@jbrowse/plugin-linear-genome-view 4.1.3 → 4.1.4

package/esm/LinearGenomeView/lazyDialogs.d.ts

@@ -0,0 +1,23 @@
+export declare const ReturnToImportFormDialog: import("react").LazyExoticComponent<({ model, handleClose, }: {
+    model: {
+        clearView: () => void;
+    };
+    handleClose: () => void;
+}) => import("react/jsx-runtime").JSX.Element>;
+export declare const SequenceSearchDialog: import("react").LazyExoticComponent<({ model, handleClose, }: {
+    model: {
+        assemblyNames: string[];
+        showTrack: (trackId: string) => void;
+    };
+    handleClose: () => void;
+}) => import("react/jsx-runtime").JSX.Element>;
+export declare const ExportSvgDialog: import("react").LazyExoticComponent<typeof import("./components/ExportSvgDialog.tsx").default>;
+export declare const GetSequenceDialog: import("react").LazyExoticComponent<({ model, handleClose, }: {
+    model: {
+        leftOffset?: import("./types.ts").BpOffset;
+        rightOffset?: import("./types.ts").BpOffset;
+        getSelectedRegions: (left?: import("./types.ts").BpOffset, right?: import("./types.ts").BpOffset) => import("@jbrowse/core/util").Region[];
+        setOffsets: (left?: import("./types.ts").BpOffset, right?: import("./types.ts").BpOffset) => void;
+    };
+    handleClose: () => void;
+}) => import("react/jsx-runtime").JSX.Element>;

package/esm/LinearGenomeView/lazyDialogs.js

@@ -0,0 +1,5 @@
+import { lazy } from 'react';
+export const ReturnToImportFormDialog = lazy(() => import('@jbrowse/core/ui/ReturnToImportFormDialog'));
+export const SequenceSearchDialog = lazy(() => import("./components/SequenceSearchDialog.js"));
+export const ExportSvgDialog = lazy(() => import("./components/ExportSvgDialog.js"));
+export const GetSequenceDialog = lazy(() => import("./components/GetSequenceDialog.js"));

package/esm/LinearGenomeView/menuItems.js

@@ -1,4 +1,3 @@
-import { lazy } from 'react';
 import { TrackSelector as TrackSelectorIcon } from '@jbrowse/core/ui/Icons';
 import { getSession, isSessionWithAddTracks, toLocale, } from '@jbrowse/core/util';
 import CenterFocusStrongIcon from '@mui/icons-material/CenterFocusStrong';
@@ -12,10 +11,7 @@ import SearchIcon from '@mui/icons-material/Search';
 import SyncAltIcon from '@mui/icons-material/SyncAlt';
 import VisibilityIcon from '@mui/icons-material/Visibility';
 import ZoomInIcon from '@mui/icons-material/ZoomIn';
-const ReturnToImportFormDialog = lazy(() => import('@jbrowse/core/ui/ReturnToImportFormDialog'));
-const SequenceSearchDialog = lazy(() => import("./components/SequenceSearchDialog.js"));
-const ExportSvgDialog = lazy(() => import("./components/ExportSvgDialog.js"));
-const GetSequenceDialog = lazy(() => import("./components/GetSequenceDialog.js"));
+import { ExportSvgDialog, GetSequenceDialog, ReturnToImportFormDialog, SequenceSearchDialog, } from "./lazyDialogs.js";
 function toLocaleRounded(n) {
     return toLocale(Math.round(n));
 }

package/esm/LinearGenomeView/model.d.ts

@@ -86,6 +86,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     readonly trackHeightsWithResizeHandles: number;
     readonly height: number;
     readonly totalBp: number;
+    getNonElidedRegionCount(bpPerPx: number): number;
+    getInterRegionPaddingPx(bpPerPx: number): number;
     readonly maxBpPerPx: number;
     readonly minBpPerPx: number;
     readonly error: unknown;
@@ -144,7 +146,6 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         end: number;
     }[];
     horizontalScroll(distance: number): number;
-    center(): void;
     showAllRegions(): void;
     showAllRegionsInAssembly(assemblyName?: string): void;
     setDraggingTrackId(idx?: string): void;

package/esm/LinearGenomeView/model.js

@@ -21,6 +21,9 @@ import { setupKeyboardHandler } from "./keyboardHandler.js";
 import { buildMenuItems, buildRubberBandMenuItems, buildRubberbandClickMenuItems, rewriteOnClicks, } from "./menuItems.js";
 import { calculateVisibleLocStrings, expandRegion, generateLocations, parseLocStrings, } from "./util.js";
 const SearchResultsDialog = lazy(() => import("./components/SearchResultsDialog.js"));
+function getCenteredOffsetPx(contentPx, viewportPx) {
+    return Math.round(contentPx / 2 - viewportPx / 2);
+}
 export function stateModelFactory(pluginManager) {
     return types
         .compose('LinearGenomeView', BaseViewModel, types.model({
@@ -201,8 +204,29 @@ export function stateModelFactory(pluginManager) {
         get totalBp() {
             return sum(self.displayedRegions.map(r => r.end - r.start));
         },
+        getNonElidedRegionCount(bpPerPx) {
+            if (bpPerPx <= 0) {
+                return self.displayedRegions.length;
+            }
+            return self.displayedRegions.filter(r => (r.end - r.start) / bpPerPx >= self.minimumBlockWidth).length;
+        },
+        getInterRegionPaddingPx(bpPerPx) {
+            const nonElidedCount = this.getNonElidedRegionCount(bpPerPx);
+            const numPaddings = Math.max(0, nonElidedCount - 1);
+            return numPaddings * self.interRegionPaddingWidth;
+        },
         get maxBpPerPx() {
-            return this.totalBp / (self.width * 0.9);
+            if (this.totalBp === 0 || self.width === 0) {
+                return 1;
+            }
+            const naiveBpPerPx = this.totalBp / (self.width * 0.9);
+            const totalPaddingPx = this.getInterRegionPaddingPx(naiveBpPerPx);
+            const targetWidth = self.width * 0.9;
+            const availableForBp = targetWidth - totalPaddingPx;
+            if (availableForBp <= 0) {
+                return naiveBpPerPx;
+            }
+            return this.totalBp / availableForBp;
         },
         get minBpPerPx() {
             return 1 / 50;
@@ -238,7 +262,11 @@ export function stateModelFactory(pluginManager) {
             return -self.width + rightPadding;
         },
         get displayedRegionsTotalPx() {
-            return this.totalBp / self.bpPerPx;
+            if (self.bpPerPx === 0) {
+                return 0;
+            }
+            const totalPaddingPx = this.getInterRegionPaddingPx(self.bpPerPx);
+            return this.totalBp / self.bpPerPx + totalPaddingPx;
         },
         renderProps() {
             return {
@@ -462,17 +490,9 @@ export function stateModelFactory(pluginManager) {
             const newOffsetPx = self.scrollTo(self.offsetPx + distance);
             return newOffsetPx - oldOffsetPx;
         },
-        center() {
-            const numPaddings = Math.max(0, self.displayedRegions.length - 1);
-            const totalPaddingPx = numPaddings * self.interRegionPaddingWidth;
-            const totalContentPx = self.totalBp / self.bpPerPx + totalPaddingPx;
-            const centerPx = totalContentPx / 2;
-            const targetOffsetPx = Math.round(centerPx - self.width / 2);
-            self.scrollTo(targetOffsetPx);
-        },
         showAllRegions() {
             self.bpPerPx = clamp(self.maxBpPerPx, self.minBpPerPx, self.maxBpPerPx);
-            this.center();
+            self.scrollTo(getCenteredOffsetPx(self.displayedRegionsTotalPx, self.width));
         },
         showAllRegionsInAssembly(assemblyName) {
             const session = getSession(self);
@@ -492,7 +512,7 @@ export function stateModelFactory(pluginManager) {
             }
             this.setDisplayedRegions(regions);
             self.zoomTo(self.maxBpPerPx);
-            this.center();
+            self.scrollTo(getCenteredOffsetPx(self.displayedRegionsTotalPx, self.width));
         },
         setDraggingTrackId(idx) {
             self.draggingTrackId = idx;
@@ -522,7 +542,38 @@ export function stateModelFactory(pluginManager) {
             const { renderToSvg } = await import("./svgcomponents/SVGLinearGenomeView.js");
             const html = await renderToSvg(self, opts);
             const { saveAs } = await import('file-saver-es');
-            saveAs(new Blob([html], { type: 'image/svg+xml' }), opts.filename || 'image.svg');
+            if (opts.format === 'png') {
+                const img = new Image();
+                const svgBlob = new Blob([html], { type: 'image/svg+xml' });
+                const url = URL.createObjectURL(svgBlob);
+                await new Promise((resolve, reject) => {
+                    img.onload = () => {
+                        const canvas = document.createElement('canvas');
+                        canvas.width = img.width;
+                        canvas.height = img.height;
+                        const ctx = canvas.getContext('2d');
+                        ctx.drawImage(img, 0, 0);
+                        URL.revokeObjectURL(url);
+                        canvas.toBlob(blob => {
+                            if (blob) {
+                                saveAs(blob, opts.filename || 'image.png');
+                                resolve();
+                            }
+                            else {
+                                reject(new Error(`Failed to create PNG. The image may be too large (${img.width}x${img.height}). Try reducing the view size or use SVG format.`));
+                            }
+                        }, 'image/png');
+                    };
+                    img.onerror = () => {
+                        URL.revokeObjectURL(url);
+                        reject(new Error('Failed to load SVG for PNG conversion'));
+                    };
+                    img.src = url;
+                });
+            }
+            else {
+                saveAs(new Blob([html], { type: 'image/svg+xml' }), opts.filename || 'image.svg');
+            }
         },
     }))
         .actions(self => {

package/esm/LinearGenomeView/types.d.ts

@@ -11,6 +11,7 @@ export interface BpOffset {
 }
 export interface ExportSvgOptions {
     rasterizeLayers?: boolean;
+    format?: 'svg' | 'png';
     filename?: string;
     Wrapper?: React.FC<{
         children: React.ReactNode;

package/esm/index.d.ts

@@ -41,6 +41,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                         statusMessage?: string;
                         reactElement?: React.ReactElement;
                         isRenderingPending?: boolean;
+                        displayHeight?: number;
                     };
                 }) => import("react/jsx-runtime").JSX.Element;
                 renderProps: any;
@@ -59,10 +60,11 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 beforeDestroy(): void;
             } & {
                 readonly statusMessage: any;
+                readonly displayHeight: number | undefined;
             } & {
                 afterAttach(): void;
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
-            configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+            configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
                 maxFeatureScreenDensity: {
                     type: string;
                     description: string;
@@ -89,7 +91,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     description: string;
                     defaultValue: never[];
                 };
-            }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
             showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
             showTooltips: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
         }, {
@@ -380,6 +382,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                                 statusMessage?: string;
                                 reactElement?: React.ReactElement;
                                 isRenderingPending?: boolean;
+                                displayHeight?: number;
                             };
                         }) => import("react/jsx-runtime").JSX.Element;
                         renderProps: any;
@@ -398,6 +401,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                         beforeDestroy(): void;
                     } & {
                         readonly statusMessage: any;
+                        readonly displayHeight: number | undefined;
                     } & {
                         afterAttach(): void;
                     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -424,6 +428,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                                 statusMessage?: string;
                                 reactElement?: React.ReactElement;
                                 isRenderingPending?: boolean;
+                                displayHeight?: number;
                             };
                         }) => import("react/jsx-runtime").JSX.Element;
                         renderProps: any;
@@ -442,6 +447,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                         beforeDestroy(): void;
                     } & {
                         readonly statusMessage: any;
+                        readonly displayHeight: number | undefined;
                     } & {
                         afterAttach(): void;
                     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
@@ -455,7 +461,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                                 [x: string]: any;
                             } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
                         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-                    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+                    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
                         maxFeatureScreenDensity: {
                             type: string;
                             description: string;
@@ -482,7 +488,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                             description: string;
                             defaultValue: never[];
                         };
-                    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>>;
+                    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>>;
                     showLegend: boolean | undefined;
                     showTooltips: boolean | undefined;
                 } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -772,6 +778,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                                 statusMessage?: string;
                                 reactElement?: React.ReactElement;
                                 isRenderingPending?: boolean;
+                                displayHeight?: number;
                             };
                         }) => import("react/jsx-runtime").JSX.Element;
                         renderProps: any;
@@ -790,10 +797,11 @@ export default class LinearGenomeViewPlugin extends Plugin {
                         beforeDestroy(): void;
                     } & {
                         readonly statusMessage: any;
+                        readonly displayHeight: number | undefined;
                     } & {
                         afterAttach(): void;
                     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
-                    configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+                    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
                         maxFeatureScreenDensity: {
                             type: string;
                             description: string;
@@ -820,7 +828,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                             description: string;
                             defaultValue: never[];
                         };
-                    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>;
+                    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
                     showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
                     showTooltips: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
                 }, {
@@ -1119,6 +1127,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                         statusMessage?: string;
                         reactElement?: React.ReactElement;
                         isRenderingPending?: boolean;
+                        displayHeight?: number;
                     };
                 }) => import("react/jsx-runtime").JSX.Element;
                 renderProps: any;
@@ -1137,10 +1146,11 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 beforeDestroy(): void;
             } & {
                 readonly statusMessage: any;
+                readonly displayHeight: number | undefined;
             } & {
                 afterAttach(): void;
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
-            configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+            configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
                 maxFeatureScreenDensity: {
                     type: string;
                     description: string;
@@ -1167,7 +1177,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     description: string;
                     defaultValue: never[];
                 };
-            }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
             showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
             showTooltips: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
         }>>, {
@@ -1181,7 +1191,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             showLegend: boolean | undefined;
             showTooltips: boolean | undefined;
         }>;
-        baseLinearDisplayConfigSchema: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+        baseLinearDisplayConfigSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
             maxFeatureScreenDensity: {
                 type: string;
                 description: string;
@@ -1208,7 +1218,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 description: string;
                 defaultValue: never[];
             };
-        }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>;
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
         SearchBox: ({ model, showHelp, }: {
             showHelp?: boolean;
             model: import("./index.ts").LinearGenomeViewModel;
@@ -1220,13 +1230,13 @@ export default class LinearGenomeViewPlugin extends Plugin {
             model: import("./index.ts").LinearGenomeViewModel;
         }) => import("react/jsx-runtime").JSX.Element;
     };
-    configurationSchema: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+    configurationSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         trackLabels: {
             type: string;
             defaultValue: string;
             model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
         };
-    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined>>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
     install(pluginManager: PluginManager): void;
     configure(pluginManager: PluginManager): void;
 }
@@ -1235,6 +1245,7 @@ export { configSchemaFactory as linearBareDisplayConfigSchemaFactory, stateModel
 export { BaseLinearDisplay, BaseLinearDisplayComponent, BlockMsg, FeatureDensityMixin, FloatingLegend, NonBlockCanvasDisplayComponent, NonBlockCanvasDisplayMixin, SVGLegend, TooLargeMessage, TrackHeightMixin, baseLinearDisplayConfigSchema, calculateSvgLegendWidth, createSubfeatureLabelMetadata, drawCanvasImageData, } from './BaseLinearDisplay/index.ts';
 export type { NonBlockCanvasDisplayMixinType, NonBlockCanvasDisplayModel, } from './BaseLinearDisplay/index.ts';
 export { type LinearGenomeViewModel, type LinearGenomeViewStateModel, RefNameAutocomplete, SearchBox, } from './LinearGenomeView/index.ts';
+export { fetchResults } from './searchUtils.ts';
 export type { BpOffset, ExportSvgOptions, HighlightType, InitState, NavLocation, VolatileGuide, } from './LinearGenomeView/types.ts';
 export { SVGGridlines, SVGRuler, SVGTracks, renderToSvg, } from './LinearGenomeView/svgcomponents/SVGLinearGenomeView.tsx';
 export { totalHeight } from './LinearGenomeView/svgcomponents/util.ts';

package/esm/index.js

@@ -55,6 +55,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
 export { configSchemaFactory as linearBareDisplayConfigSchemaFactory, stateModelFactory as linearBareDisplayStateModelFactory, } from "./LinearBareDisplay/index.js";
 export { BaseLinearDisplay, BaseLinearDisplayComponent, BlockMsg, FeatureDensityMixin, FloatingLegend, NonBlockCanvasDisplayComponent, NonBlockCanvasDisplayMixin, SVGLegend, TooLargeMessage, TrackHeightMixin, baseLinearDisplayConfigSchema, calculateSvgLegendWidth, createSubfeatureLabelMetadata, drawCanvasImageData, } from "./BaseLinearDisplay/index.js";
 export { RefNameAutocomplete, SearchBox, } from "./LinearGenomeView/index.js";
+export { fetchResults } from "./searchUtils.js";
 export { SVGGridlines, SVGRuler, SVGTracks, renderToSvg, } from "./LinearGenomeView/svgcomponents/SVGLinearGenomeView.js";
 export { totalHeight } from "./LinearGenomeView/svgcomponents/util.js";
 export { configSchema as linearBasicDisplayConfigSchemaFactory, modelFactory as linearBasicDisplayModelFactory, } from "./LinearBasicDisplay/index.js";

package/esm/searchUtils.js

@@ -1,5 +1,5 @@
 import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
-import { dedupe, getSession } from '@jbrowse/core/util';
+import { dedupe, getEnv, getSession } from '@jbrowse/core/util';
 export async function navToOption({ option, model, assemblyName, }) {
     const location = option.getLocation();
     const trackId = option.getTrackId();
@@ -9,6 +9,9 @@ export async function navToOption({ option, model, assemblyName, }) {
             model.showTrack(trackId);
         }
     }
+    const session = getSession(model);
+    const { pluginManager } = getEnv(session);
+    await pluginManager.evaluateAsyncExtensionPoint('LinearGenomeView-searchResultSelected', undefined, { session, result: option, model, assemblyName });
 }
 export async function handleSelectedRegion({ input, model, assembly, }) {
     const allRefs = assembly.allRefNamesWithLowerCase || [];

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-genome-view",
-  "version": "4.1.3",
+  "version": "4.1.4",
   "type": "module",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
@@ -22,15 +22,15 @@
   ],
   "dependencies": {
     "@jbrowse/mobx-state-tree": "^5.5.0",
-    "@mui/icons-material": "^7.3.7",
-    "@mui/material": "^7.3.7",
+    "@mui/icons-material": "^7.3.8",
+    "@mui/material": "^7.3.8",
     "@types/file-saver-es": "^2.0.3",
     "copy-to-clipboard": "^3.3.3",
     "file-saver-es": "^2.0.5",
     "mobx": "^6.15.0",
     "mobx-react": "^9.2.1",
-    "@jbrowse/product-core": "^4.1.3",
-    "@jbrowse/core": "^4.1.3"
+    "@jbrowse/product-core": "^4.1.4",
+    "@jbrowse/core": "^4.1.4"
   },
   "peerDependencies": {
     "react": ">=18.0.0",

package/esm/BaseLinearDisplay/models/calculateLabelPositions.d.ts

@@ -1,24 +0,0 @@
-import type { LinearGenomeViewModel } from '../../LinearGenomeView/index.ts';
-import type { BaseLinearDisplayModel } from '../model.ts';
-import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
-export interface RenderProps {
-    rendererType: any;
-    renderArgs: Record<string, any>;
-    renderProps: Record<string, any>;
-    displayError: unknown;
-    rpcManager: {
-        call: (...args: unknown[]) => void;
-    };
-    cannotBeRenderedReason: string;
-}
-export interface LabelData {
-    key: string;
-    label: string;
-    description: string;
-    leftPos: number;
-    topPos: number;
-}
-export interface ErrorProps {
-    displayError: string;
-}
-export declare function calculateLabelPositions(model: BaseLinearDisplayModel, view: LinearGenomeViewModel, assembly: Assembly | undefined, offsetPx: number): LabelData[];

package/esm/BaseLinearDisplay/models/calculateLabelPositions.js

@@ -1,60 +0,0 @@
-import { clamp, measureText } from '@jbrowse/core/util';
-export function calculateLabelPositions(model, view, assembly, offsetPx) {
-    if (!assembly) {
-        return [];
-    }
-    const fontSize = 11;
-    const result = [];
-    for (const [key, val] of model.layoutFeatures.entries()) {
-        if (!val?.[4]) {
-            continue;
-        }
-        const [left, , right, bottom, feature] = val;
-        const { refName, description, label, totalLayoutWidth } = feature;
-        if (!label) {
-            continue;
-        }
-        const r0 = assembly.getCanonicalRefName2(refName);
-        const px1 = view.bpToPx({
-            refName: r0,
-            coord: left,
-        })?.offsetPx;
-        const px2 = view.bpToPx({
-            refName: r0,
-            coord: right,
-        })?.offsetPx;
-        if (px1 === undefined) {
-            continue;
-        }
-        const leftPx = px2 !== undefined ? Math.min(px1, px2) : px1;
-        const rightPx = px2 !== undefined ? Math.max(px1, px2) : px1;
-        const labelWidth = getCachedMeasureText(label, fontSize);
-        const effectiveRightPx = totalLayoutWidth !== undefined ? leftPx + totalLayoutWidth : rightPx;
-        const leftPos = clamp(0, leftPx - offsetPx, effectiveRightPx - offsetPx - labelWidth);
-        const topPos = bottom - 14 * (+!!description + +!!label);
-        result.push({
-            key,
-            label,
-            description: description || '',
-            leftPos,
-            topPos,
-        });
-    }
-    return result;
-}
-const textMeasureCache = new Map();
-function getCachedMeasureText(text, fontSize) {
-    const key = `${text}:${fontSize}`;
-    let width = textMeasureCache.get(key);
-    if (width === undefined) {
-        width = measureText(text, fontSize);
-        if (textMeasureCache.size > 500) {
-            const firstKey = textMeasureCache.keys().next().value;
-            if (firstKey) {
-                textMeasureCache.delete(firstKey);
-            }
-        }
-        textMeasureCache.set(key, width);
-    }
-    return width;
-}

package/esm/BaseLinearDisplay/models/renderSvg.d.ts

@@ -1,3 +0,0 @@
-import type { BaseLinearDisplayModel } from '../model.ts';
-import type { ExportSvgDisplayOptions } from '../types.ts';
-export declare function renderBaseLinearDisplaySvg(self: BaseLinearDisplayModel, opts: ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;

package/esm/BaseLinearDisplay/models/renderSvg.js

@@ -1,55 +0,0 @@
-import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
-import { Fragment } from 'react';
-import { ReactRendering, getContainingView, getSession, } from '@jbrowse/core/util';
-import { calculateLabelPositions } from "./calculateLabelPositions.js";
-import BlockState, { renderBlockData } from "./serverSideRenderedBlock.js";
-import { getId } from "./util.js";
-import { ErrorBox } from "../../LinearGenomeView/SVGErrorBox.js";
-export async function renderBaseLinearDisplaySvg(self, opts) {
-    const { height, id } = self;
-    const { overrideHeight } = opts;
-    const view = getContainingView(self);
-    const { offsetPx: viewOffsetPx, roundedDynamicBlocks, width } = view;
-    if (self.error) {
-        return _jsx(ErrorBox, { error: self.error, width: width, height: height });
-    }
-    const renderings = await Promise.all(roundedDynamicBlocks.map(async (block) => {
-        const blockState = BlockState.create({
-            key: block.key,
-            region: block,
-        });
-        const cannotBeRenderedReason = self.regionCannotBeRenderedText(block) ||
-            self.regionCannotBeRendered(block);
-        if (cannotBeRenderedReason) {
-            return [
-                block,
-                {
-                    reactElement: (_jsxs(_Fragment, { children: [_jsx("rect", { x: 0, y: 0, width: width, height: 20, fill: "#aaa" }), _jsx("text", { x: 0, y: 15, children: cannotBeRenderedReason })] })),
-                },
-            ];
-        }
-        const { rpcManager, renderArgs, renderProps, renderingProps, rendererType, } = renderBlockData(blockState, self);
-        return [
-            block,
-            await rendererType.renderInClient(rpcManager, {
-                ...renderArgs,
-                ...renderProps,
-                renderingProps,
-                exportSVG: opts,
-                theme: opts.theme || renderProps.theme,
-            }),
-        ];
-    }));
-    const { assemblyManager } = getSession(self);
-    const { offsetPx } = view;
-    const assemblyName = view.assemblyNames[0];
-    const assembly = assemblyName ? assemblyManager.get(assemblyName) : undefined;
-    const labelData = calculateLabelPositions(self, view, assembly, offsetPx);
-    const labelsClipId = getId(id, 'labels');
-    return (_jsxs(_Fragment, { children: [renderings.map(([block, rendering], index) => {
-                const { offsetPx, widthPx } = block;
-                const offset = offsetPx - viewOffsetPx;
-                const clipid = getId(id, index);
-                return (_jsxs(Fragment, { children: [_jsx("defs", { children: _jsx("clipPath", { id: clipid, children: _jsx("rect", { x: 0, y: 0, width: widthPx, height: overrideHeight || height }) }) }), _jsx("g", { transform: `translate(${offset} 0)`, children: _jsx("g", { clipPath: `url(#${clipid})`, children: _jsx(ReactRendering, { rendering: rendering }) }) })] }, `frag-${index}`));
-            }), _jsx("defs", { children: _jsx("clipPath", { id: labelsClipId, children: _jsx("rect", { x: 0, y: 0, width: width, height: overrideHeight || height }) }) }), _jsx("g", { clipPath: `url(#${labelsClipId})`, children: labelData.map(({ key, label, description, leftPos, topPos }) => (_jsxs("g", { transform: `translate(${leftPos}, ${topPos})`, children: [_jsx("text", { x: 0, y: 11, fontSize: 11, fill: "currentColor", style: { pointerEvents: 'none' }, children: label }), description ? (_jsx("text", { x: 0, y: 25, fontSize: 11, fill: "blue", style: { pointerEvents: 'none' }, children: description })) : null] }, `label-${key}`))) })] }));
-}