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

@jbrowse/plugin-linear-genome-view 2.3.4 → 2.4.1

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Files changed (271) hide show

package/esm/LinearGenomeView/components/util.js.map CHANGED Viewed

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package/esm/LinearGenomeView/index.js CHANGED Viewed

@@ -2,12 +2,14 @@ import { lazy } from 'react';
 import { ViewType } from '@jbrowse/core/pluggableElementTypes';
 import { stateModelFactory } from './model';
 export default (pluginManager) => {
-    pluginManager.addViewType(() => new ViewType({
-        name: 'LinearGenomeView',
-        displayName: 'Linear genome view',
-        stateModel: stateModelFactory(pluginManager),
-        ReactComponent: lazy(() => import('./components/LinearGenomeView')),
-    }));
+    pluginManager.addViewType(() => {
+        return new ViewType({
+            name: 'LinearGenomeView',
+            displayName: 'Linear genome view',
+            stateModel: stateModelFactory(pluginManager),
+            ReactComponent: lazy(() => import('./components/LinearGenomeView')),
+        });
+    });
 };
 export * from './model';
 //# sourceMappingURL=index.js.map

package/esm/LinearGenomeView/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/LinearGenomeView/model.d.ts CHANGED Viewed

@@ -5,11 +5,6 @@ import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
 import { BlockSet, BaseBlock } from '@jbrowse/core/util/blockTypes';
 import { Instance } from 'mobx-state-tree';
 import PluginManager from '@jbrowse/core/PluginManager';
-import { renderToSvg } from './components/LinearGenomeViewSvg';
-import RefNameAutocomplete from './components/RefNameAutocomplete';
-import SearchBox from './components/SearchBox';
-import ZoomControls from './components/ZoomControls';
-import LinearGenomeView from './components/LinearGenomeView';
 export interface BpOffset {
     refName?: string;
     index: number;
@@ -25,6 +20,14 @@ export interface ExportSvgOptions {
     rasterizeLayers?: boolean;
     filename?: string;
     Wrapper?: React.FC<any>;
+    fontSize?: number;
+    rulerHeight?: number;
+    textHeight?: number;
+    paddingHeight?: number;
+    headerHeight?: number;
+    cytobandHeight?: number;
+    trackLabels?: string;
+    themeName?: string;
 }
 export interface NavLocation {
     refName: string;
@@ -148,15 +151,15 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #getter
      */
-    readonly trackHeights: any;
+    readonly trackHeights: number;
     /**
      * #getter
      */
-    readonly trackHeightsWithResizeHandles: any;
+    readonly trackHeightsWithResizeHandles: number;
     /**
      * #getter
      */
-    readonly height: any;
+    readonly height: number;
     /**
      * #getter
      */
@@ -250,7 +253,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #action
      */
-    zoomTo(bpPerPx: number): number;
+    zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
     /**
      * #action
      * sets offsets used in the get sequence dialog
@@ -366,7 +369,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      */
     clearView(): void;
     /**
-     * #action
+     * #method
      * creates an svg export and save using FileSaver
      */
     exportSvg(opts?: ExportSvgOptions): Promise<void>;
@@ -529,7 +532,10 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         reversed: boolean;
     } | undefined;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export { renderToSvg, RefNameAutocomplete, SearchBox, ZoomControls, LinearGenomeView, };
 export type LinearGenomeViewStateModel = ReturnType<typeof stateModelFactory>;
 export type LinearGenomeViewModel = Instance<LinearGenomeViewStateModel>;
-export { default as ReactComponent } from './components/LinearGenomeView';
+export { default as ReactComponent, default as LinearGenomeView, } from './components/LinearGenomeView';
+export { default as RefNameAutocomplete } from './components/RefNameAutocomplete';
+export { default as SearchBox } from './components/SearchBox';
+export { default as ZoomControls } from './components/ZoomControls';
+export { renderToSvg } from './svgcomponents/SVGLinearGenomeView';

package/esm/LinearGenomeView/model.js CHANGED Viewed

@@ -3,7 +3,7 @@ import { getConf } from '@jbrowse/core/configuration';
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models';
 import { ElementId, Region as MUIRegion } from '@jbrowse/core/util/types/mst';
 import { ReturnToImportFormDialog } from '@jbrowse/core/ui';
-import { assembleLocString, clamp, findLastIndex, getContainingView, getSession, isViewContainer, isSessionModelWithWidgets, isSessionWithAddTracks, localStorageGetItem, measureText, parseLocString, springAnimate, } from '@jbrowse/core/util';
+import { assembleLocString, clamp, findLastIndex, getContainingView, getSession, isViewContainer, isSessionModelWithWidgets, isSessionWithAddTracks, localStorageGetItem, measureText, parseLocString, springAnimate, sum, } from '@jbrowse/core/util';
 import calculateDynamicBlocks from '@jbrowse/core/util/calculateDynamicBlocks';
 import calculateStaticBlocks from '@jbrowse/core/util/calculateStaticBlocks';
 import { getParentRenderProps } from '@jbrowse/core/util/tracks';
@@ -23,14 +23,10 @@ import PhotoCameraIcon from '@mui/icons-material/PhotoCamera';
 import ZoomInIcon from '@mui/icons-material/ZoomIn';
 import MenuOpenIcon from '@mui/icons-material/MenuOpen';
 // locals
-import { renderToSvg } from './components/LinearGenomeViewSvg';
-import RefNameAutocomplete from './components/RefNameAutocomplete';
-import SearchBox from './components/SearchBox';
+import { renderToSvg } from './svgcomponents/SVGLinearGenomeView';
 import ExportSvgDlg from './components/ExportSvgDialog';
 import MiniControls from './components/MiniControls';
 import Header from './components/Header';
-import ZoomControls from './components/ZoomControls';
-import LinearGenomeView from './components/LinearGenomeView';
 // lazies
 const SequenceSearchDialog = lazy(() => import('./components/SequenceSearchDialog'));
 function calculateVisibleLocStrings(contentBlocks) {
@@ -249,9 +245,7 @@ export function stateModelFactory(pluginManager) {
          * #getter
          */
         get trackHeights() {
-            return self.tracks
-                .map(t => t.displays[0].height)
-                .reduce((a, b) => a + b, 0);
+            return sum(self.tracks.map(t => t.displays[0].height));
         },
         /**
          * #getter
@@ -344,12 +338,12 @@ export function stateModelFactory(pluginManager) {
          */
         rankSearchResults(results) {
             // order of rank
-            const openTrackIds = self.tracks.map(track => track.configuration.trackId);
-            results.forEach(result => {
-                if (openTrackIds.includes(result.trackId)) {
+            const openTrackIds = new Set(self.tracks.map(track => track.configuration.trackId));
+            for (const result of results) {
+                if (openTrackIds.has(result.trackId)) {
                     result.updateScore(result.getScore() + 1);
                 }
-            });
+            }
             return results;
         },
         /**
@@ -444,21 +438,21 @@ export function stateModelFactory(pluginManager) {
         /**
          * #action
          */
-        zoomTo(bpPerPx) {
+        zoomTo(bpPerPx, offset = self.width / 2, centerAtOffset = false) {
             const newBpPerPx = clamp(bpPerPx, self.minBpPerPx, self.maxBpPerPx);
             if (newBpPerPx === self.bpPerPx) {
                 return newBpPerPx;
             }
             const oldBpPerPx = self.bpPerPx;
-            self.bpPerPx = newBpPerPx;
             if (Math.abs(oldBpPerPx - newBpPerPx) < 0.000001) {
                 console.warn('zoomTo bpPerPx rounding error');
                 return oldBpPerPx;
             }
-            // tweak the offset so that the center of the view remains at the same coordinate
-            const viewWidth = self.width;
-            this.scrollTo(Math.round(((self.offsetPx + viewWidth / 2) * oldBpPerPx) / newBpPerPx -
-                viewWidth / 2));
+            self.bpPerPx = newBpPerPx;
+            // tweak the offset so that the center of the view remains at the same
+            // coordinate
+            this.scrollTo(Math.round(((self.offsetPx + offset) * oldBpPerPx) / newBpPerPx -
+                (centerAtOffset ? self.width / 2 : offset)));
             return newBpPerPx;
         },
         /**
@@ -493,8 +487,7 @@ export function stateModelFactory(pluginManager) {
          * #action
          */
         horizontallyFlip() {
-            self.displayedRegions = cast(self.displayedRegions
-                .slice()
+            self.displayedRegions = cast([...self.displayedRegions]
                 .reverse()
                 .map(region => ({ ...region, reversed: !region.reversed })));
             this.scrollTo(self.totalBp / self.bpPerPx - self.offsetPx - self.width);
@@ -513,8 +506,8 @@ export 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));
             if (!displayConf) {
                 throw new Error(`Could not find a compatible display for view type ${self.type}`);
             }
@@ -730,7 +723,7 @@ export function stateModelFactory(pluginManager) {
             self.zoomTo(10);
         },
         /**
-         * #action
+         * #method
          * creates an svg export and save using FileSaver
          */
         async exportSvg(opts = {}) {
@@ -1129,7 +1122,7 @@ export function stateModelFactory(pluginManager) {
             }
             else {
                 self.setDisplayedRegions(
-                // @ts-ignore
+                // @ts-expect-error
                 locations.map(r => (r.start === undefined ? r.parentRegion : r)));
                 self.showAllRegions();
             }
@@ -1307,12 +1300,15 @@ export function stateModelFactory(pluginManager) {
          * #getter
          */
         get centerLineInfo() {
-            return self.displayedRegions.length
+            return self.displayedRegions.length > 0
                 ? this.pxToBp(self.width / 2)
                 : undefined;
         },
     }));
 }
-export { renderToSvg, RefNameAutocomplete, SearchBox, ZoomControls, LinearGenomeView, };
-export { default as ReactComponent } from './components/LinearGenomeView';
+export { default as ReactComponent, default as LinearGenomeView, } from './components/LinearGenomeView';
+export { default as RefNameAutocomplete } from './components/RefNameAutocomplete';
+export { default as SearchBox } from './components/SearchBox';
+export { default as ZoomControls } from './components/ZoomControls';
+export { renderToSvg } from './svgcomponents/SVGLinearGenomeView';
 //# sourceMappingURL=model.js.map

package/esm/LinearGenomeView/model.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/LinearGenomeView/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/esm/LinearGenomeView/svgcomponents/SVGBackground.js ADDED Viewed

@@ -0,0 +1,7 @@
+import React from 'react';
+import { useTheme } from '@mui/material';
+export default function SVGBackground({ width, height, shift, }) {
+    const theme = useTheme();
+    return (React.createElement("rect", { width: width + shift * 2, height: height, fill: theme.palette.background.default }));
+}
+//# sourceMappingURL=SVGBackground.js.map

package/esm/LinearGenomeView/svgcomponents/SVGBackground.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"SVGBackground.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/svgcomponents/SVGBackground.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAExC,MAAM,CAAC,OAAO,UAAU,aAAa,CAAC,EACpC,KAAK,EACL,MAAM,EACN,KAAK,GAKN;IACC,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,OAAO,CACL,8BACE,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"}

package/esm/LinearGenomeView/svgcomponents/SVGHeader.d.ts ADDED Viewed

@@ -0,0 +1,10 @@
+/// <reference types="react" />
+import { LinearGenomeViewModel } from '..';
+type LGV = LinearGenomeViewModel;
+export default function SVGHeader({ model, fontSize, cytobandHeight, rulerHeight, }: {
+    model: LGV;
+    rulerHeight: number;
+    fontSize: number;
+    cytobandHeight: number;
+}): JSX.Element;
+export {};

package/esm/LinearGenomeView/svgcomponents/SVGHeader.js ADDED Viewed

@@ -0,0 +1,49 @@
+import React from 'react';
+import { getSession } from '@jbrowse/core/util';
+import Base1DView from '@jbrowse/core/util/Base1DViewModel';
+import { useTheme } from '@mui/material';
+// locals
+import { HEADER_OVERVIEW_HEIGHT } from '..';
+import Cytobands from '../components/Cytobands';
+import { Polygon } from '../components/OverviewScalebar';
+import SVGRuler from './SVGRuler';
+import SVGScalebar from './SVGScalebar';
+export default function SVGHeader({ model, fontSize, cytobandHeight, rulerHeight, }) {
+    const { width, assemblyNames, showCytobands, displayedRegions } = model;
+    const { assemblyManager } = getSession(model);
+    const assemblyName = assemblyNames.length > 1 ? '' : assemblyNames[0];
+    const assembly = assemblyManager.get(assemblyName);
+    const theme = useTheme();
+    const overview = Base1DView.create({
+        displayedRegions: JSON.parse(JSON.stringify(displayedRegions)),
+        interRegionPaddingWidth: 0,
+        minimumBlockWidth: model.minimumBlockWidth,
+    });
+    const visibleRegions = model.dynamicBlocks.contentBlocks;
+    overview.setVolatileWidth(width);
+    overview.showAllRegions();
+    const block = overview.dynamicBlocks.contentBlocks[0];
+    const first = visibleRegions[0];
+    const firstOverviewPx = overview.bpToPx({
+        ...first,
+        coord: first.reversed ? first.end : first.start,
+    }) || 0;
+    const last = visibleRegions[visibleRegions.length - 1];
+    const lastOverviewPx = overview.bpToPx({
+        ...last,
+        coord: last.reversed ? last.start : last.end,
+    }) || 0;
+    const c = +showCytobands * cytobandHeight;
+    return (React.createElement("g", { id: "header" },
+        React.createElement("text", { x: 0, y: fontSize, fontSize: fontSize, fill: theme.palette.text.primary }, assemblyName),
+        showCytobands ? (React.createElement("g", { transform: `translate(0 ${rulerHeight})` },
+            React.createElement(Cytobands, { overview: overview, assembly: assembly, block: block }),
+            React.createElement("rect", { stroke: "red", fill: "rgb(255,0,0,0.1)", width: Math.max(lastOverviewPx - firstOverviewPx, 0.5), height: HEADER_OVERVIEW_HEIGHT - 1, x: firstOverviewPx, y: 0.5 }),
+            React.createElement("g", { transform: `translate(0,${HEADER_OVERVIEW_HEIGHT})` },
+                React.createElement(Polygon, { overview: overview, model: model, useOffset: false })))) : null,
+        React.createElement("g", { transform: `translate(0 ${fontSize + c})` },
+            React.createElement(SVGScalebar, { model: model, fontSize: fontSize })),
+        React.createElement("g", { transform: `translate(0 ${rulerHeight + c})` },
+            React.createElement(SVGRuler, { model: model, fontSize: fontSize }))));
+}
+//# sourceMappingURL=SVGHeader.js.map

package/esm/LinearGenomeView/svgcomponents/SVGHeader.js.map ADDED Viewed

@@ -0,0 +1 @@

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package/esm/LinearGenomeView/svgcomponents/SVGLinearGenomeView.d.ts ADDED Viewed

@@ -0,0 +1,12 @@
+import { LinearGenomeViewModel, ExportSvgOptions } from '..';
+type LGV = LinearGenomeViewModel;
+interface Display {
+    height: number;
+}
+interface Track {
+    displays: Display[];
+}
+export declare function totalHeight(tracks: Track[], textHeight: number, trackLabels: string): number;
+export declare function renderToSvg(model: LGV, opts: ExportSvgOptions): Promise<string>;
+export { default as SVGRuler } from './SVGRuler';
+export { default as SVGTracks } from './SVGTracks';

package/esm/LinearGenomeView/svgcomponents/SVGLinearGenomeView.js ADDED Viewed

@@ -0,0 +1,47 @@
+import React from 'react';
+import { renderToStaticMarkup } from 'react-dom/server';
+import { when } from 'mobx';
+import { getSession, max, measureText, sum } from '@jbrowse/core/util';
+import { ThemeProvider } from '@mui/material';
+import { createJBrowseTheme } from '@jbrowse/core/ui';
+import SVGBackground from './SVGBackground';
+import SVGTracks from './SVGTracks';
+import SVGHeader from './SVGHeader';
+import { getTrackName } from '@jbrowse/core/util/tracks';
+export function totalHeight(tracks, textHeight, trackLabels) {
+    return sum(tracks.map(t => t.displays[0].height +
+        (['none', 'left'].includes(trackLabels) ? 0 : textHeight)));
+}
+// render LGV to SVG
+export async function renderToSvg(model, opts) {
+    var _a;
+    await when(() => model.initialized);
+    const { textHeight = 18, headerHeight = 40, rulerHeight = 50, fontSize = 13, cytobandHeight = 100, trackLabels = 'offset', themeName = 'default', Wrapper = ({ children }) => React.createElement(React.Fragment, null, children), } = opts;
+    const session = getSession(model);
+    const theme = (_a = session.allThemes) === null || _a === void 0 ? void 0 : _a.call(session)[themeName];
+    const { width, tracks, showCytobands } = model;
+    const shift = 50;
+    const c = +showCytobands * cytobandHeight;
+    const offset = headerHeight + rulerHeight + c + 10;
+    const height = totalHeight(tracks, textHeight, trackLabels) + offset + 100;
+    const displayResults = await Promise.all(tracks.map(async (track) => {
+        const display = track.displays[0];
+        await when(() => (display.ready !== undefined ? display.ready : true));
+        return { track, result: await display.renderSvg({ ...opts, theme }) };
+    }));
+    const trackLabelMaxLen = max(tracks.map(t => measureText(getTrackName(t.configuration, session), fontSize)), 0) + 40;
+    const trackLabelOffset = trackLabels === 'left' ? trackLabelMaxLen : 0;
+    const w = width + trackLabelOffset;
+    // the xlink namespace is used for rendering <image> tag
+    return renderToStaticMarkup(React.createElement(ThemeProvider, { theme: createJBrowseTheme(theme) },
+        React.createElement(Wrapper, null,
+            React.createElement("svg", { width: w, height: height, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, w + shift * 2, height].toString() },
+                React.createElement(SVGBackground, { width: w, height: height, shift: shift }),
+                React.createElement("g", { transform: `translate(${shift} 0)` },
+                    React.createElement("g", { transform: `translate(${trackLabelOffset})` },
+                        React.createElement(SVGHeader, { model: model, fontSize: fontSize, rulerHeight: rulerHeight, cytobandHeight: cytobandHeight })),
+                    React.createElement(SVGTracks, { textHeight: textHeight, fontSize: fontSize, model: model, displayResults: displayResults, offset: offset, trackLabels: trackLabels, trackLabelOffset: trackLabelOffset }))))));
+}
+export { default as SVGRuler } from './SVGRuler';
+export { default as SVGTracks } from './SVGTracks';
+//# sourceMappingURL=SVGLinearGenomeView.js.map

package/esm/LinearGenomeView/svgcomponents/SVGLinearGenomeView.js.map ADDED Viewed

@@ -0,0 +1 @@

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package/esm/LinearGenomeView/svgcomponents/SVGRegionSeparators.d.ts ADDED Viewed

@@ -0,0 +1,8 @@
+/// <reference types="react" />
+import { LinearGenomeViewModel } from '..';
+type LGV = LinearGenomeViewModel;
+export default function SVGRegionSeparators({ model, height, }: {
+    height: number;
+    model: LGV;
+}): JSX.Element;
+export {};

package/esm/LinearGenomeView/svgcomponents/SVGRegionSeparators.js ADDED Viewed

@@ -0,0 +1,7 @@
+import React from 'react';
+// SVG component, region separator
+export default function SVGRegionSeparators({ model, height, }) {
+    const { dynamicBlocks, offsetPx, interRegionPaddingWidth } = model;
+    return (React.createElement(React.Fragment, null, dynamicBlocks.contentBlocks.slice(1).map(block => (React.createElement("rect", { key: block.key, x: block.offsetPx - offsetPx - interRegionPaddingWidth, width: interRegionPaddingWidth, y: 0, height: height, fill: "grey" })))));
+}
+//# sourceMappingURL=SVGRegionSeparators.js.map

package/esm/LinearGenomeView/svgcomponents/SVGRegionSeparators.js.map ADDED Viewed

@@ -0,0 +1 @@

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package/esm/LinearGenomeView/svgcomponents/SVGRuler.d.ts ADDED Viewed

@@ -0,0 +1,8 @@
+/// <reference types="react" />
+import { LinearGenomeViewModel } from '..';
+type LGV = LinearGenomeViewModel;
+export default function SVGRuler({ model, fontSize, }: {
+    model: LGV;
+    fontSize: number;
+}): JSX.Element;
+export {};