react-msaview 1.2.9 → 1.3.1

package/dist/components/ImportForm.js

@@ -7,8 +7,9 @@ import { smallTree, smallMSA, smallMSAOnly } from './data/seq2';
 var ListItem = function (_a) {
     var onClick = _a.onClick, model = _a.model, children = _a.children;
     return (React.createElement("li", null,
-        React.createElement(Link, { onClick: function () {
+        React.createElement(Link, { onClick: function (event) {
                 model.setError(undefined);
+                event.preventDefault();
                 onClick();
             }, href: "#" },
             React.createElement(Typography, null, children))));
@@ -47,6 +48,7 @@ export default observer(function (_a) {
                     React.createElement(ListItem, { model: model, onClick: function () {
                             model.setTreeFilehandle({
                                 uri: 'https://jbrowse.org/genomes/newick_trees/sarscov2phylo.pub.ft.nh',
+                                locationType: 'UriLocation',
                             });
                         } }, "230k COVID-19 samples (tree only)"),
                     React.createElement(ListItem, { model: model, onClick: function () {
@@ -58,30 +60,36 @@ export default observer(function (_a) {
                     React.createElement(ListItem, { model: model, onClick: function () {
                             model.setMSAFilehandle({
                                 uri: 'https://ihh.github.io/abrowse/build/pfam-cov2.stock',
+                                locationType: 'UriLocation',
                             });
                         } }, "PFAM SARS-CoV2 multi-stockholm"),
                     React.createElement(ListItem, { model: model, onClick: function () {
                             model.setMSAFilehandle({
                                 uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/Lysine.stock',
+                                locationType: 'UriLocation',
                             });
                         } }, "Lysine stockholm file"),
                     React.createElement(ListItem, { model: model, onClick: function () {
                             model.setMSAFilehandle({
                                 uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/PF01601_full.txt',
+                                locationType: 'UriLocation',
                             });
                         } }, "PF01601 stockholm file (SARS-CoV2 spike protein)"),
                     React.createElement(ListItem, { model: model, onClick: function () {
                             model.setMSAFilehandle({
                                 uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/europe_covid.fa',
+                                locationType: 'UriLocation',
                             });
                         } }, "Europe COVID full genomes (LR883044.1 and 199 other sequences)"),
                     React.createElement(ListItem, { model: model, onClick: function () {
                             transaction(function () {
                                 model.setMSAFilehandle({
                                     uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/rhv_test-only.aligned_with_mafft_auto.fa',
+                                    locationType: 'UriLocation',
                                 });
                                 model.setTreeFilehandle({
                                     uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/rhv_test-only.aligned_with_mafft_auto.nh',
+                                    locationType: 'UriLocation',
                                 });
                             });
                         } }, "MAFFT+VeryFastTree(17.9k samples)"))))));

package/dist/components/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"
@@ -30,6 +29,10 @@
     "name": "react-msaview",
     "author": "Colin",
     "devDependencies": {
+        "@rollup/plugin-commonjs": "^21.0.1",
+        "@rollup/plugin-json": "^4.1.0",
+        "@rollup/plugin-node-resolve": "^13.0.6",
+        "@rollup/plugin-typescript": "^8.3.0",
         "@types/color": "^3.0.1",
         "@types/d3": "^6.7.0",
         "@types/lodash": "^4.14.170",
@@ -39,11 +42,14 @@
         "eslint-config-react-app": "^6.0.0",
         "react": "^17.0.1",
         "react-dom": "^17.0.1",
+        "rollup": "^2.60.2",
+        "rollup-plugin-node-builtins": "^2.1.2",
+        "rollup-plugin-node-polyfills": "^0.2.1",
+        "rollup-plugin-polyfill-node": "^0.7.0",
         "tslib": "^2.1.0",
         "typescript": "^4.2.3"
     },
     "dependencies": {
-        "@gmod/gff": "^1.1.2",
         "clustal-js": "^1.0.3",
         "color": "^3.1.3",
         "copy-to-clipboard": "^3.3.1",

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<{
@@ -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

@@ -78,7 +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';
@@ -187,7 +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
@@ -281,7 +295,9 @@ var MSAModel = types
         self.selectedStructures = [];
     },
     setError: function (error) {
-        console.error(error);
+        if (error) {
+            console.error(error);
+        }
         self.error = error;
     },
     setMousePos: function (col, row) {

package/package.json

@@ -1,10 +1,11 @@
 {
-  "version": "1.2.9",
+  "version": "1.3.1",
   "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"
@@ -30,6 +29,10 @@
   "name": "react-msaview",
   "author": "Colin",
   "devDependencies": {
+    "@rollup/plugin-commonjs": "^21.0.1",
+    "@rollup/plugin-json": "^4.1.0",
+    "@rollup/plugin-node-resolve": "^13.0.6",
+    "@rollup/plugin-typescript": "^8.3.0",
     "@types/color": "^3.0.1",
     "@types/d3": "^6.7.0",
     "@types/lodash": "^4.14.170",
@@ -39,11 +42,14 @@
     "eslint-config-react-app": "^6.0.0",
     "react": "^17.0.1",
     "react-dom": "^17.0.1",
+    "rollup": "^2.60.2",
+    "rollup-plugin-node-builtins": "^2.1.2",
+    "rollup-plugin-node-polyfills": "^0.2.1",
+    "rollup-plugin-polyfill-node": "^0.7.0",
     "tslib": "^2.1.0",
     "typescript": "^4.2.3"
   },
   "dependencies": {
-    "@gmod/gff": "^1.1.2",
     "clustal-js": "^1.0.3",
     "color": "^3.1.3",
     "copy-to-clipboard": "^3.3.1",