@jbrowse/plugin-linear-genome-view 2.4.2 → 2.6.1

package/esm/BaseLinearDisplay/models/FeatureDensityMixin.js

@@ -0,0 +1,184 @@
+/* eslint-disable @typescript-eslint/no-explicit-any */
+import React from 'react';
+import { getConf } from '@jbrowse/core/configuration';
+import { getContainingView } from '@jbrowse/core/util';
+import { autorun } from 'mobx';
+import { addDisposer, isAlive, types } from 'mobx-state-tree';
+import TooLargeMessage from '../components/TooLargeMessage';
+import { getDisplayStr, getFeatureDensityStatsPre } from './util';
+import autorunFeatureDensityStats from './autorunFeatureDensityStats';
+/**
+ * #stateModel FeatureDensityMixin
+ * #category display
+ */
+export default function FeatureDensityMixin() {
+    return types
+        .model({
+        /**
+         * #property
+         */
+        userBpPerPxLimit: types.maybe(types.number),
+        /**
+         * #property
+         */
+        userByteSizeLimit: types.maybe(types.number),
+    })
+        .volatile(() => ({
+        featureDensityStatsP: undefined,
+        featureDensityStats: undefined,
+        currStatsBpPerPx: 0,
+    }))
+        .views(self => ({
+        /**
+         * #getter
+         */
+        get currentBytesRequested() {
+            var _a;
+            return ((_a = self.featureDensityStats) === null || _a === void 0 ? void 0 : _a.bytes) || 0;
+        },
+        /**
+         * #getter
+         */
+        get currentFeatureScreenDensity() {
+            var _a;
+            const view = getContainingView(self);
+            return (((_a = self.featureDensityStats) === null || _a === void 0 ? void 0 : _a.featureDensity) || 0) * view.bpPerPx;
+        },
+        /**
+         * #getter
+         */
+        get maxFeatureScreenDensity() {
+            // @ts-expect-error
+            return getConf(self, 'maxFeatureScreenDensity');
+        },
+        /**
+         * #getter
+         */
+        get featureDensityStatsReady() {
+            const view = getContainingView(self);
+            return (self.currStatsBpPerPx === view.bpPerPx &&
+                (!!self.featureDensityStats || !!self.userBpPerPxLimit));
+        },
+        /**
+         * #getter
+         */
+        get maxAllowableBytes() {
+            var _a;
+            return (self.userByteSizeLimit ||
+                ((_a = self.featureDensityStats) === null || _a === void 0 ? void 0 : _a.fetchSizeLimit) ||
+                // @ts-expect-error
+                getConf(self, 'fetchSizeLimit'));
+        },
+    }))
+        .actions(self => ({
+        afterAttach() {
+            addDisposer(self, autorun(() => autorunFeatureDensityStats(self)));
+        },
+    }))
+        .actions(self => ({
+        /**
+         * #action
+         */
+        setCurrStatsBpPerPx(n) {
+            self.currStatsBpPerPx = n;
+        },
+        /**
+         * #action
+         */
+        setFeatureDensityStatsLimit(stats) {
+            const view = getContainingView(self);
+            if (stats === null || stats === void 0 ? void 0 : stats.bytes) {
+                self.userByteSizeLimit = stats.bytes;
+            }
+            else {
+                self.userBpPerPxLimit = view.bpPerPx;
+            }
+        },
+        /**
+         * #action
+         */
+        async getFeatureDensityStats() {
+            if (!self.featureDensityStatsP) {
+                self.featureDensityStatsP = getFeatureDensityStatsPre(self).catch(e => {
+                    if (isAlive(self)) {
+                        this.setFeatureDensityStatsP(undefined);
+                    }
+                    throw e;
+                });
+            }
+            return self.featureDensityStatsP;
+        },
+        /**
+         * #action
+         */
+        setFeatureDensityStatsP(arg) {
+            self.featureDensityStatsP = arg;
+        },
+        /**
+         * #action
+         */
+        setFeatureDensityStats(featureDensityStats) {
+            self.featureDensityStats = featureDensityStats;
+        },
+        /**
+         * #action
+         */
+        clearFeatureDensityStats() {
+            self.featureDensityStatsP = undefined;
+            self.featureDensityStats = undefined;
+        },
+    }))
+        .views(self => ({
+        /**
+         * #getter
+         * region is too large if:
+         * - stats are ready
+         * - region is greater than 20kb (don't warn when zoomed in less than that)
+         * - and bytes is greater than max allowed bytes or density greater than max
+         *   density
+         */
+        get regionTooLarge() {
+            const view = getContainingView(self);
+            if (!self.featureDensityStatsReady ||
+                view.dynamicBlocks.totalBp < 20000) {
+                return false;
+            }
+            return (self.currentBytesRequested > self.maxAllowableBytes ||
+                (self.userBpPerPxLimit
+                    ? view.bpPerPx > self.userBpPerPxLimit
+                    : self.currentFeatureScreenDensity > self.maxFeatureScreenDensity));
+        },
+        /**
+         * #getter
+         * only shows a message of bytes requested is defined, the feature density
+         * based stats don't produce any helpful message besides to zoom in
+         */
+        get regionTooLargeReason() {
+            const req = self.currentBytesRequested;
+            const max = self.maxAllowableBytes;
+            return req && req > max
+                ? `Requested too much data (${getDisplayStr(req)})`
+                : '';
+        },
+    }))
+        .views(self => ({
+        /**
+         * #method
+         */
+        regionCannotBeRenderedText(_region) {
+            return self.regionTooLarge ? 'Force load to see features' : '';
+        },
+        /**
+         * #method
+         * @param region -
+         * @returns falsy if the region is fine to try rendering. Otherwise,
+         *  return a react node + string of text.
+         *  string of text describes why it cannot be rendered
+         *  react node allows user to force load at current setting
+         */
+        regionCannotBeRendered(_region) {
+            return self.regionTooLarge ? (React.createElement(TooLargeMessage, { model: self })) : null;
+        },
+    }));
+}
+//# sourceMappingURL=FeatureDensityMixin.js.map

package/esm/BaseLinearDisplay/models/FeatureDensityMixin.js.map

@@ -0,0 +1 @@
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package/esm/BaseLinearDisplay/models/TrackHeightMixin.d.ts

@@ -0,0 +1,30 @@
+/**
+ * #stateModel TrackHeightMixin
+ * #category display
+ */
+export default function TrackHeightMixin(): import("mobx-state-tree").IModelType<{
+    /**
+     * #property
+     */
+    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+}, {
+    /**
+     * #property
+     */
+    scrollTop: number;
+} & {
+    readonly height: number;
+} & {
+    /**
+     * #action
+     */
+    setScrollTop(scrollTop: number): void;
+    /**
+     * #action
+     */
+    setHeight(displayHeight: number): number;
+    /**
+     * #action
+     */
+    resizeHeight(distance: number): number;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/esm/BaseLinearDisplay/models/TrackHeightMixin.js

@@ -0,0 +1,53 @@
+import { getConf } from '@jbrowse/core/configuration';
+import { types } from 'mobx-state-tree';
+const minDisplayHeight = 20;
+/**
+ * #stateModel TrackHeightMixin
+ * #category display
+ */
+export default function TrackHeightMixin() {
+    return types
+        .model({
+        /**
+         * #property
+         */
+        heightPreConfig: types.maybe(types.refinement('displayHeight', types.number, n => n >= minDisplayHeight)),
+    })
+        .volatile(() => ({
+        /**
+         * #property
+         */
+        scrollTop: 0,
+    }))
+        .views(self => ({
+        get height() {
+            var _a;
+            // @ts-expect-error
+            return (_a = self.heightPreConfig) !== null && _a !== void 0 ? _a : getConf(self, 'height');
+        },
+    }))
+        .actions(self => ({
+        /**
+         * #action
+         */
+        setScrollTop(scrollTop) {
+            self.scrollTop = scrollTop;
+        },
+        /**
+         * #action
+         */
+        setHeight(displayHeight) {
+            self.heightPreConfig = Math.max(displayHeight, minDisplayHeight);
+            return self.height;
+        },
+        /**
+         * #action
+         */
+        resizeHeight(distance) {
+            const oldHeight = self.height;
+            const newHeight = this.setHeight(self.height + distance);
+            return newHeight - oldHeight;
+        },
+    }));
+}
+//# sourceMappingURL=TrackHeightMixin.js.map

package/esm/BaseLinearDisplay/models/TrackHeightMixin.js.map

@@ -0,0 +1 @@
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package/esm/BaseLinearDisplay/models/autorunFeatureDensityStats.d.ts

@@ -0,0 +1,2 @@
+import { BaseLinearDisplayModel } from './BaseLinearDisplayModel';
+export default function autorunFeatureDensityStats(self: BaseLinearDisplayModel): Promise<void>;

package/esm/BaseLinearDisplay/models/autorunFeatureDensityStats.js

@@ -0,0 +1,39 @@
+import { getContainingView, isAbortException } from '@jbrowse/core/util';
+import { isAlive } from 'mobx-state-tree';
+// stats estimation autorun calls getFeatureDensityStats against the data
+// adapter which by default uses featureDensity, but can also respond with a
+// byte size estimate and fetch size limit (data adapter can define what is too
+// much data)
+export default async function autorunFeatureDensityStats(self) {
+    var _a;
+    try {
+        const view = getContainingView(self);
+        // extra check for contentBlocks.length
+        // https://github.com/GMOD/jbrowse-components/issues/2694
+        if (!view.initialized ||
+            !view.staticBlocks.contentBlocks.length ||
+            view.bpPerPx === self.currStatsBpPerPx ||
+            self.error) {
+            return;
+        }
+        // don't re-estimate featureDensity even if zoom level changes,
+        // jbrowse1-style assume it's sort of representative
+        if (((_a = self.featureDensityStats) === null || _a === void 0 ? void 0 : _a.featureDensity) !== undefined) {
+            self.setCurrStatsBpPerPx(view.bpPerPx);
+            return;
+        }
+        self.clearFeatureDensityStats();
+        self.setCurrStatsBpPerPx(view.bpPerPx);
+        const stats = await self.getFeatureDensityStats();
+        if (isAlive(self)) {
+            self.setFeatureDensityStats(stats);
+        }
+    }
+    catch (e) {
+        if (!isAbortException(e) && isAlive(self)) {
+            console.error(e);
+            self.setError(e);
+        }
+    }
+}
+//# sourceMappingURL=autorunFeatureDensityStats.js.map

package/esm/BaseLinearDisplay/models/autorunFeatureDensityStats.js.map

@@ -0,0 +1 @@
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package/esm/BaseLinearDisplay/models/configSchema.d.ts

@@ -1,2 +1,36 @@
-declare const baseLinearDisplayConfigSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const baseLinearDisplayConfigSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    maxFeatureScreenDensity: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    fetchSizeLimit: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    height: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    mouseover: {
+        type: string;
+        description: string;
+        defaultValue: string;
+        contextVariable: string[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 export default baseLinearDisplayConfigSchema;

package/esm/BaseLinearDisplay/models/configSchema.js

@@ -1,6 +1,7 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 /**
  * #config BaseLinearDisplay
+ * #category display
  * `BaseLinearDisplay` is a "base" config that is extended by classes like
  * `LinearBasicDisplay` (used for feature tracks, etc) and `LinearBareDisplay`
  * (more stripped down than even the basic display, not commonly used)
@@ -31,6 +32,15 @@ const baseLinearDisplayConfigSchema = ConfigurationSchema('BaseLinearDisplay', {
         defaultValue: 100,
         description: 'default height for the track',
     },
+    /**
+     * #slot
+     */
+    mouseover: {
+        type: 'string',
+        description: 'text to display when the cursor hovers over a feature',
+        defaultValue: `jexl:get(feature,'name')`,
+        contextVariable: ['feature'],
+    },
 }, {
     /**
      * #identifier

package/esm/BaseLinearDisplay/models/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../../src/BaseLinearDisplay/models/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;;;;;GAMG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,6BAA6B,GAAG,mBAAmB,CACvD,mBAAmB,EACnB;IACE;;OAEG;IACH,uBAAuB,EAAE;QACvB,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,qGAAqG;QACvG,YAAY,EAAE,GAAG;KAClB;IACD;;OAEG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,OAAS;QACvB,WAAW,EACT,4FAA4F;KAC/F;IACD;;OAEG;IACH,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,GAAG;QACjB,WAAW,EAAE,8BAA8B;KAC5C;IACD;;OAEG;IACH,SAAS,EAAE;QACT,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,uDAAuD;QACpE,YAAY,EAAE,0BAA0B;QAExC,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;CACF,EACD;IACE;;OAEG;IACH,kBAAkB,EAAE,WAAW;CAChC,CACF,CAAA;AAED,eAAe,6BAA6B,CAAA"}

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

@@ -0,0 +1,8 @@
+import React from 'react';
+import { ThemeOptions } from '@mui/material';
+import { ExportSvgOptions } from '../../LinearGenomeView';
+import { BaseLinearDisplayModel } from './BaseLinearDisplayModel';
+export default function renderBaseLinearDisplaySvg(self: BaseLinearDisplayModel, opts: ExportSvgOptions & {
+    overrideHeight: number;
+    theme: ThemeOptions;
+}): Promise<React.JSX.Element>;

package/esm/BaseLinearDisplay/models/renderSvg.js

@@ -0,0 +1,54 @@
+import React from 'react';
+import { getContainingView, getViewParams, ReactRendering, } from '@jbrowse/core/util';
+import BlockState, { renderBlockData } from './serverSideRenderedBlock';
+import { getId } from './util';
+export default async function renderBaseLinearDisplaySvg(self, opts) {
+    const { height, id } = self;
+    const { overrideHeight } = opts;
+    const view = getContainingView(self);
+    const { offsetPx: viewOffsetPx, roundedDynamicBlocks, width } = view;
+    const renderings = await Promise.all(roundedDynamicBlocks.map(async (block) => {
+        const blockState = BlockState.create({
+            key: block.key,
+            region: block,
+        });
+        // regionCannotBeRendered can return jsx so look for plaintext
+        // version, or just get the default if none available
+        const cannotBeRenderedReason = self.regionCannotBeRenderedText(block) ||
+            self.regionCannotBeRendered(block);
+        if (cannotBeRenderedReason) {
+            return [
+                block,
+                {
+                    reactElement: (React.createElement(React.Fragment, null,
+                        React.createElement("rect", { x: 0, y: 0, width: width, height: 20, fill: "#aaa" }),
+                        React.createElement("text", { x: 0, y: 15 }, cannotBeRenderedReason))),
+                },
+            ];
+        }
+        const { rpcManager, renderArgs, renderProps, rendererType } = renderBlockData(blockState, self);
+        return [
+            block,
+            await rendererType.renderInClient(rpcManager, {
+                ...renderArgs,
+                ...renderProps,
+                viewParams: getViewParams(self, true),
+                exportSVG: opts,
+                theme: opts.theme || renderProps.theme,
+            }),
+        ];
+    }));
+    return (React.createElement(React.Fragment, null, renderings.map(([block, rendering], index) => {
+        const { offsetPx, widthPx } = block;
+        const offset = offsetPx - viewOffsetPx;
+        const clipid = getId(id, index);
+        return (React.createElement(React.Fragment, { key: `frag-${index}` },
+            React.createElement("defs", null,
+                React.createElement("clipPath", { id: clipid },
+                    React.createElement("rect", { x: 0, y: 0, width: widthPx, height: overrideHeight || height }))),
+            React.createElement("g", { transform: `translate(${offset} 0)` },
+                React.createElement("g", { clipPath: `url(#${clipid})` },
+                    React.createElement(ReactRendering, { rendering: rendering })))));
+    })));
+}
+//# sourceMappingURL=renderSvg.js.map

package/esm/BaseLinearDisplay/models/renderSvg.js.map

@@ -0,0 +1 @@
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package/esm/BaseLinearDisplay/models/serverSideRenderedBlock.js

@@ -37,12 +37,16 @@ const blockState = types
         },
         afterAttach() {
             const display = getContainingDisplay(self);
-            makeAbortableReaction(self, renderBlockData, renderBlockEffect, // reaction doesn't expect async here
-            {
-                name: `${display.id}/${assembleLocString(self.region)} rendering`,
-                delay: display.renderDelay,
-                fireImmediately: true,
-            }, this.setLoading, this.setRendered, this.setError);
+            setTimeout(() => {
+                if (isAlive(self)) {
+                    makeAbortableReaction(self, renderBlockData, renderBlockEffect, // reaction doesn't expect async here
+                    {
+                        name: `${display.id}/${assembleLocString(self.region)} rendering`,
+                        delay: display.renderDelay,
+                        fireImmediately: true,
+                    }, this.setLoading, this.setRendered, this.setError);
+                }
+            }, display.renderDelay);
         },
         setStatus(message) {
             self.status = message;
@@ -124,22 +128,26 @@ const blockState = types
             getParent(self, 2).reload();
         },
         beforeDestroy() {
-            if (renderInProgress && !renderInProgress.signal.aborted) {
-                renderInProgress.abort();
-            }
-            const display = getContainingDisplay(self);
-            const { rpcManager } = getSession(self);
-            const { rendererType } = display;
-            const { renderArgs } = renderBlockData(cast(self));
-            // renderArgs can be undefined if an error occurred in this block
-            if (renderArgs) {
-                rendererType
-                    .freeResourcesInClient(rpcManager, JSON.parse(JSON.stringify(renderArgs)))
-                    .catch((e) => {
-                    // just console.error if it's something while it's being destroyed
-                    console.warn('Error while destroying block', e);
-                });
-            }
+            // eslint-disable-next-line @typescript-eslint/no-floating-promises
+            ;
+            (async () => {
+                try {
+                    if (renderInProgress && !renderInProgress.signal.aborted) {
+                        renderInProgress.abort();
+                    }
+                    const display = getContainingDisplay(self);
+                    const { rpcManager } = getSession(self);
+                    const { rendererType } = display;
+                    const { renderArgs } = renderBlockData(cast(self));
+                    // renderArgs can be undefined if an error occurred in this block
+                    if (renderArgs) {
+                        await rendererType.freeResourcesInClient(rpcManager, JSON.parse(JSON.stringify(renderArgs)));
+                    }
+                }
+                catch (e) {
+                    console.error('Error while destroying block', e);
+                }
+            })();
         },
     };
 });

package/esm/BaseLinearDisplay/models/serverSideRenderedBlock.js.map

@@ -1 +1 @@
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package/esm/BaseLinearDisplay/models/util.d.ts

@@ -1,4 +1,5 @@
-import { Stats } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { FeatureDensityStats } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { IAnyStateTreeNode } from 'mobx-state-tree';
 export interface RenderProps {
     rendererType: any;
@@ -19,4 +20,7 @@ export interface ErrorProps {
 }
 export declare function getDisplayStr(totalBytes: number): string;
 export declare function getId(id: string, index: number): string;
-export declare function estimateRegionsStatsPre(self: IAnyStateTreeNode): Promise<Stats>;
+export declare function getFeatureDensityStatsPre(self: IAnyStateTreeNode & {
+    adapterConfig?: AnyConfigurationModel;
+    setMessage: (arg: string) => void;
+}): Promise<FeatureDensityStats>;

package/esm/BaseLinearDisplay/models/util.js

@@ -19,7 +19,7 @@ export function getId(id, index) {
     const isJest = typeof jest === 'undefined';
     return `clip-${isJest ? id : 'jest'}-${index}`;
 }
-export async function estimateRegionsStatsPre(self) {
+export async function getFeatureDensityStatsPre(self) {
     const view = getContainingView(self);
     const regions = view.staticBlocks.contentBlocks;
     const { rpcManager } = getSession(self);
@@ -30,7 +30,7 @@ export async function estimateRegionsStatsPre(self) {
         return {};
     }
     const sessionId = getRpcSessionId(self);
-    return rpcManager.call(sessionId, 'CoreEstimateRegionStats', {
+    return rpcManager.call(sessionId, 'CoreGetFeatureDensityStats', {
         sessionId,
         regions,
         adapterConfig,

package/esm/BaseLinearDisplay/models/util.js.map

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