@jbrowse/plugin-config 1.7.11 → 2.1.0

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

@@ -0,0 +1,18 @@
+/// <reference types="react" />
+import { IAnyType } from 'mobx-state-tree';
+export declare const useSlotEditorStyles: (params: void, styleOverrides?: {
+    props: {
+        classes?: Record<string, string> | undefined;
+    } & Record<string, unknown>;
+    ownerState?: Record<string, unknown> | undefined;
+} | undefined) => {
+    classes: Record<"paper" | "paperContent" | "slotModeSwitch", string>;
+    theme: import("@mui/material").Theme;
+    css: import("tss-react/types").Css;
+    cx: import("tss-react/types").Cx;
+};
+declare const SlotEditor: ({ slot, slotSchema }: {
+    slot: any;
+    slotSchema: IAnyType;
+}) => JSX.Element;
+export default SlotEditor;

package/esm/ConfigurationEditorWidget/components/SlotEditor.js

@@ -0,0 +1,182 @@
+import React, { useEffect, useState } from 'react';
+import { observer } from 'mobx-react';
+import { getPropertyMembers, getEnv } from 'mobx-state-tree';
+import { FileSelector, SanitizedHTML } from '@jbrowse/core/ui';
+import { getPropertyType, getSubType, getUnionSubTypes, } from '@jbrowse/core/util/mst-reflection';
+import { Card, CardContent, CardHeader, Checkbox, FormControl, FormControlLabel, FormHelperText, IconButton, InputAdornment, InputLabel, MenuItem, Paper, SvgIcon, TextField, } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+// icons
+import DeleteIcon from '@mui/icons-material/Delete';
+import AddIcon from '@mui/icons-material/Add';
+import RadioButtonUncheckedIcon from '@mui/icons-material/RadioButtonUnchecked';
+// locals
+import StringArrayEditor from './StringArrayEditor';
+import CallbackEditor from './CallbackEditor';
+import ColorEditor from './ColorEditor';
+import JsonEditor from './JsonEditor';
+// adds ability to have html in helperText. note that FormHelperTextProps is
+// div because the default is p which does not like div children
+function MyTextField(props) {
+    const { helperText } = props;
+    return (React.createElement(TextField, { ...props, helperText: React.createElement(SanitizedHTML, { html: helperText || '' }), FormHelperTextProps: {
+            // @ts-ignore
+            component: 'div',
+        }, fullWidth: true }));
+}
+const StringEditor = observer(({ slot, }) => (React.createElement(MyTextField, { label: slot.name, helperText: slot.description, value: slot.value, onChange: evt => slot.set(evt.target.value) })));
+const TextEditor = observer(({ slot, }) => (React.createElement(TextField, { label: slot.name, helperText: slot.description, multiline: true, value: slot.value, onChange: evt => 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 useMapEditorStyles = makeStyles()(theme => ({
+    card: {
+        marginTop: theme.spacing(1),
+    },
+}));
+const StringArrayMapEditor = observer(({ slot, }) => {
+    const { classes } = useMapEditorStyles();
+    const [value, setValue] = useState('');
+    return (React.createElement(React.Fragment, null,
+        React.createElement(InputLabel, null, slot.name),
+        Array.from(slot.value, ([key, val]) => (React.createElement(Card, { raised: true, key: key, className: classes.card },
+            React.createElement(CardHeader, { title: key, action: React.createElement(IconButton, { color: "secondary", onClick: () => slot.remove(key) },
+                    React.createElement(DeleteIcon, null)) }),
+            React.createElement(CardContent, null,
+                React.createElement(StringArrayEditor, { slot: {
+                        name: slot.name,
+                        value: val,
+                        description: `Values associated with entry ${key}`,
+                        setAtIndex: (idx, val) => slot.setAtKeyIndex(key, idx, val),
+                        removeAtIndex: (idx) => slot.removeAtKeyIndex(key, idx),
+                        add: (val) => slot.addToKey(key, val),
+                    } }))))),
+        React.createElement(Card, { raised: true, className: classes.card },
+            React.createElement(CardHeader, { disableTypography: true, title: React.createElement(TextField, { fullWidth: true, value: value, placeholder: "add new", onChange: event => setValue(event.target.value), InputProps: {
+                        endAdornment: (React.createElement(InputAdornment, { position: "end" },
+                            React.createElement(IconButton, { disabled: value === '', onClick: () => {
+                                    slot.add(value, []);
+                                    setValue('');
+                                }, color: "secondary" },
+                                React.createElement(AddIcon, null)))),
+                    } }) })),
+        React.createElement(FormHelperText, null, slot.description)));
+});
+const NumberMapEditor = observer(({ slot, }) => {
+    const { classes } = useMapEditorStyles();
+    const [value, setValue] = useState('');
+    return (React.createElement(React.Fragment, null,
+        React.createElement(InputLabel, null, slot.name),
+        Array.from(slot.value, ([key, val]) => (React.createElement(Card, { raised: true, key: key, className: classes.card },
+            React.createElement(CardHeader, { title: key, action: React.createElement(IconButton, { color: "secondary", onClick: () => slot.remove(key) },
+                    React.createElement(DeleteIcon, null)) }),
+            React.createElement(CardContent, null,
+                React.createElement(NumberEditor, { slot: {
+                        value: val,
+                        set: (val) => slot.add(key, val),
+                    } }))))),
+        React.createElement(Card, { raised: true, className: classes.card },
+            React.createElement(CardHeader, { disableTypography: true, title: React.createElement(TextField, { fullWidth: true, value: value, placeholder: "add new", onChange: event => setValue(event.target.value), InputProps: {
+                        endAdornment: (React.createElement(InputAdornment, { position: "end" },
+                            React.createElement(IconButton, { disabled: value === '', onClick: () => {
+                                    slot.add(value, 0);
+                                    setValue('');
+                                }, color: "secondary" },
+                                React.createElement(AddIcon, null)))),
+                    } }) })),
+        React.createElement(FormHelperText, null, slot.description)));
+});
+const NumberEditor = observer(({ slot, }) => {
+    const [val, setVal] = useState(slot.value);
+    useEffect(() => {
+        var _a;
+        const num = parseFloat(val);
+        if (!Number.isNaN(num)) {
+            slot.set(num);
+        }
+        else {
+            (_a = slot.reset) === null || _a === void 0 ? void 0 : _a.call(slot);
+        }
+    }, [slot, val]);
+    return (React.createElement(MyTextField, { label: slot.name, helperText: slot.description, value: val, type: "number", onChange: evt => setVal(evt.target.value) }));
+});
+const IntegerEditor = observer(({ slot, }) => {
+    const [val, setVal] = useState(slot.value);
+    useEffect(() => {
+        const num = parseInt(val, 10);
+        if (!Number.isNaN(num)) {
+            slot.set(num);
+        }
+    }, [slot, val]);
+    return (React.createElement(MyTextField, { label: slot.name, helperText: slot.description, value: val, type: "number", onChange: evt => setVal(evt.target.value) }));
+});
+const BooleanEditor = observer(({ slot, }) => (React.createElement(FormControl, null,
+    React.createElement(FormControlLabel, { label: slot.name, control: React.createElement(Checkbox, { checked: slot.value, onChange: evt => slot.set(evt.target.checked) }) }),
+    React.createElement(FormHelperText, null, slot.description))));
+const StringEnumEditor = observer(
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+({ slot, slotSchema }) => {
+    const p = getPropertyMembers(getSubType(slotSchema));
+    const choices = getUnionSubTypes(getUnionSubTypes(getSubType(getPropertyType(p, 'value')))[1]).map(t => t.value);
+    return (React.createElement(MyTextField, { value: slot.value, label: slot.name, select: true, helperText: slot.description, onChange: evt => slot.set(evt.target.value) }, choices.map(str => (React.createElement(MenuItem, { key: str, value: str }, str)))));
+});
+const FileSelectorWrapper = observer(({ slot, }) => {
+    var _a;
+    return (React.createElement(FileSelector, { location: slot.value, setLocation: location => slot.set(location), name: slot.name, description: slot.description, rootModel: (_a = getEnv(slot).pluginManager) === null || _a === void 0 ? void 0 : _a.rootModel }));
+});
+const valueComponents = {
+    string: StringEditor,
+    text: TextEditor,
+    fileLocation: FileSelectorWrapper,
+    stringArray: StringArrayEditor,
+    stringArrayMap: StringArrayMapEditor,
+    numberMap: NumberMapEditor,
+    number: NumberEditor,
+    integer: IntegerEditor,
+    color: ColorEditor,
+    stringEnum: StringEnumEditor,
+    boolean: BooleanEditor,
+    frozen: JsonEditor,
+    configRelationships: JsonEditor,
+};
+export const useSlotEditorStyles = makeStyles()(theme => ({
+    paper: {
+        display: 'flex',
+        marginBottom: theme.spacing(2),
+        position: 'relative',
+    },
+    paperContent: {
+        width: '100%',
+    },
+    slotModeSwitch: {
+        width: 24,
+        background: theme.palette.secondary.light,
+        display: 'flex',
+        justifyContent: 'center',
+        alignItems: 'center',
+    },
+}));
+const SlotEditor = observer(
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+({ slot, slotSchema }) => {
+    const { classes } = useSlotEditorStyles();
+    const { type } = slot;
+    let ValueComponent = slot.isCallback
+        ? CallbackEditor
+        : // @ts-ignore
+            valueComponents[type];
+    if (!ValueComponent) {
+        console.warn(`no slot editor defined for ${type}, editing as string`);
+        ValueComponent = StringEditor;
+    }
+    if (!(type in valueComponents)) {
+        console.warn(`SlotEditor needs to implement ${type}`);
+    }
+    return (React.createElement(Paper, { className: classes.paper },
+        React.createElement("div", { className: classes.paperContent },
+            React.createElement(ValueComponent, { slot: slot, slotSchema: slotSchema })),
+        React.createElement("div", { className: classes.slotModeSwitch }, slot.contextVariable.length ? (React.createElement(IconButton, { onClick: () => slot.isCallback
+                ? slot.convertToValue()
+                : slot.convertToCallback(), title: `convert to ${slot.isCallback ? 'regular value' : 'callback'}`, color: "secondary" }, !slot.isCallback ? (React.createElement(RadioButtonUncheckedIcon, null)) : (React.createElement(SvgCheckbox, null)))) : null)));
+});
+export default SlotEditor;
+//# sourceMappingURL=SlotEditor.js.map

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

@@ -0,0 +1 @@
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package/esm/ConfigurationEditorWidget/components/StringArrayEditor.d.ts

@@ -0,0 +1,12 @@
+/// <reference types="react" />
+declare const StringArrayEditor: ({ slot, }: {
+    slot: {
+        name: string;
+        value: string[];
+        setAtIndex: Function;
+        removeAtIndex: Function;
+        add: Function;
+        description: string;
+    };
+}) => JSX.Element;
+export default StringArrayEditor;

package/esm/ConfigurationEditorWidget/components/StringArrayEditor.js

@@ -0,0 +1,36 @@
+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';
+const StringArrayEditor = observer(({ slot, }) => {
+    const [value, setValue] = useState('');
+    const [addNew, setAddNew] = useState(false);
+    return (React.createElement(React.Fragment, null,
+        slot.name ? React.createElement(InputLabel, null, slot.name) : null,
+        React.createElement(List, { disablePadding: true },
+            slot.value.map((val, idx) => (React.createElement(ListItem, { key: idx, disableGutters: true },
+                React.createElement(TextField, { value: val, onChange: evt => slot.setAtIndex(idx, evt.target.value), InputProps: {
+                        endAdornment: (React.createElement(InputAdornment, { position: "end" },
+                            React.createElement(IconButton, { color: "secondary", onClick: () => slot.removeAtIndex(idx) },
+                                React.createElement(DeleteIcon, null)))),
+                    } })))),
+            addNew ? (React.createElement(ListItem, { disableGutters: true },
+                React.createElement(TextField, { value: value, placeholder: "add new", onChange: event => setValue(event.target.value), InputProps: {
+                        endAdornment: (React.createElement(InputAdornment, { position: "end" },
+                            React.createElement(React.Fragment, null,
+                                React.createElement(Button, { color: "primary", variant: "contained", style: { margin: 2 }, "data-testid": `stringArrayAdd-${slot.name}`, onClick: () => {
+                                        setAddNew(false);
+                                        slot.add(value);
+                                        setValue('');
+                                    } }, "OK"),
+                                React.createElement(Button, { color: "primary", variant: "contained", style: { margin: 2 }, onClick: () => {
+                                        setAddNew(false);
+                                        setValue('');
+                                    } }, "Cancel")))),
+                    } }))) : null,
+            React.createElement(Button, { color: "primary", variant: "contained", style: { margin: 4 }, disabled: addNew, onClick: () => setAddNew(true) }, "Add item")),
+        React.createElement(FormHelperText, null, slot.description)));
+});
+export default StringArrayEditor;
+//# sourceMappingURL=StringArrayEditor.js.map

package/esm/ConfigurationEditorWidget/components/StringArrayEditor.js.map

@@ -0,0 +1 @@
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package/esm/ConfigurationEditorWidget/components/TypeSelector.d.ts

@@ -0,0 +1,9 @@
+import React from 'react';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+declare const TypeSelector: ({ typeNameChoices, slot, slotName, onChange, }: {
+    typeNameChoices: string[];
+    slot: AnyConfigurationModel;
+    slotName: string;
+    onChange: (event: React.ChangeEvent<HTMLInputElement>) => void;
+}) => JSX.Element;
+export default TypeSelector;

package/esm/ConfigurationEditorWidget/components/TypeSelector.js

@@ -0,0 +1,12 @@
+import React from 'react';
+import { MenuItem, Paper, TextField } from '@mui/material';
+import { observer } from 'mobx-react';
+import { useSlotEditorStyles } from './SlotEditor';
+const TypeSelector = observer(({ typeNameChoices, slot, slotName, onChange, }) => {
+    const { classes } = useSlotEditorStyles();
+    return (React.createElement(Paper, { className: classes.paper },
+        React.createElement("div", { className: classes.paperContent },
+            React.createElement(TextField, { value: slot.type, label: "Type", select: true, helperText: `Type of ${slotName} to use`, fullWidth: true, onChange: onChange }, typeNameChoices.map(str => (React.createElement(MenuItem, { key: str, value: str }, str)))))));
+});
+export default TypeSelector;
+//# sourceMappingURL=TypeSelector.js.map

package/esm/ConfigurationEditorWidget/components/TypeSelector.js.map

@@ -0,0 +1 @@
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package/esm/ConfigurationEditorWidget/index.d.ts

@@ -0,0 +1,10 @@
+/// <reference types="react" />
+export { default as stateModelFactory } from './model';
+export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export declare const HeadingComponent: ({ model }: {
+    model?: {
+        target: {
+            type: string;
+        };
+    } | undefined;
+}) => JSX.Element;

package/esm/ConfigurationEditorWidget/index.js

@@ -0,0 +1,21 @@
+import React from 'react';
+import { observer } from 'mobx-react';
+import { isStateTreeNode, getType } from 'mobx-state-tree';
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export { default as stateModelFactory } from './model';
+export const configSchema = ConfigurationSchema('ConfigurationEditorWidget', {});
+export const HeadingComponent = observer(({ model }) => {
+    if (model === null || model === void 0 ? void 0 : model.target) {
+        if (model.target.type) {
+            return React.createElement(React.Fragment, null, `${model.target.type} settings`);
+        }
+        if (isStateTreeNode(model.target)) {
+            const type = getType(model.target);
+            if (type === null || type === void 0 ? void 0 : type.name) {
+                return (React.createElement(React.Fragment, null, `${type.name.replace('ConfigurationSchema', '')} settings`));
+            }
+        }
+    }
+    return React.createElement(React.Fragment, null, "Settings");
+});
+//# sourceMappingURL=index.js.map

package/esm/ConfigurationEditorWidget/index.js.map

@@ -0,0 +1 @@
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package/esm/ConfigurationEditorWidget/model.d.ts

@@ -0,0 +1,9 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (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">;
+    target: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyModelType>>;
+}, {
+    setTarget(newTarget: any): void;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export default _default;

package/esm/ConfigurationEditorWidget/model.js

@@ -0,0 +1,17 @@
+import { types } from 'mobx-state-tree';
+import { ElementId } from '@jbrowse/core/util/types/mst';
+export default (pluginManager) => 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 => ({
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    setTarget(newTarget) {
+        self.target = newTarget;
+    },
+}));
+//# sourceMappingURL=model.js.map

package/esm/ConfigurationEditorWidget/model.js.map

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package/esm/FromConfigAdapter/FromConfigAdapter.d.ts

@@ -0,0 +1,24 @@
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import SimpleFeature, { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
+import { NoAssemblyRegion } from '@jbrowse/core/util/types';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+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 }, ... ]`
+ */
+export default class FromConfigAdapter extends BaseFeatureDataAdapter {
+    protected features: Map<string, Feature[]>;
+    constructor(conf: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    static makeFeatures(fdata: SimpleFeatureSerialized[]): Map<string, Feature[]>;
+    static makeFeature(data: SimpleFeatureSerialized): SimpleFeature;
+    getRefNames(): Promise<string[]>;
+    getRefNameAliases(): Promise<{
+        refName: string;
+        aliases: any;
+    }[]>;
+    getFeatures(region: NoAssemblyRegion): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}

package/esm/FromConfigAdapter/FromConfigAdapter.js

@@ -0,0 +1,63 @@
+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';
+/**
+ * Adapter that just returns the features defined in its `features` configuration
+ * key, like:
+ *   `"features": [ { "refName": "ctgA", "start":1, "end":20 }, ... ]`
+ */
+export default class FromConfigAdapter extends BaseFeatureDataAdapter {
+    constructor(conf, getSubAdapter, pluginManager) {
+        super(conf, getSubAdapter, pluginManager);
+        const feats = readConfObject(conf, 'features');
+        this.features = FromConfigAdapter.makeFeatures(feats || []);
+    }
+    static makeFeatures(fdata) {
+        const features = new Map();
+        for (let i = 0; i < fdata.length; i += 1) {
+            if (fdata[i]) {
+                const f = this.makeFeature(fdata[i]);
+                const refName = f.get('refName');
+                let bucket = features.get(refName);
+                if (!bucket) {
+                    bucket = [];
+                    features.set(refName, bucket);
+                }
+                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'));
+        }
+        return features;
+    }
+    static makeFeature(data) {
+        return new SimpleFeature(data);
+    }
+    async getRefNames() {
+        return [...this.features.keys()];
+    }
+    async getRefNameAliases() {
+        return Array.from(this.features.values()).map(featureArray => ({
+            refName: featureArray[0].get('refName'),
+            aliases: featureArray[0].get('aliases'),
+        }));
+    }
+    getFeatures(region) {
+        const { refName, start, end } = region;
+        return ObservableCreate(async (observer) => {
+            const features = this.features.get(refName) || [];
+            for (let i = 0; i < features.length; i++) {
+                const f = features[i];
+                if (f.get('end') > start && f.get('start') < end) {
+                    observer.next(f);
+                }
+            }
+            observer.complete();
+        });
+    }
+    freeResources( /* { region } */) { }
+}
+//# sourceMappingURL=FromConfigAdapter.js.map

package/esm/FromConfigAdapter/FromConfigAdapter.js.map

@@ -0,0 +1 @@
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package/esm/FromConfigAdapter/FromConfigRegionsAdapter.d.ts

@@ -0,0 +1,23 @@
+import { BaseAdapter, RegionsAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { ConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+import { configSchema as FromConfigAdapterConfigSchema } from './configSchema';
+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 }, ... ]`
+ */
+export default class FromConfigRegionsAdapter extends BaseAdapter implements RegionsAdapter {
+    private features;
+    constructor(config: ConfigurationModel<typeof FromConfigAdapterConfigSchema>, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    /**
+     * Get refName, start, and end for all features after collapsing any overlaps
+     */
+    getRegions(): Promise<{
+        refName: string;
+        start: number;
+        end: number;
+    }[]>;
+    freeResources(): void;
+}

package/esm/FromConfigAdapter/FromConfigRegionsAdapter.js

@@ -0,0 +1,50 @@
+import { BaseAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { readConfObject } from '@jbrowse/core/configuration';
+import FromConfigAdapter from './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 features = readConfObject(config, 'features');
+        this.features = FromConfigAdapter.makeFeatures(features || []);
+    }
+    /**
+     * 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) {
+                if (currentRegion &&
+                    currentRegion.end >= feature.get('start') &&
+                    currentRegion.start <= feature.get('end')) {
+                    currentRegion.end = feature.get('end');
+                }
+                else {
+                    if (currentRegion) {
+                        regions.push(currentRegion);
+                    }
+                    currentRegion = {
+                        refName,
+                        start: feature.get('start'),
+                        end: feature.get('end'),
+                    };
+                }
+            }
+            if (currentRegion) {
+                regions.push(currentRegion);
+            }
+        }
+        // sort the regions by refName
+        regions.sort((a, b) => a.refName.localeCompare(b.refName));
+        return regions;
+    }
+    freeResources( /* { region } */) { }
+}
+//# sourceMappingURL=FromConfigRegionsAdapter.js.map

package/esm/FromConfigAdapter/FromConfigRegionsAdapter.js.map

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package/esm/FromConfigAdapter/FromConfigSequenceAdapter.d.ts

@@ -0,0 +1,26 @@
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { NoAssemblyRegion } from '@jbrowse/core/util/types';
+import FromConfigAdapter from './FromConfigAdapter';
+import { RegionsAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+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<{
+        refName: string;
+        start: number;
+        end: number;
+    }[]>;
+    /**
+     * called to provide a hint that data tied to a certain region
+     * will not be needed for the forseeable future and can be purged
+     * from caches, etc
+     */
+    freeResources(): void;
+}