@jbrowse/plugin-alignments 2.4.2 → 2.6.0

package/dist/LinearReadArcsDisplay/model.js

@@ -26,33 +26,27 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importStar(require("react"));
-const mobx_1 = require("mobx");
+const react_1 = require("react");
 const mobx_state_tree_1 = require("mobx-state-tree");
 const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
+const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 // icons
 const Palette_1 = __importDefault(require("@mui/icons-material/Palette"));
 const ClearAll_1 = __importDefault(require("@mui/icons-material/ClearAll"));
 // locals
 const shared_1 = require("../shared");
-const drawFeats_1 = __importDefault(require("./drawFeats"));
-const fetchChains_1 = require("../shared/fetchChains");
 // async
 const FilterByTagDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../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 mobx_state_tree_1.types
-        .compose('LinearReadArcsDisplay', plugin_linear_genome_view_1.BaseLinearDisplay, mobx_state_tree_1.types.model({
+        .compose('LinearReadArcsDisplay', pluggableElementTypes_1.BaseDisplay, (0, plugin_linear_genome_view_1.TrackHeightMixin)(), (0, plugin_linear_genome_view_1.FeatureDensityMixin)(), mobx_state_tree_1.types.model({
         /**
          * #property
          */
@@ -92,22 +86,40 @@ 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;
@@ -139,81 +151,58 @@ function stateModelFactory(configSchema) {
         /**
          * #action
          */
-        setLoading(f) {
-            self.loading = f;
+        setFilterBy(filter) {
+            self.filterBy = (0, mobx_state_tree_1.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 = (0, mobx_state_tree_1.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 : (0, configuration_1.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 : (0, configuration_1.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 : (0, configuration_1.getConf)(self, 'lineWidth');
-            },
-            /**
-             * #getter
-             */
-            get jitterVal() {
-                var _a;
-                return (_a = self.jitter) !== null && _a !== void 0 ? _a : (0, configuration_1.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: (0, configuration_1.ConfigurationSchema)('empty', {}).create(),
+                    notReady: !self.chainData,
                 };
             },
             /**
@@ -254,19 +243,19 @@ 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),
                             },
@@ -315,65 +304,26 @@ function stateModelFactory(configSchema) {
          * #method
          */
         async renderSvg(opts) {
-            const view = (0, util_1.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 (0, drawFeats_1.default)(self, ctx);
-                str = (react_1.default.createElement("image", { width: width, height: height, xlinkHref: canvas.toDataURL('image/png') }));
-            }
-            else {
-                // @ts-ignore
-                const C2S = await Promise.resolve().then(() => __importStar(require('canvas2svg')));
-                const ctx = new C2S.default(width, height);
-                await (0, drawFeats_1.default)(self, ctx);
-                const clipid = getId(self.id);
-                str = (react_1.default.createElement(react_1.default.Fragment, null,
-                    react_1.default.createElement("defs", null,
-                        react_1.default.createElement("clipPath", { id: clipid },
-                            react_1.default.createElement("rect", { x: 0, y: 0, width: width, height: height }))),
-                    react_1.default.createElement("g", { 
-                        /* eslint-disable-next-line react/no-danger */
-                        dangerouslySetInnerHTML: {
-                            __html: ctx.getSvg().innerHTML,
-                        }, clipPath: `url(#${clipid})` })));
-            }
-            return react_1.default.createElement(react_1.default.Fragment, null, str);
+            const { renderSvg } = await Promise.resolve().then(() => __importStar(require('../shared/renderSvg')));
+            const { drawFeats } = await Promise.resolve().then(() => __importStar(require('./drawFeats')));
+            return renderSvg(self, opts, drawFeats);
         },
     }))
         .actions(self => ({
         afterAttach() {
-            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => (0, fetchChains_1.fetchChains)(self), { delay: 1000 }));
-            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.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 (0, drawFeats_1.default)(self, ctx);
-                    self.setDrawn(true);
+                    const { doAfterAttach } = await Promise.resolve().then(() => __importStar(require('../shared/afterAttach')));
+                    const { drawFeats } = await Promise.resolve().then(() => __importStar(require('./drawFeats')));
+                    doAfterAttach(self, drawFeats);
                 }
                 catch (e) {
                     console.error(e);
                     self.setError(e);
                 }
-            }, { delay: 1000 }));
+            })();
         },
     }));
 }

package/dist/LinearReadArcsDisplay/model.js.map

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package/dist/LinearReadArcsDisplay/util.d.ts

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

package/dist/LinearReadArcsDisplay/util.js

@@ -0,0 +1,13 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.hasPairedReads = void 0;
+function hasPairedReads(features) {
+    for (const f of features.chains.values()) {
+        if (f[0].flags & 1) {
+            return true;
+        }
+    }
+    return false;
+}
+exports.hasPairedReads = hasPairedReads;
+//# sourceMappingURL=util.js.map

package/dist/LinearReadArcsDisplay/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/LinearReadArcsDisplay/util.ts"],"names":[],"mappings":";;;AAEA,SAAgB,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;AAPD,wCAOC"}

package/dist/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/dist/LinearReadCloudDisplay/components/ReactComponent.js

@@ -1,49 +1,47 @@
 "use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importDefault(require("react"));
-const mobx_state_tree_1 = require("mobx-state-tree");
+const react_1 = __importStar(require("react"));
 const mobx_react_1 = require("mobx-react");
-const mui_1 = require("tss-react/mui");
 const util_1 = require("@jbrowse/core/util");
-const ui_1 = require("@jbrowse/core/ui");
-const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const useStyles = (0, mui_1.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',
-    },
-}));
+const BaseDisplayComponent_1 = __importDefault(require("../../shared/BaseDisplayComponent"));
 const Cloud = (0, mobx_react_1.observer)(function ({ model, }) {
     const view = (0, util_1.getContainingView)(model);
-    return (react_1.default.createElement("canvas", { "data-testid": `ReadCloud-display-${model.drawn}`, ref: ref => {
-            if ((0, mobx_state_tree_1.isAlive)(model)) {
-                model.setRef(ref);
-            }
-        }, style: {
-            position: 'absolute',
-            left: -view.offsetPx + model.lastDrawnOffsetPx,
-            width: view.dynamicBlocks.totalWidthPx,
-            height: model.height,
-        }, width: view.dynamicBlocks.totalWidthPx * 2, height: model.height * 2 }));
+    const width = Math.round(view.dynamicBlocks.totalWidthPx);
+    const height = model.height;
+    const cb = (0, react_1.useCallback)((ref) => model.setRef(ref), 
+    // eslint-disable-next-line react-hooks/exhaustive-deps
+    [model, width, height]);
+    // note: the position absolute below avoids scrollbar from appearing on track
+    return (react_1.default.createElement("canvas", { "data-testid": "cloud-canvas", ref: cb, style: { width, height, position: 'absolute' }, width: width * 2, height: height * 2 }));
 });
 exports.default = (0, mobx_react_1.observer)(function ({ model, }) {
-    const view = (0, util_1.getContainingView)(model);
-    const { classes } = useStyles();
-    const err = model.error;
-    return err ? (react_1.default.createElement(plugin_linear_genome_view_1.BlockMsg, { message: `${err}`, severity: "error", buttonText: 'Reload', action: model.reload })) : model.loading ? (react_1.default.createElement("div", { className: classes.loading, style: {
-            width: view.dynamicBlocks.totalWidthPx,
-            height: 20,
-            position: 'absolute',
-            left: Math.max(0, -view.offsetPx),
-        } },
-        react_1.default.createElement(ui_1.LoadingEllipses, { message: model.message }))) : (react_1.default.createElement(Cloud, { model: model }));
+    return (react_1.default.createElement(BaseDisplayComponent_1.default, { model: model },
+        react_1.default.createElement(Cloud, { model: model })));
 });
 //# sourceMappingURL=ReactComponent.js.map

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

@@ -1 +1 @@
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package/dist/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/dist/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;