react-msaview 1.3.1 → 2.0.0

package/bundle/parseNewick.js

@@ -1,94 +0,0 @@
-/**
- * Newick format parser in JavaScript.
- *
- * Copyright (c) Jason Davies 2010.
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in
- * all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- * THE SOFTWARE.
- *
- * Example tree (from http://en.wikipedia.org/wiki/Newick_format):
- *
- * +--0.1--A
- * F-----0.2-----B            +-------0.3----C
- * +------------------0.5-----E
- *                            +---------0.4------D
- *
- * Newick format:
- * (A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F;
- *
- * Converted to JSON:
- * {
- *   name: "F",
- *   branchset: [
- *     {name: "A", length: 0.1},
- *     {name: "B", length: 0.2},
- *     {
- *       name: "E",
- *       length: 0.5,
- *       branchset: [
- *         {name: "C", length: 0.3},
- *         {name: "D", length: 0.4}
- *       ]
- *     }
- *   ]
- * }
- *
- * Converted to JSON, but with no names or lengths:
- * {
- *   branchset: [
- *     {}, {}, {
- *       branchset: [{}, {}]
- *     }
- *   ]
- * }
- */
-export default function parse(s) {
-    var ancestors = [];
-    var tree = {};
-    var tokens = s.split(/\s*(;|\(|\)|,|:)\s*/);
-    for (var i = 0; i < tokens.length; i++) {
-        var token = tokens[i];
-        var subtree = {};
-        switch (token) {
-            case '(': // new branchset
-                tree.branchset = [subtree];
-                ancestors.push(tree);
-                tree = subtree;
-                break;
-            case ',': // another branch
-                ancestors[ancestors.length - 1].branchset.push(subtree);
-                tree = subtree;
-                break;
-            case ')': // optional name next
-                tree = ancestors.pop();
-                break;
-            case ':': // optional length next
-                break;
-            default: {
-                var x = tokens[i - 1];
-                if (x === ')' || x === '(' || x === ',') {
-                    tree.name = token;
-                }
-                else if (x === ':') {
-                    tree.length = parseFloat(token);
-                }
-            }
-        }
-    }
-    return tree;
-}

package/bundle/parsers/ClustalMSA.d.ts

@@ -1,39 +0,0 @@
-export default class ClustalMSA {
-    private MSA;
-    constructor(text: string);
-    getMSA(): {
-        header: Record<string, any>;
-        consensus?: string | undefined;
-        alns: {
-            id: string;
-            seq: string;
-        }[];
-    };
-    getRow(name: string): string[] | undefined;
-    getWidth(): number;
-    getDetails(): Record<string, any>;
-    getNames(): string[];
-    getStructures(): {};
-    get alignmentNames(): never[];
-    getTree(): {
-        id: string;
-        noTree: boolean;
-        branchset: {
-            id: string;
-            name: string;
-        }[];
-    };
-    get seqConsensus(): string | undefined;
-    get secondaryStructureConsensus(): undefined;
-    get tracks(): {
-        id: string;
-        name: string;
-        data: string;
-        customColorScheme: {
-            '*': string;
-            ':': string;
-            '.': string;
-            ' ': string;
-        };
-    }[];
-}

package/bundle/parsers/ClustalMSA.js

@@ -1,77 +0,0 @@
-import { parse } from 'clustal-js';
-var ClustalMSA = /** @class */ (function () {
-    function ClustalMSA(text) {
-        this.MSA = parse(text);
-    }
-    ClustalMSA.prototype.getMSA = function () {
-        return this.MSA;
-    };
-    ClustalMSA.prototype.getRow = function (name) {
-        var _a;
-        return (_a = this.MSA.alns.find(function (aln) { return aln.id === name; })) === null || _a === void 0 ? void 0 : _a.seq.split('');
-    };
-    ClustalMSA.prototype.getWidth = function () {
-        return this.MSA.alns[0].seq.length;
-    };
-    ClustalMSA.prototype.getDetails = function () {
-        return this.MSA.header;
-    };
-    ClustalMSA.prototype.getNames = function () {
-        return this.MSA.alns.map(function (aln) { return aln.id; });
-    };
-    ClustalMSA.prototype.getStructures = function () {
-        return {};
-    };
-    Object.defineProperty(ClustalMSA.prototype, "alignmentNames", {
-        get: function () {
-            return [];
-        },
-        enumerable: false,
-        configurable: true
-    });
-    ClustalMSA.prototype.getTree = function () {
-        return {
-            id: 'root',
-            noTree: true,
-            branchset: this.getNames().map(function (name) { return ({ id: name, name: name }); }),
-        };
-    };
-    Object.defineProperty(ClustalMSA.prototype, "seqConsensus", {
-        get: function () {
-            return this.MSA.consensus;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(ClustalMSA.prototype, "secondaryStructureConsensus", {
-        get: function () {
-            return undefined;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(ClustalMSA.prototype, "tracks", {
-        get: function () {
-            var _a;
-            return ((_a = this.seqConsensus) === null || _a === void 0 ? void 0 : _a.trim())
-                ? [
-                    {
-                        id: 'seqConsensus',
-                        name: 'Sequence consensus',
-                        data: this.seqConsensus,
-                        customColorScheme: {
-                            '*': 'white',
-                            ':': 'grey',
-                            '.': 'darkgrey',
-                            ' ': 'black',
-                        },
-                    },
-                ]
-                : [];
-        },
-        enumerable: false,
-        configurable: true
-    });
-    return ClustalMSA;
-}());
-export default ClustalMSA;

package/bundle/parsers/FastaMSA.d.ts

@@ -1,26 +0,0 @@
-export default class FastaMSA {
-    private MSA;
-    constructor(text: string);
-    getMSA(): {
-        seqdata: {
-            [key: string]: string;
-        };
-    };
-    getNames(): string[];
-    getRow(name: string): string[];
-    getWidth(): number;
-    getStructures(): {};
-    get alignmentNames(): never[];
-    getDetails(): {};
-    getTree(): {
-        id: string;
-        noTree: boolean;
-        branchset: {
-            id: string;
-            name: string;
-        }[];
-    };
-    get seqConsensus(): undefined;
-    get secondaryStructureConsensus(): undefined;
-    get tracks(): never[];
-}

package/bundle/parsers/FastaMSA.js

@@ -1,78 +0,0 @@
-var FastaMSA = /** @class */ (function () {
-    function FastaMSA(text) {
-        var seq = {};
-        var name = '';
-        var re = /^>(\S+)/;
-        text.split('\n').forEach(function (line) {
-            var match = re.exec(line);
-            if (match) {
-                seq[(name = match[1])] = '';
-            }
-            else if (name) {
-                seq[name] = seq[name] + line.replace(/[ \t]/g, '');
-            }
-        });
-        this.MSA = { seqdata: seq };
-    }
-    FastaMSA.prototype.getMSA = function () {
-        return this.MSA;
-    };
-    FastaMSA.prototype.getNames = function () {
-        return Object.keys(this.MSA.seqdata);
-    };
-    FastaMSA.prototype.getRow = function (name) {
-        var _a, _b;
-        return (_b = (_a = this.MSA) === null || _a === void 0 ? void 0 : _a.seqdata[name]) === null || _b === void 0 ? void 0 : _b.split('');
-    };
-    FastaMSA.prototype.getWidth = function () {
-        var _a;
-        var name = Object.keys((_a = this.MSA) === null || _a === void 0 ? void 0 : _a.seqdata)[0];
-        return this.getRow(name).length;
-    };
-    FastaMSA.prototype.getStructures = function () {
-        return {};
-    };
-    Object.defineProperty(FastaMSA.prototype, "alignmentNames", {
-        get: function () {
-            return [];
-        },
-        enumerable: false,
-        configurable: true
-    });
-    FastaMSA.prototype.getDetails = function () {
-        return {};
-    };
-    FastaMSA.prototype.getTree = function () {
-        return {
-            id: 'root',
-            noTree: true,
-            branchset: this.getNames().map(function (name) { return ({
-                id: name,
-                name: name,
-            }); }),
-        };
-    };
-    Object.defineProperty(FastaMSA.prototype, "seqConsensus", {
-        get: function () {
-            return undefined;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(FastaMSA.prototype, "secondaryStructureConsensus", {
-        get: function () {
-            return undefined;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(FastaMSA.prototype, "tracks", {
-        get: function () {
-            return [];
-        },
-        enumerable: false,
-        configurable: true
-    });
-    return FastaMSA;
-}());
-export default FastaMSA;

package/bundle/parsers/StockholmMSA.d.ts

@@ -1,75 +0,0 @@
-declare type StockholmEntry = {
-    gf: {
-        DE?: string[];
-        NH?: string[];
-    };
-    gs: {
-        AC: Record<string, string>;
-        DR: Record<string, string>;
-    };
-    gc?: {
-        SS_cons?: string;
-        seq_cons?: string;
-    };
-    seqdata: {
-        [key: string]: string;
-    };
-};
-export default class StockholmMSA {
-    private data;
-    private MSA;
-    constructor(text: string, currentAlignment: number);
-    getMSA(): StockholmEntry;
-    getRow(name: string): string[];
-    getWidth(): number;
-    get alignmentNames(): string[];
-    getDetails(): {
-        General: {
-            DE?: string[] | undefined;
-            NH?: string[] | undefined;
-        };
-        Accessions: Record<string, string>;
-        Dbxref: Record<string, string>;
-    };
-    getRowDetails(rowName: string): {
-        name: string;
-        accession: string;
-        dbxref: string;
-    };
-    getNames(): string[];
-    getSeqCoords(): void;
-    getStructures(): Record<string, {
-        pdb: string;
-        chain: string;
-        startPos: number;
-        endPos: number;
-    }[]>;
-    getTree(): import("../util").NodeWithIds | {
-        id: string;
-        noTree: boolean;
-        branchset: {
-            id: string;
-            name: string;
-        }[];
-    };
-    get seqConsensus(): string | undefined;
-    get secondaryStructureConsensus(): string | undefined;
-    get tracks(): ({
-        id: string;
-        name: string;
-        data: string | undefined;
-        customColorScheme: {
-            '>'?: undefined;
-            '<'?: undefined;
-        };
-    } | {
-        id: string;
-        name: string;
-        data: string | undefined;
-        customColorScheme: {
-            '>': string;
-            '<': string;
-        };
-    })[];
-}
-export {};

package/bundle/parsers/StockholmMSA.js

@@ -1,142 +0,0 @@
-var __rest = (this && this.__rest) || function (s, e) {
-    var t = {};
-    for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p) && e.indexOf(p) < 0)
-        t[p] = s[p];
-    if (s != null && typeof Object.getOwnPropertySymbols === "function")
-        for (var i = 0, p = Object.getOwnPropertySymbols(s); i < p.length; i++) {
-            if (e.indexOf(p[i]) < 0 && Object.prototype.propertyIsEnumerable.call(s, p[i]))
-                t[p[i]] = s[p[i]];
-        }
-    return t;
-};
-import Stockholm from 'stockholm-js';
-import parseNewick from '../parseNewick';
-import { generateNodeIds } from '../util';
-var StockholmMSA = /** @class */ (function () {
-    function StockholmMSA(text, currentAlignment) {
-        var res = Stockholm.parseAll(text);
-        this.data = res;
-        this.MSA = res[currentAlignment];
-    }
-    StockholmMSA.prototype.getMSA = function () {
-        return this.MSA;
-    };
-    StockholmMSA.prototype.getRow = function (name) {
-        var _a, _b;
-        return (_b = (_a = this.MSA) === null || _a === void 0 ? void 0 : _a.seqdata[name]) === null || _b === void 0 ? void 0 : _b.split('');
-    };
-    StockholmMSA.prototype.getWidth = function () {
-        var _a;
-        var name = Object.keys((_a = this.MSA) === null || _a === void 0 ? void 0 : _a.seqdata)[0];
-        return this.getRow(name).length;
-    };
-    Object.defineProperty(StockholmMSA.prototype, "alignmentNames", {
-        get: function () {
-            return this.data.map(function (aln, index) { var _a; return ((_a = aln.gf.DE) === null || _a === void 0 ? void 0 : _a[0]) || "Alignment " + (index + 1); });
-        },
-        enumerable: false,
-        configurable: true
-    });
-    StockholmMSA.prototype.getDetails = function () {
-        var _a, _b;
-        return {
-            General: this.MSA.gf,
-            Accessions: (_a = this.MSA.gs) === null || _a === void 0 ? void 0 : _a.AC,
-            Dbxref: (_b = this.MSA.gs) === null || _b === void 0 ? void 0 : _b.DR,
-        };
-    };
-    StockholmMSA.prototype.getRowDetails = function (rowName) {
-        var _a, _b;
-        return {
-            name: rowName,
-            accession: (_a = this.MSA.gs) === null || _a === void 0 ? void 0 : _a.AC[rowName],
-            dbxref: (_b = this.MSA.gs) === null || _b === void 0 ? void 0 : _b.DR[rowName],
-        };
-    };
-    StockholmMSA.prototype.getNames = function () {
-        return Object.keys(this.MSA.seqdata);
-    };
-    StockholmMSA.prototype.getSeqCoords = function () { };
-    StockholmMSA.prototype.getStructures = function () {
-        var _a;
-        var pdbRegex = /PDB; +(\S+) +(\S); ([0-9]+)-([0-9]+)/;
-        var ent = this.MSA;
-        return Object.entries(((_a = ent.gs) === null || _a === void 0 ? void 0 : _a.DR) || {})
-            .map(function (_a) {
-            var id = _a[0], dr = _a[1];
-            return [id, pdbRegex.exec(dr)];
-        })
-            .filter(function (item) { return !!item[1]; })
-            .map(function (_a) {
-            var id = _a[0], match = _a[1];
-            var pdb = match[1].toLowerCase();
-            var chain = match[2];
-            var startPos = +match[3];
-            var endPos = +match[4];
-            return { id: id, pdb: pdb, chain: chain, startPos: startPos, endPos: endPos };
-        })
-            .reduce(function (a, b) {
-            var id = b.id, rest = __rest(b, ["id"]);
-            if (!a[id]) {
-                a[id] = [];
-            }
-            a[id].push(rest);
-            return a;
-        }, {});
-    };
-    StockholmMSA.prototype.getTree = function () {
-        var _a, _b, _c;
-        var tree = (_c = (_b = (_a = this.MSA) === null || _a === void 0 ? void 0 : _a.gf) === null || _b === void 0 ? void 0 : _b.NH) === null || _c === void 0 ? void 0 : _c[0];
-        return tree
-            ? generateNodeIds(parseNewick(tree))
-            : {
-                id: 'root',
-                noTree: true,
-                branchset: this.getNames().map(function (name) { return ({
-                    id: name,
-                    name: name,
-                }); }),
-            };
-    };
-    Object.defineProperty(StockholmMSA.prototype, "seqConsensus", {
-        get: function () {
-            var _a;
-            return (_a = this.MSA.gc) === null || _a === void 0 ? void 0 : _a.seq_cons;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(StockholmMSA.prototype, "secondaryStructureConsensus", {
-        get: function () {
-            var _a;
-            return (_a = this.MSA.gc) === null || _a === void 0 ? void 0 : _a.SS_cons;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(StockholmMSA.prototype, "tracks", {
-        get: function () {
-            return [
-                {
-                    id: 'seqConsensus',
-                    name: 'Sequence consensus',
-                    data: this.seqConsensus,
-                    customColorScheme: {},
-                },
-                {
-                    id: 'secondaryStruct',
-                    name: 'Secondary-structure',
-                    data: this.secondaryStructureConsensus,
-                    customColorScheme: {
-                        '>': 'pink',
-                        '<': 'lightblue',
-                    },
-                },
-            ];
-        },
-        enumerable: false,
-        configurable: true
-    });
-    return StockholmMSA;
-}());
-export default StockholmMSA;

package/bundle/util.d.ts

@@ -1,17 +0,0 @@
-export declare function transform<T>(obj: Record<string, T>, cb: (arg0: [string, T]) => [string, T]): {
-    [k: string]: T;
-};
-export declare type Node = {
-    branchset?: Node[];
-};
-export declare type NodeWithIds = {
-    id: string;
-    branchset: NodeWithIds[];
-    noTree?: boolean;
-};
-export declare function generateNodeIds(tree: Node, parent?: string, depth?: number): NodeWithIds;
-export declare function colorContrast(colorScheme: {
-    [key: string]: string;
-}, theme: any): {
-    [k: string]: string;
-};

package/bundle/util.js

@@ -1,33 +0,0 @@
-var __assign = (this && this.__assign) || function () {
-    __assign = Object.assign || function(t) {
-        for (var s, i = 1, n = arguments.length; i < n; i++) {
-            s = arguments[i];
-            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
-                t[p] = s[p];
-        }
-        return t;
-    };
-    return __assign.apply(this, arguments);
-};
-import Color from 'color';
-export function transform(obj, cb) {
-    return Object.fromEntries(Object.entries(obj).map(cb));
-}
-export function generateNodeIds(tree, parent, depth) {
-    var _a;
-    if (parent === void 0) { parent = 'node'; }
-    if (depth === void 0) { depth = 0; }
-    var id = parent + "-" + depth;
-    return __assign(__assign({}, tree), { id: id, branchset: ((_a = tree.branchset) === null || _a === void 0 ? void 0 : _a.map(function (b, i) {
-            return generateNodeIds(b, id + "-" + i, depth + 1);
-        })) || [] });
-}
-export function colorContrast(colorScheme, theme) {
-    return transform(colorScheme, function (_a) {
-        var letter = _a[0], color = _a[1];
-        return [
-            letter,
-            theme.palette.getContrastText(Color(color).hex()),
-        ];
-    });
-}

package/dist/components/package.json

@@ -1,62 +0,0 @@
-{
-    "version": "1.3.0",
-    "license": "MIT",
-    "main": "dist/index.js",
-    "typings": "dist/index.d.ts",
-    "files": [
-        "dist",
-        "bundle"
-    ],
-    "engines": {
-        "node": ">=10"
-    },
-    "scripts": {
-        "lint": "eslint src",
-        "clean": "rimraf dist",
-        "prestart": "npm run clean",
-        "prebuild": "npm run clean",
-        "start": "yarn tsc --watch",
-        "build": "yarn tsc && rollup -c",
-        "preversion": "npm run build",
-        "postversion": "git push --follow-tags"
-    },
-    "peerDependencies": {
-        "@jbrowse/core": ">=1.5.1",
-        "@material-ui/core": ">=4.12.2",
-        "react": ">=16.8.0",
-        "react-dom": ">=16.8.0"
-    },
-    "name": "react-msaview",
-    "author": "Colin",
-    "devDependencies": {
-        "@rollup/plugin-commonjs": "^21.0.1",
-        "@rollup/plugin-json": "^4.1.0",
-        "@rollup/plugin-node-resolve": "^13.0.6",
-        "@rollup/plugin-typescript": "^8.3.0",
-        "@types/color": "^3.0.1",
-        "@types/d3": "^6.7.0",
-        "@types/lodash": "^4.14.170",
-        "@types/react": "^17.0.3",
-        "@types/react-dom": "^17.0.2",
-        "concurrently": "^6.2.0",
-        "eslint-config-react-app": "^6.0.0",
-        "react": "^17.0.1",
-        "react-dom": "^17.0.1",
-        "rollup": "^2.60.2",
-        "rollup-plugin-node-builtins": "^2.1.2",
-        "rollup-plugin-node-polyfills": "^0.2.1",
-        "rollup-plugin-polyfill-node": "^0.7.0",
-        "tslib": "^2.1.0",
-        "typescript": "^4.2.3"
-    },
-    "dependencies": {
-        "clustal-js": "^1.0.3",
-        "color": "^3.1.3",
-        "copy-to-clipboard": "^3.3.1",
-        "d3-array": "^2.12.0",
-        "d3-hierarchy": "^2.0.0",
-        "normalize-wheel": "^1.0.1",
-        "rbush": "^3.0.1",
-        "stockholm-js": "^1.0.10"
-    }
-}