@jbrowse/plugin-alignments 2.4.2 → 2.6.0

package/esm/LinearReadCloudDisplay/model.js

@@ -1,30 +1,23 @@
-import React, { lazy } from 'react';
-import { autorun } from 'mobx';
-import { addDisposer, cast, types } from 'mobx-state-tree';
-import { ConfigurationReference, ConfigurationSchema, } from '@jbrowse/core/configuration';
-import { getContainingView, getSession } from '@jbrowse/core/util';
-import { BaseLinearDisplay } from '@jbrowse/plugin-linear-genome-view';
+import { lazy } from 'react';
+import { cast, types } from 'mobx-state-tree';
+import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes';
+import { ConfigurationReference, } from '@jbrowse/core/configuration';
+import { getSession } from '@jbrowse/core/util';
+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 { fetchChains } from '../shared/fetchChains';
-import drawFeats from './drawFeats';
 // async
 const FilterByTagDlg = lazy(() => import('../shared/FilterByTag'));
-// stabilize clipid under test for snapshot
-function getId(id) {
-    const isJest = typeof jest === 'undefined';
-    return `cloud-clip-${isJest ? id : 'jest'}`;
-}
 /**
  * #stateModel LinearReadCloudDisplay
- * extends `BaseLinearDisplay`
+ * extends `BaseDisplay`, it is not a block based track, hence not BaseLinearDisplay
  */
 function stateModelFactory(configSchema) {
     return types
-        .compose('LinearReadCloudDisplay', BaseLinearDisplay, types.model({
+        .compose('LinearReadCloudDisplay', BaseDisplay, TrackHeightMixin(), FeatureDensityMixin(), types.model({
         /**
          * #property
          */
@@ -45,36 +38,36 @@ function stateModelFactory(configSchema) {
             tag: types.maybe(types.string),
             extra: types.frozen(),
         })),
+        /**
+         * #property
+         */
+        drawSingletons: true,
     }))
         .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
          */
-        reload() {
-            self.error = undefined;
+        setDrawSingletons(f) {
+            self.drawSingletons = f;
         },
         /**
          * #action
          */
-        setRef(ref) {
-            self.ref = ref;
-        },
-        setColorScheme(s) {
-            self.colorBy = cast(s);
+        setLastDrawnOffsetPx(n) {
+            self.lastDrawnOffsetPx = n;
         },
         /**
          * #action
          */
-        setChainData(args) {
-            self.chainData = args;
+        setLastDrawnBpPerPx(n) {
+            self.lastDrawnBpPerPx = n;
         },
         /**
          * #action
@@ -85,44 +78,47 @@ function stateModelFactory(configSchema) {
         /**
          * #action
          */
-        setDrawn(f) {
-            self.drawn = f;
+        reload() {
+            self.error = undefined;
         },
         /**
          * #action
+         * internal, a reference to a HTMLCanvas because we use a autorun to draw
+         * the canvas
          */
-        setFilterBy(filter) {
-            self.filterBy = cast(filter);
+        setRef(ref) {
+            self.ref = ref;
+        },
+        setColorScheme(s) {
+            self.colorBy = cast(s);
         },
         /**
          * #action
          */
-        setLastDrawnOffsetPx(n) {
-            self.lastDrawnOffsetPx = n;
+        setChainData(args) {
+            self.chainData = args;
+        },
+        /**
+         * #action
+         */
+        setFilterBy(filter) {
+            self.filterBy = cast(filter);
+        },
+    }))
+        .views(self => ({
+        get drawn() {
+            return self.lastDrawnOffsetPx !== undefined;
         },
     }))
         .views(self => {
         const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
         return {
-            /**
-             * #getter
-             */
-            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,
                 };
             },
             /**
@@ -131,6 +127,12 @@ function stateModelFactory(configSchema) {
             trackMenuItems() {
                 return [
                     ...superTrackMenuItems(),
+                    {
+                        label: 'Draw singletons',
+                        type: 'checkbox',
+                        checked: self.drawSingletons,
+                        onClick: () => self.setDrawSingletons(!self.drawSingletons),
+                    },
                     {
                         label: 'Filter by',
                         icon: FilterListIcon,
@@ -169,66 +171,27 @@ 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("g", 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 }));
+            })();
         },
     }));
 }

package/esm/LinearReadCloudDisplay/model.js.map

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package/esm/LinearReadCloudDisplay/util.d.ts

@@ -0,0 +1,2 @@
+export declare function fillRectCtx(x: number, y: number, width: number, height: number, ctx: CanvasRenderingContext2D, fillColor?: string): void;
+export declare function strokeRectCtx(x: number, y: number, width: number, height: number, ctx: CanvasRenderingContext2D, strokeColor?: string): void;

package/esm/LinearReadCloudDisplay/util.js

@@ -0,0 +1,30 @@
+// avoid drawing negative width features for SVG exports
+export function fillRectCtx(x, y, width, height, ctx, fillColor) {
+    if (width < 0) {
+        x += width;
+        width = -width;
+    }
+    if (height < 0) {
+        y += height;
+        height = -height;
+    }
+    if (fillColor) {
+        ctx.fillStyle = fillColor;
+    }
+    ctx.fillRect(x, y, width, height);
+}
+export function strokeRectCtx(x, y, width, height, ctx, strokeColor) {
+    if (width < 0) {
+        x += width;
+        width = -width;
+    }
+    if (height < 0) {
+        y += height;
+        height = -height;
+    }
+    if (strokeColor) {
+        ctx.strokeStyle = strokeColor;
+    }
+    ctx.strokeRect(x, y, width, height);
+}
+//# sourceMappingURL=util.js.map

package/esm/LinearReadCloudDisplay/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/LinearReadCloudDisplay/util.ts"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,MAAM,UAAU,WAAW,CACzB,CAAS,EACT,CAAS,EACT,KAAa,EACb,MAAc,EACd,GAA6B,EAC7B,SAAkB;IAElB,IAAI,KAAK,GAAG,CAAC,EAAE;QACb,CAAC,IAAI,KAAK,CAAA;QACV,KAAK,GAAG,CAAC,KAAK,CAAA;KACf;IACD,IAAI,MAAM,GAAG,CAAC,EAAE;QACd,CAAC,IAAI,MAAM,CAAA;QACX,MAAM,GAAG,CAAC,MAAM,CAAA;KACjB;IAED,IAAI,SAAS,EAAE;QACb,GAAG,CAAC,SAAS,GAAG,SAAS,CAAA;KAC1B;IAED,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,MAAM,CAAC,CAAA;AACnC,CAAC;AAED,MAAM,UAAU,aAAa,CAC3B,CAAS,EACT,CAAS,EACT,KAAa,EACb,MAAc,EACd,GAA6B,EAC7B,WAAoB;IAEpB,IAAI,KAAK,GAAG,CAAC,EAAE;QACb,CAAC,IAAI,KAAK,CAAA;QACV,KAAK,GAAG,CAAC,KAAK,CAAA;KACf;IACD,IAAI,MAAM,GAAG,CAAC,EAAE;QACd,CAAC,IAAI,MAAM,CAAA;QACX,MAAM,GAAG,CAAC,MAAM,CAAA;KACjB;IAED,IAAI,WAAW,EAAE;QACf,GAAG,CAAC,WAAW,GAAG,WAAW,CAAA;KAC9B;IACD,GAAG,CAAC,UAAU,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,MAAM,CAAC,CAAA;AACrC,CAAC"}

package/esm/LinearSNPCoverageDisplay/components/Tooltip.d.ts

@@ -1,4 +1,4 @@
-/// <reference types="react" />
+import React from 'react';
 import { Feature } from '@jbrowse/core/util';
 type Coord = [number, number];
 declare const SNPCoverageTooltip: (props: {
@@ -9,5 +9,5 @@ declare const SNPCoverageTooltip: (props: {
     offsetMouseCoord: Coord;
     clientMouseCoord: Coord;
     clientRect?: DOMRect;
-}) => JSX.Element | null;
+}) => React.JSX.Element | null;
 export default SNPCoverageTooltip;

package/esm/LinearSNPCoverageDisplay/models/configSchema.d.ts

@@ -1,2 +1,80 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-export default function SNPCoverageConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default function SNPCoverageConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    autoscale: {
+        type: string;
+        defaultValue: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    minScore: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    maxScore: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    scaleType: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+    /**
+     * #slot
+     */ inverted: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    multiTicks: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        SNPCoverageRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, 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;
+    };
+    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>>;