@jbrowse/plugin-arc 3.6.4 → 3.7.0

package/dist/ArcRenderer/ArcRendering.js

@@ -43,7 +43,7 @@ function Arc({ selectedFeatureId, region, bpPerPx, config, height: displayHeight
     const [isMouseOvered, setIsMouseOvered] = (0, react_1.useState)(false);
     const [left, right] = (0, util_1.bpSpanPx)(feature.get('start'), feature.get('end'), region, bpPerPx);
     const featureId = feature.id();
-    const selected = selectedFeatureId && String(selectedFeatureId) === String(feature.id());
+    const selected = selectedFeatureId && selectedFeatureId === feature.id();
     const stroke = selected ? 'red' : (0, configuration_1.readConfObject)(config, 'color', { feature });
     const textStroke = selected ? 'red' : 'black';
     const label = (0, configuration_1.readConfObject)(config, 'label', { feature });
@@ -91,7 +91,7 @@ function SemiCircles({ selectedFeatureId, region, bpPerPx, config, onFeatureClic
     const [isMouseOvered, setIsMouseOvered] = (0, react_1.useState)(false);
     const [left, right] = (0, util_1.bpSpanPx)(feature.get('start'), feature.get('end'), region, bpPerPx);
     const featureId = feature.id();
-    const selected = selectedFeatureId && String(selectedFeatureId) === String(feature.id());
+    const selected = selectedFeatureId && selectedFeatureId === feature.id();
     const stroke = selected ? 'red' : (0, configuration_1.readConfObject)(config, 'color', { feature });
     const textStroke = selected ? 'red' : 'black';
     const label = (0, configuration_1.readConfObject)(config, 'label', { feature });

package/dist/LinearArcDisplay/model.d.ts

@@ -172,6 +172,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
+    mouseoverExtraInformation: string | undefined;
     featureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
 } & {
@@ -186,9 +187,22 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
+    readonly layoutFeatures: import("@jbrowse/core/util/compositeMap").default<string, [number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]>;
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
-    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
-    searchFeatureByID(id: string): [number, number, number, number] | undefined;
+    getFeatureByID(blockKey: string, id: string): ([number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]) | undefined;
+    searchFeatureByID(id: string): ([number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]) | undefined;
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
@@ -197,6 +211,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature): void;
+    setMouseoverExtraInformation(extra?: string): void;
 } & {
     reload(): Promise<void>;
 } & {

package/dist/LinearPairedArcDisplay/components/BaseDisplayComponent.js

@@ -38,46 +38,33 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const jsx_runtime_1 = require("react/jsx-runtime");
 const react_1 = require("react");
-const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 const Refresh_1 = __importDefault(require("@mui/icons-material/Refresh"));
 const Report_1 = __importDefault(require("@mui/icons-material/Report"));
 const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
-const mui_1 = require("tss-react/mui");
+const LoadingBar_1 = __importDefault(require("./LoadingBar"));
 const ErrorMessageStackTraceDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@jbrowse/core/ui/ErrorMessageStackTraceDialog'))));
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    loading: {
-        backgroundColor: theme.palette.background.default,
-        backgroundImage: `repeating-linear-gradient(45deg, transparent, transparent 5px, ${theme.palette.action.disabledBackground} 5px, ${theme.palette.action.disabledBackground} 10px)`,
-        position: 'absolute',
-        bottom: 0,
-        height: 50,
-        width: 300,
-        right: 0,
-        pointerEvents: 'none',
-        textAlign: 'center',
-    },
-}));
+function ErrorActions({ model }) {
+    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(material_1.Tooltip, { title: "Reload", children: (0, jsx_runtime_1.jsx)(material_1.IconButton, { "data-testid": "reload_button", onClick: () => {
+                        model.reload();
+                    }, children: (0, jsx_runtime_1.jsx)(Refresh_1.default, {}) }) }), (0, jsx_runtime_1.jsx)(material_1.Tooltip, { title: "Show stack trace", children: (0, jsx_runtime_1.jsx)(material_1.IconButton, { onClick: () => {
+                        (0, util_1.getSession)(model).queueDialog(onClose => [
+                            ErrorMessageStackTraceDialog,
+                            {
+                                onClose,
+                                error: model.error,
+                            },
+                        ]);
+                    }, children: (0, jsx_runtime_1.jsx)(Report_1.default, {}) }) })] }));
+}
 const BaseDisplayComponent = (0, mobx_react_1.observer)(function ({ model, children, }) {
     const { error, regionTooLarge } = model;
-    return error ? ((0, jsx_runtime_1.jsx)(plugin_linear_genome_view_1.BlockMsg, { message: `${error}`, severity: "error", action: (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(material_1.Tooltip, { title: "Reload", children: (0, jsx_runtime_1.jsx)(material_1.IconButton, { "data-testid": "reload_button", onClick: () => {
-                            model.reload();
-                        }, children: (0, jsx_runtime_1.jsx)(Refresh_1.default, {}) }) }), (0, jsx_runtime_1.jsx)(material_1.Tooltip, { title: "Show stack trace", children: (0, jsx_runtime_1.jsx)(material_1.IconButton, { onClick: () => {
-                            (0, util_1.getSession)(model).queueDialog(onClose => [
-                                ErrorMessageStackTraceDialog,
-                                { onClose, error: model.error },
-                            ]);
-                        }, children: (0, jsx_runtime_1.jsx)(Report_1.default, {}) }) })] }) })) : regionTooLarge ? (model.regionCannotBeRendered()) : ((0, jsx_runtime_1.jsx)(DataDisplay, { model: model, children: children }));
+    return error ? ((0, jsx_runtime_1.jsx)(plugin_linear_genome_view_1.BlockMsg, { message: `${error}`, severity: "error", action: (0, jsx_runtime_1.jsx)(ErrorActions, { model: model }) })) : regionTooLarge ? (model.regionCannotBeRendered()) : ((0, jsx_runtime_1.jsx)(DataDisplay, { model: model, children: children }));
 });
 const DataDisplay = (0, mobx_react_1.observer)(function ({ model, children, }) {
     const { loading } = model;
-    return ((0, jsx_runtime_1.jsxs)("div", { children: [children, loading ? (0, jsx_runtime_1.jsx)(LoadingBar, { model: model }) : null] }));
-});
-const LoadingBar = (0, mobx_react_1.observer)(function ({ model, }) {
-    const { classes } = useStyles();
-    const { message } = model;
-    return ((0, jsx_runtime_1.jsx)("div", { className: classes.loading, children: (0, jsx_runtime_1.jsx)(ui_1.LoadingEllipses, { message: message }) }));
+    return ((0, jsx_runtime_1.jsxs)("div", { children: [children, loading ? (0, jsx_runtime_1.jsx)(LoadingBar_1.default, { model: model }) : null] }));
 });
 exports.default = BaseDisplayComponent;

package/dist/LinearPairedArcDisplay/components/LoadingBar.d.ts

@@ -0,0 +1,5 @@
+import type { LinearArcDisplayModel } from '../model';
+declare const LoadingBar: ({ model, }: {
+    model: LinearArcDisplayModel;
+}) => import("react/jsx-runtime").JSX.Element;
+export default LoadingBar;

package/dist/LinearPairedArcDisplay/components/LoadingBar.js

@@ -0,0 +1,25 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const jsx_runtime_1 = require("react/jsx-runtime");
+const ui_1 = require("@jbrowse/core/ui");
+const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
+    loading: {
+        backgroundColor: theme.palette.background.default,
+        backgroundImage: `repeating-linear-gradient(45deg, transparent, transparent 5px, ${theme.palette.action.disabledBackground} 5px, ${theme.palette.action.disabledBackground} 10px)`,
+        position: 'absolute',
+        bottom: 0,
+        height: 50,
+        width: 300,
+        right: 0,
+        pointerEvents: 'none',
+        textAlign: 'center',
+    },
+}));
+const LoadingBar = (0, mobx_react_1.observer)(function ({ model, }) {
+    const { classes } = useStyles();
+    const { message } = model;
+    return ((0, jsx_runtime_1.jsx)("div", { className: classes.loading, children: (0, jsx_runtime_1.jsx)(ui_1.LoadingEllipses, { message: message }) }));
+});
+exports.default = LoadingBar;

package/esm/ArcRenderer/ArcRendering.js

@@ -8,7 +8,7 @@ function Arc({ selectedFeatureId, region, bpPerPx, config, height: displayHeight
     const [isMouseOvered, setIsMouseOvered] = useState(false);
     const [left, right] = bpSpanPx(feature.get('start'), feature.get('end'), region, bpPerPx);
     const featureId = feature.id();
-    const selected = selectedFeatureId && String(selectedFeatureId) === String(feature.id());
+    const selected = selectedFeatureId && selectedFeatureId === feature.id();
     const stroke = selected ? 'red' : readConfObject(config, 'color', { feature });
     const textStroke = selected ? 'red' : 'black';
     const label = readConfObject(config, 'label', { feature });
@@ -56,7 +56,7 @@ function SemiCircles({ selectedFeatureId, region, bpPerPx, config, onFeatureClic
     const [isMouseOvered, setIsMouseOvered] = useState(false);
     const [left, right] = bpSpanPx(feature.get('start'), feature.get('end'), region, bpPerPx);
     const featureId = feature.id();
-    const selected = selectedFeatureId && String(selectedFeatureId) === String(feature.id());
+    const selected = selectedFeatureId && selectedFeatureId === feature.id();
     const stroke = selected ? 'red' : readConfObject(config, 'color', { feature });
     const textStroke = selected ? 'red' : 'black';
     const label = readConfObject(config, 'label', { feature });

package/esm/LinearArcDisplay/model.d.ts

@@ -172,6 +172,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
+    mouseoverExtraInformation: string | undefined;
     featureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
 } & {
@@ -186,9 +187,22 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
+    readonly layoutFeatures: import("@jbrowse/core/util/compositeMap").default<string, [number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]>;
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
-    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
-    searchFeatureByID(id: string): [number, number, number, number] | undefined;
+    getFeatureByID(blockKey: string, id: string): ([number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]) | undefined;
+    searchFeatureByID(id: string): ([number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]) | undefined;
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
@@ -197,6 +211,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature): void;
+    setMouseoverExtraInformation(extra?: string): void;
 } & {
     reload(): Promise<void>;
 } & {

package/esm/LinearPairedArcDisplay/components/BaseDisplayComponent.js

@@ -1,45 +1,32 @@
 import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
 import { lazy } from 'react';
-import { LoadingEllipses } from '@jbrowse/core/ui';
 import { getSession } from '@jbrowse/core/util';
 import { BlockMsg } from '@jbrowse/plugin-linear-genome-view';
 import RefreshIcon from '@mui/icons-material/Refresh';
 import ReportIcon from '@mui/icons-material/Report';
 import { IconButton, Tooltip } from '@mui/material';
 import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
+import LoadingBar from './LoadingBar';
 const ErrorMessageStackTraceDialog = lazy(() => import('@jbrowse/core/ui/ErrorMessageStackTraceDialog'));
-const useStyles = makeStyles()(theme => ({
-    loading: {
-        backgroundColor: theme.palette.background.default,
-        backgroundImage: `repeating-linear-gradient(45deg, transparent, transparent 5px, ${theme.palette.action.disabledBackground} 5px, ${theme.palette.action.disabledBackground} 10px)`,
-        position: 'absolute',
-        bottom: 0,
-        height: 50,
-        width: 300,
-        right: 0,
-        pointerEvents: 'none',
-        textAlign: 'center',
-    },
-}));
+function ErrorActions({ model }) {
+    return (_jsxs(_Fragment, { children: [_jsx(Tooltip, { title: "Reload", children: _jsx(IconButton, { "data-testid": "reload_button", onClick: () => {
+                        model.reload();
+                    }, children: _jsx(RefreshIcon, {}) }) }), _jsx(Tooltip, { title: "Show stack trace", children: _jsx(IconButton, { onClick: () => {
+                        getSession(model).queueDialog(onClose => [
+                            ErrorMessageStackTraceDialog,
+                            {
+                                onClose,
+                                error: model.error,
+                            },
+                        ]);
+                    }, children: _jsx(ReportIcon, {}) }) })] }));
+}
 const BaseDisplayComponent = observer(function ({ model, children, }) {
     const { error, regionTooLarge } = model;
-    return error ? (_jsx(BlockMsg, { message: `${error}`, severity: "error", action: _jsxs(_Fragment, { children: [_jsx(Tooltip, { title: "Reload", children: _jsx(IconButton, { "data-testid": "reload_button", onClick: () => {
-                            model.reload();
-                        }, children: _jsx(RefreshIcon, {}) }) }), _jsx(Tooltip, { title: "Show stack trace", children: _jsx(IconButton, { onClick: () => {
-                            getSession(model).queueDialog(onClose => [
-                                ErrorMessageStackTraceDialog,
-                                { onClose, error: model.error },
-                            ]);
-                        }, children: _jsx(ReportIcon, {}) }) })] }) })) : regionTooLarge ? (model.regionCannotBeRendered()) : (_jsx(DataDisplay, { model: model, children: children }));
+    return error ? (_jsx(BlockMsg, { message: `${error}`, severity: "error", action: _jsx(ErrorActions, { model: model }) })) : regionTooLarge ? (model.regionCannotBeRendered()) : (_jsx(DataDisplay, { model: model, children: children }));
 });
 const DataDisplay = observer(function ({ model, children, }) {
     const { loading } = model;
     return (_jsxs("div", { children: [children, loading ? _jsx(LoadingBar, { model: model }) : null] }));
 });
-const LoadingBar = observer(function ({ model, }) {
-    const { classes } = useStyles();
-    const { message } = model;
-    return (_jsx("div", { className: classes.loading, children: _jsx(LoadingEllipses, { message: message }) }));
-});
 export default BaseDisplayComponent;

package/esm/LinearPairedArcDisplay/components/LoadingBar.d.ts

@@ -0,0 +1,5 @@
+import type { LinearArcDisplayModel } from '../model';
+declare const LoadingBar: ({ model, }: {
+    model: LinearArcDisplayModel;
+}) => import("react/jsx-runtime").JSX.Element;
+export default LoadingBar;

package/esm/LinearPairedArcDisplay/components/LoadingBar.js

@@ -0,0 +1,23 @@
+import { jsx as _jsx } from "react/jsx-runtime";
+import { LoadingEllipses } from '@jbrowse/core/ui';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+const useStyles = makeStyles()(theme => ({
+    loading: {
+        backgroundColor: theme.palette.background.default,
+        backgroundImage: `repeating-linear-gradient(45deg, transparent, transparent 5px, ${theme.palette.action.disabledBackground} 5px, ${theme.palette.action.disabledBackground} 10px)`,
+        position: 'absolute',
+        bottom: 0,
+        height: 50,
+        width: 300,
+        right: 0,
+        pointerEvents: 'none',
+        textAlign: 'center',
+    },
+}));
+const LoadingBar = observer(function ({ model, }) {
+    const { classes } = useStyles();
+    const { message } = model;
+    return (_jsx("div", { className: classes.loading, children: _jsx(LoadingEllipses, { message: message }) }));
+});
+export default LoadingBar;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-arc",
-  "version": "3.6.4",
+  "version": "3.7.0",
   "description": "JBrowse 2 arc adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -36,9 +36,9 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@jbrowse/core": "^3.6.4",
-    "@jbrowse/plugin-linear-genome-view": "^3.6.4",
-    "@jbrowse/plugin-wiggle": "^3.6.4",
+    "@jbrowse/core": "^3.7.0",
+    "@jbrowse/plugin-linear-genome-view": "^3.7.0",
+    "@jbrowse/plugin-wiggle": "^3.7.0",
     "@mui/material": "^7.0.0",
     "mobx": "^6.0.0",
     "mobx-react": "^9.0.0",
@@ -55,5 +55,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "3db8e50ce2bd9c081efbf6c2e7ae5f342380a25a"
+  "gitHead": "85bdd0d58286b7adbfd408146b15847676317635"
 }