@jbrowse/plugin-linear-genome-view 2.2.1 → 2.3.0

package/dist/LinearBareDisplay/index.js

@@ -1,8 +1,24 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.stateModelFactory = exports.configSchemaFactory = void 0;
-var configSchema_1 = require("./configSchema");
+const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
+// locals
+const configSchema_1 = require("./configSchema");
 Object.defineProperty(exports, "configSchemaFactory", { enumerable: true, get: function () { return configSchema_1.configSchemaFactory; } });
-var model_1 = require("./model");
+const model_1 = require("./model");
 Object.defineProperty(exports, "stateModelFactory", { enumerable: true, get: function () { return model_1.stateModelFactory; } });
+const BaseLinearDisplay_1 = require("../BaseLinearDisplay/");
+exports.default = (pluginManager) => {
+    pluginManager.addDisplayType(() => {
+        const configSchema = (0, configSchema_1.configSchemaFactory)(pluginManager);
+        return new pluggableElementTypes_1.DisplayType({
+            name: 'LinearBareDisplay',
+            configSchema,
+            stateModel: (0, model_1.stateModelFactory)(configSchema),
+            trackType: 'BasicTrack',
+            viewType: 'LinearGenomeView',
+            ReactComponent: BaseLinearDisplay_1.BaseLinearDisplayComponent,
+        });
+    });
+};
 //# sourceMappingURL=index.js.map

package/dist/LinearBareDisplay/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearBareDisplay/index.ts"],"names":[],"mappings":";;;AACA,+EAAiE;AAEjE,SAAS;AACT,iDAAoD;AAkB3C,oGAlBA,kCAAmB,OAkBA;AAjB5B,mCAA2C;AAiBb,kGAjBrB,yBAAiB,OAiBqB;AAhB/C,6DAAkE;AAElE,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,kCAAmB,EAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,mCAAW,CAAC;YACrB,IAAI,EAAE,mBAAmB;YACzB,YAAY;YACZ,UAAU,EAAE,IAAA,yBAAiB,EAAC,YAAY,CAAC;YAC3C,SAAS,EAAE,YAAY;YACvB,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,8CAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/dist/LinearBareDisplay/model.d.ts

@@ -121,10 +121,10 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     reload(): void;
 } & {
     currBpPerPx: number;
+    scrollTop: number;
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
-    scrollTop: number;
     estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
     estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {

package/dist/LinearBasicDisplay/components/SetMaxHeight.js

@@ -22,25 +22,16 @@ var __importStar = (this && this.__importStar) || function (mod) {
     __setModuleDefault(result, mod);
     return result;
 };
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
 const mobx_react_1 = require("mobx-react");
+const ui_1 = require("@jbrowse/core/ui");
 const material_1 = require("@mui/material");
 const mui_1 = require("tss-react/mui");
-const Close_1 = __importDefault(require("@mui/icons-material/Close"));
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     root: {
         width: 500,
     },
-    closeButton: {
-        position: 'absolute',
-        right: theme.spacing(1),
-        top: theme.spacing(1),
-        color: theme.palette.grey[500],
-    },
     field: {
         margin: theme.spacing(2),
     },
@@ -49,11 +40,7 @@ function SetMaxHeightDlg({ model, handleClose, }) {
     const { classes } = useStyles();
     const { maxHeight = '' } = model;
     const [max, setMax] = (0, react_1.useState)(`${maxHeight}`);
-    return (react_1.default.createElement(material_1.Dialog, { open: true, onClose: handleClose, "aria-labelledby": "alert-dialog-title", "aria-describedby": "alert-dialog-description" },
-        react_1.default.createElement(material_1.DialogTitle, { id: "alert-dialog-title" },
-            "Filter options",
-            react_1.default.createElement(material_1.IconButton, { "aria-label": "close", className: classes.closeButton, onClick: handleClose, size: "large" },
-                react_1.default.createElement(Close_1.default, null))),
+    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Set max height" },
         react_1.default.createElement(material_1.DialogContent, { className: classes.root },
             react_1.default.createElement(material_1.Typography, null, "Set max height for the track. For example, you can increase this if the layout says \"Max height reached\""),
             react_1.default.createElement(material_1.TextField, { value: max, onChange: event => setMax(event.target.value), placeholder: "Enter max score" }),

package/dist/LinearBasicDisplay/components/SetMaxHeight.js.map

@@ -1 +1 @@
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+{"version":3,"file":"SetMaxHeight.js","sourceRoot":"","sources":["../../../src/LinearBasicDisplay/components/SetMaxHeight.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,yCAAyC;AACzC,4CAMsB;AACtB,uCAA0C;AAE1C,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,IAAI,EAAE;QACJ,KAAK,EAAE,GAAG;KACX;IAED,KAAK,EAAE;QACL,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KACzB;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,eAAe,CAAC,EACvB,KAAK,EACL,WAAW,GAOZ;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,SAAS,GAAG,EAAE,EAAE,GAAG,KAAK,CAAA;IAChC,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,IAAA,gBAAQ,EAAC,GAAG,SAAS,EAAE,CAAC,CAAA;IAE9C,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,gBAAgB;QACvD,8BAAC,wBAAa,IAAC,SAAS,EAAE,OAAO,CAAC,IAAI;YACpC,8BAAC,qBAAU,qHAGE;YACb,8BAAC,oBAAS,IACR,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAC7C,WAAW,EAAC,iBAAiB,GAC7B;YACF,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,SAAS,QACT,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,YAAY,CAChB,GAAG,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,SAAS,CACrD,CAAA;wBACD,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM;gBACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,eAAe,CAAC,CAAA"}

package/dist/LinearBasicDisplay/index.d.ts

@@ -1,2 +1,6 @@
-export { default as modelFactory } from './model';
-export { default as configSchema } from './configSchema';
+import PluginManager from '@jbrowse/core/PluginManager';
+import configSchema from './configSchema';
+import modelFactory from './model';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;
+export { modelFactory, configSchema };

package/dist/LinearBasicDisplay/index.js

@@ -4,8 +4,25 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.configSchema = exports.modelFactory = void 0;
-var model_1 = require("./model");
-Object.defineProperty(exports, "modelFactory", { enumerable: true, get: function () { return __importDefault(model_1).default; } });
-var configSchema_1 = require("./configSchema");
-Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(configSchema_1).default; } });
+const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
+const BaseLinearDisplay_1 = require("../BaseLinearDisplay");
+// locals
+const configSchema_1 = __importDefault(require("./configSchema"));
+exports.configSchema = configSchema_1.default;
+const model_1 = __importDefault(require("./model"));
+exports.modelFactory = model_1.default;
+exports.default = (pluginManager) => {
+    pluginManager.addDisplayType(() => {
+        const config = (0, configSchema_1.default)(pluginManager);
+        return new pluggableElementTypes_1.DisplayType({
+            name: 'LinearBasicDisplay',
+            displayName: 'Basic deature display',
+            configSchema: config,
+            stateModel: (0, model_1.default)(config),
+            trackType: 'FeatureTrack',
+            viewType: 'LinearGenomeView',
+            ReactComponent: BaseLinearDisplay_1.BaseLinearDisplayComponent,
+        });
+    });
+};
 //# sourceMappingURL=index.js.map

package/dist/LinearBasicDisplay/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearBasicDisplay/index.ts"],"names":[],"mappings":";;;;;;AAAA,iCAAiD;AAAxC,sHAAA,OAAO,OAAgB;AAChC,+CAAwD;AAA/C,6HAAA,OAAO,OAAgB"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearBasicDisplay/index.ts"],"names":[],"mappings":";;;;;;AACA,+EAAiE;AACjE,4DAAiE;AAEjE,SAAS;AACT,kEAAyC;AAkBlB,uBAlBhB,sBAAY,CAkBgB;AAjBnC,oDAAkC;AAiBzB,uBAjBF,eAAY,CAiBE;AAfrB,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,MAAM,GAAG,IAAA,sBAAY,EAAC,aAAa,CAAC,CAAA;QAC1C,OAAO,IAAI,mCAAW,CAAC;YACrB,IAAI,EAAE,oBAAoB;YAC1B,WAAW,EAAE,uBAAuB;YACpC,YAAY,EAAE,MAAM;YACpB,UAAU,EAAE,IAAA,eAAY,EAAC,MAAM,CAAC;YAChC,SAAS,EAAE,cAAc;YACzB,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,8CAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/dist/LinearBasicDisplay/model.d.ts

@@ -4,7 +4,8 @@ import { MenuItem } from '@jbrowse/core/ui';
 import { Instance } from 'mobx-state-tree';
 /**
  * #stateModel LinearBasicDisplay
- * used by `FeatureTrack`, has simple settings like "show/hide feature labels", etc.
+ * used by `FeatureTrack`, has simple settings like "show/hide feature labels",
+ * etc.
  */
 declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -34,14 +35,13 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         filled: boolean;
         reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
-        /**
-         * #property
-         */
         layout: any;
         status: string;
         error: unknown;
         message: string | undefined;
-        maxHeightReached: boolean;
+        maxHeightReached: boolean; /**
+         * #getter
+         */
         ReactComponent: ({ model, }: {
             model: any;
         }) => any;
@@ -49,7 +49,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     } & {
         doReload(): void;
         afterAttach(): void;
-        setStatus(message: string): void; /**
+        setStatus(message: string): void;
+        /**
          * #getter
          */
         setLoading(abortController: AbortController): void;
@@ -58,7 +59,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
             features: Map<string, import("@jbrowse/core/util").Feature>;
             layout: any;
-            maxHeightReached: boolean;
+            maxHeightReached: boolean; /**
+             * #method
+             */
             renderProps: any;
         } | undefined): void;
         setError(error: unknown): void;
@@ -107,9 +110,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
              */
             error: unknown;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>; /**
-             * #property
-             */
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
@@ -135,12 +136,15 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             rendererTypeName: string;
             error: unknown;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    }> | null;
+    }> | null; /**
+     * #action
+     */
     readonly adapterConfig: any;
     readonly parentTrack: any;
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined; /**
+    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    /**
      * #method
      */
     trackMenuItems(): MenuItem[];
@@ -152,10 +156,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     reload(): void;
 } & {
     currBpPerPx: number;
+    scrollTop: number;
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
-    scrollTop: number;
     estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
     estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {

package/dist/LinearBasicDisplay/model.js

@@ -37,7 +37,8 @@ const BaseLinearDisplay_1 = require("../BaseLinearDisplay");
 const SetMaxHeightDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SetMaxHeight'))));
 /**
  * #stateModel LinearBasicDisplay
- * used by `FeatureTrack`, has simple settings like "show/hide feature labels", etc.
+ * used by `FeatureTrack`, has simple settings like "show/hide feature labels",
+ * etc.
  */
 function stateModelFactory(configSchema) {
     return mobx_state_tree_1.types

package/dist/LinearBasicDisplay/model.js.map

@@ -1 +1 @@
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package/dist/LinearGenomeView/components/ExportSvgDialog.js

@@ -22,23 +22,10 @@ var __importStar = (this && this.__importStar) || function (mod) {
     __setModuleDefault(result, mod);
     return result;
 };
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const mui_1 = require("tss-react/mui");
 const material_1 = require("@mui/material");
 const ui_1 = require("@jbrowse/core/ui");
-const Close_1 = __importDefault(require("@mui/icons-material/Close"));
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    closeButton: {
-        position: 'absolute',
-        right: theme.spacing(1),
-        top: theme.spacing(1),
-        color: theme.palette.grey[500],
-    },
-}));
 function LoadingMessage() {
     return (react_1.default.createElement("div", null,
         react_1.default.createElement(material_1.CircularProgress, { size: 20, style: { marginRight: 20 } }),
@@ -51,12 +38,7 @@ function ExportSvgDlg({ model, handleClose, }) {
     const [loading, setLoading] = (0, react_1.useState)(false);
     const [filename, setFilename] = (0, react_1.useState)('jbrowse.svg');
     const [error, setError] = (0, react_1.useState)();
-    const { classes } = useStyles();
-    return (react_1.default.createElement(material_1.Dialog, { open: true, onClose: handleClose },
-        react_1.default.createElement(material_1.DialogTitle, null,
-            "Export SVG",
-            react_1.default.createElement(material_1.IconButton, { className: classes.closeButton, onClick: handleClose },
-                react_1.default.createElement(Close_1.default, null))),
+    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Export SVG" },
         react_1.default.createElement(material_1.DialogContent, null,
             error ? (react_1.default.createElement(ui_1.ErrorMessage, { error: error })) : loading ? (react_1.default.createElement(LoadingMessage, null)) : null,
             react_1.default.createElement(material_1.TextField, { helperText: "filename", value: filename, onChange: event => setFilename(event.target.value) }),

package/dist/LinearGenomeView/components/ExportSvgDialog.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ExportSvgDialog.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/ExportSvgDialog.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,4CASsB;AACtB,yCAAuD;AAGvD,SAAS,cAAc;IACrB,OAAO,CACL;QACE,8BAAC,2BAAgB,IAAC,IAAI,EAAE,EAAE,EAAE,KAAK,EAAE,EAAE,WAAW,EAAE,EAAE,EAAE,GAAI;QAC1D,8BAAC,qBAAU,IAAC,OAAO,EAAC,QAAQ,mBAA0B,CAClD,CACP,CAAA;AACH,CAAC;AAED,SAAwB,YAAY,CAAC,EACnC,KAAK,EACL,WAAW,GAIZ;IACC,aAAa;IACb,MAAM,eAAe,GAAG,OAAO,eAAe,KAAK,WAAW,CAAA;IAC9D,MAAM,CAAC,eAAe,EAAE,kBAAkB,CAAC,GAAG,IAAA,gBAAQ,EAAC,eAAe,CAAC,CAAA;IACvE,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,IAAA,gBAAQ,EAAC,KAAK,CAAC,CAAA;IAC7C,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,IAAA,gBAAQ,EAAC,aAAa,CAAC,CAAA;IACvD,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,IAAA,gBAAQ,GAAW,CAAA;IAC7C,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,YAAY;QACnD,8BAAC,wBAAa;YACX,KAAK,CAAC,CAAC,CAAC,CACP,8BAAC,iBAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAC/B,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CACZ,8BAAC,cAAc,OAAG,CACnB,CAAC,CAAC,CAAC,IAAI;YACR,8BAAC,oBAAS,IACR,UAAU,EAAC,UAAU,EACrB,KAAK,EAAE,QAAQ,EACf,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,WAAW,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,GAClD;YACD,eAAe,CAAC,CAAC,CAAC,CACjB,8BAAC,2BAAgB,IACf,OAAO,EACL,8BAAC,mBAAQ,IACP,OAAO,EAAE,eAAe,EACxB,QAAQ,EAAE,GAAG,EAAE,CAAC,kBAAkB,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GAC/C,EAEJ,KAAK,EAAC,8EAA8E,GACpF,CACH,CAAC,CAAC,CAAC,CACF,8BAAC,qBAAU,+FAGE,CACd,CACa;QAChB,8BAAC,wBAAa;YACZ,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB;YACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,OAAO,EAAE,KAAK,IAAI,EAAE;oBAClB,UAAU,CAAC,IAAI,CAAC,CAAA;oBAChB,QAAQ,CAAC,SAAS,CAAC,CAAA;oBACnB,IAAI;wBACF,MAAM,KAAK,CAAC,SAAS,CAAC,EAAE,eAAe,EAAE,QAAQ,EAAE,CAAC,CAAA;wBACpD,WAAW,EAAE,CAAA;qBACd;oBAAC,OAAO,CAAC,EAAE;wBACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;wBAChB,QAAQ,CAAC,CAAC,CAAC,CAAA;wBACX,UAAU,CAAC,KAAK,CAAC,CAAA;qBAClB;gBACH,CAAC,aAGM,CACK,CACT,CACV,CAAA;AACH,CAAC;AAzED,+BAyEC"}

package/dist/LinearGenomeView/components/GetSequenceDialog.js

@@ -33,26 +33,20 @@ const mobx_react_1 = require("mobx-react");
 const file_saver_1 = require("file-saver");
 const configuration_1 = require("@jbrowse/core/configuration");
 const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
+const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
 const formatFastaStrings_1 = require("@jbrowse/core/util/formatFastaStrings");
 // icons
 const Icons_1 = require("@jbrowse/core/ui/Icons");
-const Close_1 = __importDefault(require("@mui/icons-material/Close"));
 const GetApp_1 = __importDefault(require("@mui/icons-material/GetApp"));
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    closeButton: {
-        position: 'absolute',
-        right: theme.spacing(1),
-        top: theme.spacing(1),
-        color: theme.palette.grey[500],
-    },
+const useStyles = (0, mui_1.makeStyles)()({
     dialogContent: {
         width: '80em',
     },
     textAreaFont: {
         fontFamily: 'Courier New',
     },
-}));
+});
 /**
  * Fetches and returns a list features for a given list of regions
  */
@@ -131,15 +125,10 @@ function SequenceDialog({ model, handleClose, }) {
         };
     }, [model, session, regionsSelected, setSequence]);
     const sequenceTooLarge = sequence ? sequence.length > 1000000 : false;
-    return (react_1.default.createElement(material_1.Dialog, { maxWidth: "xl", open: true, onClose: handleClose },
-        react_1.default.createElement(material_1.DialogTitle, null,
-            "Reference sequence",
-            handleClose ? (react_1.default.createElement(material_1.IconButton, { className: classes.closeButton, onClick: () => {
-                    handleClose();
-                    model.setOffsets(undefined, undefined);
-                }, size: "large" },
-                react_1.default.createElement(Close_1.default, null))) : null),
-        react_1.default.createElement(material_1.Divider, null),
+    return (react_1.default.createElement(ui_1.Dialog, { maxWidth: "xl", open: true, onClose: () => {
+            handleClose();
+            model.setOffsets(undefined, undefined);
+        }, title: "Reference sequence" },
         react_1.default.createElement(material_1.DialogContent, null,
             error ? react_1.default.createElement(material_1.Typography, { color: "error" }, `${error}`) : null,
             loading && !error ? (react_1.default.createElement(material_1.Container, null,

package/dist/LinearGenomeView/components/GetSequenceDialog.js.map

@@ -1 +1 @@
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package/dist/LinearGenomeView/components/Header.js

@@ -14,7 +14,7 @@ const ArrowForward_1 = __importDefault(require("@mui/icons-material/ArrowForward
 const ArrowBack_1 = __importDefault(require("@mui/icons-material/ArrowBack"));
 // locals
 const __1 = require("..");
-const OverviewScaleBar_1 = __importDefault(require("./OverviewScaleBar"));
+const OverviewScalebar_1 = __importDefault(require("./OverviewScalebar"));
 const ZoomControls_1 = __importDefault(require("./ZoomControls"));
 const SearchBox_1 = __importDefault(require("./SearchBox"));
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
@@ -79,7 +79,7 @@ const Controls = ({ model }) => {
         react_1.default.createElement("div", { className: classes.spacer })));
 };
 const LinearGenomeViewHeader = (0, mobx_react_1.observer)(({ model }) => {
-    return !model.hideHeader ? (model.hideHeaderOverview ? (react_1.default.createElement(Controls, { model: model })) : (react_1.default.createElement(OverviewScaleBar_1.default, { model: model },
+    return !model.hideHeader ? (model.hideHeaderOverview ? (react_1.default.createElement(Controls, { model: model })) : (react_1.default.createElement(OverviewScalebar_1.default, { model: model },
         react_1.default.createElement(Controls, { model: model })))) : null;
 });
 exports.default = LinearGenomeViewHeader;

package/dist/LinearGenomeView/components/HelpDialog.js

@@ -5,24 +5,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
 const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
-const Close_1 = __importDefault(require("@mui/icons-material/Close"));
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    closeButton: {
-        position: 'absolute',
-        right: theme.spacing(1),
-        top: theme.spacing(1),
-        color: theme.palette.grey[500],
-    },
-}));
+const ui_1 = require("@jbrowse/core/ui");
 function HelpDialog({ handleClose, }) {
-    const { classes } = useStyles();
-    return (react_1.default.createElement(material_1.Dialog, { open: true, maxWidth: "xl", onClose: handleClose },
-        react_1.default.createElement(material_1.DialogTitle, null,
-            "Using the search box",
-            handleClose ? (react_1.default.createElement(material_1.IconButton, { className: classes.closeButton, onClick: () => handleClose() },
-                react_1.default.createElement(Close_1.default, null))) : null),
-        react_1.default.createElement(material_1.Divider, null),
+    return (react_1.default.createElement(ui_1.Dialog, { open: true, maxWidth: "xl", onClose: handleClose, title: "Using the search box" },
         react_1.default.createElement(material_1.DialogContent, null,
             react_1.default.createElement("h3", null, "Searching"),
             react_1.default.createElement("ul", null,

package/dist/LinearGenomeView/components/HelpDialog.js.map

@@ -1 +1 @@
-{"version":3,"file":"HelpDialog.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/HelpDialog.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,4CAQsB;AACtB,uCAA0C;AAC1C,sEAAiD;AAEjD,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,WAAW,EAAE;QACX,QAAQ,EAAE,UAAU;QACpB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACvB,GAAG,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACrB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC;KAC/B;CACF,CAAC,CAAC,CAAA;AAEH,SAAwB,UAAU,CAAC,EACjC,WAAW,GAGZ;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,CACL,8BAAC,iBAAM,IAAC,IAAI,QAAC,QAAQ,EAAC,IAAI,EAAC,OAAO,EAAE,WAAW;QAC7C,8BAAC,sBAAW;;YAET,WAAW,CAAC,CAAC,CAAC,CACb,8BAAC,qBAAU,IACT,SAAS,EAAE,OAAO,CAAC,WAAW,EAC9B,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE;gBAE5B,8BAAC,eAAS,OAAG,CACF,CACd,CAAC,CAAC,CAAC,IAAI,CACI;QACd,8BAAC,kBAAO,OAAG;QACX,8BAAC,wBAAa;YACZ,sDAAkB;YAClB;gBACE,+IAGK;gBACL;;oBAEM,6DAA2B;;oBAAI,4DAA0B;wKAI1D,CACF;YACL,6DAAyB;YACzB;gBACE;oBACE,mDAAiB;6DACd;gBACL;oBACE,mDAAiB;+CACd;gBACL;oBACE,0EAAwC;mFAErC;gBACL;oBACE,oEAAkC;0EAE/B;gBACL;oBACE,6DAA2B;8DACxB;gBACL;oBACE,yEAAuC;0FAEpC;gBACL;oBACE,2DAAyB;sEAEtB,CACF,CACS;QAChB,8BAAC,kBAAO,OAAG;QACX,8BAAC,wBAAa;YACZ,8BAAC,iBAAM,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,EAAE,KAAK,EAAC,SAAS,YAE5C,CACK,CACT,CACV,CAAA;AACH,CAAC;AAxED,6BAwEC"}
+{"version":3,"file":"HelpDialog.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/HelpDialog.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,4CAA6E;AAC7E,yCAAyC;AAEzC,SAAwB,UAAU,CAAC,EACjC,WAAW,GAGZ;IACC,OAAO,CACL,8BAAC,WAAM,IACL,IAAI,QACJ,QAAQ,EAAC,IAAI,EACb,OAAO,EAAE,WAAW,EACpB,KAAK,EAAC,sBAAsB;QAE5B,8BAAC,wBAAa;YACZ,sDAAkB;YAClB;gBACE,+IAGK;gBACL;;oBAEM,6DAA2B;;oBAAI,4DAA0B;wKAI1D,CACF;YACL,6DAAyB;YACzB;gBACE;oBACE,mDAAiB;6DACd;gBACL;oBACE,mDAAiB;+CACd;gBACL;oBACE,0EAAwC;mFAErC;gBACL;oBACE,oEAAkC;0EAE/B;gBACL;oBACE,6DAA2B;8DACxB;gBACL;oBACE,yEAAuC;0FAEpC;gBACL;oBACE,2DAAyB;sEAEtB,CACF,CACS;QAChB,8BAAC,kBAAO,OAAG;QACX,8BAAC,wBAAa;YACZ,8BAAC,iBAAM,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,EAAE,KAAK,EAAC,SAAS,YAE5C,CACK,CACT,CACV,CAAA;AACH,CAAC;AAhED,6BAgEC"}

package/dist/LinearGenomeView/components/ImportForm.js

@@ -73,11 +73,11 @@ const ImportForm = (0, mobx_react_1.observer)(({ model }) => {
     (0, react_1.useEffect)(() => {
         setValue(r0);
     }, [r0, selectedAsm]);
-    function navToOption(option) {
+    async function navToOption(option) {
         const location = option.getLocation();
         const trackId = option.getTrackId();
         if (location) {
-            model.navToLocString(location, selectedAsm);
+            await model.navToLocString(location, selectedAsm);
             if (trackId) {
                 model.showTrack(trackId);
             }
@@ -89,16 +89,20 @@ const ImportForm = (0, mobx_react_1.observer)(({ model }) => {
     // 2) if it's a single result navigate to it
     // 3) else assume it's a locstring and navigate to it
     async function handleSelectedRegion(input) {
+        var _a;
         try {
             if ((option === null || option === void 0 ? void 0 : option.getDisplayString()) === input && option.hasLocation()) {
-                navToOption(option);
+                await navToOption(option);
+            }
+            else if ((_a = option === null || option === void 0 ? void 0 : option.results) === null || _a === void 0 ? void 0 : _a.length) {
+                model.setSearchResults(option.results, option.getLabel());
             }
             else {
                 const [ref, rest] = (0, util_2.splitLast)(input, ':');
                 const allRefs = (assembly === null || assembly === void 0 ? void 0 : assembly.allRefNamesWithLowerCase) || [];
                 if (allRefs.includes(input) ||
                     (allRefs.includes(ref) && !Number.isNaN(parseInt(rest, 10)))) {
-                    model.navToLocString(input, selectedAsm);
+                    await model.navToLocString(input, selectedAsm);
                 }
                 else {
                     const results = await (0, util_2.fetchResults)({
@@ -113,10 +117,10 @@ const ImportForm = (0, mobx_react_1.observer)(({ model }) => {
                         model.setSearchResults(results, input.toLowerCase());
                     }
                     else if (results.length === 1) {
-                        navToOption(results[0]);
+                        await navToOption(results[0]);
                     }
                     else {
-                        model.navToLocString(input, selectedAsm);
+                        await model.navToLocString(input, selectedAsm);
                     }
                 }
             }
@@ -131,11 +135,12 @@ const ImportForm = (0, mobx_react_1.observer)(({ model }) => {
     return (react_1.default.createElement("div", { className: classes.container },
         displayError ? react_1.default.createElement(ui_1.ErrorMessage, { error: displayError }) : null,
         react_1.default.createElement(material_1.Container, { className: classes.importFormContainer },
-            react_1.default.createElement("form", { onSubmit: event => {
+            react_1.default.createElement("form", { onSubmit: async (event) => {
                     event.preventDefault();
                     model.setError(undefined);
                     if (value) {
-                        handleSelectedRegion(value);
+                        // has it's own error handling
+                        await handleSelectedRegion(value);
                     }
                 } },
                 react_1.default.createElement(material_1.Grid, { container: true, spacing: 1, justifyContent: "center", alignItems: "center" },
@@ -144,7 +149,7 @@ const ImportForm = (0, mobx_react_1.observer)(({ model }) => {
                             react_1.default.createElement(ui_1.AssemblySelector, { onChange: val => {
                                     setSelectedAsm(val);
                                     setValue('');
-                                }, session: session, selected: selectedAsm }))),
+                                }, localStorageKey: "lgv", session: session, selected: selectedAsm }))),
                     react_1.default.createElement(material_1.Grid, { item: true }, selectedAsm ? (assemblyError ? (react_1.default.createElement(Close_1.default, { style: { color: 'red' } })) : value ? (react_1.default.createElement(material_1.FormControl, null,
                         react_1.default.createElement(RefNameAutocomplete_1.default, { fetchResults: queryString => (0, util_2.fetchResults)({
                                 queryString,
@@ -153,7 +158,7 @@ const ImportForm = (0, mobx_react_1.observer)(({ model }) => {
                                 rankSearchResults,
                                 searchScope,
                             }), model: model, assemblyName: assemblyError ? undefined : selectedAsm, value: value, 
-                            // note: minWidth 270 accomodates full width of helperText
+                            // note: minWidth 270 accommodates full width of helperText
                             minWidth: 270, onChange: str => setValue(str), onSelect: val => setOption(val), TextFieldProps: {
                                 variant: 'outlined',
                                 helperText: 'Enter sequence name, feature name, or location',

package/dist/LinearGenomeView/components/ImportForm.js.map

@@ -1 +1 @@
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package/dist/LinearGenomeView/components/LinearGenomeViewSvg.js

@@ -14,8 +14,8 @@ const Base1DViewModel_1 = __importDefault(require("@jbrowse/core/util/Base1DView
 // locals
 const Ruler_1 = __importDefault(require("./Ruler"));
 const __1 = require("..");
-const OverviewScaleBar_1 = require("./OverviewScaleBar");
-function ScaleBar({ model, fontSize }) {
+const OverviewScalebar_1 = require("./OverviewScalebar");
+function Scalebar({ model, fontSize }) {
     const { offsetPx, dynamicBlocks: { totalWidthPxWithoutBorders: totalWidthPx, totalBp }, } = model;
     const displayBp = (0, util_1.getBpDisplayStr)(totalBp);
     const x0 = Math.max(-offsetPx, 0);
@@ -83,12 +83,12 @@ const SVGHeader = ({ model }) => {
     return (react_1.default.createElement("g", { id: "header" },
         react_1.default.createElement("text", { x: 0, y: fontSize, fontSize: fontSize }, assemblyName),
         showCytobands ? (react_1.default.createElement("g", { transform: `translate(0 ${rulerHeight})` },
-            react_1.default.createElement(OverviewScaleBar_1.Cytobands, { overview: overview, assembly: assembly, block: block }),
+            react_1.default.createElement(OverviewScalebar_1.Cytobands, { overview: overview, assembly: assembly, block: block }),
             react_1.default.createElement("rect", { stroke: "red", fill: "rgb(255,0,0,0.1)", width: Math.max(lastOverviewPx - firstOverviewPx, 0.5), height: __1.HEADER_OVERVIEW_HEIGHT - 1, x: firstOverviewPx, y: 0.5 }),
             react_1.default.createElement("g", { transform: `translate(0,${__1.HEADER_OVERVIEW_HEIGHT})` },
-                react_1.default.createElement(OverviewScaleBar_1.Polygon, { overview: overview, model: model, useOffset: false })))) : null,
+                react_1.default.createElement(OverviewScalebar_1.Polygon, { overview: overview, model: model, useOffset: false })))) : null,
         react_1.default.createElement("g", { transform: `translate(0 ${fontSize + cytobandHeight})` },
-            react_1.default.createElement(ScaleBar, { model: model, fontSize: fontSize })),
+            react_1.default.createElement(Scalebar, { model: model, fontSize: fontSize })),
         react_1.default.createElement("g", { transform: `translate(0 ${rulerHeight + cytobandHeight})` },
             react_1.default.createElement(SVGRuler, { model: model, fontSize: fontSize, width: width }))));
 };
@@ -127,8 +127,7 @@ async function renderToSvg(model, opts) {
     const displayResults = await Promise.all(tracks.map(async (track) => {
         const display = track.displays[0];
         await (0, mobx_1.when)(() => (display.ready !== undefined ? display.ready : true));
-        const result = await display.renderSvg(opts);
-        return { track, result };
+        return { track, result: await display.renderSvg(opts) };
     }));
     // the xlink namespace is used for rendering <image> tag
     return (0, server_1.renderToStaticMarkup)(react_1.default.createElement(Wrapper, null,