@jbrowse/plugin-config 2.17.0 → 2.18.0

package/dist/ConfigurationEditorWidget/components/BooleanEditor.js

@@ -4,8 +4,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
-const mobx_react_1 = require("mobx-react");
 const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
 const BooleanEditor = (0, mobx_react_1.observer)(function ({ slot, }) {
     return (react_1.default.createElement(material_1.FormControl, null,
         react_1.default.createElement(material_1.FormControlLabel, { label: slot.name, control: react_1.default.createElement(material_1.Checkbox, { checked: slot.value, onChange: evt => {

package/dist/ConfigurationEditorWidget/components/CallbackEditor.js

@@ -27,16 +27,13 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const material_1 = require("@mui/material");
 const util_1 = require("@jbrowse/core/util");
 const jexlStrings_1 = require("@jbrowse/core/util/jexlStrings");
-const mobx_state_tree_1 = require("mobx-state-tree");
+const Help_1 = __importDefault(require("@mui/icons-material/Help"));
+const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
+const mobx_state_tree_1 = require("mobx-state-tree");
 const mui_1 = require("tss-react/mui");
-// icons
-const Help_1 = __importDefault(require("@mui/icons-material/Help"));
-// Optimize by using system default fonts:
-// https://css-tricks.com/snippets/css/font-stacks/
 const fontFamily = 'Consolas, "Andale Mono WT", "Andale Mono", "Lucida Console", "Lucida Sans Typewriter", "DejaVu Sans Mono", "Bitstream Vera Sans Mono", "Liberation Mono", "Nimbus Mono L", Monaco, "Courier New", Courier, monospace';
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     callbackEditor: {
@@ -80,8 +77,6 @@ const CallbackEditor = (0, mobx_react_1.observer)(function ({ slot, }) {
             setCodeError(e);
         }
     }, [debouncedCode, slot]);
-    // if default value is a callback, will have to remove jexl:
-    // do this last
     return (react_1.default.createElement(react_1.default.Fragment, null,
         error ? react_1.default.createElement("p", { className: classes.error }, `${error}`) : null,
         react_1.default.createElement("div", { className: classes.callbackContainer },

package/dist/ConfigurationEditorWidget/components/ColorEditor.js

@@ -28,9 +28,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.ColorSlot = void 0;
 const react_1 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
-const material_1 = require("@mui/material");
 const ColorPicker_1 = __importDefault(require("@jbrowse/core/ui/ColorPicker"));
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
 const ColorSlot = (props) => {
     const { value = '#000', label = '', TextFieldProps = {}, onChange } = props;
     const [displayed, setDisplayed] = (0, react_1.useState)(false);

package/dist/ConfigurationEditorWidget/components/ConfigurationEditor.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
-import { AbstractSessionModel } from '@jbrowse/core/util';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { AbstractSessionModel } from '@jbrowse/core/util';
 declare const ConfigurationEditor: ({ model, }: {
     model: {
         target: AnyConfigurationModel;

package/dist/ConfigurationEditorWidget/components/ConfigurationEditor.js

@@ -4,16 +4,14 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
+const configuration_1 = require("@jbrowse/core/configuration");
+const SanitizedHTML_1 = __importDefault(require("@jbrowse/core/ui/SanitizedHTML"));
+const ExpandMore_1 = __importDefault(require("@mui/icons-material/ExpandMore"));
 const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
 const mobx_react_1 = require("mobx-react");
 const mobx_state_tree_1 = require("mobx-state-tree");
 const pluralize_1 = require("pluralize");
-const SanitizedHTML_1 = __importDefault(require("@jbrowse/core/ui/SanitizedHTML"));
-const configuration_1 = require("@jbrowse/core/configuration");
-// icons
-const ExpandMore_1 = __importDefault(require("@mui/icons-material/ExpandMore"));
-// locals
+const mui_1 = require("tss-react/mui");
 const SlotEditor_1 = __importDefault(require("./SlotEditor"));
 const TypeSelector_1 = __importDefault(require("./TypeSelector"));
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
@@ -44,8 +42,6 @@ const Member = (0, mobx_react_1.observer)(function (props) {
                 return react_1.default.createElement(Member, { key: key, ...props, slot: subslot, slotName: key });
             });
         }
-        // if this is an explicitly typed schema, make a type-selecting dropdown
-        // that can be used to change its type
         const typeNameChoices = (0, configuration_1.getTypeNamesFromExplicitlyTypedUnion)(slotSchema);
         return (react_1.default.createElement(material_1.Accordion, { defaultExpanded: true, className: classes.accordion },
             react_1.default.createElement(material_1.AccordionSummary, { expandIcon: react_1.default.createElement(ExpandMore_1.default, { className: classes.icon }) },
@@ -72,9 +68,6 @@ const Schema = (0, mobx_react_1.observer)(function ({ schema, path = [], }) {
 });
 const ConfigurationEditor = (0, mobx_react_1.observer)(function ({ model, }) {
     const { classes } = useStyles();
-    // key forces a re-render, otherwise the same field can end up being used for
-    // different tracks since only the backing model changes for example see pr
-    // #804
     const { target } = model;
     const key = (0, configuration_1.readConfObject)(target, 'trackId');
     const name = (0, configuration_1.readConfObject)(target, 'name');

package/dist/ConfigurationEditorWidget/components/ConfigurationTextField.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { TextFieldProps } from '@mui/material';
+import type { TextFieldProps } from '@mui/material';
 export default function ConfigurationTextField(props: {
     helperText?: string;
 } & TextFieldProps): React.JSX.Element;

package/dist/ConfigurationEditorWidget/components/ConfigurationTextField.js

@@ -5,10 +5,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = ConfigurationTextField;
 const react_1 = __importDefault(require("react"));
-const material_1 = require("@mui/material");
 const ui_1 = require("@jbrowse/core/ui");
-// adds ability to have html in helperText. note that FormHelperTextProps is
-// div because the default is p which does not like div children
+const material_1 = require("@mui/material");
 function ConfigurationTextField(props) {
     const { helperText } = props;
     return (react_1.default.createElement(material_1.TextField, { ...props, helperText: react_1.default.createElement(ui_1.SanitizedHTML, { html: helperText || '' }), fullWidth: true, slotProps: {

package/dist/ConfigurationEditorWidget/components/JsonEditor.js

@@ -25,11 +25,9 @@ var __importStar = (this && this.__importStar) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
 const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
 const mobx_react_1 = require("mobx-react");
-// fontSize and fontFamily have to match between Editor and SyntaxHighlighter
+const mui_1 = require("tss-react/mui");
 const fontSize = '12px';
-// Optimize by using system default fonts: https://css-tricks.com/snippets/css/font-stacks/
 const fontFamily = 'Consolas, "Andale Mono WT", "Andale Mono", "Lucida Console", "Lucida Sans Typewriter", "DejaVu Sans Mono", "Bitstream Vera Sans Mono", "Liberation Mono", "Nimbus Mono L", Monaco, "Courier New", Courier, monospace';
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     error: {

package/dist/ConfigurationEditorWidget/components/NumberMapEditor.js

@@ -27,12 +27,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
+const Add_1 = __importDefault(require("@mui/icons-material/Add"));
+const Delete_1 = __importDefault(require("@mui/icons-material/Delete"));
 const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
 const mui_1 = require("tss-react/mui");
-// icons
-const Delete_1 = __importDefault(require("@mui/icons-material/Delete"));
-const Add_1 = __importDefault(require("@mui/icons-material/Add"));
 const NumberEditor_1 = __importDefault(require("./NumberEditor"));
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     card: {

package/dist/ConfigurationEditorWidget/components/SlotEditor.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { IAnyType } from 'mobx-state-tree';
+import type { IAnyType } from 'mobx-state-tree';
 declare const SlotEditor: ({ slot, slotSchema, }: {
     slot: any;
     slotSchema: IAnyType;

package/dist/ConfigurationEditorWidget/components/SlotEditor.js

@@ -27,24 +27,22 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const util_1 = require("@jbrowse/core/util");
 const ui_1 = require("@jbrowse/core/ui");
+const util_1 = require("@jbrowse/core/util");
 const mst_reflection_1 = require("@jbrowse/core/util/mst-reflection");
-const material_1 = require("@mui/material");
-// icons
 const RadioButtonUnchecked_1 = __importDefault(require("@mui/icons-material/RadioButtonUnchecked"));
-// locals
-const StringArrayEditor_1 = __importDefault(require("./StringArrayEditor"));
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const BooleanEditor_1 = __importDefault(require("./BooleanEditor"));
 const CallbackEditor_1 = __importDefault(require("./CallbackEditor"));
 const ColorEditor_1 = __importDefault(require("./ColorEditor"));
-const JsonEditor_1 = __importDefault(require("./JsonEditor"));
-const StringArrayMapEditor_1 = __importDefault(require("./StringArrayMapEditor"));
 const ConfigurationTextField_1 = __importDefault(require("./ConfigurationTextField"));
-const NumberMapEditor_1 = __importDefault(require("./NumberMapEditor"));
+const JsonEditor_1 = __importDefault(require("./JsonEditor"));
 const NumberEditor_1 = __importDefault(require("./NumberEditor"));
-const BooleanEditor_1 = __importDefault(require("./BooleanEditor"));
+const NumberMapEditor_1 = __importDefault(require("./NumberMapEditor"));
+const StringArrayEditor_1 = __importDefault(require("./StringArrayEditor"));
+const StringArrayMapEditor_1 = __importDefault(require("./StringArrayMapEditor"));
 const useSlotEditorStyles_1 = require("./useSlotEditorStyles");
 const StringEditor = (0, mobx_react_1.observer)(function ({ slot, }) {
     return (react_1.default.createElement(ConfigurationTextField_1.default, { label: slot.name, helperText: slot.description, value: slot.value, onChange: evt => {
@@ -56,7 +54,6 @@ const TextEditor = (0, mobx_react_1.observer)(function ({ slot, }) {
             slot.set(evt.target.value);
         } }));
 });
-// checked checkbox, looks like a styled (x)
 const SvgCheckbox = () => (react_1.default.createElement(material_1.SvgIcon, null,
     react_1.default.createElement("path", { d: "M20.41,3C21.8,5.71 22.35,8.84 22,12C21.8,15.16 20.7,18.29 18.83,21L17.3,20C18.91,17.57 19.85,14.8 20,12C20.34,9.2 19.89,6.43 18.7,4L20.41,3M5.17,3L6.7,4C5.09,6.43 4.15,9.2 4,12C3.66,14.8 4.12,17.57 5.3,20L3.61,21C2.21,18.29 1.65,15.17 2,12C2.2,8.84 3.3,5.71 5.17,3M12.08,10.68L14.4,7.45H16.93L13.15,12.45L15.35,17.37H13.09L11.71,14L9.28,17.33H6.76L10.66,12.21L8.53,7.45H10.8L12.08,10.68Z" })));
 const IntegerEditor = (0, mobx_react_1.observer)(function ({ slot, }) {
@@ -82,9 +79,7 @@ const FileSelectorWrapper = (0, mobx_react_1.observer)(function ({ slot, }) {
     var _a;
     return (react_1.default.createElement(ui_1.FileSelector, { location: slot.value, setLocation: location => {
             slot.set(location);
-        }, name: slot.name, description: slot.description, 
-        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
-        rootModel: (_a = (0, util_1.getEnv)(slot).pluginManager) === null || _a === void 0 ? void 0 : _a.rootModel }));
+        }, name: slot.name, description: slot.description, rootModel: (_a = (0, util_1.getEnv)(slot).pluginManager) === null || _a === void 0 ? void 0 : _a.rootModel }));
 });
 const valueComponents = {
     string: StringEditor,
@@ -106,7 +101,7 @@ const SlotEditor = (0, mobx_react_1.observer)(function ({ slot, slotSchema, }) {
     const { type } = slot;
     let ValueComponent = slot.isCallback
         ? CallbackEditor_1.default
-        : // @ts-expect-error
+        :
             valueComponents[type];
     if (!ValueComponent) {
         console.warn(`no slot editor defined for ${type}, editing as string`);

package/dist/ConfigurationEditorWidget/components/StringArrayEditor.js

@@ -27,10 +27,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
-const material_1 = require("@mui/material");
-// icons
 const Delete_1 = __importDefault(require("@mui/icons-material/Delete"));
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
 const StringArrayEditor = (0, mobx_react_1.observer)(function ({ slot, }) {
     const [value, setValue] = (0, react_1.useState)('');
     const [addNew, setAddNew] = (0, react_1.useState)(false);

package/dist/ConfigurationEditorWidget/components/StringArrayMapEditor.js

@@ -27,13 +27,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
+const Add_1 = __importDefault(require("@mui/icons-material/Add"));
+const Delete_1 = __importDefault(require("@mui/icons-material/Delete"));
 const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
 const mui_1 = require("tss-react/mui");
-// icons
-const Delete_1 = __importDefault(require("@mui/icons-material/Delete"));
-const Add_1 = __importDefault(require("@mui/icons-material/Add"));
-// locals
 const StringArrayEditor_1 = __importDefault(require("./StringArrayEditor"));
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     card: {

package/dist/ConfigurationEditorWidget/components/TypeSelector.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 declare const TypeSelector: ({ typeNameChoices, slot, slotName, onChange, }: {
     typeNameChoices: string[];
     slot: AnyConfigurationModel;

package/dist/ConfigurationEditorWidget/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function registerConfigurationEditorWidget(pluginManager: PluginManager): void;

package/dist/ConfigurationEditorWidget/index.js

@@ -30,8 +30,8 @@ exports.default = registerConfigurationEditorWidget;
 const react_1 = require("react");
 const configuration_1 = require("@jbrowse/core/configuration");
 const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
-const model_1 = __importDefault(require("./model"));
 const HeadingComponent_1 = __importDefault(require("./components/HeadingComponent"));
+const model_1 = __importDefault(require("./model"));
 const configSchema = (0, configuration_1.ConfigurationSchema)('ConfigurationEditorWidget', {});
 const LazyConfigurationEditorComponent = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ConfigurationEditor'))));
 function registerConfigurationEditorWidget(pluginManager) {

package/dist/ConfigurationEditorWidget/model.d.ts

@@ -1,4 +1,4 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<"ConfigurationEditorWidget">;

package/dist/ConfigurationEditorWidget/model.js

@@ -1,15 +1,13 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = stateModelFactory;
-const mobx_state_tree_1 = require("mobx-state-tree");
 const mst_1 = require("@jbrowse/core/util/types/mst");
+const mobx_state_tree_1 = require("mobx-state-tree");
 function stateModelFactory(pluginManager) {
     return mobx_state_tree_1.types
         .model('ConfigurationEditorWidget', {
         id: mst_1.ElementId,
         type: mobx_state_tree_1.types.literal('ConfigurationEditorWidget'),
-        // If you add different types of targets, don't forget to account for that
-        // in the key of ./components/ConfigurationEditor.js
         target: mobx_state_tree_1.types.safeReference(pluginManager.pluggableConfigSchemaType('track')),
     })
         .actions(self => ({

package/dist/FromConfigAdapter/FromConfigAdapter.d.ts

@@ -1,9 +1,9 @@
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
-import { NoAssemblyRegion } from '@jbrowse/core/util/types';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import type { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
+import type { NoAssemblyRegion } from '@jbrowse/core/util/types';
 export declare function makeFeatures(fdata: SimpleFeatureSerialized[]): Map<string, Feature[]>;
 export default class FromConfigAdapter extends BaseFeatureDataAdapter {
     protected features: Map<string, Feature[]>;

package/dist/FromConfigAdapter/FromConfigAdapter.js

@@ -4,10 +4,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.makeFeatures = makeFeatures;
+const configuration_1 = require("@jbrowse/core/configuration");
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
-const configuration_1 = require("@jbrowse/core/configuration");
+const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
 function makeFeatures(fdata) {
     const features = new Map();
     for (const entry of fdata) {
@@ -20,7 +20,6 @@ function makeFeatures(fdata) {
         }
         bucket.push(f);
     }
-    // sort the features on each reference sequence by start coordinate
     for (const refFeatures of features.values()) {
         refFeatures.sort((a, b) => a.get('start') - b.get('start'));
     }
@@ -53,6 +52,6 @@ class FromConfigAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }
 exports.default = FromConfigAdapter;

package/dist/FromConfigAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     features: {
         type: string;
         defaultValue: never[];

package/dist/FromConfigAdapter/configSchema.js

@@ -1,14 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config FromConfigAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const configSchema = (0, configuration_1.ConfigurationSchema)('FromConfigAdapter', {
-    /**
-     * #slot
-     */
     features: {
         type: 'frozen',
         defaultValue: [],

package/dist/FromConfigAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function FromConfigAdapterF(pluginManager: PluginManager): void;

package/dist/FromConfigRegionsAdapter/FromConfigRegionsAdapter.d.ts

@@ -1,18 +1,11 @@
-import { BaseAdapter, RegionsAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
-/**
- * Adapter that just returns the features defined in its `features` configuration
- * key, like:
- *   `"features": [ { "refName": "ctgA", "start":1, "end":20 }, ... ]`
- */
+import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { RegionsAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
 export default class FromConfigRegionsAdapter extends BaseAdapter implements RegionsAdapter {
     private features;
     constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
-    /**
-     * Get refName, start, and end for all features after collapsing any overlaps
-     */
     getRegions(): Promise<{
         refName: string;
         start: number;

package/dist/FromConfigRegionsAdapter/FromConfigRegionsAdapter.js

@@ -1,25 +1,16 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const configuration_1 = require("@jbrowse/core/configuration");
+const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const FromConfigAdapter_1 = require("../FromConfigAdapter/FromConfigAdapter");
-/**
- * Adapter that just returns the features defined in its `features` configuration
- * key, like:
- *   `"features": [ { "refName": "ctgA", "start":1, "end":20 }, ... ]`
- */
 class FromConfigRegionsAdapter extends BaseAdapter_1.BaseAdapter {
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
         const f = (0, configuration_1.readConfObject)(config, 'features');
         this.features = (0, FromConfigAdapter_1.makeFeatures)(f);
     }
-    /**
-     * Get refName, start, and end for all features after collapsing any overlaps
-     */
     async getRegions() {
         const regions = [];
-        // recall: features are stored in this object sorted by start coordinate
         for (const [refName, features] of this.features) {
             let currentRegion;
             for (const feature of features) {
@@ -43,10 +34,9 @@ class FromConfigRegionsAdapter extends BaseAdapter_1.BaseAdapter {
                 regions.push(currentRegion);
             }
         }
-        // sort the regions by refName
         regions.sort((a, b) => a.refName.localeCompare(b.refName));
         return regions;
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }
 exports.default = FromConfigRegionsAdapter;

package/dist/FromConfigRegionsAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const regionsConfigSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     features: {
         type: string;
         defaultValue: never[];

package/dist/FromConfigRegionsAdapter/configSchema.js

@@ -1,15 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config FromConfigRegionsAdapter
- * used for specifying refNames+sizes of an assembly
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const regionsConfigSchema = (0, configuration_1.ConfigurationSchema)('FromConfigRegionsAdapter', {
-    /**
-     * #slot
-     */
     features: {
         type: 'frozen',
         defaultValue: [],

package/dist/FromConfigRegionsAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function FromConfigRegionsAdapterF(pluginManager: PluginManager): void;

package/dist/FromConfigSequenceAdapter/FromConfigSequenceAdapter.d.ts

@@ -1,26 +1,13 @@
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { NoAssemblyRegion } from '@jbrowse/core/util/types';
-import { RegionsAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import FromConfigAdapter from '../FromConfigAdapter/FromConfigAdapter';
+import type { RegionsAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature } from '@jbrowse/core/util/simpleFeature';
+import type { NoAssemblyRegion } from '@jbrowse/core/util/types';
 export default class FromConfigSequenceAdapter extends FromConfigAdapter implements RegionsAdapter {
-    /**
-     * Fetch features for a certain region
-     * @param region - Region
-     * @returns Observable of Feature objects in the region
-     */
     getFeatures(region: NoAssemblyRegion): import("rxjs").Observable<Feature>;
-    /**
-     * Get refName, start, and end for all features after collapsing any overlaps
-     */
     getRegions(): Promise<{
         start: number;
         end: number;
         refName: string;
     }[]>;
-    /**
-     * called to provide a hint that data tied to a certain region
-     * will not be needed for the foreseeable future and can be purged
-     * from caches, etc
-     */
     freeResources(): void;
 }

package/dist/FromConfigSequenceAdapter/FromConfigSequenceAdapter.js

@@ -3,18 +3,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
+const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
+const rxjs_2 = require("rxjs");
 const operators_1 = require("rxjs/operators");
-// locals
 const FromConfigAdapter_1 = __importDefault(require("../FromConfigAdapter/FromConfigAdapter"));
-const rxjs_2 = require("rxjs");
 class FromConfigSequenceAdapter extends FromConfigAdapter_1.default {
-    /**
-     * Fetch features for a certain region
-     * @param region - Region
-     * @returns Observable of Feature objects in the region
-     */
     getFeatures(region) {
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
             const feats = await (0, rxjs_2.firstValueFrom)(super.getFeatures(region).pipe((0, operators_1.toArray)()));
@@ -31,12 +25,8 @@ class FromConfigSequenceAdapter extends FromConfigAdapter_1.default {
             observer.complete();
         });
     }
-    /**
-     * Get refName, start, and end for all features after collapsing any overlaps
-     */
     async getRegions() {
         const regions = [];
-        // recall: features are stored in this object sorted by start coordinate
         for (const [refName, features] of this.features) {
             let currentRegion;
             for (const feature of features) {
@@ -62,11 +52,6 @@ class FromConfigSequenceAdapter extends FromConfigAdapter_1.default {
         }
         return regions;
     }
-    /**
-     * called to provide a hint that data tied to a certain region
-     * will not be needed for the foreseeable future and can be purged
-     * from caches, etc
-     */
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }
 exports.default = FromConfigSequenceAdapter;

package/dist/FromConfigSequenceAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const sequenceConfigSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     features: {
         type: string;
         defaultValue: never[];

package/dist/FromConfigSequenceAdapter/configSchema.js

@@ -1,14 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config FromConfigSequenceAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const sequenceConfigSchema = (0, configuration_1.ConfigurationSchema)('FromConfigSequenceAdapter', {
-    /**
-     * #slot
-     */
     features: {
         type: 'frozen',
         defaultValue: [],

package/dist/FromConfigSequenceAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function FromConfigSequenceAdapterF(pluginManager: PluginManager): void;

package/dist/NcbiSequenceReportAliasAdapter/NcbiSequenceReportAliasAdapter.d.ts

@@ -1,4 +1,5 @@
-import { BaseRefNameAliasAdapter, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseRefNameAliasAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 export default class NcbiSequenceReportAliasAdapter extends BaseAdapter implements BaseRefNameAliasAdapter {
     getRefNameAliases(): Promise<{
         refName: string;

package/dist/NcbiSequenceReportAliasAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const NcbiSequenceReportAliasAdapterConfigSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     location: {
         type: string;
         defaultValue: {

package/dist/NcbiSequenceReportAliasAdapter/configSchema.js

@@ -1,15 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config NcbiSequenceReportAliasAdapter
- * can read "sequence_report.tsv" type files from NCBI
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const NcbiSequenceReportAliasAdapterConfigSchema = (0, configuration_1.ConfigurationSchema)('NcbiSequenceReportAliasAdapter', {
-    /**
-     * #slot
-     */
     location: {
         type: 'fileLocation',
         defaultValue: {