react-msaview 2.0.0 → 2.1.1

package/dist/components/{TracklistDlg.js → dialogs/TracklistDlg.js}

@@ -2,9 +2,9 @@ import React from 'react';
 import { Dialog } from '@jbrowse/core/ui';
 import { DialogContent, FormControlLabel, FormGroup, Checkbox, DialogActions, Button, Typography, } from '@mui/material';
 import { observer } from 'mobx-react';
-export default observer(function ({ model, onClose, open, }) {
+export default observer(function ({ model, onClose, }) {
     const { tracks } = model;
-    return (React.createElement(Dialog, { onClose: () => onClose(), open: open, title: "Add track" },
+    return (React.createElement(Dialog, { onClose: () => onClose(), open: true, title: "Add track" },
         React.createElement(DialogContent, null,
             React.createElement(Typography, null, "Open relevant per-alignment tracks e.g. protein domains"),
             React.createElement(FormGroup, null, tracks.map(track => {

package/dist/components/dialogs/TracklistDlg.js.map

@@ -0,0 +1 @@
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package/dist/components/util.js

@@ -37,7 +37,6 @@ export function makeTicks(start, end, bpPerPx, emitMajor = true, emitMinor = tru
         return [];
     }
     if (bpPerPx < 0) {
-        // eslint-disable-next-line @typescript-eslint/no-extra-semi
         ;
         [minBase, maxBase] = [maxBase, minBase];
     }

package/dist/components/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/components/util.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AACH,MAAM,UAAU,eAAe,CAC7B,KAAa,EACb,eAAuB,EACvB,eAAuB;IAEvB,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;IACvB,MAAM,eAAe,GAAG,eAAe,GAAG,KAAK,CAAA;IAC/C,MAAM,cAAc,GAAG,QAAQ,CAC7B,MAAM,CAAC,eAAe,CAAC,CAAC,aAAa,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,EACtD,EAAE,CACH,CAAA;IAED,IAAI,UAAU,GAAG,EAAE,IAAI,cAAc,CAAA;IACrC,OAAO,UAAU,GAAG,eAAe,EAAE;QACnC,UAAU,IAAI,CAAC,CAAA;QACf,IAAI,UAAU,IAAI,eAAe,EAAE;YACjC,MAAK;SACN;QACD,UAAU,IAAI,GAAG,CAAA;KAClB;IAED,UAAU,GAAG,IAAI,CAAC,GAAG,CAAC,UAAU,EAAE,CAAC,CAAC,CAAA;IAEpC,MAAM,YAAY,GAAG,UAAU,GAAG,KAAK,CAAA;IAEvC,IAAI,UAAU,GAAG,CAAC,CAAA;IAClB,IAAI,CAAC,CAAC,UAAU,GAAG,EAAE,CAAC,IAAI,YAAY,GAAG,EAAE,IAAI,eAAe,EAAE;QAC9D,UAAU,GAAG,UAAU,GAAG,EAAE,CAAA;KAC7B;SAAM,IAAI,CAAC,CAAC,UAAU,GAAG,CAAC,CAAC,IAAI,YAAY,GAAG,CAAC,IAAI,eAAe,EAAE;QACnE,UAAU,GAAG,UAAU,GAAG,CAAC,CAAA;KAC5B;SAAM,IAAI,CAAC,CAAC,UAAU,GAAG,CAAC,CAAC,IAAI,YAAY,GAAG,CAAC,IAAI,eAAe,EAAE;QACnE,UAAU,GAAG,UAAU,GAAG,CAAC,CAAA;KAC5B;IAED,OAAO,EAAE,UAAU,EAAE,UAAU,EAAE,CAAA;AACnC,CAAC;AACD,MAAM,UAAU,SAAS,CACvB,KAAa,EACb,GAAW,EACX,OAAe,EACf,SAAS,GAAG,IAAI,EAChB,SAAS,GAAG,IAAI;IAEhB,MAAM,SAAS,GAAG,eAAe,CAAC,OAAO,EAAE,EAAE,EAAE,EAAE,CAAC,CAAA;IAElD,IAAI,OAAO,GAAG,KAAK,CAAA;IACnB,IAAI,OAAO,GAAG,GAAG,CAAA;IACjB,IAAI,OAAO,KAAK,IAAI,IAAI,OAAO,KAAK,IAAI,EAAE;QACxC,OAAO,EAAE,CAAA;KACV;IAED,IAAI,OAAO,GAAG,CAAC,EAAE;QACf,CAAC;QAAA,CAAC,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,OAAO,EAAE,OAAO,CAAC,CAAA;KACzC;IAED,4EAA4E;IAC5E,8CAA8C;IAC9C,OAAO,IAAI,IAAI,CAAC,GAAG,CAAC,EAAE,GAAG,OAAO,CAAC,CAAA;IACjC,OAAO,IAAI,IAAI,CAAC,GAAG,CAAC,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,CAAA;IAErC,MAAM,SAAS,GAAG,SAAS,CAAC,UAAU,IAAI,SAAS,CAAC,UAAU,CAAA;IAC9D,IAAI,KAAK,GAAG,CAAC,CAAA;IACb,MAAM,KAAK,GAAG,EAAE,CAAA;IAChB,KACE,IAAI,IAAI,GAAG,IAAI,CAAC,IAAI,CAAC,OAAO,GAAG,SAAS,CAAC,GAAG,SAAS,EACrD,IAAI,GAAG,OAAO,EACd,IAAI,IAAI,SAAS,EACjB;QACA,IAAI,SAAS,IAAI,IAAI,GAAG,CAAC,SAAS,CAAC,UAAU,GAAG,CAAC,CAAC,EAAE;YAClD,KAAK,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,IAAI,GAAG,CAAC,EAAE,KAAK,EAAE,CAAC,CAAA;YACpD,KAAK,IAAI,CAAC,CAAA;SACX;aAAM,IAAI,SAAS,IAAI,CAAC,CAAC,IAAI,GAAG,CAAC,SAAS,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,EAAE;YAC5D,KAAK,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,IAAI,GAAG,CAAC,EAAE,KAAK,EAAE,CAAC,CAAA;YACpD,KAAK,IAAI,CAAC,CAAA;SACX;KACF;IACD,OAAO,KAAK,CAAA;AACd,CAAC;AAED,MAAM,UAAU,SAAS,CAAC,GAAW;IACnC,IAAI,GAAG,GAAG,GAAG,EAAE;QACb,OAAO,MAAM,CAAC,GAAG,CAAC,CAAA;KACnB;IACD,OAAO,GAAG,SAAS,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,IAAI,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAC,GAAG,GAAG,IAAI,CAAC,EAAE,CAAC,KAAK,CAChE,CAAC,CAAC,EACF,CAAC,CAAC,GAAG,CAAC,CACP,EAAE,CAAA;AACL,CAAC"}

package/dist/model.d.ts

@@ -1,4 +1,4 @@
-/// <reference types="react" />
+import React from 'react';
 import { Instance, SnapshotIn } from 'mobx-state-tree';
 import { HierarchyNode } from 'd3-hierarchy';
 import { FileLocation as FileLocationType } from '@jbrowse/core/util/types';
@@ -22,9 +22,7 @@ interface BasicTrackModel {
     height: number;
 }
 export interface TextTrackModel extends BasicTrackModel {
-    customColorScheme?: {
-        [key: string]: string;
-    };
+    customColorScheme?: Record<string, string>;
     data: string;
 }
 export interface BoxTrackModel extends BasicTrackModel {
@@ -107,7 +105,17 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
     }> | import("mobx-state-tree").ModelSnapshotType<{
         locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
         localPath: import("mobx-state-tree").ISimpleType<string>;
-    }>, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+    }>, import("mobx-state-tree").ModelInstanceType<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree").ISimpleType<string>;
+    }, {}> | import("mobx-state-tree").ModelInstanceType<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }, {}> | ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
         locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
         uri: import("mobx-state-tree").ISimpleType<string>;
         baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -116,14 +124,7 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
             internetAccountType: import("mobx-state-tree").ISimpleType<string>;
             authInfo: import("mobx-state-tree").IType<any, any, any>;
         }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    }>> | import("mobx-state-tree").ModelInstanceType<{
-        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
-        name: import("mobx-state-tree").ISimpleType<string>;
-        blobId: import("mobx-state-tree").ISimpleType<string>;
-    }, {}> | import("mobx-state-tree").ModelInstanceType<{
-        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-        localPath: import("mobx-state-tree").ISimpleType<string>;
-    }, {}>>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     msaFilehandle: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
         locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
         uri: import("mobx-state-tree").ISimpleType<string>;
@@ -155,7 +156,17 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
     }> | import("mobx-state-tree").ModelSnapshotType<{
         locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
         localPath: import("mobx-state-tree").ISimpleType<string>;
-    }>, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+    }>, import("mobx-state-tree").ModelInstanceType<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree").ISimpleType<string>;
+    }, {}> | import("mobx-state-tree").ModelInstanceType<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }, {}> | ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
         locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
         uri: import("mobx-state-tree").ISimpleType<string>;
         baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -164,14 +175,7 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
             internetAccountType: import("mobx-state-tree").ISimpleType<string>;
             authInfo: import("mobx-state-tree").IType<any, any, any>;
         }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    }>> | import("mobx-state-tree").ModelInstanceType<{
-        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
-        name: import("mobx-state-tree").ISimpleType<string>;
-        blobId: import("mobx-state-tree").ISimpleType<string>;
-    }, {}> | import("mobx-state-tree").ModelInstanceType<{
-        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-        localPath: import("mobx-state-tree").ISimpleType<string>;
-    }, {}>>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     currentAlignment: import("mobx-state-tree").IType<number | undefined, number, number>;
     collapsed: import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>;
     showOnly: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -224,12 +228,13 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
     setWidth(newWidth: number): void;
     setMinimized(flag: boolean): void;
 } & {
+    rulerHeight: number;
     error: unknown;
     margin: {
         left: number;
         top: number;
     };
-    DialogComponent: import("react").FC<any> | undefined;
+    DialogComponent: React.FC<any> | undefined;
     DialogProps: any;
     annotPos: {
         left: number;
@@ -282,9 +287,7 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
 } & {
     readonly blocks2d: number[][];
     readonly done: string | false | undefined;
-    readonly colorScheme: {
-        [key: string]: string;
-    };
+    readonly colorScheme: Record<string, string>;
     readonly header: {};
     getRowData(name: string): {
         range?: {
@@ -308,13 +311,11 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
     readonly mouseOverRowName: string | undefined;
     getMouseOverResidue(rowName: string): string;
     readonly root: HierarchyNode<NodeWithIds>;
-    readonly structures: {
-        [key: string]: {
-            pdb: string;
-            startPos: number;
-            endPos: number;
-        }[];
-    };
+    readonly structures: Record<string, {
+        pdb: string;
+        startPos: number;
+        endPos: number;
+    }[]>;
     readonly inverseStructures: {
         [k: string]: {
             id: string;
@@ -327,9 +328,7 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
         [k: string]: string;
     };
     readonly columns2d: string[];
-    readonly colStats: {
-        [key: string]: number;
-    }[];
+    readonly colStats: Record<string, number>[];
     readonly hierarchy: HierarchyNode<NodeWithIdsAndLength>;
     readonly totalHeight: number;
 } & {
@@ -353,9 +352,7 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
     relativePxToBp(rowName: string, position: number): number;
     getPos(pos: number): number;
 } & {
-    addAnnotation(start: number, end: number, attributes: {
-        [key: string]: string[];
-    }): void;
+    addAnnotation(start: number, end: number, attributes: Record<string, string[]>): void;
     setOffsets(left: number, right: number): void;
     clearAnnotPos(): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, import("mobx-state-tree")._NotCustomized, {

package/dist/model.js

@@ -67,6 +67,7 @@ const MSAModel = types
     })), { tree: '', msa: '' }),
 })
     .volatile(() => ({
+    rulerHeight: 20,
     error: undefined,
     margin: { left: 20, top: 20 },
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
@@ -373,8 +374,8 @@ const MSAModel = types
             .filter((item) => !!item);
         for (let i = 0; i < ((_a = strs[0]) === null || _a === void 0 ? void 0 : _a.length); i++) {
             let counter = 0;
-            for (let j = 0; j < strs.length; j++) {
-                if (strs[j][i] === '-') {
+            for (const str of strs) {
+                if (str[i] === '-') {
                     counter++;
                 }
             }
@@ -398,14 +399,14 @@ const MSAModel = types
     },
     get colStats() {
         const r = [];
-        const m = this.columns2d;
-        for (let i = 0; i < m.length; i++) {
-            for (let j = 0; j < m[i].length; j++) {
+        const columns = this.columns2d;
+        for (const column of columns) {
+            for (let j = 0; j < column.length; j++) {
                 const l = r[j] || {};
-                if (!l[m[i][j]]) {
-                    l[m[i][j]] = 0;
+                if (!l[column[j]]) {
+                    l[column[j]] = 0;
                 }
-                l[m[i][j]]++;
+                l[column[j]]++;
                 r[j] = l;
             }
         }
@@ -483,12 +484,11 @@ const MSAModel = types
         return (_a = self.MSA) === null || _a === void 0 ? void 0 : _a.seqConsensus;
     },
     get conservation() {
-        const m = self.columns2d;
-        if (m.length) {
-            for (let i = 0; i < m[0].length; i++) {
+        if (self.columns2d.length) {
+            for (let i = 0; i < self.columns2d[0].length; i++) {
                 const col = [];
-                for (let j = 0; j < m.length; j++) {
-                    col.push(m[j][i]);
+                for (const column of self.columns2d) {
+                    col.push(column[i]);
                 }
             }
         }
@@ -597,17 +597,20 @@ const MSAModel = types
     relativePxToBp(rowName, position) {
         const { rowNames, rows } = self;
         const index = rowNames.indexOf(rowName);
-        const row = rows[index][1];
-        let k = 0;
-        for (let i = 0; i < position; i++) {
-            if (row[i] !== '-') {
-                k++;
-            }
-            else if (k >= position) {
-                break;
+        if (index !== -1) {
+            const row = rows[index][1];
+            let k = 0;
+            for (let i = 0; i < position; i++) {
+                if (row[i] !== '-') {
+                    k++;
+                }
+                else if (k >= position) {
+                    break;
+                }
             }
+            return k;
         }
-        return k;
+        return 0;
     },
     getPos(pos) {
         let j = 0;

package/dist/model.js.map

@@ -1 +1 @@
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package/dist/parseNewick.js

@@ -58,6 +58,7 @@
  * }
  */
 export default function parse(s) {
+    var _a;
     const ancestors = [];
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
     let tree = {};
@@ -72,11 +73,10 @@ export default function parse(s) {
                 tree = subtree;
                 break;
             case ',': // another branch
-                ancestors[ancestors.length - 1].branchset.push(subtree);
+                (_a = ancestors.at(-1)) === null || _a === void 0 ? void 0 : _a.branchset.push(subtree);
                 tree = subtree;
                 break;
             case ')': // optional name next
-                // eslint-disable-next-line @typescript-eslint/no-explicit-any
                 tree = ancestors.pop();
                 break;
             case ':': // optional length next

package/dist/parseNewick.js.map

@@ -1 +1 @@
-{"version":3,"file":"parseNewick.js","sourceRoot":"","sources":["../src/parseNewick.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA0DG;AACH,MAAM,CAAC,OAAO,UAAU,KAAK,CAAC,CAAS;IACrC,MAAM,SAAS,GAAG,EAAE,CAAA;IACpB,8DAA8D;IAC9D,IAAI,IAAI,GAAG,EAAyB,CAAA;IACpC,MAAM,MAAM,GAAG,CAAC,CAAC,KAAK,CAAC,qBAAqB,CAAC,CAAA;IAC7C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QACtC,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;QACvB,MAAM,OAAO,GAAG,EAAE,CAAA;QAClB,QAAQ,KAAK,EAAE;YACb,KAAK,GAAG,EAAE,gBAAgB;gBACxB,IAAI,CAAC,SAAS,GAAG,CAAC,OAAO,CAAC,CAAA;gBAC1B,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBACpB,IAAI,GAAG,OAAO,CAAA;gBACd,MAAK;YACP,KAAK,GAAG,EAAE,iBAAiB;gBACzB,SAAS,CAAC,SAAS,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,SAAS,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACvD,IAAI,GAAG,OAAO,CAAA;gBACd,MAAK;YACP,KAAK,GAAG,EAAE,qBAAqB;gBAC7B,8DAA8D;gBAC9D,IAAI,GAAG,SAAS,CAAC,GAAG,EAAyB,CAAA;gBAC7C,MAAK;YACP,KAAK,GAAG,EAAE,uBAAuB;gBAC/B,MAAK;YACP,OAAO,CAAC,CAAC;gBACP,MAAM,CAAC,GAAG,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;gBACvB,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,EAAE;oBACvC,IAAI,CAAC,IAAI,GAAG,KAAK,CAAA;iBAClB;qBAAM,IAAI,CAAC,KAAK,GAAG,EAAE;oBACpB,IAAI,CAAC,MAAM,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;iBAChC;aACF;SACF;KACF;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}
+{"version":3,"file":"parseNewick.js","sourceRoot":"","sources":["../src/parseNewick.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA0DG;AACH,MAAM,CAAC,OAAO,UAAU,KAAK,CAAC,CAAS;;IACrC,MAAM,SAAS,GAAG,EAAE,CAAA;IACpB,8DAA8D;IAC9D,IAAI,IAAI,GAAG,EAAyB,CAAA;IACpC,MAAM,MAAM,GAAG,CAAC,CAAC,KAAK,CAAC,qBAAqB,CAAC,CAAA;IAC7C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QACtC,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;QACvB,MAAM,OAAO,GAAG,EAAE,CAAA;QAClB,QAAQ,KAAK,EAAE;YACb,KAAK,GAAG,EAAE,gBAAgB;gBACxB,IAAI,CAAC,SAAS,GAAG,CAAC,OAAO,CAAC,CAAA;gBAC1B,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBACpB,IAAI,GAAG,OAAO,CAAA;gBACd,MAAK;YACP,KAAK,GAAG,EAAE,iBAAiB;gBACzB,MAAA,SAAS,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,0CAAE,SAAS,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACzC,IAAI,GAAG,OAAO,CAAA;gBACd,MAAK;YACP,KAAK,GAAG,EAAE,qBAAqB;gBAC7B,IAAI,GAAG,SAAS,CAAC,GAAG,EAAG,CAAA;gBACvB,MAAK;YACP,KAAK,GAAG,EAAE,uBAAuB;gBAC/B,MAAK;YACP,OAAO,CAAC,CAAC;gBACP,MAAM,CAAC,GAAG,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;gBACvB,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,EAAE;oBACvC,IAAI,CAAC,IAAI,GAAG,KAAK,CAAA;iBAClB;qBAAM,IAAI,CAAC,KAAK,GAAG,EAAE;oBACpB,IAAI,CAAC,MAAM,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;iBAChC;aACF;SACF;KACF;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}

package/dist/parsers/FastaMSA.d.ts

@@ -3,9 +3,7 @@ export default class FastaMSA {
     private MSA;
     constructor(text: string);
     getMSA(): {
-        seqdata: {
-            [key: string]: string;
-        };
+        seqdata: Record<string, string>;
     };
     getRowData(): undefined;
     getNames(): string[];

package/dist/parsers/FastaMSA.js

@@ -7,14 +7,14 @@ function parseSmallFasta(text) {
         const [id, ...description] = defLine.split(' ');
         const descriptionStr = description.join(' ');
         const seqLinesStr = seqLines.join('');
-        const sequence = seqLinesStr.replace(/\s/g, '');
+        const sequence = seqLinesStr.replaceAll(/\s/g, '');
         return { id, description: descriptionStr, sequence };
     });
 }
 export default class FastaMSA {
     constructor(text) {
         this.MSA = {
-            seqdata: Object.fromEntries(parseSmallFasta(text).map((m, i) => [`${m.id}-${i}`, m.sequence])),
+            seqdata: Object.fromEntries(parseSmallFasta(text).map(m => [`${m.id}`, m.sequence])),
         };
     }
     getMSA() {

package/dist/parsers/FastaMSA.js.map

@@ -1 +1 @@
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+{"version":3,"file":"FastaMSA.js","sourceRoot":"","sources":["../../src/parsers/FastaMSA.ts"],"names":[],"mappings":"AAEA,SAAS,eAAe,CAAC,IAAY;IACnC,OAAO,IAAI;SACR,KAAK,CAAC,GAAG,CAAC;SACV,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;SACzB,GAAG,CAAC,SAAS,CAAC,EAAE;QACf,MAAM,CAAC,OAAO,EAAE,GAAG,QAAQ,CAAC,GAAG,SAAS,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACpD,MAAM,CAAC,EAAE,EAAE,GAAG,WAAW,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QAC/C,MAAM,cAAc,GAAG,WAAW,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QAC5C,MAAM,WAAW,GAAG,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;QACrC,MAAM,QAAQ,GAAG,WAAW,CAAC,UAAU,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;QAClD,OAAO,EAAE,EAAE,EAAE,WAAW,EAAE,cAAc,EAAE,QAAQ,EAAE,CAAA;IACtD,CAAC,CAAC,CAAA;AACN,CAAC;AACD,MAAM,CAAC,OAAO,OAAO,QAAQ;IAE3B,YAAY,IAAY;QACtB,IAAI,CAAC,GAAG,GAAG;YACT,OAAO,EAAE,MAAM,CAAC,WAAW,CACzB,eAAe,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CACxD;SACF,CAAA;IACH,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,UAAU;QACR,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IACtC,CAAC;IAED,MAAM,CAAC,IAAY;;QACjB,OAAO,MAAA,MAAA,IAAI,CAAC,GAAG,0CAAE,OAAO,CAAC,IAAI,CAAC,0CAAE,KAAK,CAAC,EAAE,CAAC,CAAA;IAC3C,CAAC;IAED,QAAQ;;QACN,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,MAAA,IAAI,CAAC,GAAG,0CAAE,OAAO,CAAC,CAAC,CAAC,CAAC,CAAA;QAC9C,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,CAAA;IACjC,CAAC;IAED,aAAa;QACX,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,EAAE,CAAA;IACX,CAAC;IAED,SAAS;QACP,OAAO,EAAE,CAAA;IACX,CAAC;IAED,OAAO;QACL,OAAO;YACL,EAAE,EAAE,MAAM;YACV,IAAI,EAAE,MAAM;YACZ,MAAM,EAAE,IAAI;YACZ,SAAS,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACtC,EAAE,EAAE,IAAI;gBACR,SAAS,EAAE,EAAE;gBACb,IAAI;aACL,CAAC,CAAC;SACJ,CAAA;IACH,CAAC;IAED,IAAI,YAAY;QACd,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,IAAI,2BAA2B;QAC7B,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,MAAM;QACR,OAAO,EAAE,CAAA;IACX,CAAC;CACF"}

package/dist/parsers/StockholmMSA.d.ts

@@ -1,5 +1,5 @@
 import { NodeWithIds } from '../util';
-type StockholmEntry = {
+interface StockholmEntry {
     gf: {
         DE?: string[];
         NH?: string[];
@@ -12,10 +12,8 @@ type StockholmEntry = {
         SS_cons?: string;
         seq_cons?: string;
     };
-    seqdata: {
-        [key: string]: string;
-    };
-};
+    seqdata: Record<string, string>;
+}
 export default class StockholmMSA {
     private data;
     private MSA;

package/dist/parsers/StockholmMSA.js

@@ -31,11 +31,11 @@ export default class StockholmMSA {
         };
     }
     getRowData(rowName) {
-        var _a, _b;
+        var _a, _b, _c, _d;
         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],
+            accession: (_b = (_a = this.MSA.gs) === null || _a === void 0 ? void 0 : _a.AC) === null || _b === void 0 ? void 0 : _b[rowName],
+            dbxref: (_d = (_c = this.MSA.gs) === null || _c === void 0 ? void 0 : _c.DR) === null || _d === void 0 ? void 0 : _d[rowName],
         };
     }
     getNames() {

package/dist/parsers/StockholmMSA.js.map

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

@@ -8,24 +8,22 @@ interface Node {
     name?: string;
     [key: string]: unknown;
 }
-export type NodeWithIds = {
+export interface NodeWithIds {
     id: string;
     name: string;
     branchset: NodeWithIds[];
     length?: number;
     noTree?: boolean;
-};
-export type NodeWithIdsAndLength = {
+}
+export interface 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: Theme): {
+export declare function colorContrast(colorScheme: Record<string, string>, theme: Theme): {
     [k: string]: string;
 };
 export declare function parseGFF(str?: string): {

package/dist/util.js

@@ -1,5 +1,7 @@
-import Color from 'color';
 import { max } from 'd3-array';
+import { colord, extend } from 'colord';
+import namesPlugin from 'colord/plugins/names';
+extend([namesPlugin]);
 export function transform(obj, cb) {
     return Object.fromEntries(Object.entries(obj).map(cb));
 }
@@ -16,7 +18,7 @@ export function generateNodeIds(tree, parent = 'node', depth = 0) {
 export function colorContrast(colorScheme, theme) {
     return transform(colorScheme, ([letter, color]) => [
         letter,
-        theme.palette.getContrastText(Color(color).hex()),
+        theme.palette.getContrastText(colord(color).toHex()),
     ]);
 }
 export function parseGFF(str) {

package/dist/util.js.map

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package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "1.3.2";
+export declare const version = "2.1.1";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = "1.3.2";
+export const version = '2.1.1';
 //# sourceMappingURL=version.js.map

package/dist/version.js.map

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