@jbrowse/plugin-alignments 2.4.2 → 2.6.0

package/esm/LinearReadArcsDisplay/model.js

@@ -1,30 +1,24 @@
-import React, { lazy } from 'react';
-import { autorun } from 'mobx';
-import { addDisposer, cast, types } from 'mobx-state-tree';
-import { ConfigurationReference, ConfigurationSchema, getConf, } from '@jbrowse/core/configuration';
-import { getSession, getContainingView } from '@jbrowse/core/util';
-import { BaseLinearDisplay, } from '@jbrowse/plugin-linear-genome-view';
+import { lazy } from 'react';
+import { cast, types } from 'mobx-state-tree';
+import { ConfigurationReference, getConf, } from '@jbrowse/core/configuration';
+import { getSession } from '@jbrowse/core/util';
+import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes';
+import { FeatureDensityMixin, TrackHeightMixin, } from '@jbrowse/plugin-linear-genome-view';
 // icons
 import PaletteIcon from '@mui/icons-material/Palette';
 import FilterListIcon from '@mui/icons-material/ClearAll';
 // locals
 import { FilterModel } from '../shared';
-import drawFeats from './drawFeats';
-import { fetchChains } from '../shared/fetchChains';
 // async
 const FilterByTagDlg = lazy(() => import('../shared/FilterByTag'));
-// stabilize clipid under test for snapshot
-function getId(id) {
-    const isJest = typeof jest === 'undefined';
-    return `arc-clip-${isJest ? id : 'jest'}`;
-}
 /**
  * #stateModel LinearReadArcsDisplay
- * extends `BaseLinearDisplay`
+ * extends `BaseDisplay`, it is not a block based track, hence not
+ * BaseLinearDisplay
  */
 function stateModelFactory(configSchema) {
     return types
-        .compose('LinearReadArcsDisplay', BaseLinearDisplay, types.model({
+        .compose('LinearReadArcsDisplay', BaseDisplay, TrackHeightMixin(), FeatureDensityMixin(), types.model({
         /**
          * #property
          */
@@ -64,22 +58,40 @@ function stateModelFactory(configSchema) {
     }))
         .volatile(() => ({
         loading: false,
-        drawn: false,
         chainData: undefined,
+        lastDrawnOffsetPx: undefined,
+        lastDrawnBpPerPx: 0,
         ref: null,
-        lastDrawnOffsetPx: 0,
     }))
         .actions(self => ({
         /**
          * #action
-         * internal, a reference to a HTMLCanvas because we use a autorun to draw the canvas
+         */
+        setLastDrawnOffsetPx(n) {
+            self.lastDrawnOffsetPx = n;
+        },
+        /**
+         * #action
+         */
+        setLastDrawnBpPerPx(n) {
+            self.lastDrawnBpPerPx = n;
+        },
+        /**
+         * #action
+         */
+        setLoading(f) {
+            self.loading = f;
+        },
+        /**
+         * #action
          */
         reload() {
             self.error = undefined;
         },
         /**
          * #action
-         * internal, a reference to a HTMLCanvas because we use a autorun to draw the canvas
+         * internal, a reference to a HTMLCanvas because we use a autorun to draw
+         * the canvas
          */
         setRef(ref) {
             self.ref = ref;
@@ -111,81 +123,58 @@ function stateModelFactory(configSchema) {
         /**
          * #action
          */
-        setLoading(f) {
-            self.loading = f;
+        setFilterBy(filter) {
+            self.filterBy = cast(filter);
         },
         /**
          * #action
-         * used during tests to detect when we can complete a snapshot test
+         * thin, bold, extrabold, etc
          */
-        setDrawn(f) {
-            self.drawn = f;
+        setLineWidth(n) {
+            self.lineWidth = n;
         },
         /**
          * #action
+         * jitter val, helpful to jitter the x direction so you see better
+         * evidence when e.g. 100 long reads map to same x position
          */
-        setFilterBy(filter) {
-            self.filterBy = cast(filter);
+        setJitter(n) {
+            self.jitter = n;
         },
+    }))
+        .views(self => ({
         /**
-         * #action
-         * allows the drawing to slide around a little bit if it takes a long time to refresh
+         * #getter
          */
-        setLastDrawnOffsetPx(n) {
-            self.lastDrawnOffsetPx = n;
+        get drawn() {
+            return self.lastDrawnOffsetPx !== undefined;
         },
         /**
-         * #action
-         * thin, bold, extrabold, etc
+         * #getter
          */
-        setLineWidth(n) {
-            self.lineWidth = n;
+        get lineWidthSetting() {
+            var _a;
+            return (_a = self.lineWidth) !== null && _a !== void 0 ? _a : getConf(self, 'lineWidth');
         },
         /**
-         * #action
-         * jitter val, helpful to jitter the x direction so you see better evidence when e.g. 100
-         * long reads map to same x position
+         * #getter
          */
-        setJitter(n) {
-            self.jitter = n;
+        get jitterVal() {
+            var _a;
+            return (_a = self.jitter) !== null && _a !== void 0 ? _a : getConf(self, 'jitter');
         },
     }))
         .views(self => {
         const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
         return {
             /**
-             * #getter
-             */
-            get lineWidthSetting() {
-                var _a;
-                return (_a = self.lineWidth) !== null && _a !== void 0 ? _a : getConf(self, 'lineWidth');
-            },
-            /**
-             * #getter
-             */
-            get jitterVal() {
-                var _a;
-                return (_a = self.jitter) !== null && _a !== void 0 ? _a : getConf(self, 'jitter');
-            },
-            /**
-             * #getter
+             * #method
+             * only used to tell system it's ready for export
              */
-            get ready() {
-                return !!self.chainData;
-            },
-            // we don't use a server side renderer, but we need to provide this
-            // to avoid confusing the system currently
-            get rendererTypeName() {
-                return 'PileupRenderer';
-            },
-            // we don't use a server side renderer, so this fills in minimal
-            // info so as not to crash
             renderProps() {
                 return {
                     ...superRenderProps(),
-                    // never ready, we don't want to use server side render
-                    notReady: true,
-                    config: ConfigurationSchema('empty', {}).create(),
+                    notReady: !self.chainData,
                 };
             },
             /**
@@ -226,19 +215,19 @@ function stateModelFactory(configSchema) {
                         subMenu: [
                             {
                                 type: 'checkbox',
-                                checked: this.jitterVal === 0,
+                                checked: self.jitterVal === 0,
                                 label: 'None',
                                 onClick: () => self.setJitter(0),
                             },
                             {
                                 type: 'checkbox',
-                                checked: this.jitterVal === 2,
+                                checked: self.jitterVal === 2,
                                 label: 'Small',
                                 onClick: () => self.setJitter(2),
                             },
                             {
                                 type: 'checkbox',
-                                checked: this.jitterVal === 10,
+                                checked: self.jitterVal === 10,
                                 label: 'Large',
                                 onClick: () => self.setJitter(10),
                             },
@@ -287,65 +276,26 @@ function stateModelFactory(configSchema) {
          * #method
          */
         async renderSvg(opts) {
-            const view = getContainingView(self);
-            const width = view.dynamicBlocks.totalWidthPx;
-            const height = self.height;
-            let str;
-            if (opts.rasterizeLayers) {
-                const canvas = document.createElement('canvas');
-                canvas.width = width * 2;
-                canvas.height = height * 2;
-                const ctx = canvas.getContext('2d');
-                if (!ctx) {
-                    return;
-                }
-                ctx.scale(2, 2);
-                await drawFeats(self, ctx);
-                str = (React.createElement("image", { width: width, height: height, xlinkHref: canvas.toDataURL('image/png') }));
-            }
-            else {
-                // @ts-ignore
-                const C2S = await import('canvas2svg');
-                const ctx = new C2S.default(width, height);
-                await drawFeats(self, ctx);
-                const clipid = getId(self.id);
-                str = (React.createElement(React.Fragment, null,
-                    React.createElement("defs", null,
-                        React.createElement("clipPath", { id: clipid },
-                            React.createElement("rect", { x: 0, y: 0, width: width, height: height }))),
-                    React.createElement("g", { 
-                        /* eslint-disable-next-line react/no-danger */
-                        dangerouslySetInnerHTML: {
-                            __html: ctx.getSvg().innerHTML,
-                        }, clipPath: `url(#${clipid})` })));
-            }
-            return React.createElement(React.Fragment, null, str);
+            const { renderSvg } = await import('../shared/renderSvg');
+            const { drawFeats } = await import('./drawFeats');
+            return renderSvg(self, opts, drawFeats);
         },
     }))
         .actions(self => ({
         afterAttach() {
-            addDisposer(self, autorun(() => fetchChains(self), { delay: 1000 }));
-            addDisposer(self, autorun(async () => {
+            // eslint-disable-next-line @typescript-eslint/no-floating-promises
+            ;
+            (async () => {
                 try {
-                    const canvas = self.ref;
-                    if (!canvas) {
-                        return;
-                    }
-                    const ctx = canvas.getContext('2d');
-                    if (!ctx) {
-                        return;
-                    }
-                    ctx.clearRect(0, 0, canvas.width, self.height * 2);
-                    ctx.resetTransform();
-                    ctx.scale(2, 2);
-                    await drawFeats(self, ctx);
-                    self.setDrawn(true);
+                    const { doAfterAttach } = await import('../shared/afterAttach');
+                    const { drawFeats } = await import('./drawFeats');
+                    doAfterAttach(self, drawFeats);
                 }
                 catch (e) {
                     console.error(e);
                     self.setError(e);
                 }
-            }, { delay: 1000 }));
+            })();
         },
     }));
 }

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package/esm/LinearReadArcsDisplay/util.d.ts

@@ -0,0 +1,2 @@
+import { ChainData } from '../shared/fetchChains';
+export declare function hasPairedReads(features: ChainData): boolean;

package/esm/LinearReadArcsDisplay/util.js

@@ -0,0 +1,9 @@
+export function hasPairedReads(features) {
+    for (const f of features.chains.values()) {
+        if (f[0].flags & 1) {
+            return true;
+        }
+    }
+    return false;
+}
+//# sourceMappingURL=util.js.map

package/esm/LinearReadArcsDisplay/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/LinearReadArcsDisplay/util.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,cAAc,CAAC,QAAmB;IAChD,KAAK,MAAM,CAAC,IAAI,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,EAAE;QACxC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,EAAE;YAClB,OAAO,IAAI,CAAA;SACZ;KACF;IACD,OAAO,KAAK,CAAA;AACd,CAAC"}

package/esm/LinearReadCloudDisplay/components/ReactComponent.d.ts

@@ -1,6 +1,6 @@
-/// <reference types="react" />
+import React from 'react';
 import { LinearReadCloudDisplayModel } from '../model';
 declare const _default: ({ model, }: {
     model: LinearReadCloudDisplayModel;
-}) => JSX.Element;
+}) => React.JSX.Element;
 export default _default;

package/esm/LinearReadCloudDisplay/components/ReactComponent.js

@@ -1,44 +1,19 @@
-import React from 'react';
-import { isAlive } from 'mobx-state-tree';
+import React, { useCallback } from 'react';
 import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
 import { getContainingView } from '@jbrowse/core/util';
-import { LoadingEllipses } from '@jbrowse/core/ui';
-import { BlockMsg, } from '@jbrowse/plugin-linear-genome-view';
-const useStyles = makeStyles()(theme => ({
-    loading: {
-        paddingLeft: '0.6em',
-        backgroundColor: theme.palette.action.disabledBackground,
-        backgroundImage: 'repeating-linear-gradient(45deg, transparent, transparent 5px, rgba(255,255,255,.5) 5px, rgba(255,255,255,.5) 10px)',
-        height: '100%',
-        width: '100%',
-        pointerEvents: 'none',
-        textAlign: 'center',
-    },
-}));
+import BaseDisplayComponent from '../../shared/BaseDisplayComponent';
 const Cloud = observer(function ({ model, }) {
     const view = getContainingView(model);
-    return (React.createElement("canvas", { "data-testid": `ReadCloud-display-${model.drawn}`, ref: ref => {
-            if (isAlive(model)) {
-                model.setRef(ref);
-            }
-        }, style: {
-            position: 'absolute',
-            left: -view.offsetPx + model.lastDrawnOffsetPx,
-            width: view.dynamicBlocks.totalWidthPx,
-            height: model.height,
-        }, width: view.dynamicBlocks.totalWidthPx * 2, height: model.height * 2 }));
+    const width = Math.round(view.dynamicBlocks.totalWidthPx);
+    const height = model.height;
+    const cb = useCallback((ref) => model.setRef(ref), 
+    // eslint-disable-next-line react-hooks/exhaustive-deps
+    [model, width, height]);
+    // note: the position absolute below avoids scrollbar from appearing on track
+    return (React.createElement("canvas", { "data-testid": "cloud-canvas", ref: cb, style: { width, height, position: 'absolute' }, width: width * 2, height: height * 2 }));
 });
 export default observer(function ({ model, }) {
-    const view = getContainingView(model);
-    const { classes } = useStyles();
-    const err = model.error;
-    return err ? (React.createElement(BlockMsg, { message: `${err}`, severity: "error", buttonText: 'Reload', action: model.reload })) : model.loading ? (React.createElement("div", { className: classes.loading, style: {
-            width: view.dynamicBlocks.totalWidthPx,
-            height: 20,
-            position: 'absolute',
-            left: Math.max(0, -view.offsetPx),
-        } },
-        React.createElement(LoadingEllipses, { message: model.message }))) : (React.createElement(Cloud, { model: model }));
+    return (React.createElement(BaseDisplayComponent, { model: model },
+        React.createElement(Cloud, { model: model })));
 });
 //# sourceMappingURL=ReactComponent.js.map

package/esm/LinearReadCloudDisplay/components/ReactComponent.js.map

@@ -1 +1 @@
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package/esm/LinearReadCloudDisplay/configSchema.d.ts

@@ -2,5 +2,56 @@ import PluginManager from '@jbrowse/core/PluginManager';
 /**
  * #config LinearReadCloudDisplay
  */
-declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    maxFeatureScreenDensity: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    featureHeight: {
+        type: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    colorScheme: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    renderer: import("mobx-state-tree").IAnyModelType;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    maxFeatureScreenDensity: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    fetchSizeLimit: {
+        type: string;
+        defaultValue: number;
+        description: string; /**
+         * #slot
+         */
+    };
+    height: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    mouseover: {
+        type: string;
+        description: string;
+        defaultValue: string;
+        contextVariable: string[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;
 export default configSchemaF;

package/esm/LinearReadCloudDisplay/drawFeats.d.ts

@@ -1,10 +1,2 @@
-import { ChainData } from '../shared/fetchChains';
-export default function drawFeats(self: {
-    setLastDrawnOffsetPx: (n: number) => void;
-    setError: (e: unknown) => void;
-    colorBy?: {
-        type: string;
-    };
-    height: number;
-    chainData?: ChainData;
-}, ctx: CanvasRenderingContext2D): Promise<void>;
+import { LinearReadCloudDisplayModel } from './model';
+export declare function drawFeats(self: LinearReadCloudDisplayModel, ctx: CanvasRenderingContext2D): void;

package/esm/LinearReadCloudDisplay/drawFeats.js

@@ -1,142 +1,25 @@
-import { getConf } from '@jbrowse/core/configuration';
 import { getContainingView, getSession } from '@jbrowse/core/util';
-// locals
-import { getOrientationColor, getInsertSizeColor, getInsertSizeAndOrientationColor, } from '../shared/color';
-// avoid drawing negative width features for SVG exports
-function fillRectCtx(x, y, width, height, ctx, color) {
-    if (width < 0) {
-        x += width;
-        width = -width;
-    }
-    if (height < 0) {
-        y += height;
-        height = -height;
-    }
-    if (color) {
-        ctx.fillStyle = color;
-    }
-    ctx.fillRect(x, y, width, height);
-}
-export default async function drawFeats(self, ctx) {
-    var _a;
+import { hasPairedReads } from '../shared/util';
+import { drawPairChains } from './drawPairChains';
+import { drawLongReadChains } from './drawLongReadChains';
+export function drawFeats(self, ctx) {
     const { chainData } = self;
     if (!chainData) {
         return;
     }
     const { assemblyManager } = getSession(self);
-    const featureHeight = getConf(self, 'featureHeight');
-    const displayHeight = self.height;
     const view = getContainingView(self);
     const assemblyName = view.assemblyNames[0];
     const asm = assemblyManager.get(assemblyName);
     if (!asm) {
         return;
     }
-    self.setLastDrawnOffsetPx(view.offsetPx);
-    const { chains, stats } = chainData;
-    const coords = [];
-    for (let i = 0; i < chains.length; i++) {
-        const chain = chains[i];
-        // if we're looking at a paired read (flag 1) then assume it is just two
-        // reads (some small cases may defy this assumption such as secondary
-        // alignments but this may be uncommon)
-        if (chain[0].flags & 1 && chain.length > 1) {
-            const v0 = chain[0];
-            const v1 = chain[1];
-            const ra1 = asm.getCanonicalRefName(v0.refName);
-            const ra2 = asm.getCanonicalRefName(v1.refName);
-            const r1s = view.bpToPx({ refName: ra1, coord: v0.start });
-            const r1e = view.bpToPx({ refName: ra1, coord: v0.end });
-            const r2s = view.bpToPx({ refName: ra2, coord: v1.start });
-            const r2e = view.bpToPx({ refName: ra2, coord: v1.end });
-            let distance = 0;
-            if (r1s !== undefined &&
-                r1e !== undefined &&
-                r2s !== undefined &&
-                r2e !== undefined) {
-                if (v0.refName === v1.refName) {
-                    const s = Math.min(v0.start, v1.start);
-                    const e = Math.max(v0.end, v1.end);
-                    distance = Math.abs(e - s);
-                }
-                coords.push({
-                    r1s: r1s.offsetPx,
-                    r1e: r1e.offsetPx,
-                    r2s: r2s.offsetPx,
-                    r2e: r2e.offsetPx,
-                    v0,
-                    v1,
-                    distance,
-                });
-            }
-        }
-        else {
-            // if we're not looking at pairs, then it could be a multiply-split-long
-            // read, so traverse chain
-            for (let i = 1; i < chain.length; i++) {
-                const v0 = chain[i - 1];
-                const v1 = chain[i];
-                const ra1 = asm.getCanonicalRefName(v0.refName);
-                const ra2 = asm.getCanonicalRefName(v1.refName);
-                const r1s = view.bpToPx({ refName: ra1, coord: v0.start });
-                const r1e = view.bpToPx({ refName: ra1, coord: v0.end });
-                const r2s = view.bpToPx({ refName: ra2, coord: v1.start });
-                const r2e = view.bpToPx({ refName: ra2, coord: v1.end });
-                let distance = 0;
-                if (r1s !== undefined &&
-                    r1e !== undefined &&
-                    r2s !== undefined &&
-                    r2e !== undefined) {
-                    if (v0.refName === v1.refName) {
-                        const s = Math.min(v0.start, v1.start);
-                        const e = Math.max(v0.end, v1.end);
-                        distance = Math.abs(e - s);
-                    }
-                    coords.push({
-                        r1s: r1s.offsetPx,
-                        r1e: r1e.offsetPx,
-                        r2s: r2s.offsetPx,
-                        r2e: r2e.offsetPx,
-                        v0,
-                        v1,
-                        distance,
-                    });
-                }
-            }
-        }
-    }
-    let max = 0;
-    for (let i = 0; i < coords.length; i++) {
-        const { distance } = coords[i];
-        max = Math.max(max, distance);
+    const hasPaired = hasPairedReads(chainData);
+    if (hasPaired) {
+        drawPairChains({ self, view, asm, ctx, chainData });
     }
-    const halfHeight = featureHeight / 2 - 0.5;
-    const scaler = (displayHeight - 20) / Math.log(max);
-    for (let i = 0; i < coords.length; i++) {
-        const { r1s, r1e, r2s, r2e, v0, v1, distance } = coords[i];
-        const type = ((_a = self.colorBy) === null || _a === void 0 ? void 0 : _a.type) || 'insertSizeAndOrientation';
-        const top = Math.log(distance) * scaler;
-        ctx.fillStyle = 'black';
-        const w = r2s - r1e;
-        fillRectCtx(r1e - view.offsetPx, top + halfHeight, w, 1, ctx);
-        if (type === 'insertSizeAndOrientation') {
-            ctx.fillStyle = getInsertSizeAndOrientationColor(v0, v1, stats);
-        }
-        else if (type === 'orientation') {
-            ctx.fillStyle = getOrientationColor(v0);
-        }
-        else if (type === 'insertSize') {
-            ctx.fillStyle = getInsertSizeColor(v0, v1, stats) || 'grey';
-        }
-        else if (type === 'gradient') {
-            const s = Math.min(v0.start, v1.start);
-            const e = Math.max(v0.end, v1.end);
-            ctx.fillStyle = `hsl(${Math.log10(Math.abs(e - s)) * 10},50%,50%)`;
-        }
-        const w1 = Math.max(r1e - r1s, 2);
-        const w2 = Math.max(r2e - r2s, 2);
-        fillRectCtx(r1s - view.offsetPx, top, w1, featureHeight, ctx);
-        fillRectCtx(r2s - view.offsetPx, top, w2, featureHeight, ctx);
+    else {
+        drawLongReadChains({ self, view, asm, ctx, chainData });
     }
 }
 //# sourceMappingURL=drawFeats.js.map