react-msaview 1.3.1 → 2.0.0

package/dist/parsers/StockholmMSA.js

@@ -1,142 +1,113 @@
-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);
+export default class StockholmMSA {
+    constructor(text, currentAlignment) {
+        const res = Stockholm.parseAll(text);
         this.data = res;
         this.MSA = res[currentAlignment];
     }
-    StockholmMSA.prototype.getMSA = function () {
+    getMSA() {
         return this.MSA;
-    };
-    StockholmMSA.prototype.getRow = function (name) {
+    }
+    getRow(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 () {
+    }
+    getWidth() {
         var _a;
-        var name = Object.keys((_a = this.MSA) === null || _a === void 0 ? void 0 : _a.seqdata)[0];
+        const 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 () {
+    }
+    get alignmentNames() {
+        return this.data.map((aln, idx) => { var _a; return ((_a = aln.gf.DE) === null || _a === void 0 ? void 0 : _a[0]) || `Alignment ${idx + 1}`; });
+    }
+    getHeader() {
         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) {
+    }
+    getRowData(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 () {
+    }
+    getNames() {
         return Object.keys(this.MSA.seqdata);
-    };
-    StockholmMSA.prototype.getSeqCoords = function () { };
-    StockholmMSA.prototype.getStructures = function () {
+    }
+    getSeqCoords() { }
+    getStructures() {
         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] = [];
+        const pdbRegex = /PDB; +(\S+) +(\S); ([0-9]+)-([0-9]+)/;
+        const ent = this.MSA;
+        const args = Object.entries(((_a = ent.gs) === null || _a === void 0 ? void 0 : _a.DR) || {})
+            .map(([id, dr]) => [id, pdbRegex.exec(dr)])
+            .filter((item) => !!item[1])
+            .map(([id, match]) => {
+            const pdb = match[1].toLowerCase();
+            const chain = match[2];
+            const startPos = +match[3];
+            const endPos = +match[4];
+            return { id, pdb, chain, startPos, endPos };
+        });
+        const ret = {};
+        for (const entry of args) {
+            const { id, ...rest } = entry;
+            if (!ret[id]) {
+                ret[id] = [];
             }
-            a[id].push(rest);
-            return a;
-        }, {});
-    };
-    StockholmMSA.prototype.getTree = function () {
+            ret[id].push(rest);
+        }
+        return ret;
+    }
+    getTree() {
         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];
+        const 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',
+                name: 'root',
                 noTree: true,
-                branchset: this.getNames().map(function (name) { return ({
+                branchset: this.getNames().map(name => ({
                     id: name,
-                    name: name,
-                }); }),
+                    branchset: [],
+                    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',
-                    },
+    }
+    get seqConsensus() {
+        var _a;
+        return (_a = this.MSA.gc) === null || _a === void 0 ? void 0 : _a.seq_cons;
+    }
+    get secondaryStructureConsensus() {
+        var _a;
+        return (_a = this.MSA.gc) === null || _a === void 0 ? void 0 : _a.SS_cons;
+    }
+    get tracks() {
+        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;
+            },
+        ];
+    }
+}
+//# sourceMappingURL=StockholmMSA.js.map

package/dist/parsers/StockholmMSA.js.map

@@ -0,0 +1 @@
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package/dist/util.d.ts

@@ -1,17 +1,46 @@
+import { HierarchyNode } from 'd3-hierarchy';
+import { Theme } from '@mui/material';
 export declare function transform<T>(obj: Record<string, T>, cb: (arg0: [string, T]) => [string, T]): {
     [k: string]: T;
 };
-export declare type Node = {
+interface Node {
     branchset?: Node[];
-};
-export declare type NodeWithIds = {
+    name?: string;
+    [key: string]: unknown;
+}
+export type NodeWithIds = {
     id: string;
+    name: string;
     branchset: NodeWithIds[];
+    length?: number;
+    noTree?: boolean;
+};
+export type NodeWithIdsAndLength = {
+    id: string;
+    name: string;
+    branchset: NodeWithIdsAndLength[];
     noTree?: boolean;
+    length: number;
 };
 export declare function generateNodeIds(tree: Node, parent?: string, depth?: number): NodeWithIds;
 export declare function colorContrast(colorScheme: {
     [key: string]: string;
-}, theme: any): {
+}, theme: Theme): {
     [k: string]: string;
 };
+export declare function parseGFF(str?: string): {
+    seq_id: string;
+    source: string;
+    type: string;
+    start: number;
+    end: number;
+    score: number;
+    strand: string;
+    phase: string;
+}[] | undefined;
+export declare function skipBlanks(blanks: number[], arg: string | string[]): string;
+export declare function setBrLength(d: HierarchyNode<NodeWithIds>, y0: number, k: number): void;
+export declare function maxLength(d: HierarchyNode<NodeWithIds>): number;
+export declare function collapse(d: HierarchyNode<NodeWithIds>): void;
+export declare function clamp(min: number, num: number, max: number): number;
+export {};

package/dist/util.js

@@ -1,33 +1,85 @@
-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';
+import { max } from 'd3-array';
 export function transform(obj, cb) {
     return Object.fromEntries(Object.entries(obj).map(cb));
 }
-export function generateNodeIds(tree, parent, depth) {
+export function generateNodeIds(tree, parent = 'node', depth = 0) {
     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);
-        })) || [] });
+    const id = `${parent}-${depth}`;
+    return {
+        ...tree,
+        id,
+        name: tree.name || id,
+        branchset: ((_a = tree.branchset) === null || _a === void 0 ? void 0 : _a.map((b, i) => 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()),
-        ];
+    return transform(colorScheme, ([letter, color]) => [
+        letter,
+        theme.palette.getContrastText(Color(color).hex()),
+    ]);
+}
+export function parseGFF(str) {
+    return str === null || str === void 0 ? void 0 : str.split('\n').map(f => f.trim()).filter(f => !!f && !f.startsWith('#')).map(f => {
+        const [seq_id, source, type, start, end, score, strand, phase, col9] = f.split('\t');
+        return {
+            seq_id,
+            source,
+            type,
+            start: +start,
+            end: +end,
+            score: +score,
+            strand,
+            phase,
+            ...Object.fromEntries(col9
+                .split(';')
+                .map(f => f.trim())
+                .filter(f => !!f)
+                .map(f => f.split('='))
+                .map(([key, val]) => [
+                key.trim(),
+                decodeURIComponent(val).trim().split(',').join(' '),
+            ])),
+        };
     });
 }
+export function skipBlanks(blanks, arg) {
+    let s = '';
+    let b = 0;
+    for (let j = 0; j < arg.length; j++) {
+        if (j === blanks[b]) {
+            b++;
+        }
+        else {
+            s += arg[j];
+        }
+    }
+    return s;
+}
+export function setBrLength(d, y0, k) {
+    var _a;
+    // @ts-expect-error
+    d.len = (y0 += Math.max(d.data.length || 0, 0)) * k;
+    (_a = d.children) === null || _a === void 0 ? void 0 : _a.forEach(d => {
+        setBrLength(d, y0, k);
+    });
+}
+export function maxLength(d) {
+    return ((d.data.length || 1) + (d.children ? max(d.children, maxLength) || 0 : 0));
+}
+// Collapse the node and all it's children, from
+// https://bl.ocks.org/d3noob/43a860bc0024792f8803bba8ca0d5ecd
+export function collapse(d) {
+    if (d.children) {
+        // @ts-expect-error
+        d._children = d.children;
+        // @ts-expect-error
+        d._children.forEach(collapse);
+        // @ts-expect-error
+        d.children = null;
+    }
+}
+export function clamp(min, num, max) {
+    return Math.min(Math.max(num, min), max);
+}
+//# sourceMappingURL=util.js.map

package/dist/util.js.map

@@ -0,0 +1 @@
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package/dist/version.d.ts

@@ -0,0 +1 @@
+export declare const version = "1.3.2";

package/dist/version.js

@@ -0,0 +1,2 @@
+export const version = "1.3.2";
+//# sourceMappingURL=version.js.map

package/dist/version.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"version.js","sourceRoot":"","sources":["../src/version.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,OAAO,GAAG,OAAO,CAAC"}

package/package.json

@@ -1,11 +1,14 @@
 {
-  "version": "1.3.1",
+  "name": "react-msaview",
+  "type": "module",
+  "author": "Colin",
+  "version": "2.0.0",
   "license": "MIT",
   "main": "dist/index.js",
-  "typings": "dist/index.d.ts",
   "files": [
     "dist",
-    "bundle"
+    "bundle",
+    "src"
   ],
   "engines": {
     "node": ">=10"
@@ -13,50 +16,47 @@
   "scripts": {
     "lint": "eslint src",
     "clean": "rimraf dist",
-    "prestart": "npm run clean",
     "prebuild": "npm run clean",
-    "start": "yarn tsc --watch",
-    "build": "yarn tsc && rollup -c",
+    "prepublishOnly": "node -p \"'export const version = ' + JSON.stringify(require('./package.json').version) + ';'\" > src/version.ts",
+    "build": "tsc && rollup -c",
     "preversion": "npm run build",
     "postversion": "git push --follow-tags"
   },
   "peerDependencies": {
-    "@jbrowse/core": ">=1.5.1",
-    "@material-ui/core": ">=4.12.2",
+    "@jbrowse/core": ">=2.0.0",
+    "@mui/icons-material": ">=5.0.0",
+    "@mui/material": ">=5.0.0",
+    "mobx": ">=6.0.0",
+    "mobx-react": ">=7.0.0",
+    "mobx-state-tree": ">=5.0.0",
     "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",
+    "@rollup/plugin-commonjs": "^24.1.0",
+    "@rollup/plugin-json": "^6.0.0",
+    "@rollup/plugin-node-resolve": "^15.0.2",
+    "@rollup/plugin-replace": "^5.0.2",
+    "@rollup/plugin-terser": "^0.4.1",
+    "@rollup/plugin-typescript": "^11.1.0",
     "@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",
+    "@types/d3": "^7.4.0",
+    "@types/react": "^18.2.0",
+    "@types/react-dom": "^18.2.1",
+    "rollup": "^3.21.3",
+    "rollup-plugin-polyfill-node": "^0.12.0",
     "tslib": "^2.1.0",
-    "typescript": "^4.2.3"
+    "typescript": "^5.0.4"
   },
   "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",
+    "d3-array": "^3.2.3",
+    "d3-hierarchy": "^3.1.2",
     "normalize-wheel": "^1.0.1",
     "rbush": "^3.0.1",
-    "stockholm-js": "^1.0.10"
+    "stockholm-js": "^1.0.10",
+    "tss-react": "^4.8.3"
   }
 }

package/src/StructureModel.ts

@@ -0,0 +1,11 @@
+import { types } from 'mobx-state-tree'
+
+export const StructureModel = types.model({
+  id: types.identifier,
+  structure: types.model({
+    pdb: types.string,
+    startPos: types.number,
+    endPos: types.number,
+  }),
+  range: types.maybe(types.string),
+})

package/src/UniprotTrack.ts

@@ -0,0 +1,60 @@
+import { types, addDisposer } from 'mobx-state-tree'
+import { autorun } from 'mobx'
+
+// locals
+import { parseGFF } from './util'
+
+export const UniprotTrack = types
+  .model({
+    id: types.string,
+    accession: types.string,
+    name: types.string,
+    associatedRowName: types.string,
+    height: types.optional(types.number, 100),
+  })
+  .volatile(() => ({
+    error: undefined as unknown,
+    data: undefined as string | undefined,
+  }))
+  .actions(self => ({
+    setError(error: unknown) {
+      self.error = error
+    },
+    setData(data: string) {
+      self.data = data
+    },
+  }))
+  .actions(self => ({
+    afterCreate() {
+      addDisposer(
+        self,
+        autorun(async () => {
+          try {
+            const { accession } = self
+            const url = `https://rest.uniprot.org/uniprotkb/${accession}.gff`
+            const response = await fetch(url)
+            if (!response.ok) {
+              throw new Error(
+                `HTTP ${
+                  response.status
+                } fetching ${url}: ${await response.text()}`,
+              )
+            }
+            self.setData(await response.text())
+          } catch (e) {
+            console.error(e)
+            self.setError(e)
+          }
+        }),
+      )
+    },
+  }))
+  .views(self => ({
+    get loading() {
+      return !self.data
+    },
+
+    get features() {
+      return parseGFF(self.data)
+    },
+  }))