react-msaview 1.2.8 → 1.3.0

package/dist/model.d.ts

@@ -74,54 +74,102 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
     drawNodeBubbles: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     highResScaleFactor: import("mobx-state-tree").IType<number | undefined, number, number>;
     colorSchemeName: import("mobx-state-tree").IType<string | undefined, string, string>;
-    treeFilehandle: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+    treeFilehandle: 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>;
         baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+            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").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        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<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
         name: import("mobx-state-tree").ISimpleType<string>;
         blobId: import("mobx-state-tree").ISimpleType<string>;
     }>>, {
+        locationType: "UriLocation";
         uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
     } | import("mobx-state-tree").ModelSnapshotType<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
         localPath: import("mobx-state-tree").ISimpleType<string>;
     }> | import("mobx-state-tree").ModelSnapshotType<{
+        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").ModelCreationType<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>>;
+        internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+            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").ModelInstanceTypeProps<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
         localPath: import("mobx-state-tree").ISimpleType<string>;
     }> | import("mobx-state-tree").ModelInstanceTypeProps<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
         name: import("mobx-state-tree").ISimpleType<string>;
         blobId: import("mobx-state-tree").ISimpleType<string>;
-    }>>>;
-    msaFilehandle: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+    }>>, 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>;
         baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+            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").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        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<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
         name: import("mobx-state-tree").ISimpleType<string>;
         blobId: import("mobx-state-tree").ISimpleType<string>;
     }>>, {
+        locationType: "UriLocation";
         uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
     } | import("mobx-state-tree").ModelSnapshotType<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
         localPath: import("mobx-state-tree").ISimpleType<string>;
     }> | import("mobx-state-tree").ModelSnapshotType<{
+        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").ModelCreationType<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>>;
+        internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+            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").ModelInstanceTypeProps<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
         localPath: import("mobx-state-tree").ISimpleType<string>;
     }> | import("mobx-state-tree").ModelInstanceTypeProps<{
+        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")._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>>;
@@ -141,7 +189,16 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
         afterCreate(): void;
     } & {
         readonly loading: boolean;
-        readonly features: any;
+        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>>;
     turnedOffTracks: import("mobx-state-tree").IMapType<import("mobx-state-tree").ISimpleType<boolean>>;
     annotatedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
@@ -159,7 +216,7 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
 }, {
     width: number;
 } & {
-    readonly menuItems: import("@jbrowse/core/ui").MenuItem[];
+    menuItems(): import("@jbrowse/core/ui").MenuItem[];
 } & {
     setDisplayName(name: string): void;
     setWidth(newWidth: number): void;
@@ -314,18 +371,34 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
     highResScaleFactor: number;
     colorSchemeName: string;
     treeFilehandle: {
+        locationType: "UriLocation";
         uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
     } | import("mobx-state-tree").ModelSnapshotType<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
         localPath: import("mobx-state-tree").ISimpleType<string>;
     }> | import("mobx-state-tree").ModelSnapshotType<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
         name: import("mobx-state-tree").ISimpleType<string>;
         blobId: import("mobx-state-tree").ISimpleType<string>;
     }> | undefined;
     msaFilehandle: {
+        locationType: "UriLocation";
         uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
     } | import("mobx-state-tree").ModelSnapshotType<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
         localPath: import("mobx-state-tree").ISimpleType<string>;
     }> | import("mobx-state-tree").ModelSnapshotType<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
         name: import("mobx-state-tree").ISimpleType<string>;
         blobId: import("mobx-state-tree").ISimpleType<string>;
     }> | undefined;

package/dist/model.js

@@ -56,10 +56,14 @@ var __rest = (this && this.__rest) || function (s, e) {
         }
     return t;
 };
-var __spreadArray = (this && this.__spreadArray) || function (to, from) {
-    for (var i = 0, il = from.length, j = to.length; i < il; i++, j++)
-        to[j] = from[i];
-    return to;
+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 { cast, types, addDisposer } from 'mobx-state-tree';
 import { hierarchy, cluster } from 'd3-hierarchy';
@@ -74,7 +78,6 @@ import StockholmMSA from './parsers/StockholmMSA';
 import FastaMSA from './parsers/FastaMSA';
 import parseNewick from './parseNewick';
 import colorSchemes from './colorSchemes';
-import gff from '@gmod/gff';
 import { generateNodeIds } from './util';
 import TextTrack from './components/TextTrack';
 import BoxTrack from './components/BoxTrack';
@@ -183,7 +186,22 @@ var UniprotTrack = types
         return !self.data;
     },
     get features() {
-        return gff.parseStringSync(self.data).map(function (f) { return f[0]; });
+        var _a;
+        return (_a = self.data) === null || _a === void 0 ? void 0 : _a.split('\n').map(function (f) { return f.trim(); }).filter(function (f) { return !!f; }).filter(function (f) { return !f.startsWith('#'); }).map(function (f) {
+            var _a = f.split('\t'), seq_id = _a[0], source = _a[1], type = _a[2], start = _a[3], end = _a[4], score = _a[5], strand = _a[6], phase = _a[7], col9 = _a[8];
+            return __assign({ seq_id: seq_id, source: source, type: type, start: +start, end: +end, score: +score, strand: strand, phase: phase }, Object.fromEntries(col9
+                .split(';')
+                .map(function (f) { return f.trim(); })
+                .filter(function (f) { return !!f; })
+                .map(function (f) { return f.split('='); })
+                .map(function (_a) {
+                var key = _a[0], val = _a[1];
+                return [
+                    key.trim(),
+                    decodeURIComponent(val).trim().split(',').join(' '),
+                ];
+            })));
+        });
     },
 }); });
 var MSAModel = types
@@ -776,7 +794,7 @@ var MSAModel = types
                 },
             ]
             : [];
-        return __spreadArray(__spreadArray(__spreadArray([], adapterTracks), boxTracks), annotationTracks);
+        return __spreadArray(__spreadArray(__spreadArray([], adapterTracks, true), boxTracks, true), annotationTracks, true);
     },
     get turnedOnTracks() {
         return this.tracks.filter(function (f) { return !self.turnedOffTracks.has(f.model.id); });

package/package.json

@@ -1,10 +1,11 @@
 {
-  "version": "1.2.8",
+  "version": "1.3.0",
   "license": "MIT",
   "main": "dist/index.js",
   "typings": "dist/index.d.ts",
   "files": [
-    "dist"
+    "dist",
+    "bundle"
   ],
   "engines": {
     "node": ">=10"
@@ -15,14 +16,12 @@
     "prestart": "npm run clean",
     "prebuild": "npm run clean",
     "start": "yarn tsc --watch",
-    "build": "yarn tsc",
-    "size": "size-limit",
-    "analyze": "size-limit --why",
+    "build": "yarn tsc && rollup -c",
     "preversion": "npm run build",
     "postversion": "git push --follow-tags"
   },
   "peerDependencies": {
-    "@jbrowse/core": ">=1.3.0",
+    "@jbrowse/core": ">=1.5.1",
     "@material-ui/core": ">=4.12.2",
     "react": ">=16.8.0",
     "react-dom": ">=16.8.0"
@@ -30,21 +29,27 @@
   "name": "react-msaview",
   "author": "Colin",
   "devDependencies": {
-    "@size-limit/preset-small-lib": "^4.10.1",
+    "@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",
-    "husky": "^5.1.3",
     "react": "^17.0.1",
     "react-dom": "^17.0.1",
-    "size-limit": "^4.10.1",
+    "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": {
-    "@gmod/gff": "^1.1.2",
     "clustal-js": "^1.0.3",
     "color": "^3.1.3",
     "copy-to-clipboard": "^3.3.1",