@jbrowse/plugin-legacy-jbrowse 2.10.3 → 2.11.1

package/dist/GuessNCList/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function GuessNCListF(pluginManager: PluginManager): void;

package/dist/GuessNCList/index.js

@@ -1,7 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const tracks_1 = require("@jbrowse/core/util/tracks");
-exports.default = (pluginManager) => {
+function GuessNCListF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {
             const regexGuess = /trackData.jsonz?$/i;
@@ -16,4 +16,5 @@ exports.default = (pluginManager) => {
             return adapterGuesser(file, index, adapterHint);
         };
     });
-};
+}
+exports.default = GuessNCListF;

package/dist/JBrowse1Connection/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function JBrowse1ConnectionF(pluginManager: PluginManager): void;

package/dist/JBrowse1Connection/index.js

@@ -7,7 +7,7 @@ const ConnectionType_1 = __importDefault(require("@jbrowse/core/pluggableElement
 // locals
 const model_1 = __importDefault(require("./model"));
 const configSchema_1 = __importDefault(require("./configSchema"));
-exports.default = (pluginManager) => {
+function JBrowse1ConnectionF(pluginManager) {
     pluginManager.addConnectionType(() => new ConnectionType_1.default({
         name: 'JBrowse1Connection',
         configSchema: configSchema_1.default,
@@ -16,4 +16,5 @@ exports.default = (pluginManager) => {
         description: 'A JBrowse 1 data directory',
         url: '//jbrowse.org/',
     }));
-};
+}
+exports.default = JBrowse1ConnectionF;

package/dist/JBrowse1Connection/jb1ConfigParse.js

@@ -293,10 +293,11 @@ function regularizeClass(root, className) {
     return className;
 }
 function guessStoreClass(trackConfig, urlTemplate) {
+    var _a, _b;
     if (!trackConfig) {
         return '';
     }
-    if (trackConfig.type && trackConfig.type.includes('/FixedImage')) {
+    if ((_a = trackConfig.type) === null || _a === void 0 ? void 0 : _a.includes('/FixedImage')) {
         return `JBrowse/Store/TiledImage/Fixed${trackConfig.backendVersion === 0 ? '_v0' : ''}`;
     }
     if (/\.jsonz?$/i.test(urlTemplate)) {
@@ -338,7 +339,7 @@ function guessStoreClass(trackConfig, urlTemplate) {
     if (/\.2bit$/i.test(urlTemplate)) {
         return 'JBrowse/Store/SeqFeature/TwoBit';
     }
-    if (trackConfig.type && trackConfig.type.endsWith('/Sequence')) {
+    if ((_b = trackConfig.type) === null || _b === void 0 ? void 0 : _b.endsWith('/Sequence')) {
         return 'JBrowse/Store/Sequence/StaticChunked';
     }
     return '';

package/dist/JBrowse1Connection/jb1ToJb2.js

@@ -5,7 +5,7 @@ const io_1 = require("@jbrowse/core/util/io");
 const util_1 = require("@jbrowse/core/util");
 const tracks_1 = require("@jbrowse/core/util/tracks");
 function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
-    var _a;
+    var _a, _b, _c, _d, _e;
     const jb2TrackConfig = {
         trackId: (0, util_1.objectHash)(jb1TrackConfig),
         name: jb1TrackConfig.key || jb1TrackConfig.label,
@@ -19,7 +19,7 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
     jb2TrackConfig.category = category ? category.split(/\s*\/\s*/) : [];
     const { storeClass } = jb1TrackConfig;
     if (!jb1TrackConfig.urlTemplate) {
-        if (!(storeClass && storeClass.endsWith('FromConfig'))) {
+        if (!(storeClass === null || storeClass === void 0 ? void 0 : storeClass.endsWith('FromConfig'))) {
             const trackIdentifier = jb1TrackConfig.key || jb1TrackConfig.label;
             console.warn(`Could not import JBrowse1 track "${trackIdentifier}" because it does not have a "urlTemplate" or is not a "FromConfig" track`);
             return (0, tracks_1.generateUnsupportedTrackConf)(jb2TrackConfig.name, trackIdentifier, jb2TrackConfig.category);
@@ -99,11 +99,10 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
         }
         if (storeClass === 'JBrowse/Store/SeqFeature/BigWig' ||
             storeClass === 'JBrowse/Store/BigWig') {
-            if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('XYPlot')) {
+            if ((_b = jb1TrackConfig.type) === null || _b === void 0 ? void 0 : _b.endsWith('XYPlot')) {
                 jb2TrackConfig.defaultRendering = 'xyplot';
             }
-            else if (jb1TrackConfig.type &&
-                jb1TrackConfig.type.endsWith('Density')) {
+            else if ((_c = jb1TrackConfig.type) === null || _c === void 0 ? void 0 : _c.endsWith('Density')) {
                 jb2TrackConfig.defaultRendering = 'density';
             }
             return {
@@ -330,10 +329,10 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
     }
     jb2TrackConfig.type = (0, tracks_1.guessTrackType)(jb2TrackConfig.adapter.type);
     if (jb2TrackConfig.type === 'QuantitativeTrack') {
-        if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('XYPlot')) {
+        if ((_d = jb1TrackConfig.type) === null || _d === void 0 ? void 0 : _d.endsWith('XYPlot')) {
             jb2TrackConfig.defaultRendering = 'xyplot';
         }
-        else if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('Density')) {
+        else if ((_e = jb1TrackConfig.type) === null || _e === void 0 ? void 0 : _e.endsWith('Density')) {
             jb2TrackConfig.defaultRendering = 'density';
         }
     }

package/dist/JBrowse1Connection/model.d.ts

@@ -1,5 +1,5 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-export default function (pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
+export default function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     name: import("mobx-state-tree").ISimpleType<string>;
     tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
     configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{

package/dist/JBrowse1Connection/model.js

@@ -32,7 +32,7 @@ const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
 const mobx_state_tree_1 = require("mobx-state-tree");
 // locals
 const configSchema_1 = __importDefault(require("./configSchema"));
-function default_1(pluginManager) {
+function stateModelFactory(pluginManager) {
     return mobx_state_tree_1.types
         .compose('JBrowse1Connection', (0, models_1.BaseConnectionModelFactory)(pluginManager), mobx_state_tree_1.types.model({
         configuration: (0, configuration_1.ConfigurationReference)(configSchema_1.default),
@@ -65,10 +65,10 @@ function default_1(pluginManager) {
             }
             catch (error) {
                 console.error(error);
-                session.notify(`There was a problem connecting to the JBrowse 1 data directory "${self.name}". Please make sure you have entered a valid location. The error that was thrown is: "${error}"`, 'error');
+                session.notifyError(`There was a problem connecting to the JBrowse 1 data directory "${self.name}". Please make sure you have entered a valid location. The error that was thrown is: "${error}"`, error);
                 (_b = session.breakConnection) === null || _b === void 0 ? void 0 : _b.call(session, self.configuration);
             }
         },
     }));
 }
-exports.default = default_1;
+exports.default = stateModelFactory;

package/dist/JBrowse1TextSearchAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function JBrowse1TextSearchAdapterF(pluginManager: PluginManager): void;

package/dist/JBrowse1TextSearchAdapter/index.js

@@ -7,11 +7,12 @@ const TextSearchAdapterType_1 = __importDefault(require("@jbrowse/core/pluggable
 // locals
 const JBrowse1TextSearchAdapter_1 = __importDefault(require("./JBrowse1TextSearchAdapter"));
 const configSchema_1 = __importDefault(require("./configSchema"));
-exports.default = (pluginManager) => {
+function JBrowse1TextSearchAdapterF(pluginManager) {
     pluginManager.addTextSearchAdapterType(() => new TextSearchAdapterType_1.default({
         name: 'JBrowse1TextSearchAdapter',
         configSchema: configSchema_1.default,
         AdapterClass: JBrowse1TextSearchAdapter_1.default,
         description: 'A JBrowse 1 text search adapter',
     }));
-};
+}
+exports.default = JBrowse1TextSearchAdapterF;

package/dist/NCListAdapter/NCListFeature.js

@@ -60,6 +60,7 @@ class NCListFeature {
         return this.get('subfeatures');
     }
     toJSON() {
+        // @ts-expect-error
         const data = { uniqueId: this.id() };
         this.ncFeature.tags().forEach((tag) => {
             const mappedTag = this.jb1TagToJb2Tag(tag);

package/dist/NCListAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function NCListAdapterF(pluginManager: PluginManager): void;

package/dist/NCListAdapter/index.js

@@ -28,11 +28,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
 const configSchema_1 = __importDefault(require("./configSchema"));
-exports.default = (pluginManager) => {
+function NCListAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new pluggableElementTypes_1.AdapterType({
         name: 'NCListAdapter',
         displayName: 'NCList adapter',
         configSchema: configSchema_1.default,
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./NCListAdapter'))).then(r => r.default),
     }));
-};
+}
+exports.default = NCListAdapterF;

package/esm/GuessNCList/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function GuessNCListF(pluginManager: PluginManager): void;

package/esm/GuessNCList/index.js

@@ -1,5 +1,5 @@
 import { getFileName } from '@jbrowse/core/util/tracks';
-export default (pluginManager) => {
+export default function GuessNCListF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {
             const regexGuess = /trackData.jsonz?$/i;
@@ -14,4 +14,4 @@ export default (pluginManager) => {
             return adapterGuesser(file, index, adapterHint);
         };
     });
-};
+}

package/esm/JBrowse1Connection/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function JBrowse1ConnectionF(pluginManager: PluginManager): void;

package/esm/JBrowse1Connection/index.js

@@ -2,7 +2,7 @@ import ConnectionType from '@jbrowse/core/pluggableElementTypes/ConnectionType';
 // locals
 import modelFactory from './model';
 import configSchema from './configSchema';
-export default (pluginManager) => {
+export default function JBrowse1ConnectionF(pluginManager) {
     pluginManager.addConnectionType(() => new ConnectionType({
         name: 'JBrowse1Connection',
         configSchema,
@@ -11,4 +11,4 @@ export default (pluginManager) => {
         description: 'A JBrowse 1 data directory',
         url: '//jbrowse.org/',
     }));
-};
+}

package/esm/JBrowse1Connection/jb1ConfigParse.js

@@ -284,10 +284,11 @@ function regularizeClass(root, className) {
     return className;
 }
 function guessStoreClass(trackConfig, urlTemplate) {
+    var _a, _b;
     if (!trackConfig) {
         return '';
     }
-    if (trackConfig.type && trackConfig.type.includes('/FixedImage')) {
+    if ((_a = trackConfig.type) === null || _a === void 0 ? void 0 : _a.includes('/FixedImage')) {
         return `JBrowse/Store/TiledImage/Fixed${trackConfig.backendVersion === 0 ? '_v0' : ''}`;
     }
     if (/\.jsonz?$/i.test(urlTemplate)) {
@@ -329,7 +330,7 @@ function guessStoreClass(trackConfig, urlTemplate) {
     if (/\.2bit$/i.test(urlTemplate)) {
         return 'JBrowse/Store/SeqFeature/TwoBit';
     }
-    if (trackConfig.type && trackConfig.type.endsWith('/Sequence')) {
+    if ((_b = trackConfig.type) === null || _b === void 0 ? void 0 : _b.endsWith('/Sequence')) {
         return 'JBrowse/Store/Sequence/StaticChunked';
     }
     return '';

package/esm/JBrowse1Connection/jb1ToJb2.js

@@ -2,7 +2,7 @@ import { openLocation } from '@jbrowse/core/util/io';
 import { objectHash } from '@jbrowse/core/util';
 import { generateUnknownTrackConf, generateUnsupportedTrackConf, guessAdapter, guessTrackType, UNKNOWN, UNSUPPORTED, } from '@jbrowse/core/util/tracks';
 export function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
-    var _a;
+    var _a, _b, _c, _d, _e;
     const jb2TrackConfig = {
         trackId: objectHash(jb1TrackConfig),
         name: jb1TrackConfig.key || jb1TrackConfig.label,
@@ -16,7 +16,7 @@ export function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
     jb2TrackConfig.category = category ? category.split(/\s*\/\s*/) : [];
     const { storeClass } = jb1TrackConfig;
     if (!jb1TrackConfig.urlTemplate) {
-        if (!(storeClass && storeClass.endsWith('FromConfig'))) {
+        if (!(storeClass === null || storeClass === void 0 ? void 0 : storeClass.endsWith('FromConfig'))) {
             const trackIdentifier = jb1TrackConfig.key || jb1TrackConfig.label;
             console.warn(`Could not import JBrowse1 track "${trackIdentifier}" because it does not have a "urlTemplate" or is not a "FromConfig" track`);
             return generateUnsupportedTrackConf(jb2TrackConfig.name, trackIdentifier, jb2TrackConfig.category);
@@ -96,11 +96,10 @@ export function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
         }
         if (storeClass === 'JBrowse/Store/SeqFeature/BigWig' ||
             storeClass === 'JBrowse/Store/BigWig') {
-            if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('XYPlot')) {
+            if ((_b = jb1TrackConfig.type) === null || _b === void 0 ? void 0 : _b.endsWith('XYPlot')) {
                 jb2TrackConfig.defaultRendering = 'xyplot';
             }
-            else if (jb1TrackConfig.type &&
-                jb1TrackConfig.type.endsWith('Density')) {
+            else if ((_c = jb1TrackConfig.type) === null || _c === void 0 ? void 0 : _c.endsWith('Density')) {
                 jb2TrackConfig.defaultRendering = 'density';
             }
             return {
@@ -327,10 +326,10 @@ export function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
     }
     jb2TrackConfig.type = guessTrackType(jb2TrackConfig.adapter.type);
     if (jb2TrackConfig.type === 'QuantitativeTrack') {
-        if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('XYPlot')) {
+        if ((_d = jb1TrackConfig.type) === null || _d === void 0 ? void 0 : _d.endsWith('XYPlot')) {
             jb2TrackConfig.defaultRendering = 'xyplot';
         }
-        else if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('Density')) {
+        else if ((_e = jb1TrackConfig.type) === null || _e === void 0 ? void 0 : _e.endsWith('Density')) {
             jb2TrackConfig.defaultRendering = 'density';
         }
     }

package/esm/JBrowse1Connection/model.d.ts

@@ -1,5 +1,5 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-export default function (pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
+export default function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     name: import("mobx-state-tree").ISimpleType<string>;
     tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
     configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{

package/esm/JBrowse1Connection/model.js

@@ -4,7 +4,7 @@ import { BaseConnectionModelFactory } from '@jbrowse/core/pluggableElementTypes/
 import { types } from 'mobx-state-tree';
 // locals
 import configSchema from './configSchema';
-export default function (pluginManager) {
+export default function stateModelFactory(pluginManager) {
     return types
         .compose('JBrowse1Connection', BaseConnectionModelFactory(pluginManager), types.model({
         configuration: ConfigurationReference(configSchema),
@@ -37,7 +37,7 @@ export default function (pluginManager) {
             }
             catch (error) {
                 console.error(error);
-                session.notify(`There was a problem connecting to the JBrowse 1 data directory "${self.name}". Please make sure you have entered a valid location. The error that was thrown is: "${error}"`, 'error');
+                session.notifyError(`There was a problem connecting to the JBrowse 1 data directory "${self.name}". Please make sure you have entered a valid location. The error that was thrown is: "${error}"`, error);
                 (_b = session.breakConnection) === null || _b === void 0 ? void 0 : _b.call(session, self.configuration);
             }
         },

package/esm/JBrowse1TextSearchAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function JBrowse1TextSearchAdapterF(pluginManager: PluginManager): void;

package/esm/JBrowse1TextSearchAdapter/index.js

@@ -2,11 +2,11 @@ import TextSearchAdapterType from '@jbrowse/core/pluggableElementTypes/TextSearc
 // locals
 import AdapterClass from './JBrowse1TextSearchAdapter';
 import configSchema from './configSchema';
-export default (pluginManager) => {
+export default function JBrowse1TextSearchAdapterF(pluginManager) {
     pluginManager.addTextSearchAdapterType(() => new TextSearchAdapterType({
         name: 'JBrowse1TextSearchAdapter',
         configSchema,
         AdapterClass,
         description: 'A JBrowse 1 text search adapter',
     }));
-};
+}

package/esm/NCListAdapter/NCListFeature.js

@@ -58,6 +58,7 @@ export default class NCListFeature {
         return this.get('subfeatures');
     }
     toJSON() {
+        // @ts-expect-error
         const data = { uniqueId: this.id() };
         this.ncFeature.tags().forEach((tag) => {
             const mappedTag = this.jb1TagToJb2Tag(tag);

package/esm/NCListAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function NCListAdapterF(pluginManager: PluginManager): void;

package/esm/NCListAdapter/index.js

@@ -1,10 +1,10 @@
 import { AdapterType } from '@jbrowse/core/pluggableElementTypes';
 import configSchema from './configSchema';
-export default (pluginManager) => {
+export default function NCListAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'NCListAdapter',
         displayName: 'NCList adapter',
         configSchema,
         getAdapterClass: () => import('./NCListAdapter').then(r => r.default),
     }));
-};
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-legacy-jbrowse",
-  "version": "2.10.3",
+  "version": "2.11.1",
   "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data",
   "keywords": [
     "jbrowse",
@@ -55,5 +55,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "c8fc800cd17decd72b2e971c7a6add3b95214e72"
+  "gitHead": "11b28d66d782eb06f92ccb993108bb6c3c82819e"
 }