react-msaview 1.3.2 → 2.0.0

package/dist/StructureModel.d.ts

@@ -0,0 +1,9 @@
+export declare const StructureModel: import("mobx-state-tree").IModelType<{
+    id: import("mobx-state-tree").ISimpleType<string>;
+    structure: import("mobx-state-tree").IModelType<{
+        pdb: import("mobx-state-tree").ISimpleType<string>;
+        startPos: import("mobx-state-tree").ISimpleType<number>;
+        endPos: import("mobx-state-tree").ISimpleType<number>;
+    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+    range: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+}, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/dist/StructureModel.js

@@ -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),
+});
+//# sourceMappingURL=StructureModel.js.map

package/dist/StructureModel.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"StructureModel.js","sourceRoot":"","sources":["../src/StructureModel.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC,MAAM,CAAC,MAAM,cAAc,GAAG,KAAK,CAAC,KAAK,CAAC;IACxC,EAAE,EAAE,KAAK,CAAC,UAAU;IACpB,SAAS,EAAE,KAAK,CAAC,KAAK,CAAC;QACrB,GAAG,EAAE,KAAK,CAAC,MAAM;QACjB,QAAQ,EAAE,KAAK,CAAC,MAAM;QACtB,MAAM,EAAE,KAAK,CAAC,MAAM;KACrB,CAAC;IACF,KAAK,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;CACjC,CAAC,CAAA"}

package/dist/UniprotTrack.d.ts

@@ -0,0 +1,27 @@
+export declare const UniprotTrack: import("mobx-state-tree").IModelType<{
+    id: import("mobx-state-tree").ISimpleType<string>;
+    accession: import("mobx-state-tree").ISimpleType<string>;
+    name: import("mobx-state-tree").ISimpleType<string>;
+    associatedRowName: import("mobx-state-tree").ISimpleType<string>;
+    height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+}, {
+    error: unknown;
+    data: string | undefined;
+} & {
+    setError(error: unknown): void;
+    setData(data: string): void;
+} & {
+    afterCreate(): void;
+} & {
+    readonly loading: boolean;
+    readonly features: {
+        seq_id: string;
+        source: string;
+        type: string;
+        start: number;
+        end: number;
+        score: number;
+        strand: string;
+        phase: string;
+    }[] | undefined;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/dist/UniprotTrack.js

@@ -0,0 +1,52 @@
+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,
+    data: undefined,
+}))
+    .actions(self => ({
+    setError(error) {
+        self.error = error;
+    },
+    setData(data) {
+        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);
+    },
+}));
+//# sourceMappingURL=UniprotTrack.js.map

package/dist/UniprotTrack.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"UniprotTrack.js","sourceRoot":"","sources":["../src/UniprotTrack.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAA;AACpD,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAE9B,SAAS;AACT,OAAO,EAAE,QAAQ,EAAE,MAAM,QAAQ,CAAA;AAEjC,MAAM,CAAC,MAAM,YAAY,GAAG,KAAK;KAC9B,KAAK,CAAC;IACL,EAAE,EAAE,KAAK,CAAC,MAAM;IAChB,SAAS,EAAE,KAAK,CAAC,MAAM;IACvB,IAAI,EAAE,KAAK,CAAC,MAAM;IAClB,iBAAiB,EAAE,KAAK,CAAC,MAAM;IAC/B,MAAM,EAAE,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,MAAM,EAAE,GAAG,CAAC;CAC1C,CAAC;KACD,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;IACf,KAAK,EAAE,SAAoB;IAC3B,IAAI,EAAE,SAA+B;CACtC,CAAC,CAAC;KACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IAChB,QAAQ,CAAC,KAAc;QACrB,IAAI,CAAC,KAAK,GAAG,KAAK,CAAA;IACpB,CAAC;IACD,OAAO,CAAC,IAAY;QAClB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;IAClB,CAAC;CACF,CAAC,CAAC;KACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IAChB,WAAW;QACT,WAAW,CACT,IAAI,EACJ,OAAO,CAAC,KAAK,IAAI,EAAE;YACjB,IAAI;gBACF,MAAM,EAAE,SAAS,EAAE,GAAG,IAAI,CAAA;gBAC1B,MAAM,GAAG,GAAG,sCAAsC,SAAS,MAAM,CAAA;gBACjE,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,GAAG,CAAC,CAAA;gBACjC,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE;oBAChB,MAAM,IAAI,KAAK,CACb,QACE,QAAQ,CAAC,MACX,aAAa,GAAG,KAAK,MAAM,QAAQ,CAAC,IAAI,EAAE,EAAE,CAC7C,CAAA;iBACF;gBACD,IAAI,CAAC,OAAO,CAAC,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC,CAAA;aACpC;YAAC,OAAO,CAAC,EAAE;gBACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;gBAChB,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;aACjB;QACH,CAAC,CAAC,CACH,CAAA;IACH,CAAC;CACF,CAAC,CAAC;KACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACd,IAAI,OAAO;QACT,OAAO,CAAC,IAAI,CAAC,IAAI,CAAA;IACnB,CAAC;IAED,IAAI,QAAQ;QACV,OAAO,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;IAC5B,CAAC;CACF,CAAC,CAAC,CAAA"}

package/dist/colorSchemes.d.ts

@@ -8,9 +8,9 @@ export declare function getClustalXColor(stats: {
     [key: string]: number;
 }, model: {
     columns: Record<string, string>;
-}, row: number, col: number): "rgb(128,179,230)" | "#d88" | "rgb(192, 72, 192)" | "rgb(204, 77, 204)" | "#8f8" | "rgb(26,204,26)" | "rgb(240, 128, 128)" | "rgb(240, 144, 72)" | "rgb(204, 204, 0)" | "rgb(26, 179, 179)" | undefined;
+}, row: string, col: number): "rgb(128,179,230)" | "#d88" | "rgb(192, 72, 192)" | "rgb(204, 77, 204)" | "#8f8" | "rgb(26,204,26)" | "rgb(240, 128, 128)" | "rgb(240, 144, 72)" | "rgb(204, 204, 0)" | "rgb(26, 179, 179)" | undefined;
 export declare function getPercentIdentityColor(stats: {
     [key: string]: number;
 }, model: {
     columns: Record<string, string>;
-}, row: number, col: number): string | undefined;
+}, row: string, col: number): string | undefined;

package/dist/colorSchemes.js

@@ -1,6 +1,6 @@
 import Color from 'color';
 import { transform } from './util';
-var colorSchemes = {
+const colorSchemes = {
     clustal: {
         G: 'orange',
         P: 'orange',
@@ -62,7 +62,7 @@ var colorSchemes = {
         T: 'red',
     },
     percent_identity_dynamic: {},
-    //https://github.com/biotite-dev/biotite/blob/8c460972f8ab904312f130dfb80f3efc8c9bd7c5/src/biotite/sequence/graphics/color_schemes/flower.json
+    // https://github.com/biotite-dev/biotite/blob/8c460972f8ab904312f130dfb80f3efc8c9bd7c5/src/biotite/sequence/graphics/color_schemes/flower.json
     flower: {
         A: '#b18a51',
         C: '#ff5701',
@@ -92,7 +92,7 @@ var colorSchemes = {
         T: '#f53737',
         U: '#f53737',
     },
-    //https://github.com/biotite-dev/biotite/blob/8c460972f8ab904312f130dfb80f3efc8c9bd7c5/src/biotite/sequence/graphics/color_schemes/clustalx_protein.json
+    // https://github.com/biotite-dev/biotite/blob/8c460972f8ab904312f130dfb80f3efc8c9bd7c5/src/biotite/sequence/graphics/color_schemes/clustalx_protein.json
     clustalx_protein: {
         A: '#197fe5',
         C: '#e57f7f',
@@ -323,30 +323,24 @@ var colorSchemes = {
 };
 // turn all supplied colors to hex colors which getContrastText from mui
 // requires
-export default transform(colorSchemes, function (_a) {
-    var key = _a[0], val = _a[1];
-    return [
-        key,
-        transform(val, function (_a) {
-            var letter = _a[0], color = _a[1];
-            return [letter, Color(color).hex()];
-        }),
-    ];
-});
+export default transform(colorSchemes, ([key, val]) => [
+    key,
+    transform(val, ([letter, color]) => [letter, Color(color).hex()]),
+]);
 // info http://www.jalview.org/help/html/colourSchemes/clustal.html
 // modifications:
 // reference to clustalX source code scheme modifies what the jalview.org
 // scheme says there the jalview.org colorscheme says WLVIMAFCHP but it
 // should be WLVIMAFCHPY, colprot.xml says e.g. %#ACFHILMVWYPp" which has Y
 export function getClustalXColor(stats, model, row, col) {
-    var total = Object.values(stats).reduce(function (a, b) { return a + b; }, 0);
-    var l = model.columns[row][col];
-    var _a = stats.W, W = _a === void 0 ? 0 : _a, _b = stats.L, L = _b === void 0 ? 0 : _b, _c = stats.V, V = _c === void 0 ? 0 : _c, _d = stats.I, I = _d === void 0 ? 0 : _d, _e = stats.M, M = _e === void 0 ? 0 : _e, _f = stats.A, A = _f === void 0 ? 0 : _f, _g = stats.F, F = _g === void 0 ? 0 : _g, _h = stats.C, C = _h === void 0 ? 0 : _h, _j = stats.H, H = _j === void 0 ? 0 : _j, _k = stats.P, P = _k === void 0 ? 0 : _k, _l = stats.R, R = _l === void 0 ? 0 : _l, _m = stats.K, K = _m === void 0 ? 0 : _m, _o = stats.Q, Q = _o === void 0 ? 0 : _o, _p = stats.E, E = _p === void 0 ? 0 : _p, _q = stats.D, D = _q === void 0 ? 0 : _q, _r = stats.T, T = _r === void 0 ? 0 : _r, _s = stats.S, S = _s === void 0 ? 0 : _s, _t = stats.G, G = _t === void 0 ? 0 : _t, _u = stats.Y, Y = _u === void 0 ? 0 : _u, _v = stats.N, N = _v === void 0 ? 0 : _v;
-    var WLVIMAFCHP = W + L + V + I + M + A + F + C + H + P + Y;
-    var KR = K + R;
-    var QE = Q + E;
-    var ED = E + D;
-    var TS = T + S;
+    const total = Object.values(stats).reduce((a, b) => a + b, 0);
+    const l = model.columns[row][col];
+    const { W = 0, L = 0, V = 0, I = 0, M = 0, A = 0, F = 0, C = 0, H = 0, P = 0, R = 0, K = 0, Q = 0, E = 0, D = 0, T = 0, S = 0, G = 0, Y = 0, N = 0, } = stats;
+    const WLVIMAFCHP = W + L + V + I + M + A + F + C + H + P + Y;
+    const KR = K + R;
+    const QE = Q + E;
+    const ED = E + D;
+    const TS = T + S;
     if (WLVIMAFCHP / total > 0.6) {
         if (l === 'W' ||
             l === 'L' ||
@@ -434,22 +428,23 @@ export function getClustalXColor(stats, model, row, col) {
 // scheme says there the jalview.org colorscheme says WLVIMAFCHP but it
 // should be WLVIMAFCHPY, colprot.xml says e.g. %#ACFHILMVWYPp" which has Y
 export function getPercentIdentityColor(stats, model, row, col) {
-    var total = Object.values(stats).reduce(function (a, b) { return a + b; }, 0);
-    var l = model.columns[row][col];
-    var entries = Object.entries(stats);
-    var ent = 0;
-    var letter = '';
-    for (var i = 0; i < entries.length; i++) {
+    const total = Object.values(stats).reduce((a, b) => a + b, 0);
+    const l = model.columns[row][col];
+    const entries = Object.entries(stats);
+    let ent = 0;
+    let letter = '';
+    for (let i = 0; i < entries.length; i++) {
         if (entries[i][1] > ent && entries[i][0] !== '-') {
             letter = entries[i][0];
             ent = entries[i][1];
         }
     }
-    var proportion = ent / total;
-    var thresh = "hsl(240, 30%, ".concat(100 * Math.max(1 - ent / total / 3, 0.3), "%)");
+    const proportion = ent / total;
+    const thresh = `hsl(240, 30%, ${100 * Math.max(1 - ent / total / 3, 0.3)}%)`;
     if (proportion > 0.4) {
         if (l === letter) {
             return thresh;
         }
     }
 }
+//# sourceMappingURL=colorSchemes.js.map

package/dist/colorSchemes.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"colorSchemes.js","sourceRoot":"","sources":["../src/colorSchemes.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,SAAS,EAAE,MAAM,QAAQ,CAAA;AAElC,MAAM,YAAY,GAAG;IACnB,OAAO,EAAE;QACP,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,KAAK;QACR,CAAC,EAAE,KAAK;QACR,CAAC,EAAE,KAAK;QACR,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;KACX;IACD,IAAI,EAAE;QACJ,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,KAAK;QACR,CAAC,EAAE,KAAK;QACR,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,MAAM;KACV;IACD,QAAQ,EAAE;QACR,CAAC,EAAE,YAAY;QACf,CAAC,EAAE,YAAY;QACf,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,WAAW;QACd,CAAC,EAAE,WAAW;QACd,CAAC,EAAE,WAAW;QACd,CAAC,EAAE,WAAW;QACd,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,UAAU;QACb,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,KAAK;QACR,CAAC,EAAE,KAAK;KACT;IAED,wBAAwB,EAAE,EAAE;IAC5B,+IAA+I;IAC/I,MAAM,EAAE;QACN,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IACD,WAAW,EAAE;QACX,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IAED,yJAAyJ;IACzJ,gBAAgB,EAAE;QAChB,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IAED,4BAA4B;IAC5B,wBAAwB,EAAE,EAAE;IAE5B,YAAY,EAAE;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IACD,cAAc,EAAE;QACd,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IAED,sBAAsB,EAAE;QACtB,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IAED,iBAAiB,EAAE;QACjB,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IAED,kBAAkB,EAAE;QAClB,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IAED,gBAAgB,EAAE;QAChB,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IAED,cAAc,EAAE;QACd,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SA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package/dist/components/AboutDlg.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 export default function AboutDialog({ onClose, open, }: {
     onClose: () => void;
     open: boolean;

package/dist/components/AboutDlg.js

@@ -1,50 +1,40 @@
-import React, { useState } from 'react';
-import { Dialog, DialogTitle, DialogContent, Typography, Link, } from '@material-ui/core';
-import { version } from './package.json';
-function LicenseDialog(_a) {
-    var onClose = _a.onClose, open = _a.open;
-    return (React.createElement(Dialog, { onClose: function () { return onClose(); }, open: open },
-        React.createElement(DialogTitle, null, "Biotite License"),
+import React from 'react';
+import { Dialog } from '@jbrowse/core/ui';
+import { DialogContent, Typography, Link } from '@mui/material';
+import { version } from '../version';
+export default function AboutDialog({ onClose, open, }) {
+    return (React.createElement(Dialog, { onClose: () => onClose(), open: open, title: "About this plugin" },
         React.createElement(DialogContent, null,
-            React.createElement("pre", { style: { height: 100, overflow: 'auto' } }, "\nCopyright 2017 - 2020, The Biotite contributors\nAll rights reserved.\n\nRedistribution and use in source and binary forms, with or without modification,\nare permitted provided that the following conditions are met:\n\n1. Redistributions of source code must retain the above copyright notice, this\nlist of conditions and the following disclaimer.\n\n2. Redistributions in binary form must reproduce the above copyright notice,\nthis list of conditions and the following disclaimer in the documentation and/or\nother materials provided with the distribution.\n\n3. Neither the name of the copyright holder nor the names of its contributors\nmay be used to endorse or promote products derived from this software without\nspecific prior written permission.\n\nTHIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\" AND\nANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED\nWARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\nDISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR\nANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES\n(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;\nLOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON\nANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT\n(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS\nSOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n        "))));
-}
-export default function AboutDialog(_a) {
-    var onClose = _a.onClose, open = _a.open;
-    var _b = useState(false), dlgOpen = _b[0], setDlgOpen = _b[1];
-    return (React.createElement(React.Fragment, null,
-        React.createElement(LicenseDialog, { onClose: function () { return setDlgOpen(false); }, open: dlgOpen }),
-        React.createElement(Dialog, { onClose: function () { return onClose(); }, open: open },
-            React.createElement(DialogTitle, null, "About this plugin"),
-            React.createElement(DialogContent, null,
-                React.createElement(Typography, null,
-                    "MSAView ",
-                    version,
-                    " (",
-                    React.createElement(Link, { href: "https://github.com/gmod/jbrowse-plugin-msaview" }, "Github"),
-                    ")"),
-                React.createElement("ul", null,
-                    React.createElement("li", null,
-                        React.createElement(Typography, null,
-                            "We use some color schemes from the",
-                            ' ',
-                            React.createElement(Link, { href: "https://github.com/biotite-dev/biotite" }, "biotite"),
-                            ' ',
-                            "project, and their license is reproduced",
-                            ' ',
-                            React.createElement(Link, { onClick: function () { return setDlgOpen(true); } }, "here"))),
-                    React.createElement("li", null,
-                        React.createElement(Typography, null,
-                            "See this page for some information on jalview colorings",
-                            ' ',
-                            React.createElement(Link, { href: "https://www.jalview.org/help/html/colourSchemes/" }, "here"))),
-                    React.createElement("li", null,
-                        React.createElement(Typography, null,
-                            "See this page for some info on the clustal, cinema, maeditor, and lesk color schemes",
-                            ' ',
-                            React.createElement(Link, { href: "http://www.bioinformatics.nl/~berndb/aacolour.html" }, "here"))),
-                    React.createElement("li", null,
-                        React.createElement(Typography, null,
-                            "See this paper about the flower color scheme",
-                            ' ',
-                            React.createElement(Link, { href: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7245768/" }, "here"))))))));
+            React.createElement(Typography, null,
+                "MSAView ",
+                version,
+                " (",
+                React.createElement(Link, { href: "https://github.com/gmod/jbrowse-plugin-msaview" }, "Github"),
+                ")"),
+            React.createElement("ul", null,
+                React.createElement("li", null,
+                    React.createElement(Typography, null,
+                        "We use some color schemes from the",
+                        ' ',
+                        React.createElement(Link, { href: "https://github.com/biotite-dev/biotite" }, "biotite"),
+                        ' ',
+                        "project, and their license is reproduced",
+                        ' ',
+                        React.createElement(Link, { href: "https://github.com/biotite-dev/biotite/blob/master/LICENSE.rst" }, "here"))),
+                React.createElement("li", null,
+                    React.createElement(Typography, null,
+                        "See this page for some information on jalview colorings",
+                        ' ',
+                        React.createElement(Link, { href: "https://www.jalview.org/help/html/colourSchemes/" }, "here"))),
+                React.createElement("li", null,
+                    React.createElement(Typography, null,
+                        "See this page for some info on the clustal, cinema, maeditor, and lesk color schemes",
+                        ' ',
+                        React.createElement(Link, { href: "http://www.bioinformatics.nl/~berndb/aacolour.html" }, "here"))),
+                React.createElement("li", null,
+                    React.createElement(Typography, null,
+                        "See this paper about the flower color scheme",
+                        ' ',
+                        React.createElement(Link, { href: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7245768/" }, "here")))))));
 }
+//# sourceMappingURL=AboutDlg.js.map

package/dist/components/AboutDlg.js.map

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

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { MsaViewModel } from '../model';
 declare const _default: ({ model, onClose, open, }: {
     model: MsaViewModel;

package/dist/components/AddTrackDlg.js

@@ -1,26 +1,26 @@
 import React, { useState } from 'react';
-import { Dialog, DialogTitle, DialogContent, DialogActions, Button, TextField, MenuItem, Typography, } from '@material-ui/core';
-import { FileSelector } from '@jbrowse/core/ui';
+import { DialogContent, DialogActions, Button, TextField, MenuItem, Typography, } from '@mui/material';
+import { Dialog, FileSelector } from '@jbrowse/core/ui';
 import { observer } from 'mobx-react';
-export default observer(function (_a) {
-    var model = _a.model, onClose = _a.onClose, open = _a.open;
-    var options = model.rows.map(function (r) { return r[0]; });
-    var _b = useState(), trackFile = _b[0], setTrackFile = _b[1];
-    var _c = useState(''), currentOption = _c[0], setCurrentOption = _c[1];
-    return (React.createElement(Dialog, { onClose: function () { return onClose(); }, open: open },
-        React.createElement(DialogTitle, null, "Add track"),
+export default observer(function ({ model, onClose, open, }) {
+    const options = model.rows.map(r => r[0]);
+    const [trackFile, setTrackFile] = useState();
+    const [currentOption, setCurrentOption] = useState('');
+    return (React.createElement(Dialog, { onClose: () => onClose(), open: open, title: "Add track" },
         React.createElement(DialogContent, null,
             React.createElement(Typography, null, "Open relevant per-alignment tracks e.g. protein domains"),
-            React.createElement(TextField, { select: true, helperText: "Which row does this track apply to?", value: currentOption, onChange: function (event) {
+            React.createElement(TextField, { select: true, helperText: "Which row does this track apply to?", value: currentOption, onChange: event => {
                     setCurrentOption(event.target.value);
-                } }, options.map(function (option, index) { return (React.createElement(MenuItem, { key: "".concat(option, "-").concat(index), value: option }, option)); })),
+                } }, options.map((option, index) => (React.createElement(MenuItem, { key: `${option}-${index}`, value: option }, option)))),
             React.createElement(FileSelector, { location: trackFile, setLocation: setTrackFile }),
             React.createElement(DialogActions, null,
-                React.createElement(Button, { onClick: function () {
+                React.createElement(Button, { onClick: () => {
                         model.setError(undefined);
                         if (trackFile) {
+                            // eslint-disable-next-line @typescript-eslint/no-floating-promises
                             model.setMSAFilehandle(trackFile);
                         }
                     }, variant: "contained", color: "primary" }, "Open"),
-                React.createElement(Button, { color: "secondary", variant: "contained", onClick: function () { return onClose(); } }, "Cancel")))));
+                React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => onClose() }, "Cancel")))));
 });
+//# sourceMappingURL=AddTrackDlg.js.map

package/dist/components/AddTrackDlg.js.map

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

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { MsaViewModel } from '../model';
 declare const _default: ({ onClose, data, model, }: {
     model: MsaViewModel;

package/dist/components/AnnotationDlg.js

@@ -1,45 +1,35 @@
-var __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
-    if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
-        if (ar || !(i in from)) {
-            if (!ar) ar = Array.prototype.slice.call(from, 0, i);
-            ar[i] = from[i];
-        }
-    }
-    return to.concat(ar || Array.prototype.slice.call(from));
-};
 import React, { useState } from 'react';
 import { observer } from 'mobx-react';
-import { Button, Dialog, DialogActions, DialogTitle, DialogContent, IconButton, TextField, Typography, } from '@material-ui/core';
-import DeleteIcon from '@material-ui/icons/Delete';
-var specialFromEntries = function (val) {
-    var ret = {};
-    val.forEach(function (_a) {
-        var key = _a[0], val = _a[1];
-        if (!ret[key])
+import { Button, DialogActions, DialogContent, IconButton, TextField, Typography, } from '@mui/material';
+import { Dialog } from '@jbrowse/core/ui';
+// icons
+import DeleteIcon from '@mui/icons-material/Delete';
+const specialFromEntries = (val) => {
+    const ret = {};
+    val.forEach(([key, val]) => {
+        if (!ret[key]) {
             ret[key] = [];
+        }
         ret[key].push(val);
     });
     return ret;
 };
-var Row = observer(function (_a) {
-    var name = _a.name, value = _a.value, setValue = _a.setValue, setName = _a.setName, onDelete = _a.onDelete;
+const Row = observer(function ({ name, value, setValue, setName, onDelete, }) {
     return (React.createElement("div", null,
         React.createElement(IconButton, { onClick: onDelete, style: { margin: 10 } },
             React.createElement(DeleteIcon, null)),
-        React.createElement(TextField, { value: name, onChange: function (event) { return setName(event.target.value); }, label: "Key" }),
-        React.createElement(TextField, { value: value, onChange: function (event) { return setValue(event.target.value); }, label: "Value" })));
+        React.createElement(TextField, { value: name, onChange: event => setName(event.target.value), label: "Key" }),
+        React.createElement(TextField, { value: value, onChange: event => setValue(event.target.value), label: "Value" })));
 });
-export default observer(function (_a) {
-    var onClose = _a.onClose, data = _a.data, model = _a.model;
-    var blanks = model.blanks;
-    var l = data.left, r = data.right;
-    var _b = useState([
+export default observer(({ onClose, data, model, }) => {
+    const { blanks } = model;
+    const { left: l, right: r } = data;
+    const [rows, setRows] = useState([
         ['Name', ''],
         ['ID', ''],
         ['Note', ''],
-    ]), rows = _b[0], setRows = _b[1];
-    return (React.createElement(Dialog, { onClose: function () { return onClose(); }, open: true },
-        React.createElement(DialogTitle, null, "Create new region annotation"),
+    ]);
+    return (React.createElement(Dialog, { onClose: () => onClose(), open: true, title: "Create new region annotation" },
         React.createElement(DialogContent, null,
             React.createElement(Typography, null,
                 "Do you want to add an annotation to the MSA at ",
@@ -48,30 +38,28 @@ export default observer(function (_a) {
                 r,
                 ' ',
                 blanks.length
-                    ? " (gapped ".concat(model.getPos(l), "..").concat(model.getPos(r))
+                    ? ` (gapped ${model.getPos(l)}..${model.getPos(r)}`
                     : ''),
-            rows.map(function (_a, index) {
-                var key = _a[0], val = _a[1];
-                return (React.createElement(Row, { key: index, name: key, value: val, setValue: function (newValue) {
-                        var newRows = __spreadArray([], rows, true);
-                        newRows[index][1] = newValue;
-                        setRows(newRows);
-                    }, setName: function (newName) {
-                        var newRows = __spreadArray([], rows, true);
-                        newRows[index][0] = newName;
-                        setRows(newRows);
-                    }, onDelete: function () {
-                        rows.splice(index, 1);
-                        setRows(__spreadArray([], rows, true));
-                    } }));
-            }),
-            React.createElement(Button, { onClick: function () {
-                    setRows(__spreadArray(__spreadArray([], rows, true), [['', '']], false));
+            rows.map(([key, val], index) => (React.createElement(Row, { key: index, name: key, value: val, setValue: newValue => {
+                    const newRows = [...rows];
+                    newRows[index][1] = newValue;
+                    setRows(newRows);
+                }, setName: newName => {
+                    const newRows = [...rows];
+                    newRows[index][0] = newName;
+                    setRows(newRows);
+                }, onDelete: () => {
+                    rows.splice(index, 1);
+                    setRows([...rows]);
+                } }))),
+            React.createElement(Button, { onClick: () => {
+                    setRows([...rows, ['', '']]);
                 } }, "Add row"),
             React.createElement(DialogActions, null,
-                React.createElement(Button, { onClick: function () {
+                React.createElement(Button, { onClick: () => {
                         model.addAnnotation(l, r, specialFromEntries(rows));
                         onClose();
                     }, variant: "contained", color: "primary" }, "Submit"),
-                React.createElement(Button, { variant: "contained", color: "secondary", onClick: function () { return onClose(); } }, "Cancel")))));
+                React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => onClose() }, "Cancel")))));
 });
+//# sourceMappingURL=AnnotationDlg.js.map

package/dist/components/AnnotationDlg.js.map

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

@@ -1,7 +1,6 @@
-/// <reference types="react" />
-import { MsaViewModel } from '../model';
-declare const AnnotationTrack: ({ model, track }: {
+import { IBoxTrack, MsaViewModel } from '../model';
+declare const AnnotationTrack: ({ model, track, }: {
     model: MsaViewModel;
-    track: any;
+    track: IBoxTrack;
 }) => JSX.Element;
 export default AnnotationTrack;