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

package/src/LinearGenomeView/svgcomponents/SVGRuler.tsx

@@ -0,0 +1,125 @@
+import React from 'react'
+import { getTickDisplayStr } from '@jbrowse/core/util'
+import { useTheme } from '@mui/material'
+
+// locals
+import { makeTicks } from '../util'
+
+import { LinearGenomeViewModel } from '..'
+import SVGRegionSeparators from './SVGRegionSeparators'
+
+type LGV = LinearGenomeViewModel
+
+function Ruler({
+  start,
+  end,
+  bpPerPx,
+  reversed = false,
+  major = true,
+  minor = true,
+  hideText = false,
+}: {
+  start: number
+  end: number
+  bpPerPx: number
+  reversed?: boolean
+  major?: boolean
+  minor?: boolean
+  hideText?: boolean
+}) {
+  const ticks = makeTicks(start, end, bpPerPx, major, minor)
+  const theme = useTheme()
+  return (
+    <>
+      {ticks.map(tick => {
+        const x = (reversed ? end - tick.base : tick.base - start) / bpPerPx
+        return (
+          <line
+            key={tick.base}
+            x1={x}
+            x2={x}
+            y1={0}
+            y2={tick.type === 'major' ? 6 : 4}
+            strokeWidth={1}
+            stroke={theme.palette.text.secondary}
+          />
+        )
+      })}
+      {!hideText
+        ? ticks
+            .filter(tick => tick.type === 'major')
+            .map(tick => {
+              const x =
+                (reversed ? end - tick.base : tick.base - start) / bpPerPx
+              return (
+                <text
+                  x={x - 3}
+                  y={7 + 11}
+                  key={`label-${tick.base}`}
+                  fontSize={11}
+                  fill={theme.palette.text.primary}
+                >
+                  {getTickDisplayStr(tick.base + 1, bpPerPx)}
+                </text>
+              )
+            })
+        : null}
+    </>
+  )
+}
+
+export default function SVGRuler({
+  model,
+  fontSize,
+}: {
+  model: LGV
+  fontSize: number
+}) {
+  const {
+    dynamicBlocks: { contentBlocks },
+    offsetPx: viewOffsetPx,
+    bpPerPx,
+  } = model
+  const renderRuler = contentBlocks.length < 5
+  const theme = useTheme()
+  return (
+    <>
+      <SVGRegionSeparators model={model} height={30} />
+      {contentBlocks.map(block => {
+        const { start, end, key, reversed, offsetPx, refName, widthPx } = block
+        const offset = offsetPx - viewOffsetPx
+        const clipid = `clip-${key}`
+        return (
+          <g key={key}>
+            <defs>
+              <clipPath id={clipid}>
+                <rect x={0} y={0} width={widthPx} height={100} />
+              </clipPath>
+            </defs>
+            <g transform={`translate(${offset} 0)`}>
+              <g clipPath={`url(#${clipid})`}>
+                <text
+                  x={4}
+                  y={fontSize}
+                  fontSize={fontSize}
+                  fill={theme.palette.text.primary}
+                >
+                  {refName}
+                </text>
+                <g transform="translate(0 20)">
+                  <Ruler
+                    hideText={!renderRuler}
+                    start={start}
+                    end={end}
+                    bpPerPx={bpPerPx}
+                    reversed={reversed}
+                  />
+                </g>
+              </g>
+            </g>
+          </g>
+        )
+      })}
+    </>
+  )
+}

package/src/LinearGenomeView/svgcomponents/SVGScalebar.tsx

@@ -0,0 +1,57 @@
+import React from 'react'
+import { getBpDisplayStr } from '@jbrowse/core/util'
+import { useTheme } from '@mui/material'
+import { LinearGenomeViewModel } from '..'
+
+type LGV = LinearGenomeViewModel
+
+export default function SVGScalebar({
+  model,
+  fontSize,
+}: {
+  model: LGV
+  fontSize: number
+}) {
+  const {
+    offsetPx,
+    dynamicBlocks: { totalWidthPxWithoutBorders: totalWidthPx, totalBp },
+  } = model
+  const theme = useTheme()
+  const displayBp = getBpDisplayStr(totalBp)
+  const x0 = Math.max(-offsetPx, 0)
+  const x1 = x0 + totalWidthPx
+  return (
+    <>
+      <line
+        x1={x0}
+        x2={x1}
+        y1={10}
+        y2={10}
+        stroke={theme.palette.text.secondary}
+      />
+      <line
+        x1={x0}
+        x2={x0}
+        y1={5}
+        y2={15}
+        stroke={theme.palette.text.secondary}
+      />
+      <line
+        x1={x1}
+        x2={x1}
+        y1={5}
+        y2={15}
+        stroke={theme.palette.text.secondary}
+      />
+      <text
+        x={x0 + (x1 - x0) / 2}
+        y={fontSize * 2}
+        textAnchor="middle"
+        fontSize={fontSize}
+        fill={theme.palette.text.primary}
+      >
+        {displayBp}
+      </text>
+    </>
+  )
+}

package/src/LinearGenomeView/svgcomponents/SVGTrackLabel.tsx

@@ -0,0 +1,47 @@
+import React from 'react'
+import { useTheme } from '@mui/material'
+
+export default function SVGTrackLabel({
+  trackLabels,
+  trackName,
+  fontSize,
+  trackLabelOffset,
+  x,
+}: {
+  trackName: string
+  trackLabels: string
+  fontSize: number
+  trackLabelOffset: number
+  x: number
+}) {
+  const theme = useTheme()
+  const fill = theme.palette.text.primary
+  const xoff = trackLabels === 'overlay' ? 5 : 0
+  const yoff = trackLabels === 'offset' ? 5 : 0
+  return trackLabels !== 'none' ? (
+    <g>
+      {trackLabels === 'left' ? (
+        <text
+          x={trackLabelOffset - 40}
+          y={20}
+          fill={fill}
+          fontSize={fontSize}
+          dominantBaseline="hanging"
+          textAnchor="end"
+        >
+          {trackName}
+        </text>
+      ) : (
+        <text
+          x={x + xoff}
+          y={yoff}
+          fill={fill}
+          fontSize={fontSize}
+          dominantBaseline="hanging"
+        >
+          {trackName}
+        </text>
+      )}
+    </g>
+  ) : null
+}

package/src/LinearGenomeView/svgcomponents/SVGTracks.tsx

@@ -0,0 +1,67 @@
+import React from 'react'
+import { AnyConfigurationModel } from '@jbrowse/core/configuration'
+import { getTrackName } from '@jbrowse/core/util/tracks'
+import { getSession } from '@jbrowse/core/util'
+// locals
+import { LinearGenomeViewModel } from '..'
+import SVGRegionSeparators from './SVGRegionSeparators'
+import SVGTrackLabel from './SVGTrackLabel'
+
+type LGV = LinearGenomeViewModel
+
+interface DisplayResult {
+  track: {
+    configuration: AnyConfigurationModel
+    displays: { height: number }[]
+  }
+  result: string
+}
+
+// SVG component, tracks
+export default function SVGTracks({
+  displayResults,
+  model,
+  offset,
+  textHeight,
+  fontSize,
+  trackLabels = 'offset',
+  trackLabelOffset = 0,
+}: {
+  displayResults: DisplayResult[]
+  model: LGV
+  offset: number
+  textHeight: number
+  fontSize: number
+  trackLabels?: string
+  trackLabelOffset?: number
+}) {
+  const session = getSession(model)
+  const textOffset = trackLabels === 'offset' ? textHeight : 0
+  return (
+    <>
+      {displayResults.map(({ track, result }) => {
+        const current = offset
+        const conf = track.configuration
+        const trackName = getTrackName(conf, session)
+        const display = track.displays[0]
+        const x = Math.max(-model.offsetPx, 0)
+        offset += display.height + textOffset
+        return (
+          <g key={conf.trackId} transform={`translate(0 ${current})`}>
+            <g transform={`translate(${trackLabelOffset} ${textOffset})`}>
+              <SVGRegionSeparators model={model} height={display.height} />
+              {result}
+            </g>
+            <SVGTrackLabel
+              trackName={trackName}
+              fontSize={fontSize}
+              trackLabels={trackLabels}
+              trackLabelOffset={trackLabelOffset}
+              x={x}
+            />
+          </g>
+        )
+      })}
+    </>
+  )
+}

package/src/LinearGenomeView/util.test.ts

@@ -16,15 +16,18 @@ describe('tick calculation', () => {
       { type: 'minor', base: 8, index: 9 },
       { type: 'major', base: 9, index: 10 },
       { type: 'minor', base: 10, index: 11 },
+      { type: 'minor', base: 11, index: 12 },
     ])
   })
   test('two', () => {
     const result = Array.from(makeTicks(0, 50, 1))
     expect(result).toEqual([
-      { type: 'major', base: -1, index: 0 },
-      { type: 'minor', base: 19, index: 1 },
-      { type: 'minor', base: 39, index: 2 },
-      { type: 'minor', base: 59, index: 3 },
+      { type: 'minor', base: -21, index: 0 },
+      { type: 'major', base: -1, index: 1 },
+      { type: 'minor', base: 19, index: 2 },
+      { type: 'minor', base: 39, index: 3 },
+      { type: 'minor', base: 59, index: 4 },
+      { type: 'minor', base: 79, index: 5 },
     ])
   })
 })

package/src/LinearGenomeView/util.ts

@@ -10,7 +10,7 @@ export function chooseGridPitch(
 ) {
   scale = Math.abs(scale)
   const minMajorPitchBp = minMajorPitchPx * scale
-  const majorMagnitude = parseInt(
+  const majorMagnitude = Number.parseInt(
     Number(minMajorPitchBp).toExponential().split(/e/i)[1],
     10,
   )
@@ -68,8 +68,8 @@ export function makeTicks(
   let index = 0
   const ticks = []
   for (
-    let base = Math.ceil(minBase / iterPitch) * iterPitch;
-    base < maxBase;
+    let base = Math.floor(minBase / iterPitch) * iterPitch;
+    base < Math.ceil(maxBase / iterPitch) * iterPitch + 1;
     base += iterPitch
   ) {
     if (emitMinor && base % (gridPitch.majorPitch * 2)) {

package/src/index.ts

@@ -9,26 +9,16 @@ import LineStyleIcon from '@mui/icons-material/LineStyle'
 import {
   BaseLinearDisplay,
   BaseLinearDisplayComponent,
-  BlockModel,
-  BlockMsg,
   baseLinearDisplayConfigSchema,
 } from './BaseLinearDisplay'
-import LinearBareDisplayF, {
-  configSchemaFactory as linearBareDisplayConfigSchemaFactory,
-} from './LinearBareDisplay'
+import LinearBareDisplayF from './LinearBareDisplay'
 import LinearGenomeViewF, {
-  renderToSvg,
-  LinearGenomeViewModel,
-  LinearGenomeViewStateModel,
-  RefNameAutocomplete,
   SearchBox,
   ZoomControls,
   LinearGenomeView,
 } from './LinearGenomeView'
-import LinearBasicDisplayF, {
-  configSchema as linearBasicDisplayConfigSchemaFactory,
-  modelFactory as linearBasicDisplayModelFactory,
-} from './LinearBasicDisplay'
+
+import LinearBasicDisplayF from './LinearBasicDisplay'
 
 import FeatureTrackF from './FeatureTrack'
 import BasicTrackF from './BasicTrack'
@@ -68,19 +58,28 @@ export default class LinearGenomeViewPlugin extends Plugin {
   }
 }
 
+export type { BaseLinearDisplayModel, BlockModel } from './BaseLinearDisplay'
+
+export { configSchemaFactory as linearBareDisplayConfigSchemaFactory } from './LinearBareDisplay'
 export {
+  BlockMsg,
   baseLinearDisplayConfigSchema,
-  linearBareDisplayConfigSchemaFactory,
-  linearBasicDisplayConfigSchemaFactory,
-  linearBasicDisplayModelFactory,
-  renderToSvg,
   BaseLinearDisplayComponent,
   BaseLinearDisplay,
+} from './BaseLinearDisplay'
+export {
+  type LinearGenomeViewModel,
   RefNameAutocomplete,
+  type LinearGenomeViewStateModel,
   SearchBox,
-  BlockMsg,
-}
-
-export type { LinearGenomeViewModel, LinearGenomeViewStateModel, BlockModel }
-
-export type { BaseLinearDisplayModel } from './BaseLinearDisplay'
+} from './LinearGenomeView'
+export {
+  renderToSvg,
+  SVGTracks,
+  totalHeight,
+  SVGRuler,
+} from './LinearGenomeView/svgcomponents/SVGLinearGenomeView'
+export {
+  configSchema as linearBasicDisplayConfigSchemaFactory,
+  modelFactory as linearBasicDisplayModelFactory,
+} from './LinearBasicDisplay'

package/dist/LinearGenomeView/components/LinearGenomeViewSvg.d.ts

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

package/dist/LinearGenomeView/components/LinearGenomeViewSvg.js

@@ -1,141 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderToSvg = void 0;
-const react_1 = __importDefault(require("react"));
-const server_1 = require("react-dom/server");
-const mobx_1 = require("mobx");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const configuration_1 = require("@jbrowse/core/configuration");
-const util_1 = require("@jbrowse/core/util");
-const Base1DViewModel_1 = __importDefault(require("@jbrowse/core/util/Base1DViewModel"));
-// locals
-const Ruler_1 = __importDefault(require("./Ruler"));
-const __1 = require("..");
-const OverviewScalebar_1 = require("./OverviewScalebar");
-function Scalebar({ model, fontSize }) {
-    const { offsetPx, dynamicBlocks: { totalWidthPxWithoutBorders: totalWidthPx, totalBp }, } = model;
-    const displayBp = (0, util_1.getBpDisplayStr)(totalBp);
-    const x0 = Math.max(-offsetPx, 0);
-    const x1 = x0 + totalWidthPx;
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement("line", { x1: x0, x2: x1, y1: 10, y2: 10, stroke: "black" }),
-        react_1.default.createElement("line", { x1: x0, x2: x0, y1: 5, y2: 15, stroke: "black" }),
-        react_1.default.createElement("line", { x1: x1, x2: x1, y1: 5, y2: 15, stroke: "black" }),
-        react_1.default.createElement("text", { x: x0 + (x1 - x0) / 2, y: fontSize * 2, textAnchor: "middle", fontSize: fontSize }, displayBp)));
-}
-function SVGRuler({ model, fontSize, width, }) {
-    const { dynamicBlocks: { contentBlocks }, offsetPx: viewOffsetPx, bpPerPx, } = model;
-    const renderRuler = contentBlocks.length < 5;
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement("defs", null,
-            react_1.default.createElement("clipPath", { id: "clip-ruler" },
-                react_1.default.createElement("rect", { x: 0, y: 0, width: width, height: 20 }))),
-        contentBlocks.map(block => {
-            const { key, start, end, reversed, offsetPx, refName } = block;
-            const offsetLeft = offsetPx - viewOffsetPx;
-            return (react_1.default.createElement("g", { key: `${key}`, transform: `translate(${offsetLeft} 0)` },
-                react_1.default.createElement("text", { x: offsetLeft / bpPerPx, y: fontSize, fontSize: fontSize }, refName),
-                renderRuler ? (react_1.default.createElement("g", { transform: "translate(0 20)", clipPath: "url(#clip-ruler)" },
-                    react_1.default.createElement(Ruler_1.default, { start: start, end: end, bpPerPx: bpPerPx, reversed: reversed }))) : (react_1.default.createElement("line", { strokeWidth: 1, stroke: "black", x1: start / bpPerPx, x2: end / bpPerPx, y1: 20, y2: 20 }))));
-        })));
-}
-const fontSize = 15;
-const rulerHeight = 50;
-const textHeight = fontSize + 5;
-const paddingHeight = 20;
-const headerHeight = textHeight + 20;
-const cytobandHeightIfExists = 100;
-const totalHeight = (tracks) => {
-    return tracks.reduce((accum, track) => {
-        const display = track.displays[0];
-        return accum + display.height + paddingHeight + textHeight;
-    }, 0);
-};
-// SVG component, ruler and assembly name
-const SVGHeader = ({ model }) => {
-    const { width, assemblyNames, showCytobands, displayedRegions } = model;
-    const { assemblyManager } = (0, util_1.getSession)(model);
-    const assemblyName = assemblyNames.length > 1 ? '' : assemblyNames[0];
-    const assembly = assemblyManager.get(assemblyName);
-    const overview = Base1DViewModel_1.default.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 cytobandHeight = showCytobands ? cytobandHeightIfExists : 0;
-    return (react_1.default.createElement("g", { id: "header" },
-        react_1.default.createElement("text", { x: 0, y: fontSize, fontSize: fontSize }, assemblyName),
-        showCytobands ? (react_1.default.createElement("g", { transform: `translate(0 ${rulerHeight})` },
-            react_1.default.createElement(OverviewScalebar_1.Cytobands, { overview: overview, assembly: assembly, block: block }),
-            react_1.default.createElement("rect", { stroke: "red", fill: "rgb(255,0,0,0.1)", width: Math.max(lastOverviewPx - firstOverviewPx, 0.5), height: __1.HEADER_OVERVIEW_HEIGHT - 1, x: firstOverviewPx, y: 0.5 }),
-            react_1.default.createElement("g", { transform: `translate(0,${__1.HEADER_OVERVIEW_HEIGHT})` },
-                react_1.default.createElement(OverviewScalebar_1.Polygon, { overview: overview, model: model, useOffset: false })))) : null,
-        react_1.default.createElement("g", { transform: `translate(0 ${fontSize + cytobandHeight})` },
-            react_1.default.createElement(Scalebar, { model: model, fontSize: fontSize })),
-        react_1.default.createElement("g", { transform: `translate(0 ${rulerHeight + cytobandHeight})` },
-            react_1.default.createElement(SVGRuler, { model: model, fontSize: fontSize, width: width }))));
-};
-// SVG component, region separator
-const SVGRegionSeparators = ({ model, height, }) => {
-    const { dynamicBlocks, offsetPx, interRegionPaddingWidth } = model;
-    return (react_1.default.createElement(react_1.default.Fragment, null, dynamicBlocks.contentBlocks.slice(1).map(block => (react_1.default.createElement("rect", { key: block.key, x: block.offsetPx - offsetPx - interRegionPaddingWidth, width: interRegionPaddingWidth, y: 0, height: height, stroke: "none", fill: "grey" })))));
-};
-// SVG component, tracks
-function SVGTracks({ displayResults, model, offset, }) {
-    return (react_1.default.createElement(react_1.default.Fragment, null, displayResults.map(({ track, result }) => {
-        const current = offset;
-        const trackName = (0, configuration_1.getConf)(track, 'name') ||
-            `Reference sequence (${(0, configuration_1.readConfObject)((0, mobx_state_tree_1.getParent)(track.configuration), 'displayName') ||
-                (0, configuration_1.readConfObject)((0, mobx_state_tree_1.getParent)(track.configuration), 'name')})`;
-        const display = track.displays[0];
-        offset += display.height + paddingHeight + textHeight;
-        return (react_1.default.createElement("g", { key: track.configuration.trackId, transform: `translate(0 ${current})` },
-            react_1.default.createElement("text", { fontSize: fontSize, x: Math.max(-model.offsetPx, 0) }, trackName),
-            react_1.default.createElement("g", { transform: `translate(0 ${textHeight})` },
-                result,
-                react_1.default.createElement(SVGRegionSeparators, { model: model, height: display.height }))));
-    })));
-}
-// render LGV to SVG
-async function renderToSvg(model, opts) {
-    await (0, mobx_1.when)(() => model.initialized);
-    const { Wrapper = ({ children }) => react_1.default.createElement(react_1.default.Fragment, null, children) } = opts;
-    const { width, tracks, showCytobands } = model;
-    const shift = 50;
-    const offset = headerHeight +
-        rulerHeight +
-        (showCytobands ? cytobandHeightIfExists : 0) +
-        20;
-    const height = totalHeight(tracks) + offset;
-    const displayResults = await Promise.all(tracks.map(async (track) => {
-        const display = track.displays[0];
-        await (0, mobx_1.when)(() => (display.ready !== undefined ? display.ready : true));
-        return { track, result: await display.renderSvg(opts) };
-    }));
-    // the xlink namespace is used for rendering <image> tag
-    return (0, server_1.renderToStaticMarkup)(react_1.default.createElement(Wrapper, null,
-        react_1.default.createElement("svg", { width: width, height: height, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, width + shift * 2, height].toString() },
-            react_1.default.createElement("rect", { width: width + shift * 2, height: height, fill: "white" }),
-            react_1.default.createElement("g", { stroke: "none", transform: `translate(${shift} ${fontSize})` },
-                react_1.default.createElement(SVGHeader, { model: model }),
-                react_1.default.createElement(SVGTracks, { model: model, displayResults: displayResults, offset: offset })))));
-}
-exports.renderToSvg = renderToSvg;
-//# sourceMappingURL=LinearGenomeViewSvg.js.map

package/dist/LinearGenomeView/components/LinearGenomeViewSvg.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"LinearGenomeViewSvg.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/LinearGenomeViewSvg.tsx"],"names":[],"mappings":";;;;;;AAAA,kDAAyB;AACzB,6CAAuD;AACvD,+BAA2B;AAC3B,qDAA2C;AAC3C,+DAAqE;AACrE,6CAAgE;AAEhE,yFAA2D;AAE3D,SAAS;AACT,oDAA2B;AAC3B,0BAIW;AACX,yDAAuD;AAIvD,SAAS,QAAQ,CAAC,EAAE,KAAK,EAAE,QAAQ,EAAoC;IACrE,MAAM,EACJ,QAAQ,EACR,aAAa,EAAE,EAAE,0BAA0B,EAAE,YAAY,EAAE,OAAO,EAAE,GACrE,GAAG,KAAK,CAAA;IACT,MAAM,SAAS,GAAG,IAAA,sBAAe,EAAC,OAAO,CAAC,CAAA;IAC1C,MAAM,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAA;IACjC,MAAM,EAAE,GAAG,EAAE,GAAG,YAAY,CAAA;IAC5B,OAAO,CACL;QACE,wCAAM,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,MAAM,EAAC,OAAO,GAAG;QACvD,wCAAM,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE,MAAM,EAAC,OAAO,GAAG;QACtD,wCAAM,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE,MAAM,EAAC,OAAO,GAAG;QACtD,wCACE,CAAC,EAAE,EAAE,GAAG,CAAC,EAAE,GAAG,EAAE,CAAC,GAAG,CAAC,EACrB,CAAC,EAAE,QAAQ,GAAG,CAAC,EACf,UAAU,EAAC,QAAQ,EACnB,QAAQ,EAAE,QAAQ,IAEjB,SAAS,CACL,CACN,CACJ,CAAA;AACH,CAAC;AAED,SAAS,QAAQ,CAAC,EAChB,KAAK,EACL,QAAQ,EACR,KAAK,GAKN;IACC,MAAM,EACJ,aAAa,EAAE,EAAE,aAAa,EAAE,EAChC,QAAQ,EAAE,YAAY,EACtB,OAAO,GACR,GAAG,KAAK,CAAA;IACT,MAAM,WAAW,GAAG,aAAa,CAAC,MAAM,GAAG,CAAC,CAAA;IAC5C,OAAO,CACL;QACE;YACE,4CAAU,EAAE,EAAC,YAAY;gBACvB,wCAAM,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,EAAE,GAAI,CACrC,CACN;QACN,aAAa,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE;YACzB,MAAM,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,EAAE,QAAQ,EAAE,QAAQ,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;YAC9D,MAAM,UAAU,GAAG,QAAQ,GAAG,YAAY,CAAA;YAC1C,OAAO,CACL,qCAAG,GAAG,EAAE,GAAG,GAAG,EAAE,EAAE,SAAS,EAAE,aAAa,UAAU,KAAK;gBACvD,wCAAM,CAAC,EAAE,UAAU,GAAG,OAAO,EAAE,CAAC,EAAE,QAAQ,EAAE,QAAQ,EAAE,QAAQ,IAC3D,OAAO,CACH;gBACN,WAAW,CAAC,CAAC,CAAC,CACb,qCAAG,SAAS,EAAC,iBAAiB,EAAC,QAAQ,EAAC,kBAAkB;oBACxD,8BAAC,eAAK,IACJ,KAAK,EAAE,KAAK,EACZ,GAAG,EAAE,GAAG,EACR,OAAO,EAAE,OAAO,EAChB,QAAQ,EAAE,QAAQ,GAClB,CACA,CACL,CAAC,CAAC,CAAC,CACF,wCACE,WAAW,EAAE,CAAC,EACd,MAAM,EAAC,OAAO,EACd,EAAE,EAAE,KAAK,GAAG,OAAO,EACnB,EAAE,EAAE,GAAG,GAAG,OAAO,EACjB,EAAE,EAAE,EAAE,EACN,EAAE,EAAE,EAAE,GACN,CACH,CACC,CACL,CAAA;QACH,CAAC,CAAC,CACD,CACJ,CAAA;AACH,CAAC;AAED,MAAM,QAAQ,GAAG,EAAE,CAAA;AACnB,MAAM,WAAW,GAAG,EAAE,CAAA;AACtB,MAAM,UAAU,GAAG,QAAQ,GAAG,CAAC,CAAA;AAC/B,MAAM,aAAa,GAAG,EAAE,CAAA;AACxB,MAAM,YAAY,GAAG,UAAU,GAAG,EAAE,CAAA;AACpC,MAAM,sBAAsB,GAAG,GAAG,CAAA;AASlC,MAAM,WAAW,GAAG,CAAC,MAAe,EAAE,EAAE;IACtC,OAAO,MAAM,CAAC,MAAM,CAAC,CAAC,KAAK,EAAE,KAAK,EAAE,EAAE;QACpC,MAAM,OAAO,GAAG,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;QACjC,OAAO,KAAK,GAAG,OAAO,CAAC,MAAM,GAAG,aAAa,GAAG,UAAU,CAAA;IAC5D,CAAC,EAAE,CAAC,CAAC,CAAA;AACP,CAAC,CAAA;AAED,yCAAyC;AACzC,MAAM,SAAS,GAAG,CAAC,EAAE,KAAK,EAAkB,EAAE,EAAE;IAC9C,MAAM,EAAE,KAAK,EAAE,aAAa,EAAE,aAAa,EAAE,gBAAgB,EAAE,GAAG,KAAK,CAAA;IACvE,MAAM,EAAE,eAAe,EAAE,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;IAC7C,MAAM,YAAY,GAAG,aAAa,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,CAAA;IACrE,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;IAElD,MAAM,QAAQ,GAAG,yBAAU,CAAC,MAAM,CAAC;QACjC,gBAAgB,EAAE,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,gBAAgB,CAAC,CAAC;QAC9D,uBAAuB,EAAE,CAAC;QAC1B,iBAAiB,EAAE,KAAK,CAAC,iBAAiB;KAC3C,CAAC,CAAA;IACF,MAAM,cAAc,GAAG,KAAK,CAAC,aAAa,CAAC,aAAa,CAAA;IAExD,QAAQ,CAAC,gBAAgB,CAAC,KAAK,CAAC,CAAA;IAChC,QAAQ,CAAC,cAAc,EAAE,CAAA;IACzB,MAAM,KAAK,GAAG,QAAQ,CAAC,aAAa,CAAC,aAAa,CAAC,CAAC,CAAC,CAAA;IAErD,MAAM,KAAK,GAAG,cAAc,CAAC,CAAC,CAAC,CAAA;IAC/B,MAAM,eAAe,GACnB,QAAQ,CAAC,MAAM,CAAC;QACd,GAAG,KAAK;QACR,KAAK,EAAE,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK;KAChD,CAAC,IAAI,CAAC,CAAA;IAET,MAAM,IAAI,GAAG,cAAc,CAAC,cAAc,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;IACtD,MAAM,cAAc,GAClB,QAAQ,CAAC,MAAM,CAAC;QACd,GAAG,IAAI;QACP,KAAK,EAAE,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG;KAC7C,CAAC,IAAI,CAAC,CAAA;IAET,MAAM,cAAc,GAAG,aAAa,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,CAAC,CAAA;IAEjE,OAAO,CACL,qCAAG,EAAE,EAAC,QAAQ;QACZ,wCAAM,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,QAAQ,EAAE,QAAQ,EAAE,QAAQ,IACxC,YAAY,CACR;QAEN,aAAa,CAAC,CAAC,CAAC,CACf,qCAAG,SAAS,EAAE,eAAe,WAAW,GAAG;YACzC,8BAAC,4BAAS,IAAC,QAAQ,EAAE,QAAQ,EAAE,QAAQ,EAAE,QAAQ,EAAE,KAAK,EAAE,KAAK,GAAI;YACnE,wCACE,MAAM,EAAC,KAAK,EACZ,IAAI,EAAC,kBAAkB,EACvB,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,cAAc,GAAG,eAAe,EAAE,GAAG,CAAC,EACtD,MAAM,EAAE,0BAAsB,GAAG,CAAC,EAClC,CAAC,EAAE,eAAe,EAClB,CAAC,EAAE,GAAG,GACN;YACF,qCAAG,SAAS,EAAE,eAAe,0BAAsB,GAAG;gBACpD,8BAAC,0BAAO,IAAC,QAAQ,EAAE,QAAQ,EAAE,KAAK,EAAE,KAAK,EAAE,SAAS,EAAE,KAAK,GAAI,CAC7D,CACF,CACL,CAAC,CAAC,CAAC,IAAI;QAER,qCAAG,SAAS,EAAE,eAAe,QAAQ,GAAG,cAAc,GAAG;YACvD,8BAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,QAAQ,GAAI,CAC5C;QACJ,qCAAG,SAAS,EAAE,eAAe,WAAW,GAAG,cAAc,GAAG;YAC1D,8BAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,QAAQ,EAAE,KAAK,EAAE,KAAK,GAAI,CAC1D,CACF,CACL,CAAA;AACH,CAAC,CAAA;AAED,kCAAkC;AAClC,MAAM,mBAAmB,GAAG,CAAC,EAC3B,KAAK,EACL,MAAM,GAIP,EAAE,EAAE;IACH,MAAM,EAAE,aAAa,EAAE,QAAQ,EAAE,uBAAuB,EAAE,GAAG,KAAK,CAAA;IAClE,OAAO,CACL,8DACG,aAAa,CAAC,aAAa,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CACjD,wCACE,GAAG,EAAE,KAAK,CAAC,GAAG,EACd,CAAC,EAAE,KAAK,CAAC,QAAQ,GAAG,QAAQ,GAAG,uBAAuB,EACtD,KAAK,EAAE,uBAAuB,EAC9B,CAAC,EAAE,CAAC,EACJ,MAAM,EAAE,MAAM,EACd,MAAM,EAAC,MAAM,EACb,IAAI,EAAC,MAAM,GACX,CACH,CAAC,CACD,CACJ,CAAA;AACH,CAAC,CAAA;AAED,wBAAwB;AACxB,SAAS,SAAS,CAAC,EACjB,cAAc,EACd,KAAK,EACL,MAAM,GAWP;IACC,OAAO,CACL,8DACG,cAAc,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,EAAE,MAAM,EAAE,EAAE,EAAE;QACxC,MAAM,OAAO,GAAG,MAAM,CAAA;QACtB,MAAM,SAAS,GACb,IAAA,uBAAO,EAAC,KAAK,EAAE,MAAM,CAAC;YACtB,uBACE,IAAA,8BAAc,EAAC,IAAA,2BAAS,EAAC,KAAK,CAAC,aAAa,CAAC,EAAE,aAAa,CAAC;gBAC7D,IAAA,8BAAc,EAAC,IAAA,2BAAS,EAAC,KAAK,CAAC,aAAa,CAAC,EAAE,MAAM,CACvD,GAAG,CAAA;QACL,MAAM,OAAO,GAAG,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;QACjC,MAAM,IAAI,OAAO,CAAC,MAAM,GAAG,aAAa,GAAG,UAAU,CAAA;QACrD,OAAO,CACL,qCACE,GAAG,EAAE,KAAK,CAAC,aAAa,CAAC,OAAO,EAChC,SAAS,EAAE,eAAe,OAAO,GAAG;YAEpC,wCAAM,QAAQ,EAAE,QAAQ,EAAE,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,KAAK,CAAC,QAAQ,EAAE,CAAC,CAAC,IACtD,SAAS,CACL;YACP,qCAAG,SAAS,EAAE,eAAe,UAAU,GAAG;gBACvC,MAAM;gBACP,8BAAC,mBAAmB,IAAC,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,OAAO,CAAC,MAAM,GAAI,CAC3D,CACF,CACL,CAAA;IACH,CAAC,CAAC,CACD,CACJ,CAAA;AACH,CAAC;AAED,oBAAoB;AACb,KAAK,UAAU,WAAW,CAAC,KAAU,EAAE,IAAsB;IAClE,MAAM,IAAA,WAAI,EAAC,GAAG,EAAE,CAAC,KAAK,CAAC,WAAW,CAAC,CAAA;IACnC,MAAM,EAAE,OAAO,GAAG,CAAC,EAAE,QAAQ,EAAE,EAAE,EAAE,CAAC,8DAAG,QAAQ,CAAI,EAAE,GAAG,IAAI,CAAA;IAC5D,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IAC9C,MAAM,KAAK,GAAG,EAAE,CAAA;IAChB,MAAM,MAAM,GACV,YAAY;QACZ,WAAW;QACX,CAAC,aAAa,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,CAAC,CAAC;QAC5C,EAAE,CAAA;IACJ,MAAM,MAAM,GAAG,WAAW,CAAC,MAAM,CAAC,GAAG,MAAM,CAAA;IAC3C,MAAM,cAAc,GAAG,MAAM,OAAO,CAAC,GAAG,CACtC,MAAM,CAAC,GAAG,CAAC,KAAK,EAAC,KAAK,EAAC,EAAE;QACvB,MAAM,OAAO,GAAG,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;QACjC,MAAM,IAAA,WAAI,EAAC,GAAG,EAAE,CAAC,CAAC,OAAO,CAAC,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAA;QACtE,OAAO,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,OAAO,CAAC,SAAS,CAAC,IAAI,CAAC,EAAE,CAAA;IACzD,CAAC,CAAC,CACH,CAAA;IAED,wDAAwD;IACxD,OAAO,IAAA,6BAAoB,EACzB,8BAAC,OAAO;QACN,uCACE,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,EACd,KAAK,EAAC,4BAA4B,EAClC,UAAU,EAAC,8BAA8B,EACzC,OAAO,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,GAAG,KAAK,GAAG,CAAC,EAAE,MAAM,CAAC,CAAC,QAAQ,EAAE;YAGrD,wCAAM,KAAK,EAAE,KAAK,GAAG,KAAK,GAAG,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,IAAI,EAAC,OAAO,GAAG;YAE/D,qCAAG,MAAM,EAAC,MAAM,EAAC,SAAS,EAAE,aAAa,KAAK,IAAI,QAAQ,GAAG;gBAC3D,8BAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI;gBAC3B,8BAAC,SAAS,IACR,KAAK,EAAE,KAAK,EACZ,cAAc,EAAE,cAAc,EAC9B,MAAM,EAAE,MAAM,GACd,CACA,CACA,CACE,CACX,CAAA;AACH,CAAC;AA3CD,kCA2CC"}

package/dist/LinearGenomeView/components/Ruler.d.ts

@@ -1,11 +0,0 @@
-/// <reference types="react" />
-declare function Ruler({ start, end, bpPerPx, reversed, major, minor, }: {
-    start: number;
-    end: number;
-    bpPerPx: number;
-    reversed?: boolean;
-    major?: boolean;
-    minor?: boolean;
-}): JSX.Element;
-declare const _default: typeof Ruler;
-export default _default;

package/dist/LinearGenomeView/components/Ruler.js

@@ -1,39 +0,0 @@
-"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 mui_1 = require("tss-react/mui");
-const mobx_react_1 = require("mobx-react");
-const util_1 = require("@jbrowse/core/util");
-// locals
-const util_2 = require("../util");
-const useStyles = (0, mui_1.makeStyles)()({
-    majorTickLabel: {
-        fontSize: '11px',
-    },
-    majorTick: {
-        stroke: '#555',
-    },
-    minorTick: {
-        stroke: '#999',
-    },
-});
-function Ruler({ start, end, bpPerPx, reversed = false, major = true, minor = true, }) {
-    const { classes } = useStyles();
-    const ticks = (0, util_2.makeTicks)(start, end, bpPerPx, major, minor);
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        ticks.map(tick => {
-            const x = (reversed ? end - tick.base : tick.base - start) / bpPerPx;
-            return (react_1.default.createElement("line", { key: tick.base, x1: x, x2: x, y1: 0, y2: tick.type === 'major' ? 6 : 4, strokeWidth: 1, stroke: tick.type === 'major' ? '#555' : '#999', className: tick.type === 'major' ? classes.majorTick : classes.minorTick, "data-bp": tick.base }));
-        }),
-        ticks
-            .filter(tick => tick.type === 'major')
-            .map(tick => {
-            const x = (reversed ? end - tick.base : tick.base - start) / bpPerPx;
-            return (react_1.default.createElement("text", { x: x - 3, y: 7 + 11, key: `label-${tick.base}`, style: { fontSize: '11px' }, className: classes.majorTickLabel }, (0, util_1.getTickDisplayStr)(tick.base + 1, bpPerPx)));
-        })));
-}
-exports.default = (0, mobx_react_1.observer)(Ruler);
-//# sourceMappingURL=Ruler.js.map

package/dist/LinearGenomeView/components/Ruler.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"Ruler.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/Ruler.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,uCAA0C;AAC1C,2CAAqC;AACrC,6CAAsD;AAEtD,SAAS;AACT,kCAAmC;AAEnC,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC;IAC7B,cAAc,EAAE;QACd,QAAQ,EAAE,MAAM;KACjB;IACD,SAAS,EAAE;QACT,MAAM,EAAE,MAAM;KACf;IACD,SAAS,EAAE;QACT,MAAM,EAAE,MAAM;KACf;CACF,CAAC,CAAA;AAEF,SAAS,KAAK,CAAC,EACb,KAAK,EACL,GAAG,EACH,OAAO,EACP,QAAQ,GAAG,KAAK,EAChB,KAAK,GAAG,IAAI,EACZ,KAAK,GAAG,IAAI,GAQb;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,KAAK,GAAG,IAAA,gBAAS,EAAC,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,KAAK,EAAE,KAAK,CAAC,CAAA;IAC1D,OAAO,CACL;QACG,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE;YAChB,MAAM,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAC,GAAG,GAAG,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,GAAG,KAAK,CAAC,GAAG,OAAO,CAAA;YACpE,OAAO,CACL,wCACE,GAAG,EAAE,IAAI,CAAC,IAAI,EACd,EAAE,EAAE,CAAC,EACL,EAAE,EAAE,CAAC,EACL,EAAE,EAAE,CAAC,EACL,EAAE,EAAE,IAAI,CAAC,IAAI,KAAK,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EACjC,WAAW,EAAE,CAAC,EACd,MAAM,EAAE,IAAI,CAAC,IAAI,KAAK,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,EAC/C,SAAS,EACP,IAAI,CAAC,IAAI,KAAK,OAAO,CAAC,CAAC,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,CAAC,OAAO,CAAC,SAAS,aAEtD,IAAI,CAAC,IAAI,GAClB,CACH,CAAA;QACH,CAAC,CAAC;QACD,KAAK;aACH,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,IAAI,KAAK,OAAO,CAAC;aACrC,GAAG,CAAC,IAAI,CAAC,EAAE;YACV,MAAM,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAC,GAAG,GAAG,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,GAAG,KAAK,CAAC,GAAG,OAAO,CAAA;YACpE,OAAO,CACL,wCACE,CAAC,EAAE,CAAC,GAAG,CAAC,EACR,CAAC,EAAE,CAAC,GAAG,EAAE,EACT,GAAG,EAAE,SAAS,IAAI,CAAC,IAAI,EAAE,EACzB,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,EAAE,EAC3B,SAAS,EAAE,OAAO,CAAC,cAAc,IAEhC,IAAA,wBAAiB,EAAC,IAAI,CAAC,IAAI,GAAG,CAAC,EAAE,OAAO,CAAC,CACrC,CACR,CAAA;QACH,CAAC,CAAC,CACH,CACJ,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,KAAK,CAAC,CAAA"}

package/esm/LinearGenomeView/components/LinearGenomeViewSvg.d.ts

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