@jbrowse/plugin-config 2.17.0 → 2.18.0

package/dist/NcbiSequenceReportAliasAdapter/index.d.ts

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

package/dist/RefNameAliasAdapter/RefNameAliasAdapter.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 RefNameAliasAdapter extends BaseAdapter implements BaseRefNameAliasAdapter {
     getRefNameAliases(): Promise<{
         refName: string;

package/dist/RefNameAliasAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const RefNameAliasAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     location: {
         type: string;
         defaultValue: {
@@ -9,11 +6,6 @@ declare const RefNameAliasAdapter: import("@jbrowse/core/configuration/configura
             locationType: string;
         };
     };
-    /**
-     * #slot
-     * by default, the "ref names that match the fasta" are assumed to be in the
-     * first column (0), change this variable if needed
-     */
     refNameColumn: {
         type: string;
         defaultValue: number;

package/dist/RefNameAliasAdapter/configSchema.js

@@ -1,16 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config RefNameAliasAdapter
- * can read "chromAliases" type files from UCSC or any tab separated file of
- * refName aliases
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const RefNameAliasAdapter = (0, configuration_1.ConfigurationSchema)('RefNameAliasAdapter', {
-    /**
-     * #slot
-     */
     location: {
         type: 'fileLocation',
         defaultValue: {
@@ -18,11 +10,6 @@ const RefNameAliasAdapter = (0, configuration_1.ConfigurationSchema)('RefNameAli
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     * by default, the "ref names that match the fasta" are assumed to be in the
-     * first column (0), change this variable if needed
-     */
     refNameColumn: {
         type: 'number',
         defaultValue: 0,

package/dist/RefNameAliasAdapter/index.d.ts

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

package/dist/index.d.ts

@@ -1,5 +1,5 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 declare const LazyConfigurationEditorComponent: import("react").LazyExoticComponent<({ model, }: {
     model: {
         target: import("@jbrowse/core/configuration").AnyConfigurationModel;

package/dist/index.js

@@ -29,12 +29,12 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.ConfigurationEditor = void 0;
 const react_1 = require("react");
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
+const ConfigurationEditorWidget_1 = __importDefault(require("./ConfigurationEditorWidget"));
 const FromConfigAdapter_1 = __importDefault(require("./FromConfigAdapter"));
 const FromConfigRegionsAdapter_1 = __importDefault(require("./FromConfigRegionsAdapter"));
 const FromConfigSequenceAdapter_1 = __importDefault(require("./FromConfigSequenceAdapter"));
-const RefNameAliasAdapter_1 = __importDefault(require("./RefNameAliasAdapter"));
-const ConfigurationEditorWidget_1 = __importDefault(require("./ConfigurationEditorWidget"));
 const NcbiSequenceReportAliasAdapter_1 = __importDefault(require("./NcbiSequenceReportAliasAdapter"));
+const RefNameAliasAdapter_1 = __importDefault(require("./RefNameAliasAdapter"));
 const LazyConfigurationEditorComponent = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./ConfigurationEditorWidget/components/ConfigurationEditor'))));
 exports.ConfigurationEditor = LazyConfigurationEditorComponent;
 class ConfigurationPlugin extends Plugin_1.default {

package/esm/ConfigurationEditorWidget/components/BooleanEditor.js

@@ -1,6 +1,6 @@
 import React from 'react';
-import { observer } from 'mobx-react';
 import { Checkbox, FormControl, FormControlLabel, FormHelperText, } from '@mui/material';
+import { observer } from 'mobx-react';
 const BooleanEditor = observer(function ({ slot, }) {
     return (React.createElement(FormControl, null,
         React.createElement(FormControlLabel, { label: slot.name, control: React.createElement(Checkbox, { checked: slot.value, onChange: evt => {

package/esm/ConfigurationEditorWidget/components/CallbackEditor.js

@@ -1,14 +1,11 @@
 import React, { useEffect, useState } from 'react';
-import { Tooltip, IconButton, TextField } from '@mui/material';
 import { useDebounce } from '@jbrowse/core/util';
 import { stringToJexlExpression } from '@jbrowse/core/util/jexlStrings';
-import { getEnv } from 'mobx-state-tree';
+import HelpIcon from '@mui/icons-material/Help';
+import { IconButton, TextField, Tooltip } from '@mui/material';
 import { observer } from 'mobx-react';
+import { getEnv } from 'mobx-state-tree';
 import { makeStyles } from 'tss-react/mui';
-// icons
-import HelpIcon from '@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 = makeStyles()(theme => ({
     callbackEditor: {
@@ -52,8 +49,6 @@ const CallbackEditor = observer(function ({ slot, }) {
             setCodeError(e);
         }
     }, [debouncedCode, slot]);
-    // if default value is a callback, will have to remove jexl:
-    // do this last
     return (React.createElement(React.Fragment, null,
         error ? React.createElement("p", { className: classes.error }, `${error}`) : null,
         React.createElement("div", { className: classes.callbackContainer },

package/esm/ConfigurationEditorWidget/components/ColorEditor.js

@@ -1,7 +1,7 @@
 import React, { useState } from 'react';
-import { observer } from 'mobx-react';
-import { TextField } from '@mui/material';
 import ColorPicker from '@jbrowse/core/ui/ColorPicker';
+import { TextField } from '@mui/material';
+import { observer } from 'mobx-react';
 export const ColorSlot = (props) => {
     const { value = '#000', label = '', TextFieldProps = {}, onChange } = props;
     const [displayed, setDisplayed] = useState(false);

package/esm/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/esm/ConfigurationEditorWidget/components/ConfigurationEditor.js

@@ -1,14 +1,12 @@
 import React from 'react';
-import { FormGroup, Accordion, AccordionDetails, AccordionSummary, Typography, } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
+import { getTypeNamesFromExplicitlyTypedUnion, isConfigurationSchemaType, isConfigurationSlotType, readConfObject, } from '@jbrowse/core/configuration';
+import SanitizedHTML from '@jbrowse/core/ui/SanitizedHTML';
+import ExpandMoreIcon from '@mui/icons-material/ExpandMore';
+import { Accordion, AccordionDetails, AccordionSummary, FormGroup, Typography, } from '@mui/material';
 import { observer } from 'mobx-react';
 import { getMembers } from 'mobx-state-tree';
 import { singular } from 'pluralize';
-import SanitizedHTML from '@jbrowse/core/ui/SanitizedHTML';
-import { readConfObject, getTypeNamesFromExplicitlyTypedUnion, isConfigurationSchemaType, isConfigurationSlotType, } from '@jbrowse/core/configuration';
-// icons
-import ExpandMoreIcon from '@mui/icons-material/ExpandMore';
-// locals
+import { makeStyles } from 'tss-react/mui';
 import SlotEditor from './SlotEditor';
 import TypeSelector from './TypeSelector';
 const useStyles = makeStyles()(theme => ({
@@ -39,8 +37,6 @@ const Member = observer(function (props) {
                 return React.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 = getTypeNamesFromExplicitlyTypedUnion(slotSchema);
         return (React.createElement(Accordion, { defaultExpanded: true, className: classes.accordion },
             React.createElement(AccordionSummary, { expandIcon: React.createElement(ExpandMoreIcon, { className: classes.icon }) },
@@ -67,9 +63,6 @@ const Schema = observer(function ({ schema, path = [], }) {
 });
 const ConfigurationEditor = 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 = readConfObject(target, 'trackId');
     const name = readConfObject(target, 'name');

package/esm/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/esm/ConfigurationEditorWidget/components/ConfigurationTextField.js

@@ -1,8 +1,6 @@
 import React from 'react';
-import { TextField } from '@mui/material';
 import { SanitizedHTML } from '@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
+import { TextField } from '@mui/material';
 export default function ConfigurationTextField(props) {
     const { helperText } = props;
     return (React.createElement(TextField, { ...props, helperText: React.createElement(SanitizedHTML, { html: helperText || '' }), fullWidth: true, slotProps: {

package/esm/ConfigurationEditorWidget/components/HeadingComponent.js

@@ -1,6 +1,6 @@
 import React from 'react';
 import { observer } from 'mobx-react';
-import { isStateTreeNode, getType } from 'mobx-state-tree';
+import { getType, isStateTreeNode } from 'mobx-state-tree';
 const HeadingComponent = observer(function ({ model, }) {
     if (model === null || model === void 0 ? void 0 : model.target) {
         if (model.target.type) {

package/esm/ConfigurationEditorWidget/components/JsonEditor.js

@@ -1,10 +1,8 @@
 import React, { useEffect, useState } from 'react';
 import { InputLabel, TextField } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
 import { observer } from 'mobx-react';
-// fontSize and fontFamily have to match between Editor and SyntaxHighlighter
+import { makeStyles } from '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 = makeStyles()(theme => ({
     error: {

package/esm/ConfigurationEditorWidget/components/NumberMapEditor.js

@@ -1,10 +1,9 @@
 import React, { useState } from 'react';
-import { observer } from 'mobx-react';
+import AddIcon from '@mui/icons-material/Add';
+import DeleteIcon from '@mui/icons-material/Delete';
 import { Card, CardContent, CardHeader, FormHelperText, IconButton, InputAdornment, InputLabel, TextField, } from '@mui/material';
+import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
-// icons
-import DeleteIcon from '@mui/icons-material/Delete';
-import AddIcon from '@mui/icons-material/Add';
 import NumberEditor from './NumberEditor';
 const useStyles = makeStyles()(theme => ({
     card: {

package/esm/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/esm/ConfigurationEditorWidget/components/SlotEditor.js

@@ -1,22 +1,20 @@
 import React, { useEffect, useState } from 'react';
-import { observer } from 'mobx-react';
-import { getPropertyMembers } from 'mobx-state-tree';
-import { getEnv } from '@jbrowse/core/util';
 import { FileSelector } from '@jbrowse/core/ui';
-import { getSubType, getUnionSubTypes, } from '@jbrowse/core/util/mst-reflection';
-import { IconButton, MenuItem, Paper, SvgIcon, TextField } from '@mui/material';
-// icons
+import { getEnv } from '@jbrowse/core/util';
+import { getSubType, getUnionSubTypes } from '@jbrowse/core/util/mst-reflection';
 import RadioButtonUncheckedIcon from '@mui/icons-material/RadioButtonUnchecked';
-// locals
-import StringArrayEditor from './StringArrayEditor';
+import { IconButton, MenuItem, Paper, SvgIcon, TextField } from '@mui/material';
+import { observer } from 'mobx-react';
+import { getPropertyMembers } from 'mobx-state-tree';
+import BooleanEditor from './BooleanEditor';
 import CallbackEditor from './CallbackEditor';
 import ColorEditor from './ColorEditor';
-import JsonEditor from './JsonEditor';
-import StringArrayMapEditor from './StringArrayMapEditor';
 import ConfigurationTextField from './ConfigurationTextField';
-import NumberMapEditor from './NumberMapEditor';
+import JsonEditor from './JsonEditor';
 import NumberEditor from './NumberEditor';
-import BooleanEditor from './BooleanEditor';
+import NumberMapEditor from './NumberMapEditor';
+import StringArrayEditor from './StringArrayEditor';
+import StringArrayMapEditor from './StringArrayMapEditor';
 import { useSlotEditorStyles } from './useSlotEditorStyles';
 const StringEditor = observer(function ({ slot, }) {
     return (React.createElement(ConfigurationTextField, { label: slot.name, helperText: slot.description, value: slot.value, onChange: evt => {
@@ -28,7 +26,6 @@ const TextEditor = observer(function ({ slot, }) {
             slot.set(evt.target.value);
         } }));
 });
-// checked checkbox, looks like a styled (x)
 const SvgCheckbox = () => (React.createElement(SvgIcon, null,
     React.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 = observer(function ({ slot, }) {
@@ -54,9 +51,7 @@ const FileSelectorWrapper = observer(function ({ slot, }) {
     var _a;
     return (React.createElement(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 = getEnv(slot).pluginManager) === null || _a === void 0 ? void 0 : _a.rootModel }));
+        }, name: slot.name, description: slot.description, rootModel: (_a = getEnv(slot).pluginManager) === null || _a === void 0 ? void 0 : _a.rootModel }));
 });
 const valueComponents = {
     string: StringEditor,
@@ -78,7 +73,7 @@ const SlotEditor = observer(function ({ slot, slotSchema, }) {
     const { type } = slot;
     let ValueComponent = slot.isCallback
         ? CallbackEditor
-        : // @ts-expect-error
+        :
             valueComponents[type];
     if (!ValueComponent) {
         console.warn(`no slot editor defined for ${type}, editing as string`);

package/esm/ConfigurationEditorWidget/components/StringArrayEditor.js

@@ -1,8 +1,7 @@
 import React, { useState } from 'react';
-import { observer } from 'mobx-react';
-import { Button, FormHelperText, IconButton, InputAdornment, InputLabel, List, ListItem, TextField, } from '@mui/material';
-// icons
 import DeleteIcon from '@mui/icons-material/Delete';
+import { Button, FormHelperText, IconButton, InputAdornment, InputLabel, List, ListItem, TextField, } from '@mui/material';
+import { observer } from 'mobx-react';
 const StringArrayEditor = observer(function ({ slot, }) {
     const [value, setValue] = useState('');
     const [addNew, setAddNew] = useState(false);

package/esm/ConfigurationEditorWidget/components/StringArrayMapEditor.js

@@ -1,11 +1,9 @@
 import React, { useState } from 'react';
-import { observer } from 'mobx-react';
+import AddIcon from '@mui/icons-material/Add';
+import DeleteIcon from '@mui/icons-material/Delete';
 import { Card, CardContent, CardHeader, FormHelperText, IconButton, InputAdornment, InputLabel, TextField, } from '@mui/material';
+import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
-// icons
-import DeleteIcon from '@mui/icons-material/Delete';
-import AddIcon from '@mui/icons-material/Add';
-// locals
 import StringArrayEditor from './StringArrayEditor';
 const useStyles = makeStyles()(theme => ({
     card: {

package/esm/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/esm/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/esm/ConfigurationEditorWidget/index.js

@@ -1,8 +1,8 @@
 import { lazy } from 'react';
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { WidgetType } from '@jbrowse/core/pluggableElementTypes';
-import stateModelFactory from './model';
 import HeadingComponent from './components/HeadingComponent';
+import stateModelFactory from './model';
 const configSchema = ConfigurationSchema('ConfigurationEditorWidget', {});
 const LazyConfigurationEditorComponent = lazy(() => import('./components/ConfigurationEditor'));
 export default function registerConfigurationEditorWidget(pluginManager) {

package/esm/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/esm/ConfigurationEditorWidget/model.js

@@ -1,12 +1,10 @@
-import { types } from 'mobx-state-tree';
 import { ElementId } from '@jbrowse/core/util/types/mst';
+import { types } from 'mobx-state-tree';
 export default function stateModelFactory(pluginManager) {
     return types
         .model('ConfigurationEditorWidget', {
         id: ElementId,
         type: 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: types.safeReference(pluginManager.pluggableConfigSchemaType('track')),
     })
         .actions(self => ({

package/esm/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/esm/FromConfigAdapter/FromConfigAdapter.js

@@ -1,7 +1,7 @@
+import { readConfObject } from '@jbrowse/core/configuration';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import SimpleFeature from '@jbrowse/core/util/simpleFeature';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { readConfObject, } from '@jbrowse/core/configuration';
+import SimpleFeature from '@jbrowse/core/util/simpleFeature';
 export function makeFeatures(fdata) {
     const features = new Map();
     for (const entry of fdata) {
@@ -14,7 +14,6 @@ export 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'));
     }
@@ -47,5 +46,5 @@ export default class FromConfigAdapter extends BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }

package/esm/FromConfigAdapter/configSchema.d.ts

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

package/esm/FromConfigAdapter/configSchema.js

@@ -1,12 +1,6 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config FromConfigAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const configSchema = ConfigurationSchema('FromConfigAdapter', {
-    /**
-     * #slot
-     */
     features: {
         type: 'frozen',
         defaultValue: [],

package/esm/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/esm/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/esm/FromConfigRegionsAdapter/FromConfigRegionsAdapter.js

@@ -1,23 +1,14 @@
-import { BaseAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { readConfObject, } from '@jbrowse/core/configuration';
+import { readConfObject } from '@jbrowse/core/configuration';
+import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { makeFeatures } from '../FromConfigAdapter/FromConfigAdapter';
-/**
- * Adapter that just returns the features defined in its `features` configuration
- * key, like:
- *   `"features": [ { "refName": "ctgA", "start":1, "end":20 }, ... ]`
- */
 export default class FromConfigRegionsAdapter extends BaseAdapter {
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
         const f = readConfObject(config, 'features');
         this.features = 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) {
@@ -41,9 +32,8 @@ export default class FromConfigRegionsAdapter extends BaseAdapter {
                 regions.push(currentRegion);
             }
         }
-        // sort the regions by refName
         regions.sort((a, b) => a.refName.localeCompare(b.refName));
         return regions;
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }

package/esm/FromConfigRegionsAdapter/configSchema.d.ts

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

package/esm/FromConfigRegionsAdapter/configSchema.js

@@ -1,13 +1,6 @@
 import { ConfigurationSchema } from '@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 = ConfigurationSchema('FromConfigRegionsAdapter', {
-    /**
-     * #slot
-     */
     features: {
         type: 'frozen',
         defaultValue: [],

package/esm/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/esm/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;
 }