of every chain'  }),
+        'residue-test': Argument(Type.Bool, { isOptional: true, defaultValue: true, description: 'Test for the 1st atom every residue'  }),
+        'atom-test': Argument(Type.Bool, { isOptional: true, defaultValue: true }),
+        'group-by': Argument(Type.Any, { isOptional: true, defaultValue: `atom-key`, description: 'Group atoms to sets based on this property. Default: each atom has its own set' }),
+    }), Types.ElementSelectionQuery, 'Return all atoms for which the tests are satisfied, grouped into sets.'),
+
+    rings: symbol(Arguments.List(Types.RingFingerprint), Types.ElementSelectionQuery, 'Return rings with the specified fingerprint(s). If no fingerprints are given, return all rings.'),
+
+    queryInSelection: symbol(Arguments.Dictionary({
+        0: Argument(Types.ElementSelectionQuery),
+        query: Argument(Types.ElementSelectionQuery),
+        'in-complement': Argument(Type.Bool, { isOptional: true, defaultValue: false })
+    }), Types.ElementSelectionQuery, 'Executes query only on atoms that are in the source selection.'),
+
+    empty: symbol(Arguments.None, Types.ElementSelectionQuery, 'Nada.'),
+}
+
+const modifier = {
+    '@header': 'Selection Modifications',
+
+    queryEach: symbol(Arguments.Dictionary({
+        0: Argument(Types.ElementSelectionQuery),
+        query: Argument(Types.ElementSelectionQuery)
+    }), Types.ElementSelectionQuery, 'Query every atom set in the input selection separately.'),
+
+    intersectBy: symbol(Arguments.Dictionary({
+        0: Argument(Types.ElementSelectionQuery),
+        by: Argument(Types.ElementSelectionQuery)
+    }), Types.ElementSelectionQuery, 'Intersect each atom set from the first sequence from atoms in the second one.'),
+
+    exceptBy: symbol(Arguments.Dictionary({
+        0: Argument(Types.ElementSelectionQuery),
+        by: Argument(Types.ElementSelectionQuery)
+    }), Types.ElementSelectionQuery, `Remove all atoms from 'selection' that occur in 'by'.`),
+
+    unionBy: symbol(Arguments.Dictionary({
+        0: Argument(Types.ElementSelectionQuery),
+        by: Argument(Types.ElementSelectionQuery)
+    }), Types.ElementSelectionQuery, 'For each atom set A in the orginal sequence, combine all atoms sets in the target selection that intersect with A.'),
+
+    union: symbol(Arguments.Dictionary({
+        0: Argument(Types.ElementSelectionQuery)
+    }), Types.ElementSelectionQuery, 'Collects all atom sets in the sequence into a single atom set.'),
+
+    cluster: symbol(Arguments.Dictionary({
+        0: Argument(Types.ElementSelectionQuery),
+        'min-distance': Argument(Type.Num, { isOptional: true, defaultValue: 0 }),
+        'max-distance': Argument(Type.Num),
+        'min-size': Argument(Type.Num, { description: 'Minimal number of sets to merge, must be at least 2', isOptional: true, defaultValue: 2 }),
+        'max-size': Argument(Type.Num, { description: 'Maximal number of sets to merge, if not set, no limit', isOptional: true }),
+    }), Types.ElementSelectionQuery, 'Combines atom sets that have mutual distance in the interval [min-radius, max-radius]. Minimum/maximum size determines how many atom sets can be combined.'),
+
+    includeSurroundings: symbol(Arguments.Dictionary({
+        0: Argument(Types.ElementSelectionQuery),
+        radius: Argument(Type.Num),
+        'atom-radius': Argument(Type.Num, { isOptional: true, defaultValue: 0, description: 'Value added to each atom before the distance check, for example VDW radius. Using this argument is computationally demanding.' }),
+        'as-whole-residues': Argument(Type.Bool, { isOptional: true })
+    }), Types.ElementSelectionQuery, 'For each atom set in the selection, include all surrouding atoms/residues that are within the specified radius.'),
+
+    includeConnected: symbol(Arguments.Dictionary({
+        0: Argument(Types.ElementSelectionQuery),
+        'bond-test': Argument(Type.Bool, { isOptional: true, defaultValue: 'true for covalent bonds' as any }),
+        'layer-count': Argument(Type.Num, { isOptional: true, defaultValue: 1, description: 'Number of bonded layers to include.' }),
+        'as-whole-residues': Argument(Type.Bool, { isOptional: true })
+    }), Types.ElementSelectionQuery, 'Pick all atom sets that are connected to the target.'),
+
+    expandProperty: symbol(Arguments.Dictionary({
+        0: Argument(Types.ElementSelectionQuery),
+        property: Argument(Type.AnyValue)
+    }), Types.ElementSelectionQuery, 'To each atom set in the selection, add all atoms that have the same property value that was already present in the set.')
+}
+
+const filter = {
+    '@header': 'Selection Filters',
+    pick: symbol(Arguments.Dictionary({
+        0: Argument(Types.ElementSelectionQuery),
+        test: Argument(Type.Bool)
+    }), Types.ElementSelectionQuery, 'Pick all atom sets that satisfy the test.'),
+
+    withSameAtomProperties: symbol(Arguments.Dictionary({
+        0: Argument(Types.ElementSelectionQuery),
+        source: Argument(Types.ElementSelectionQuery),
+        property: Argument(Type.Any)
+    }), Types.ElementSelectionQuery, 'Pick all atom sets for which the set of given atom properties is a subset of the source properties.'),
+
+    intersectedBy: symbol(Arguments.Dictionary({
+        0: Argument(Types.ElementSelectionQuery),
+        by: Argument(Types.ElementSelectionQuery)
+    }), Types.ElementSelectionQuery, 'Pick all atom sets that have non-zero intersection with the target.'),
+
+    within: symbol(Arguments.Dictionary({
+        0: Argument(Types.ElementSelectionQuery),
+        target: Argument(Types.ElementSelectionQuery),
+        'min-radius': Argument(Type.Num, { isOptional: true, defaultValue: 0 }),
+        'max-radius': Argument(Type.Num),
+        'atom-radius': Argument(Type.Num, { isOptional: true, defaultValue: 0, description: 'Value added to each atom before the distance check, for example VDW radius. Using this argument is computationally demanding.' }),
+        invert: Argument(Type.Bool, { isOptional: true, defaultValue: false, description: 'If true, pick only atom sets that are further than the specified radius.' }),
+    }), Types.ElementSelectionQuery, 'Pick all atom sets from selection that have any atom within the radius of any atom from target.'),
+
+    isConnectedTo: symbol(Arguments.Dictionary({
+        0: Argument(Types.ElementSelectionQuery),
+        target: Argument(Types.ElementSelectionQuery),
+        'bond-test': Argument(Type.Bool, { isOptional: true, defaultValue: 'true for covalent bonds' as any }),
+        disjunct: Argument(Type.Bool, { isOptional: true, defaultValue: true, description: 'If true, there must exist a bond to an atom that lies outside the given atom set to pass test.' }),
+        invert: Argument(Type.Bool, { isOptional: true, defaultValue: false, description: 'If true, return atom sets that are not connected.' })
+    }), Types.ElementSelectionQuery, 'Pick all atom sets that are connected to the target.'),
+}
+
+const combinator = {
+    '@header': 'Selection Combinators',
+    intersect: symbol(Arguments.List(Types.ElementSelectionQuery), Types.ElementSelectionQuery, 'Return all unique atom sets that appear in all of the source selections.'),
+    merge: symbol(Arguments.List(Types.ElementSelectionQuery), Types.ElementSelectionQuery, 'Merges multiple selections into a single one. Only unique atom sets are kept.'),
+    distanceCluster: symbol(Arguments.Dictionary({
+        matrix: Argument(Core.Types.List(Core.Types.List(Type.Num)), { description: 'Distance matrix, represented as list of rows (num[][])). Lower triangle is min distance, upper triangle is max distance.' }),
+        selections: Argument(Core.Types.List(Types.ElementSelectionQuery), { description: 'A list of held selections.' })
+    }), Types.ElementSelectionQuery, 'Pick combinations of atom sets from the source sequences that are mutually within distances specified by a matrix.')
+}
+
+const atomSet = {
+    '@header': 'Atom Sets',
+
+    atomCount: symbol(Arguments.None, Type.Num),
+
+    countQuery: symbol(Arguments.Dictionary({
+        0: Argument(Types.ElementSelectionQuery)
+    }), Type.Num, 'Counts the number of occurences of a specific query inside the current atom set.'),
+
+    reduce: symbol(Arguments.Dictionary({
+        initial: Argument(Type.Variable('a', Type.AnyValue, true), { description: 'Initial value assigned to slot.atom-set-reduce. Current atom is set to the 1st atom of the current set for this.' }),
+        value: Argument(Type.Variable('a', Type.AnyValue, true), { description: 'Expression executed for each atom in the set' })
+    }), Type.Variable('a', Type.AnyValue, true), 'Execute the value expression for each atom in the current atom set and return the result. Works the same way as Array.reduce in JavaScript (``result = value(value(...value(initial)))``)'),
+
+    propertySet: symbol(Arguments.Dictionary({
+        0: Argument(Core.Types.ConstrainedVar),
+    }), Core.Types.Set(Core.Types.ConstrainedVar), 'Returns a set with all values of the given property in the current atom set.'),
+}
+
+const atomProperty = {
+    '@header': 'Atom Properties',
+
+    core: {
+        '@header': 'Core Properties',
+
+        elementSymbol: atomProp(Types.ElementSymbol),
+
+        vdw: atomProp(Type.Num, 'Van der Waals radius'),
+        mass: atomProp(Type.Num, 'Atomic weight'),
+        atomicNumber: atomProp(Type.Num, 'Atomic number'),
+
+        x: atomProp(Type.Num, 'Cartesian X coordinate'),
+        y: atomProp(Type.Num, 'Cartesian Y coordinate'),
+        z: atomProp(Type.Num, 'Cartesian Z coordinate'),
+
+        atomKey: atomProp(Type.AnyValue, 'Unique value for each atom. Main use case is grouping of atoms.'),
+
+        bondCount: symbol(Arguments.Dictionary({
+            0: Argument(Types.ElementReference, { isOptional: true, defaultValue: 'slot.current-atom' }),
+            flags: Argument(Types.BondFlags, { isOptional: true, defaultValue: 'covalent' as any }),
+        }), Type.Num, 'Number of bonds (by default only covalent bonds are counted).')
+    },
+
+    topology: {
+        connectedComponentKey: atomProp(Type.AnyValue, 'Unique value for each connected component.')
+    },
+
+    macromolecular: {
+        '@header': 'Macromolecular Properties (derived from the mmCIF format)',
+
+        authResidueId: atomProp(Types.ResidueId, `type.auth-residue-id symbol executed on current atom's residue`),
+        labelResidueId: atomProp(Types.ResidueId, `type.label-residue-id symbol executed on current atom's residue`),
+
+        residueKey: atomProp(Type.AnyValue, 'Unique value for each tuple ``(label_entity_id,auth_asym_id,auth_seq_id,pdbx_PDB_ins_code)``, main use case is grouping of atoms'),
+        chainKey: atomProp(Type.AnyValue, 'Unique value for each tuple ``(label_entity_id,auth_asym_id)``, main use case is grouping of atoms'),
+        entityKey: atomProp(Type.AnyValue, 'Unique value for each tuple ``label_entity_id``, main use case is grouping of atoms'),
+
+        isHet: atomProp(Type.Bool, 'Equivalent to atom_site.group_PDB !== ATOM'),
+
+        id: atomProp(Type.Num, '_atom_site.id'),
+
+        label_atom_id: atomProp(Types.AtomName),
+        label_alt_id: atomProp(Type.Str),
+        label_comp_id: atomProp(Type.Str),
+        label_asym_id: atomProp(Type.Str),
+        label_entity_id: atomProp(Type.Str),
+        label_seq_id: atomProp(Type.Num),
+
+        auth_atom_id: atomProp(Types.AtomName),
+        auth_comp_id: atomProp(Type.Str),
+        auth_asym_id: atomProp(Type.Str),
+        auth_seq_id: atomProp(Type.Num),
+
+        pdbx_PDB_ins_code: atomProp(Type.Str),
+        pdbx_formal_charge: atomProp(Type.Num),
+
+        occupancy: atomProp(Type.Num),
+        B_iso_or_equiv: atomProp(Type.Num),
+
+        entityType: atomProp(Types.EntityType, 'Type of the entity as defined in mmCIF (polymer, non-polymer, water, unknown)'),
+
+        secondaryStructureKey: atomProp(Type.AnyValue, 'Unique value for each secondary structure element.'),
+        secondaryStructureFlags: atomProp(Types.SecondaryStructureFlags),
+
+        isModified: atomProp(Type.Bool, 'True if the atom bolongs to modification of a standard residue.'),
+        modifiedParentName: atomProp(Type.Str, `'3-letter' code of the modifed parent residue.`),
+    }
+}
+
+const bondProperty = {
+    '@header': 'Bond Properties',
+
+    flags: bondProp(Types.BondFlags),
+    order: bondProp(Type.Num)
+}
+
+function atomProp(type: Type, description?: string) {
+    return symbol(Arguments.Dictionary({ 0: Argument(Types.ElementReference, { isOptional: true, defaultValue: 'slot.current-atom' }) }), type, description);
+}
+
+function bondProp(type: Type, description?: string) {
+    return symbol(Arguments.None, type, description);
+}
+
+export default {
+    '@header': 'Structure Queries',
+    type,
+    slot,
+    generator,
+    modifier,
+    filter,
+    combinator,
+    atomSet,
+    atomProperty,
+    bondProperty
+}
\ No newline at end of file

src/mol-util/_spec/monadic-parser.spec.ts

+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { MonadicParser as P } from '../monadic-parser'
+
+describe('parser', () => {
+    it('string', () => {
+        const p = P.string('abc');
+        expect(p.parse('abc').success).toBe(true);
+        expect(p.parse('cabc').success).toBe(false);
+    });
+
+    it('alt', () => {
+        const p = P.alt(P.string('abc'), P.string('123'));
+        expect(p.parse('abc').success).toBe(true);
+        expect(p.parse('123').success).toBe(true);
+        expect(p.parse('123a').success).toBe(false);
+    });
+
+    it('trim', () => {
+        const p = P.string('abc').trim(P.whitespace);
+        expect(p.tryParse(' abc ')).toBe('abc');
+    });
+
+    it('wrap', () => {
+        const p = P.string('abc').wrap(P.string('('), P.string(')'));
+        expect(p.tryParse('(abc)')).toBe('abc');
+    });
+
+    it('then', () => {
+        const p = P.string('abc').then(P.string('123'));
+        expect(p.tryParse('abc123')).toBe('123');
+    });
+
+    it('many', () => {
+        const p = P.string('1').many();
+        expect(p.tryParse('111')).toEqual(['1', '1', '1']);
+    });
+
+    it('times', () => {
+        const p = P.string('1').times(2);
+        expect(p.tryParse('11')).toEqual(['1', '1']);
+    });
+
+    it('sepBy', () => {
+        const p = P.sepBy(P.digits, P.string(',')).map(xs => xs.map(x => +x));
+        expect(p.tryParse('1,2,3,4')).toEqual([1, 2, 3, 4]);
+    });
+});
\ No newline at end of file

src/mol-util/monadic-parser.ts

+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+/**
+ * Adapted from Parsimmon (https://github.com/jneen/parsimmon)
+ * Copyright (c) 2011-present J. Adkisson (http://jneen.net).
+ */
+
+export class MonadicParser<A> {
+    constructor(public _: MonadicParser.Action<A>) { }
+
+    parse(input: string): MonadicParser.ParseResult<A> {
+        const result = this.skip(MonadicParser.eof)._(input, 0);
+        if (result.status) {
+            return { success: true, value: result.value };
+        }
+        return { success: false, index: makeLineColumnIndex(input, result.furthest), expected: result.expected };
+    };
+
+    tryParse(str: string) {
+        const result = this.parse(str);
+        if (result.success) {
+            return result.value;
+        } else {
+            const msg = formatError(str, result);
+            const err = new Error(msg);
+            throw err;
+        }
+    }
+
+    or<B>(alternative: MonadicParser<B>): MonadicParser<A | B> {
+        return MonadicParser.alt(this, alternative);
+    }
+
+    trim<B>(parser: MonadicParser<B>): MonadicParser<A> {
+        return this.wrap(parser, parser);
+    }
+
+    wrap<L, R>(leftParser: MonadicParser<L>, rightParser: MonadicParser<R>): MonadicParser<A> {
+        return seqPick(1, leftParser, this, rightParser);
+    }
+
+    thru<B>(wrapper: (p: MonadicParser<A>) => MonadicParser<B>) {
+        return wrapper(this);
+    }
+
+    then<B>(next: MonadicParser<B>): MonadicParser<B> {
+        return seqPick(1, this, next);
+    }
+
+    many() {
+        return new MonadicParser((input, i) => {
+            const accum: A[] = [];
+            let result: MonadicParser.Result<A> | undefined = void 0;
+
+            while (true) {
+                result = mergeReplies(this._(input, i), result);
+                if (result.status) {
+                    if (i === result.index) {
+                        throw new Error('infinite loop detected in .many() parser --- calling .many() on a parser which can accept zero characters is usually the cause');
+                    }
+                    i = result.index;
+                    accum.push(result.value);
+                } else {
+                    return mergeReplies(makeSuccess(i, accum), result);
+                }
+            }
+        });
+    };
+
+    times(min: number, _max?: number): MonadicParser<A[]> {
+        const max = typeof _max === 'undefined' ? min : _max;
+        return new MonadicParser((input, i) => {
+            const accum: A[] = [];
+            let result: MonadicParser.Result<A> | undefined = void 0;
+            let prevResult: MonadicParser.Result<A> | undefined = void 0;
+            let times: number;
+            for (times = 0; times < min; times++) {
+                result = this._(input, i);
+                prevResult = mergeReplies(result, prevResult);
+                if (result.status) {
+                    i = result.index;
+                    accum.push(result.value);
+                } else {
+                    return prevResult as any;
+                }
+            }
+            for (; times < max; times += 1) {
+                result = this._(input, i);
+                prevResult = mergeReplies(result, prevResult);
+                if (result.status) {
+                    i = result.index;
+                    accum.push(result.value);
+                } else {
+                    break;
+                }
+            }
+            return mergeReplies(makeSuccess(i, accum), prevResult);
+        });
+    };
+
+    result<B>(res: B) {
+        return this.map(() => res);
+    };
+
+    atMost(n: number) {
+        return this.times(0, n);
+    };
+
+    atLeast(n: number) {
+        return MonadicParser.seq(this.times(n), this.many()).map(r => [...r[0], ...r[1]]);
+    };
+
+    map<B>(f: (a: A) => B): MonadicParser<B> {
+        return new MonadicParser((input, i) => {
+            const result = this._(input, i);
+            if (!result.status) {
+                return result;
+            }
+            return mergeReplies(makeSuccess(result.index, f(result.value)), result);
+        });
+    }
+
+    skip<B>(next: MonadicParser<B>): MonadicParser<A> {
+        return seqPick(0, this, next);
+    }
+
+    mark(): MonadicParser<MonadicParser.Mark<A>> {
+        return MonadicParser.seq(MonadicParser.index, this, MonadicParser.index).map(r => ({ start: r[0], value: r[1], end: r[2] }));
+    }
+
+    node(name: string): MonadicParser<MonadicParser.Node<A>> {
+        return MonadicParser.seq(MonadicParser.index, this, MonadicParser.index).map(r => ({ name, start: r[0], value: r[1], end: r[2] }));
+    };
+
+    sepBy<B>(separator: MonadicParser<B>): MonadicParser<A[]> {
+        return MonadicParser.sepBy(this, separator);
+    }
+
+    sepBy1<B>(separator: MonadicParser<B>): MonadicParser<A[]> {
+        return MonadicParser.sepBy1(this, separator);
+    }
+
+    lookahead<B>(x: MonadicParser<B>) {
+        return this.skip(MonadicParser.lookahead(x));
+    };
+
+    notFollowedBy<B>(x: MonadicParser<B>) {
+        return this.skip(MonadicParser.notFollowedBy(x));
+    };
+
+    desc(expected: string) {
+        return new MonadicParser((input, i) => {
+            const reply = this._(input, i);
+            if (!reply.status) {
+                reply.expected = [expected];
+            }
+            return reply;
+        });
+    };
+
+    fallback<B>(result: B) {
+        return this.or(MonadicParser.succeed(result));
+    };
+
+    ap<B>(other: MonadicParser<(x: A) => B>): MonadicParser<B> {
+        return MonadicParser.seq(other, this).map(([f, x]) => f(x));
+    };
+
+    chain<B>(f: (a: A) => MonadicParser<B>): MonadicParser<B> {
+        return new MonadicParser<B>((input, i) => {
+            const result = this._(input, i);
+            if (!result.status) {
+                return result as any;
+            }
+            const nextParser = f(result.value);
+            return mergeReplies(nextParser._(input, result.index), result);
+        });
+    };
+}
+
+export namespace MonadicParser {
+    export type Action<T> = (input: string, i: number) => MonadicParser.Result<T>
+
+    export type ParseResult<T> = ParseSuccess<T> | ParseFailure;
+
+    export interface Index {
+        /** zero-based character offset */
+        offset: number;
+        /** one-based line offset */
+        line: number;
+        /** one-based column offset */
+        column: number;
+    }
+
+    export interface ParseSuccess<T> {
+        success: true,
+        value: T
+    }
+
+    export interface ParseFailure {
+        success: false,
+        index: Index,
+        expected: string[],
+    }
+
+    export interface Mark<T> {
+        start: Index;
+        end: Index;
+        value: T;
+    }
+
+    export interface Node<T> extends Mark<T> {
+        name: string
+    }
+
+    export interface Success<T> {
+        status: true,
+        value: T,
+        index: number
+    }
+
+    export interface Failure {
+        status: false,
+        furthest: number,
+        expected: string[]
+    }
+
+    export type Result<T> = Success<T> | Failure
+
+    // export function createLanguage(parsers: any) {
+    //     const language: any = {};
+    //     for (const key of Object.keys(parsers)) {
+    //         (function (key) {
+    //             language[key] = lazy(() => parsers[key](language));
+    //         })(key);
+    //     }
+    //     return language;
+    // }
+
+    export function seq<A>(a: MonadicParser<A>): MonadicParser<[A]>
+    export function seq<A, B>(a: MonadicParser<A>, b: MonadicParser<B>): MonadicParser<[A, B]>
+    export function seq<A, B, C>(a: MonadicParser<A>, b: MonadicParser<B>, c: MonadicParser<C>): MonadicParser<[A, B, C]>
+    export function seq<A, B, C, D>(a: MonadicParser<A>, b: MonadicParser<B>, c: MonadicParser<C>, d: MonadicParser<D>): MonadicParser<[A, B, C, D]>
+    export function seq<A, B, C, D, E>(a: MonadicParser<A>, b: MonadicParser<B>, c: MonadicParser<C>, d: MonadicParser<D>, e: MonadicParser<E>): MonadicParser<[A, B, C, D, E]>
+    export function seq<T>(...parsers: MonadicParser<T>[]): MonadicParser<T[]>
+    export function seq(...parsers: MonadicParser<any>[]): MonadicParser<any[]> {
+        const numParsers = parsers.length;
+        return new MonadicParser<any[]>((input, index) => {
+            let result: MonadicParser.Result<any> | undefined;
+            let accum = new Array(numParsers);
+            let i = index;
+            for (let j = 0; j < numParsers; j++) {
+                result = mergeReplies(parsers[j]._(input, i), result);
+                if (!result.status) {
+                    return result;
+                }
+                accum[j] = result.value;
+                i = result.index;
+            }
+            return mergeReplies(makeSuccess(i, accum), result);
+        });
+    }
+
+    export function alt<A>(a: MonadicParser<A>): MonadicParser<A>
+    export function alt<A, B>(a: MonadicParser<A>, b: MonadicParser<B>): MonadicParser<A | B>
+    export function alt<A, B, C>(a: MonadicParser<A>, b: MonadicParser<B>, c: MonadicParser<C>): MonadicParser<A | B | C>
+    export function alt<A, B, C, D>(a: MonadicParser<A>, b: MonadicParser<B>, c: MonadicParser<C>, d: MonadicParser<D>): MonadicParser<A | B | C | D>
+    export function alt<A, B, C, D, E>(a: MonadicParser<A>, b: MonadicParser<B>, c: MonadicParser<C>, d: MonadicParser<D>, e: MonadicParser<E>): MonadicParser<A | B | C | D | E>
+    export function alt<T>(...parsers: MonadicParser<T>[]): MonadicParser<T[]>
+    export function alt(...parsers: MonadicParser<any>[]): MonadicParser<any> {
+        const numParsers = parsers.length;
+        if (numParsers === 0) {
+            return fail('zero alternates');
+        }
+        return new MonadicParser((input, i) => {
+            let result: MonadicParser.Result<any> | undefined;
+            for (let j = 0; j < parsers.length; j++) {
+                result = mergeReplies(parsers[j]._(input, i), result);
+                if (result.status) {
+                    return result;
+                }
+            }
+            return result!;
+        });
+    }
+
+    export function sepBy<A, B>(parser: MonadicParser<A>, separator: MonadicParser<B>): MonadicParser<A[]> {
+        return sepBy1(parser, separator).or(succeed([]));
+    }
+
+    export function sepBy1<A, B>(parser: MonadicParser<A>, separator: MonadicParser<B>) {
+        const pairs = separator.then(parser).many();
+        return seq(parser, pairs).map(r => [r[0], ...r[1]]);
+    }
+
+    export function string(str: string) {
+        const expected = `'${str}'`;
+        return new MonadicParser((input, i) => {
+            const j = i + str.length;
+            const head = input.slice(i, j);
+            if (head === str) {
+                return makeSuccess(j, head);
+            } else {
+                return makeFailure(i, expected);
+            }
+        });
+    }
+
+    function flags(re: RegExp) {
+        const s = '' + re;
+        return s.slice(s.lastIndexOf('/') + 1);
+    }
+
+    function anchoredRegexp(re: RegExp) {
+        return RegExp('^(?:' + re.source + ')', flags(re));
+    }
+
+    export function regexp(re: RegExp, groupNumber?: number) {
+        const anchored = anchoredRegexp(re);
+        const expected = '' + re;
+        const group = groupNumber || 0;
+        return new MonadicParser(function (input, i) {
+            const match = anchored.exec(input.slice(i));
+            if (match) {
+                if (0 <= group && group <= match.length) {
+                    const fullMatch = match[0];
+                    const groupMatch = match[group];
+                    return makeSuccess(i + fullMatch.length, groupMatch);
+                }
+                const message = `invalid match group (0 to ${match.length}) in ${expected}`;
+                return makeFailure(i, message);
+            }
+            return makeFailure(i, expected);
+        });
+    }
+
+    export function succeed<A>(value: A) {
+        return new MonadicParser((input, i) => makeSuccess(i, value));
+    }
+
+    export function fail(expected: string): MonadicParser<any> {
+        return new MonadicParser((input, i) => makeFailure(i, expected));
+    }
+
+    export function lookahead<A>(x: MonadicParser<A> | string | RegExp): MonadicParser<null> {
+        if (isParser(x)) {
+            return new MonadicParser((input, i) => {
+                const result = x._(input, i);
+                if (result.status) {
+                    result.index = i;
+                    result.value = null as any;
+                }
+                return result as any;
+            });
+        } else if (typeof x === 'string') {
+            return lookahead(string(x));
+        } else if (x instanceof RegExp) {
+            return lookahead(regexp(x));
+        }
+        throw new Error('not a string, regexp, or parser: ' + x);
+    }
+
+    export function notFollowedBy<A>(parser: MonadicParser<A>): MonadicParser<null> {
+        return new MonadicParser((input, i) => {
+            const result = parser._(input, i);
+            return result.status
+                ? makeFailure(i, 'not "' + input.slice(i, result.index) + '"')
+                : makeSuccess(i, null);
+        });
+    }
+
+    export function test(predicate: (char: string) => boolean): MonadicParser<string> {
+        return new MonadicParser((input, i) => {
+            const char = input.charAt(i);
+            if (i < input.length && predicate(char)) {
+                return makeSuccess(i + 1, char);
+            } else {
+                return makeFailure(i, 'a character ' + predicate);
+            }
+        });
+    }
+
+    export function oneOf(str: string) {
+        return test(ch => str.indexOf(ch) >= 0);
+    }
+
+    export function noneOf(str: string) {
+        return test(ch => str.indexOf(ch) < 0);
+    }
+
+    export function range(begin: string, end: string) {
+        return test(ch => begin <= ch && ch <= end).desc(begin + '-' + end);
+    }
+
+    export function takeWhile(predicate: (ch: string) => boolean) {
+        return new MonadicParser((input, i) => {
+            let j = i;
+            while (j < input.length && predicate(input.charAt(j))) {
+                j++;
+            }
+            return makeSuccess(j, input.slice(i, j));
+        });
+    }
+
+    export function lazy<T>(f: () => MonadicParser<T>) {
+        const parser = new MonadicParser((input, i) => {
+            const a = f()._;
+            parser._ = a;
+            return a(input, i);
+        });
+        return parser;
+    }
+
+    export function empty() {
+        return fail('empty');
+    }
+
+    export const index = new MonadicParser(function (input, i) {
+        return makeSuccess(i, makeLineColumnIndex(input, i));
+    });
+
+    export const anyChar = new MonadicParser<string>((input, i) => {
+        if (i >= input.length) {
+            return makeFailure(i, 'any character');
+        }
+        return makeSuccess(i + 1, input.charAt(i));
+    });
+
+    export const all = new MonadicParser(function (input, i) {
+        return makeSuccess(input.length, input.slice(i));
+    });
+
+    export const eof = new MonadicParser(function (input, i) {
+        if (i < input.length) {
+            return makeFailure(i, 'EOF');
+        }
+        return makeSuccess(i, null);
+    });
+
+    export const digit = regexp(/[0-9]/).desc('a digit');
+    export const digits = regexp(/[0-9]*/).desc('optional digits');
+    export const letter = regexp(/[a-z]/i).desc('a letter');
+    export const letters = regexp(/[a-z]*/i).desc('optional letters');
+    export const optWhitespace = regexp(/\s*/).desc('optional whitespace');
+    export const whitespace = regexp(/\s+/).desc('whitespace');
+    export const cr = string('\r');
+    export const lf = string('\n');
+    export const crlf = string('\r\n');
+    export const newline = alt(crlf, lf, cr).desc('newline');
+    export const end = alt(newline, eof);
+}
+
+function seqPick(idx: number, ...parsers: MonadicParser<any>[]): MonadicParser<any> {
+    const numParsers = parsers.length;
+    return new MonadicParser<any[]>((input, index) => {
+        let result: MonadicParser.Result<any> | undefined;
+        let picked: any;
+        let i = index;
+        for (let j = 0; j < numParsers; j++) {
+            result = mergeReplies(parsers[j]._(input, i), result);
+            if (!result.status) {
+                return result;
+            }
+            if (idx === j) picked = result.value;
+            i = result.index;
+        }
+        return mergeReplies(makeSuccess(i, picked), result);
+    });
+}
+
+
+function makeSuccess<T>(index: number, value: T): MonadicParser.Success<T> {
+    return { status: true, index, value };
+}
+
+function makeFailure(index: number, expected: string): MonadicParser.Failure {
+    return { status: false, furthest: index, expected: [expected] };
+}
+
+function mergeReplies<A, B>(result: MonadicParser.Result<A>, last?: MonadicParser.Result<B>): MonadicParser.Result<A> {
+    if (!last || result.status || last.status || result.furthest > last.furthest) {
+        return result;
+    }
+    const expected = result.furthest === last.furthest
+        ? unsafeUnion(result.expected, last.expected)
+        : last.expected;
+    return { status: result.status, furthest: last.furthest, expected };
+}
+
+function makeLineColumnIndex(input: string, i: number): MonadicParser.Index {
+    const lines = input.slice(0, i).split('\n');
+    // Note that unlike the character offset, the line and column offsets are
+    // 1-based.
+    const lineWeAreUpTo = lines.length;
+    const columnWeAreUpTo = lines[lines.length - 1].length + 1;
+    return { offset: i, line: lineWeAreUpTo, column: columnWeAreUpTo };
+}
+
+function formatExpected(expected: string[]) {
+    if (expected.length === 1) {
+        return expected[0];
+    }
+    return 'one of ' + expected.join(', ');
+}
+
+function formatGot(input: string, error: MonadicParser.ParseFailure) {
+    const index = error.index;
+    const i = index.offset;
+    if (i === input.length) {
+        return ', got the end of the input';
+    }
+    const prefix = i > 0 ? '\'...' : '\'';
+    const suffix = input.length - i > 12 ? '...\'' : '\'';
+    return (
+        ' at line ' +
+        index.line +
+        ' column ' +
+        index.column +
+        ', got ' +
+        prefix +
+        input.slice(i, i + 12) +
+        suffix
+    );
+}
+
+function formatError(input: string, error: MonadicParser.ParseFailure) {
+    return 'expected ' + formatExpected(error.expected) + formatGot(input, error);
+}
+
+function unsafeUnion(xs: string[], ys: string[]) {
+    const xn = xs.length;
+    const yn = ys.length;
+    if (xn === 0) return ys;
+    else if (yn === 0) return xs;
+
+    const set = new Set<string>();
+    const ret: string[] = [];
+    for (let i = 0; i < xn; i++) {
+        if (!set.has(xs[i])) {
+            ret[ret.length] = xs[i];
+            set.add(xs[i]);
+        }
+    }
+    for (let i = 0; i < yn; i++) {
+        if (!set.has(ys[i])) {
+            ret[ret.length] = ys[i];
+            set.add(ys[i]);
+        }
+    }
+    ret.sort();
+    return ret;
+}
+
+function isParser(obj: any): obj is MonadicParser<any> {
+    return obj instanceof MonadicParser;
+}
\ No newline at end of file