@jbrowse/plugin-dotplot-view 2.6.2 → 2.7.0

package/esm/DotplotView/model.d.ts

@@ -58,15 +58,15 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
         readonly width: number;
         readonly assemblyNames: string[];
         readonly displayedRegionsTotalPx: number;
-        readonly maxOffset: number; /**
-         * #property
+        readonly maxOffset: number;
+        readonly minOffset: number; /**
+         * #stateModel DotplotView
+         * #category view
+         * extends  `BaseViewModel`
          */
-        readonly minOffset: number;
         readonly totalBp: number;
     } & {
-        readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet; /**
-         * #property
-         */
+        readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
         readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
         readonly currBp: number;
     } & {
@@ -82,14 +82,20 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
             reversed: boolean;
         };
         bpToPx({ refName, coord, regionNumber, }: {
-            refName: string;
+            refName: string; /**
+             * #property
+             */
             coord: number;
-            regionNumber?: number | undefined;
+            regionNumber?: number | undefined; /**
+             * #property
+             */
         }): number | undefined;
     } & {
         setFeatures(features: import("@jbrowse/core/util").Feature[]): void;
         showAllRegions(): void;
-        zoomOut(): void;
+        zoomOut(): void; /**
+         * #property
+         */
         zoomIn(): void;
         zoomTo(bpPerPx: number, offset?: number | undefined): number;
         scrollTo(offsetPx: number): number;
@@ -137,15 +143,15 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
         readonly width: number;
         readonly assemblyNames: string[];
         readonly displayedRegionsTotalPx: number;
-        readonly maxOffset: number; /**
-         * #property
+        readonly maxOffset: number;
+        readonly minOffset: number; /**
+         * #stateModel DotplotView
+         * #category view
+         * extends  `BaseViewModel`
          */
-        readonly minOffset: number;
         readonly totalBp: number;
     } & {
-        readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet; /**
-         * #property
-         */
+        readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
         readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
         readonly currBp: number;
     } & {
@@ -161,14 +167,20 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
             reversed: boolean;
         };
         bpToPx({ refName, coord, regionNumber, }: {
-            refName: string;
+            refName: string; /**
+             * #property
+             */
             coord: number;
-            regionNumber?: number | undefined;
+            regionNumber?: number | undefined; /**
+             * #property
+             */
         }): number | undefined;
     } & {
         setFeatures(features: import("@jbrowse/core/util").Feature[]): void;
         showAllRegions(): void;
-        zoomOut(): void;
+        zoomOut(): void; /**
+         * #property
+         */
         zoomIn(): void;
         zoomTo(bpPerPx: number, offset?: number | undefined): number;
         scrollTo(offsetPx: number): number;
@@ -201,28 +213,33 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
         readonly textSearchAdapter: any;
         readonly adapterType: import("@jbrowse/core/pluggableElementTypes").AdapterType;
         readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
-        readonly canConfigure: any;
+        readonly canConfigure: boolean | ({
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: unknown): any;
+        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | undefined;
     } & {
         setMinimized(flag: boolean): void;
-        activateConfigurationUI(): void;
-        showDisplay(displayId: string, initialSnapshot?: {} | undefined): void;
+        showDisplay(displayId: string, initialSnapshot?: {} | undefined): void; /**
+         * #property
+         */
         hideDisplay(displayId: string): number;
         replaceDisplay(oldId: string, newId: string, initialSnapshot?: {} | undefined): void;
     } & {
         trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
-            type: string; /**
+            type: string;
+            label: string; /**
              * #property
              */
-            label: string;
             subMenu: {
                 type: string;
-                label: string; /**
-                 * #property
-                 */
+                label: string;
                 checked: boolean;
                 onClick: () => void;
             }[];
-        })[];
+        })[]; /**
+         * #property
+         */
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     viewTrackConfigs: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
 }, {
@@ -329,15 +346,15 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
         readonly width: number;
         readonly assemblyNames: string[];
         readonly displayedRegionsTotalPx: number;
-        readonly maxOffset: number; /**
-         * #property
+        readonly maxOffset: number;
+        readonly minOffset: number; /**
+         * #stateModel DotplotView
+         * #category view
+         * extends  `BaseViewModel`
          */
-        readonly minOffset: number;
         readonly totalBp: number;
     } & {
-        readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet; /**
-         * #property
-         */
+        readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
         readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
         readonly currBp: number;
     } & {
@@ -353,14 +370,20 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
             reversed: boolean;
         };
         bpToPx({ refName, coord, regionNumber, }: {
-            refName: string;
+            refName: string; /**
+             * #property
+             */
             coord: number;
-            regionNumber?: number | undefined;
+            regionNumber?: number | undefined; /**
+             * #property
+             */
         }): number | undefined;
     } & {
         setFeatures(features: import("@jbrowse/core/util").Feature[]): void;
         showAllRegions(): void;
-        zoomOut(): void;
+        zoomOut(): void; /**
+         * #property
+         */
         zoomIn(): void;
         zoomTo(bpPerPx: number, offset?: number | undefined): number;
         scrollTo(offsetPx: number): number;
@@ -407,15 +430,15 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
         readonly width: number;
         readonly assemblyNames: string[];
         readonly displayedRegionsTotalPx: number;
-        readonly maxOffset: number; /**
-         * #property
+        readonly maxOffset: number;
+        readonly minOffset: number; /**
+         * #stateModel DotplotView
+         * #category view
+         * extends  `BaseViewModel`
          */
-        readonly minOffset: number;
         readonly totalBp: number;
     } & {
-        readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet; /**
-         * #property
-         */
+        readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
         readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
         readonly currBp: number;
     } & {
@@ -431,14 +454,20 @@ export default function stateModelFactory(pm: PluginManager): import("mobx-state
             reversed: boolean;
         };
         bpToPx({ refName, coord, regionNumber, }: {
-            refName: string;
+            refName: string; /**
+             * #property
+             */
             coord: number;
-            regionNumber?: number | undefined;
+            regionNumber?: number | undefined; /**
+             * #property
+             */
         }): number | undefined;
     } & {
         setFeatures(features: import("@jbrowse/core/util").Feature[]): void;
         showAllRegions(): void;
-        zoomOut(): void;
+        zoomOut(): void; /**
+         * #property
+         */
         zoomIn(): void;
         zoomTo(bpPerPx: number, offset?: number | undefined): number;
         scrollTo(offsetPx: number): number;

package/esm/DotplotView/model.js

@@ -17,6 +17,15 @@ import { getBlockLabelKeysToHide, makeTicks } from './components/util';
 // lazies
 const ExportSvgDialog = lazy(() => import('./components/ExportSvgDialog'));
 const ReturnToImportFormDialog = lazy(() => import('@jbrowse/core/ui/ReturnToImportFormDialog'));
+const len = (a) => measureText(a.slice(0, 30));
+const pxWidthForBlocks = (blocks, hide) => {
+    return max([
+        ...blocks.filter(b => !hide.has(b.key)).map(b => len(b.refName)),
+        ...blocks
+            .filter(b => !hide.has(b.key))
+            .map(b => len(b.end.toLocaleString('en-us'))),
+    ]);
+};
 /**
  * #stateModel DotplotView
  * #category view
@@ -469,8 +478,11 @@ export default function stateModelFactory(pm) {
         },
         // if any of our assemblies are temporary assemblies
         beforeDestroy() {
+            var _a;
             const session = getSession(self);
-            self.assemblyNames.forEach(asm => session.removeTemporaryAssembly(asm));
+            for (const name in self.assemblyNames) {
+                (_a = session.removeTemporaryAssembly) === null || _a === void 0 ? void 0 : _a.call(session, name);
+            }
         },
         afterAttach() {
             addDisposer(self, autorun(() => {
@@ -518,9 +530,8 @@ export default function stateModelFactory(pm) {
                 const voffset = vview.offsetPx;
                 const vhide = getBlockLabelKeysToHide(vblocks, viewHeight, voffset);
                 const hhide = getBlockLabelKeysToHide(hblocks, viewWidth, hoffset);
-                const len = (a) => measureText(a.slice(0, 30));
-                const by = max(hblocks.filter(b => !hhide.has(b.key)).map(b => len(b.refName)));
-                const bx = max(vblocks.filter(b => !vhide.has(b.key)).map(b => len(b.refName)));
+                const by = pxWidthForBlocks(hblocks, hhide);
+                const bx = pxWidthForBlocks(vblocks, vhide);
                 // these are set via autorun to avoid dependency cycle
                 self.setBorderY(Math.max(by + padding, 50));
                 self.setBorderX(Math.max(bx + padding, 50));

package/esm/DotplotView/svgcomponents/SVGBackground.js

@@ -1,6 +1,7 @@
 import React from 'react';
 import { useTheme } from '@mui/material';
+import { stripAlpha } from '@jbrowse/core/util';
 export default function SVGBackground({ width, height, }) {
     const theme = useTheme();
-    return (React.createElement("rect", { x: 0, y: 0, width: width, height: height, fill: theme.palette.background.default }));
+    return (React.createElement("rect", { x: 0, y: 0, width: width, height: height, fill: stripAlpha(theme.palette.background.default) }));
 }

package/esm/ServerSideRenderedBlockContent.d.ts

@@ -1,5 +1,5 @@
 import React, { CSSProperties } from 'react';
-declare const _default: ({ model, style, }: {
+declare const ServerSideRenderedDotplotContent: ({ model, style, }: {
     model: {
         error?: unknown;
         message?: string;
@@ -9,4 +9,4 @@ declare const _default: ({ model, style, }: {
     };
     style: CSSProperties;
 }) => React.JSX.Element | null;
-export default _default;
+export default ServerSideRenderedDotplotContent;

package/esm/ServerSideRenderedBlockContent.js

@@ -44,7 +44,7 @@ function BlockError({ error }) {
     return (React.createElement("div", { className: classes.blockError },
         React.createElement(Typography, null, `${error}`)));
 }
-export default observer(function ({ model, style, }) {
+const ServerSideRenderedDotplotContent = observer(function ({ model, style, }) {
     if (model.error) {
         return React.createElement(BlockError, { error: model.error, "data-testid": "reload_button" });
     }
@@ -59,3 +59,4 @@ export default observer(function ({ model, style, }) {
     }
     return null;
 });
+export default ServerSideRenderedDotplotContent;

package/esm/ServerSideSyntenyRendering.d.ts

@@ -3,21 +3,16 @@ import React from 'react';
  * A block whose content is rendered outside of the main thread and hydrated by this
  * component.
  */
-declare function ServerSideSyntenyRendering({ model, }: {
-    model: {
-        imageData: string;
-        style: Record<string, string>;
-        renderProps: {
-            width: number;
-            height: number;
-            highResolutionScaling?: number;
-        };
-    };
-}): React.JSX.Element;
-declare namespace ServerSideSyntenyRendering {
-    var propTypes: {
-        model: import("prop-types").Validator<any>;
+interface ModelType {
+    imageData: string;
+    style: Record<string, string>;
+    renderProps: {
+        width: number;
+        height: number;
+        highResolutionScaling?: number;
     };
 }
-declare const _default: typeof ServerSideSyntenyRendering;
-export default _default;
+declare const ServerSideSyntenyRendering: ({ model, }: {
+    model: ModelType;
+}) => React.JSX.Element;
+export default ServerSideSyntenyRendering;

package/esm/ServerSideSyntenyRendering.js

@@ -1,12 +1,7 @@
-/* eslint-disable @typescript-eslint/no-non-null-assertion */
 import React, { useRef, useState, useEffect } from 'react';
-import { observer, PropTypes } from 'mobx-react';
+import { observer } from 'mobx-react';
 import { drawImageOntoCanvasContext } from '@jbrowse/core/util/offscreenCanvasPonyfill';
-/**
- * A block whose content is rendered outside of the main thread and hydrated by this
- * component.
- */
-function ServerSideSyntenyRendering({ model, }) {
+const ServerSideSyntenyRendering = observer(function ({ model, }) {
     const { imageData, style, renderProps } = model;
     const { width, height, highResolutionScaling = 1 } = renderProps;
     const featureCanvas = useRef(null);
@@ -21,8 +16,5 @@ function ServerSideSyntenyRendering({ model, }) {
         setDone(true);
     }, [height, imageData, width]);
     return (React.createElement("canvas", { "data-testid": `prerendered_canvas${done ? '_done' : ''}`, ref: featureCanvas, width: width * highResolutionScaling, height: height * highResolutionScaling, style: { width, height, ...style } }));
-}
-ServerSideSyntenyRendering.propTypes = {
-    model: PropTypes.observableObject.isRequired,
-};
-export default observer(ServerSideSyntenyRendering);
+});
+export default ServerSideSyntenyRendering;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-dotplot-view",
-  "version": "2.6.2",
+  "version": "2.7.0",
   "description": "JBrowse 2 dotplot view",
   "keywords": [
     "jbrowse",
@@ -51,7 +51,7 @@
     "@jbrowse/plugin-alignments": "^2.0.0",
     "@mui/material": "^5.0.0",
     "mobx": "^6.0.0",
-    "mobx-react": "^7.0.0",
+    "mobx-react": "^9.0.0",
     "mobx-state-tree": "^5.0.0",
     "react": ">=16.8.0",
     "react-dom": ">=16.8.0",
@@ -64,5 +64,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "bbea587a402d9974acdd804a33f4b77f31a2fd5f"
+  "gitHead": "dbe7fb1af01fc89f833d2744635eb44a17365b41"
 }