@jbrowse/plugin-circular-view 2.3.3 → 2.4.0

package/src/CircularView/models/CircularView.ts

@@ -1,3 +1,4 @@
+import React from 'react'
 import PluginManager from '@jbrowse/core/PluginManager'
 import {
   cast,
@@ -10,22 +11,38 @@ import {
 } from 'mobx-state-tree'
 import { Region } from '@jbrowse/core/util/types/mst'
 import { transaction } from 'mobx'
+import { saveAs } from 'file-saver'
+import { renderToSvg } from '../svgcomponents/SVGCircularView'
 import {
   AnyConfigurationModel,
   readConfObject,
 } from '@jbrowse/core/configuration'
-
+import { MenuItem } from '@jbrowse/core/ui'
 import {
   getSession,
   clamp,
   isSessionModelWithWidgets,
-  Region as IRegion,
 } from '@jbrowse/core/util'
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models'
-import { calculateStaticSlices, sliceIsVisible } from './slices'
 
+// icons
+import { TrackSelector as TrackSelectorIcon } from '@jbrowse/core/ui/Icons'
+import FolderOpenIcon from '@mui/icons-material/FolderOpen'
+import PhotoCameraIcon from '@mui/icons-material/PhotoCamera'
+
+// locals
+import ExportSvgDlg from '../components/ExportSvgDialog'
+import { calculateStaticSlices, sliceIsVisible, SliceRegion } from './slices'
 import { viewportVisibleSection } from './viewportVisibleRegion'
 
+export interface ExportSvgOptions {
+  rasterizeLayers?: boolean
+  filename?: string
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  Wrapper?: React.FC<any>
+  themeName?: string
+}
+
 /**
  * #stateModel CircularView
  * extends `BaseViewModel`
@@ -121,12 +138,6 @@ function stateModelFactory(pluginManager: PluginManager) {
         }
         return self.volatileWidth
       },
-      /**
-       * #getter
-       */
-      get staticSlices() {
-        return calculateStaticSlices(self)
-      },
 
       /**
        * #getter
@@ -262,20 +273,7 @@ function stateModelFactory(pluginManager: PluginManager) {
        * elide regions that are too small to see reasonably
        */
       get elidedRegions() {
-        const visible: (
-          | {
-              elided: true
-              widthBp: number
-              regions: IRegion[]
-            }
-          | {
-              elided: false
-              widthBp: number
-              start: number
-              end: number
-              refName: string
-            }
-        )[] = []
+        const visible: SliceRegion[] = []
         self.displayedRegions.forEach(region => {
           const widthBp = region.end - region.start
           const widthPx = widthBp / self.bpPerPx
@@ -330,6 +328,14 @@ function stateModelFactory(pluginManager: PluginManager) {
         )
       },
     }))
+    .views(self => ({
+      /**
+       * #getter
+       */
+      get staticSlices() {
+        return calculateStaticSlices(self)
+      },
+    }))
     .views(self => ({
       /**
        * #getter
@@ -529,14 +535,15 @@ function stateModelFactory(pluginManager: PluginManager) {
         const displayConf = configuration.displays.find(
           (d: AnyConfigurationModel) => supportedDisplays.includes(d.type),
         )
-        const track = trackType.stateModel.create({
-          ...initialSnapshot,
-          name,
-          type,
-          configuration,
-          displays: [{ type: displayConf.type, configuration: displayConf }],
-        })
-        self.tracks.push(track)
+        self.tracks.push(
+          trackType.stateModel.create({
+            ...initialSnapshot,
+            name,
+            type,
+            configuration,
+            displays: [{ type: displayConf.type, configuration: displayConf }],
+          }),
+        )
       },
 
       /**
@@ -560,19 +567,50 @@ function stateModelFactory(pluginManager: PluginManager) {
         this.setModelViewWhenAdjust(self.atMinBpPerPx)
         return self.lockedFitToWindow
       },
+      /**
+       * #action
+       * creates an svg export and save using FileSaver
+       */
+      async exportSvg(opts: ExportSvgOptions = {}) {
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        const html = await renderToSvg(self as any, opts)
+        const blob = new Blob([html], { type: 'image/svg+xml' })
+        saveAs(blob, opts.filename || 'image.svg')
+      },
+    }))
+    .views(self => ({
+      /**
+       * #method
+       * return the view menu items
+       */
+      menuItems(): MenuItem[] {
+        return [
+          {
+            label: 'Return to import form',
+            onClick: () => self.setDisplayedRegions([]),
+            icon: FolderOpenIcon,
+          },
+          {
+            label: 'Export SVG',
+            icon: PhotoCameraIcon,
+            onClick: () => {
+              getSession(self).queueDialog(handleClose => [
+                ExportSvgDlg,
+                { model: self, handleClose },
+              ])
+            },
+          },
+          {
+            label: 'Open track selector',
+            onClick: self.activateTrackSelector,
+            icon: TrackSelectorIcon,
+          },
+        ]
+      },
     }))
 }
 
 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/src/CircularView/models/slices.ts

@@ -1,11 +1,25 @@
 import { polarToCartesian, assembleLocString, Region } from '@jbrowse/core/util'
 import { thetaRangesOverlap } from './viewportVisibleRegion'
 
+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 class Slice {
   key: string
 
-  offsetRadians: number
-
   startRadians: number
 
   endRadians: number
@@ -16,18 +30,20 @@ export class Slice {
 
   constructor(
     view: { bpPerRadian: number },
-    public region: Region & { widthBp: number; elided: boolean },
-    currentRadianOffset: number,
+    public region: SliceRegion,
+    public offsetRadians: number,
     public radianWidth: number,
   ) {
     const { bpPerRadian } = view
-    this.key = assembleLocString(region)
-    this.offsetRadians = currentRadianOffset
+    this.key =
+      'regions' in region
+        ? JSON.stringify(region.regions)
+        : 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)
   }
 
@@ -49,13 +65,17 @@ export class Slice {
   }
 }
 
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-function calculateStaticSlices(self: any) {
+function calculateStaticSlices(self: {
+  elidedRegions: SliceRegion[]
+  bpPerRadian: number
+  spacingPx: number
+  pxPerRadian: number
+}) {
   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/src/CircularView/svgcomponents/SVGBackground.tsx

@@ -0,0 +1,21 @@
+import React from 'react'
+import { useTheme } from '@mui/material'
+
+export default function SVGBackground({
+  width,
+  height,
+  shift,
+}: {
+  width: number
+  height: number
+  shift: number
+}) {
+  const theme = useTheme()
+  return (
+    <rect
+      width={width + shift * 2}
+      height={height}
+      fill={theme.palette.background.default}
+    />
+  )
+}

package/src/CircularView/svgcomponents/SVGCircularView.tsx

@@ -0,0 +1,58 @@
+import React from 'react'
+import { ThemeProvider } from '@mui/material'
+import { renderToStaticMarkup } from 'react-dom/server'
+import { when } from 'mobx'
+import { getSession, radToDeg } from '@jbrowse/core/util'
+import { createJBrowseTheme } from '@jbrowse/core/ui'
+
+// locals
+import { ExportSvgOptions, CircularViewModel } from '../models/CircularView'
+import SVGBackground from './SVGBackground'
+import Ruler from '../components/Ruler'
+
+type CGV = CircularViewModel
+
+export async function renderToSvg(model: CGV, opts: ExportSvgOptions) {
+  await when(() => model.initialized)
+  const { themeName = 'default', Wrapper = ({ children }) => <>{children}</> } =
+    opts
+  const session = getSession(model)
+  const theme = session.allThemes?.()[themeName]
+  const { width, tracks, height } = model
+  const shift = 50
+  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 { staticSlices, offsetRadians, centerXY } = model
+  const deg = radToDeg(offsetRadians)
+
+  // the xlink namespace is used for rendering <image> tag
+  return renderToStaticMarkup(
+    <ThemeProvider theme={createJBrowseTheme(theme)}>
+      <Wrapper>
+        <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()}
+        >
+          <SVGBackground width={width} height={height} shift={shift} />
+          <g transform={`translate(${centerXY}) rotate(${deg})`}>
+            {staticSlices.map((slice, i) => (
+              <Ruler key={i} model={model} slice={slice} />
+            ))}
+            {displayResults.map(({ result }, i) => (
+              <React.Fragment key={i}>{result}</React.Fragment>
+            ))}
+          </g>
+        </svg>
+      </Wrapper>
+    </ThemeProvider>,
+  )
+}

package/dist/BaseChordDisplay/models/BaseChordDisplayModel.js.map

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package/dist/BaseChordDisplay/models/baseChordDisplayConfig.js.map

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package/esm/BaseChordDisplay/models/BaseChordDisplayModel.js.map

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package/esm/BaseChordDisplay/models/baseChordDisplayConfig.js.map

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