npm - @jbrowse/plugin-circular-view - Versions diffs - 2.3.4 → 2.4.1 - Mend

@jbrowse/plugin-circular-view 2.3.4 → 2.4.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (107) hide show

package/dist/CircularView/components/Ruler.js CHANGED Viewed

@@ -39,24 +39,20 @@ function sliceArcPath(slice, radiusPx, startBase, endBase) {
         ...endXY,
     ].join(' ');
 }
-const ElisionRulerArc = (0, mobx_react_1.observer)(({ model, slice }) => {
+const ElisionRulerArc = (0, mobx_react_1.observer)(function ({ model, slice, region, }) {
     const theme = (0, styles_1.useTheme)();
     const { radiusPx: modelRadiusPx } = model;
     const radiusPx = modelRadiusPx + 1;
-    const { endRadians, startRadians, region } = slice;
+    const { endRadians, startRadians } = slice;
     const startXY = (0, util_1.polarToCartesian)(radiusPx, startRadians);
     const endXY = (0, util_1.polarToCartesian)(radiusPx, endRadians);
     const widthPx = (endRadians - startRadians) * radiusPx;
     const largeArc = endRadians - startRadians > Math.PI ? '1' : '0';
     // TODO: draw the elision
     const centerRadians = (endRadians + startRadians) / 2;
-    const regionCountString = `[${Number(
-    // @ts-ignore
-    region.regions.length).toLocaleString()}]`;
+    const regionCount = `[${Number(region.regions.length).toLocaleString()}]`;
     return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement(RulerLabel, { text: regionCountString, view: model, maxWidthPx: widthPx, radians: centerRadians, radiusPx: radiusPx, title: `${Number(
-            // @ts-ignore
-            region.regions.length).toLocaleString()} more regions`, color: theme.palette.text.primary }),
+        react_1.default.createElement(RulerLabel, { text: regionCount, view: model, maxWidthPx: widthPx, radians: centerRadians, radiusPx: radiusPx, title: `${regionCount} more regions`, color: theme.palette.text.primary }),
         react_1.default.createElement("path", { d: [
                 'M',
                 ...startXY,
@@ -69,7 +65,7 @@ const ElisionRulerArc = (0, mobx_react_1.observer)(({ model, slice }) => {
                 ...endXY,
             ].join(' '), stroke: theme.palette.text.secondary, strokeWidth: 2, strokeDasharray: "2,2", fill: "none" })));
 });
-const RulerLabel = (0, mobx_react_1.observer)(({ view, text, maxWidthPx, radians, radiusPx, title, color, }) => {
+const RulerLabel = (0, mobx_react_1.observer)(function ({ view, text, maxWidthPx, radians, radiusPx, title, color, }) {
     const { classes } = useStyles();
     const textXY = (0, util_1.polarToCartesian)(radiusPx + 5, radians);
     if (!text) {
@@ -96,15 +92,15 @@ const RulerLabel = (0, mobx_react_1.observer)(({ view, text, maxWidthPx, radians
     // if you get here there is no room for the text at all
     return null;
 });
-const RegionRulerArc = (0, mobx_react_1.observer)(({ model, slice }) => {
+const RegionRulerArc = (0, mobx_react_1.observer)(function ({ model, slice, region, }) {
     const theme = (0, styles_1.useTheme)();
     const { radiusPx } = model;
-    const { region, endRadians, startRadians } = slice;
+    const { endRadians, startRadians } = slice;
     const centerRadians = (endRadians + startRadians) / 2;
     const widthPx = (endRadians - startRadians) * radiusPx;
     const session = (0, util_1.getSession)(model);
     let color;
-    const assembly = session.assemblyManager.get(slice.region.assemblyName);
+    const assembly = session.assemblyManager.get(region.assemblyName);
     if (assembly) {
         color = assembly.getRefNameColor(region.refName);
     }
@@ -122,16 +118,12 @@ const RegionRulerArc = (0, mobx_react_1.observer)(({ model, slice }) => {
     // TODO: slice flipping
     return (react_1.default.createElement(react_1.default.Fragment, null,
         react_1.default.createElement(RulerLabel, { text: region.refName, view: model, maxWidthPx: widthPx, radians: centerRadians, radiusPx: radiusPx, color: color }),
-        react_1.default.createElement("path", { d: sliceArcPath(slice, radiusPx + 1, region.start, region.end), stroke: color, strokeWidth: 2, fill: "none" },
-            react_1.default.createElement("title", null, region.refName))));
+        react_1.default.createElement("path", { d: sliceArcPath(slice, radiusPx + 1, region.start, region.end), stroke: color, strokeWidth: 2, fill: "none" })));
 });
-const CircularRuler = (0, mobx_react_1.observer)(({ model, slice }) => {
+exports.default = (0, mobx_react_1.observer)(function ({ model, slice, }) {
     if (slice.region.elided) {
-        return (react_1.default.createElement(ElisionRulerArc, { key:
-            /* @ts-ignore */
-            (0, util_1.assembleLocString)(slice.region.regions[0]), model: model, slice: slice }));
+        return (react_1.default.createElement(ElisionRulerArc, { key: (0, util_1.assembleLocString)(slice.region.regions[0]), model: model, region: slice.region, slice: slice }));
     }
-    return (react_1.default.createElement(RegionRulerArc, { key: (0, util_1.assembleLocString)(slice.region), model: model, slice: slice }));
+    return (react_1.default.createElement(RegionRulerArc, { key: (0, util_1.assembleLocString)(slice.region), region: slice.region, model: model, slice: slice }));
 });
-exports.default = CircularRuler;
 //# sourceMappingURL=Ruler.js.map

package/dist/CircularView/components/Ruler.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ 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package/dist/CircularView/models/CircularView.d.ts CHANGED Viewed

@@ -1,8 +1,16 @@
+import React from 'react';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { SnapshotOrInstance, Instance } from 'mobx-state-tree';
 import { Region } from '@jbrowse/core/util/types/mst';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { Region as IRegion } from '@jbrowse/core/util';
+import { MenuItem } from '@jbrowse/core/ui';
+import { SliceRegion } from './slices';
+export interface ExportSvgOptions {
+    rasterizeLayers?: boolean;
+    filename?: string;
+    Wrapper?: React.FC<any>;
+    themeName?: string;
+}
 /**
  * #stateModel CircularView
  * extends `BaseViewModel`
@@ -27,7 +35,9 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         end: import("mobx-state-tree").ISimpleType<number>;
         reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     } & {
-        assemblyName: import("mobx-state-tree").ISimpleType<string>;
+        assemblyName: import("mobx-state-tree").ISimpleType<string>; /**
+         * #property
+         */
     }, {
         setRefName(newRefName: string): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -43,7 +53,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
 }, {
     width: number;
 } & {
-    menuItems(): import("@jbrowse/core/ui").MenuItem[];
+    menuItems(): MenuItem[];
 } & {
     setDisplayName(name: string): void;
     setWidth(newWidth: number): void;
@@ -56,10 +66,6 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
      * #getter
      */
     readonly width: number;
-    /**
-     * #getter
-     */
-    readonly staticSlices: import("./slices").Slice[];
     /**
      * #getter
      */
@@ -132,17 +138,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
      * this is displayedRegions, post-processed to
      * elide regions that are too small to see reasonably
      */
-    readonly elidedRegions: ({
-        elided: true;
-        widthBp: number;
-        regions: IRegion[];
-    } | {
-        elided: false;
-        widthBp: number;
-        start: number;
-        end: number;
-        refName: string;
-    })[];
+    readonly elidedRegions: SliceRegion[];
     /**
      * #getter
      */
@@ -151,6 +147,11 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
      * #getter
      */
     readonly initialized: boolean;
+} & {
+    /**
+     * #getter
+     */
+    readonly staticSlices: import("./slices").Slice[];
 } & {
     /**
      * #getter
@@ -241,15 +242,18 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
      * #action
      */
     toggleFitToWindowLock(): boolean;
+    /**
+     * #action
+     * creates an svg export and save using FileSaver
+     */
+    exportSvg(opts?: ExportSvgOptions): Promise<void>;
+} & {
+    /**
+     * #method
+     * return the view menu items
+     */
+    menuItems(): MenuItem[];
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export type CircularViewStateModel = ReturnType<typeof stateModelFactory>;
 export type CircularViewModel = Instance<CircularViewStateModel>;
-/**
-PLANS
-- tracks
-- ruler tick marks
-- set viewport scroll from state snapshot
-*/
 export default stateModelFactory;

package/dist/CircularView/models/CircularView.js CHANGED Viewed

@@ -1,11 +1,22 @@
 "use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
 const mobx_state_tree_1 = require("mobx-state-tree");
 const mst_1 = require("@jbrowse/core/util/types/mst");
 const mobx_1 = require("mobx");
+const file_saver_1 = require("file-saver");
+const SVGCircularView_1 = require("../svgcomponents/SVGCircularView");
 const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
 const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
+// icons
+const Icons_1 = require("@jbrowse/core/ui/Icons");
+const FolderOpen_1 = __importDefault(require("@mui/icons-material/FolderOpen"));
+const PhotoCamera_1 = __importDefault(require("@mui/icons-material/PhotoCamera"));
+// locals
+const ExportSvgDialog_1 = __importDefault(require("../components/ExportSvgDialog"));
 const slices_1 = require("./slices");
 const viewportVisibleRegion_1 = require("./viewportVisibleRegion");
 /**
@@ -89,12 +100,6 @@ function stateModelFactory(pluginManager) {
             }
             return self.volatileWidth;
         },
-        /**
-         * #getter
-         */
-        get staticSlices() {
-            return (0, slices_1.calculateStaticSlices)(self);
-        },
         /**
          * #getter
          */
@@ -271,6 +276,14 @@ function stateModelFactory(pluginManager) {
             return (self.volatileWidth !== undefined &&
                 this.assemblyNames.every(a => { var _a; return (_a = assemblyManager.get(a)) === null || _a === void 0 ? void 0 : _a.initialized; }));
         },
+    }))
+        .views(self => ({
+        /**
+         * #getter
+         */
+        get staticSlices() {
+            return (0, slices_1.calculateStaticSlices)(self);
+        },
     }))
         .views(self => ({
         /**
@@ -425,8 +438,8 @@ function stateModelFactory(pluginManager) {
                 throw new Error(`unknown track type ${conf.type}`);
             }
             const viewType = pluginManager.getViewType(self.type);
-            const supportedDisplays = viewType.displayTypes.map(d => d.name);
-            const displayConf = conf.displays.find((d) => supportedDisplays.includes(d.type));
+            const supportedDisplays = new Set(viewType.displayTypes.map(d => d.name));
+            const displayConf = conf.displays.find((d) => supportedDisplays.has(d.type));
             const track = trackType.stateModel.create({
                 ...initialSnapshot,
                 type: conf.type,
@@ -443,19 +456,18 @@ function stateModelFactory(pluginManager) {
             const name = (0, configuration_1.readConfObject)(configuration, 'name');
             const trackType = pluginManager.getTrackType(type);
             if (!trackType) {
-                throw new Error(`unknown track type ${configuration.type}`);
+                throw new Error(`unknown track type ${type}`);
             }
             const viewType = pluginManager.getViewType(self.type);
-            const supportedDisplays = viewType.displayTypes.map(d => d.name);
-            const displayConf = configuration.displays.find((d) => supportedDisplays.includes(d.type));
-            const track = trackType.stateModel.create({
+            const supportedDisplays = new Set(viewType.displayTypes.map(d => d.name));
+            const displayConf = configuration.displays.find((d) => supportedDisplays.has(d.type));
+            self.tracks.push(trackType.stateModel.create({
                 ...initialSnapshot,
                 name,
                 type,
                 configuration,
                 displays: [{ type: displayConf.type, configuration: displayConf }],
-            });
-            self.tracks.push(track);
+            }));
         },
         /**
          * #action
@@ -477,15 +489,47 @@ function stateModelFactory(pluginManager) {
             this.setModelViewWhenAdjust(self.atMinBpPerPx);
             return self.lockedFitToWindow;
         },
+        /**
+         * #action
+         * creates an svg export and save using FileSaver
+         */
+        async exportSvg(opts = {}) {
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            const html = await (0, SVGCircularView_1.renderToSvg)(self, opts);
+            const blob = new Blob([html], { type: 'image/svg+xml' });
+            (0, file_saver_1.saveAs)(blob, opts.filename || 'image.svg');
+        },
+    }))
+        .views(self => ({
+        /**
+         * #method
+         * return the view menu items
+         */
+        menuItems() {
+            return [
+                {
+                    label: 'Return to import form',
+                    onClick: () => self.setDisplayedRegions([]),
+                    icon: FolderOpen_1.default,
+                },
+                {
+                    label: 'Export SVG',
+                    icon: PhotoCamera_1.default,
+                    onClick: () => {
+                        (0, util_1.getSession)(self).queueDialog(handleClose => [
+                            ExportSvgDialog_1.default,
+                            { model: self, handleClose },
+                        ]);
+                    },
+                },
+                {
+                    label: 'Open track selector',
+                    onClick: self.activateTrackSelector,
+                    icon: Icons_1.TrackSelector,
+                },
+            ];
+        },
     }));
 }
-/**
-PLANS
-- tracks
-- ruler tick marks
-- set viewport scroll from state snapshot
-*/
 exports.default = stateModelFactory;
 //# sourceMappingURL=CircularView.js.map

package/dist/CircularView/models/CircularView.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/CircularView/models/slices.d.ts CHANGED Viewed

@@ -1,28 +1,41 @@
 import { Region } from '@jbrowse/core/util';
+export type SliceElidedRegion = {
+    elided: true;
+    widthBp: number;
+    regions: Region[];
+};
+export type SliceNonElidedRegion = {
+    elided: false;
+    widthBp: number;
+    start: number;
+    end: number;
+    refName: string;
+    assemblyName: string;
+};
+export type SliceRegion = SliceNonElidedRegion | SliceElidedRegion;
 export declare class Slice {
-    region: Region & {
-        widthBp: number;
-        elided: boolean;
-    };
+    region: SliceRegion;
+    offsetRadians: number;
     radianWidth: number;
     key: string;
-    offsetRadians: number;
     startRadians: number;
     endRadians: number;
     bpPerRadian: number;
     flipped: boolean;
     constructor(view: {
         bpPerRadian: number;
-    }, region: Region & {
-        widthBp: number;
-        elided: boolean;
-    }, currentRadianOffset: number, radianWidth: number);
+    }, region: SliceRegion, offsetRadians: number, radianWidth: number);
     bpToXY(bp: number, radiusPx: number): [number, number];
     toJSON(): {
         [k: string]: any;
     };
 }
-declare function calculateStaticSlices(self: any): Slice[];
+declare function calculateStaticSlices(self: {
+    elidedRegions: SliceRegion[];
+    bpPerRadian: number;
+    spacingPx: number;
+    pxPerRadian: number;
+}): Slice[];
 declare function sliceIsVisible(self: {
     offsetRadians: number;
     visibleSection: {

package/dist/CircularView/models/slices.js CHANGED Viewed

@@ -4,16 +4,19 @@ exports.sliceIsVisible = exports.calculateStaticSlices = exports.Slice = void 0;
 const util_1 = require("@jbrowse/core/util");
 const viewportVisibleRegion_1 = require("./viewportVisibleRegion");
 class Slice {
-    constructor(view, region, currentRadianOffset, radianWidth) {
+    constructor(view, region, offsetRadians, radianWidth) {
         this.region = region;
+        this.offsetRadians = offsetRadians;
         this.radianWidth = radianWidth;
         const { bpPerRadian } = view;
-        this.key = (0, util_1.assembleLocString)(region);
-        this.offsetRadians = currentRadianOffset;
+        this.key =
+            'regions' in region
+                ? JSON.stringify(region.regions)
+                : (0, util_1.assembleLocString)(region);
         this.bpPerRadian = bpPerRadian;
         this.flipped = false;
-        this.startRadians = this.offsetRadians;
-        this.endRadians = region.widthBp / this.bpPerRadian + this.offsetRadians;
+        this.startRadians = offsetRadians;
+        this.endRadians = region.widthBp / this.bpPerRadian + offsetRadians;
         Object.freeze(this);
     }
     bpToXY(bp, radiusPx) {
@@ -35,12 +38,12 @@ class Slice {
     }
 }
 exports.Slice = Slice;
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
 function calculateStaticSlices(self) {
     const slices = [];
     let currentRadianOffset = 0;
+    const { bpPerRadian, spacingPx, pxPerRadian } = self;
     for (const region of self.elidedRegions) {
-        const radianWidth = region.widthBp / self.bpPerRadian + self.spacingPx / self.pxPerRadian;
+        const radianWidth = region.widthBp / bpPerRadian + spacingPx / pxPerRadian;
         slices.push(new Slice(self, region, currentRadianOffset, radianWidth));
         currentRadianOffset += radianWidth;
     }

package/dist/CircularView/models/slices.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/CircularView/models/viewportVisibleRegion.js CHANGED Viewed

@@ -10,8 +10,7 @@ function findCircleIntersectionX(y, cx, cy, r, resultArray) {
         resultArray.push([cx, y]);
     }
     const solution = Math.sqrt(r * r - d * d);
-    resultArray.push([cx - solution, y]);
-    resultArray.push([cx + solution, y]);
+    resultArray.push([cx - solution, y], [cx + solution, y]);
 }
 function findCircleIntersectionY(x, cx, cy, r, resultArray) {
     const d = Math.abs(x - cx);
@@ -22,8 +21,7 @@ function findCircleIntersectionY(x, cx, cy, r, resultArray) {
         resultArray.push([x, cy]);
     }
     const solution = Math.sqrt(r * r - d * d);
-    resultArray.push([x, cy - solution]);
-    resultArray.push([x, cy + solution]);
+    resultArray.push([x, cy - solution], [x, cy + solution]);
 }
 function cartesianToTheta(x, y) {
     let theta = (Math.atan(y / x) + 2 * Math.PI) % (2 * Math.PI);

package/dist/CircularView/models/viewportVisibleRegion.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ 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package/dist/CircularView/svgcomponents/SVGBackground.d.ts ADDED Viewed

@@ -0,0 +1,6 @@
+/// <reference types="react" />
+export default function SVGBackground({ width, height, shift, }: {
+    width: number;
+    height: number;
+    shift: number;
+}): JSX.Element;

package/dist/CircularView/svgcomponents/SVGBackground.js ADDED Viewed

@@ -0,0 +1,13 @@
+"use strict";
+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 material_1 = require("@mui/material");
+function SVGBackground({ width, height, shift, }) {
+    const theme = (0, material_1.useTheme)();
+    return (react_1.default.createElement("rect", { width: width + shift * 2, height: height, fill: theme.palette.background.default }));
+}
+exports.default = SVGBackground;
+//# sourceMappingURL=SVGBackground.js.map

package/dist/CircularView/svgcomponents/SVGBackground.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"SVGBackground.js","sourceRoot":"","sources":["../../../src/CircularView/svgcomponents/SVGBackground.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,4CAAwC;AAExC,SAAwB,aAAa,CAAC,EACpC,KAAK,EACL,MAAM,EACN,KAAK,GAKN;IACC,MAAM,KAAK,GAAG,IAAA,mBAAQ,GAAE,CAAA;IACxB,OAAO,CACL,wCACE,KAAK,EAAE,KAAK,GAAG,KAAK,GAAG,CAAC,EACxB,MAAM,EAAE,MAAM,EACd,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,OAAO,GACtC,CACH,CAAA;AACH,CAAC;AAjBD,gCAiBC"}

package/dist/CircularView/svgcomponents/SVGCircularView.d.ts ADDED Viewed

@@ -0,0 +1,4 @@
+import { ExportSvgOptions, CircularViewModel } from '../models/CircularView';
+type CGV = CircularViewModel;
+export declare function renderToSvg(model: CGV, opts: ExportSvgOptions): Promise<string>;
+export {};