@jbrowse/plugin-circular-view 2.3.1 → 2.3.3

package/src/CircularView/models/CircularView.ts

@@ -19,6 +19,7 @@ import {
   getSession,
   clamp,
   isSessionModelWithWidgets,
+  Region as IRegion,
 } from '@jbrowse/core/util'
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models'
 import { calculateStaticSlices, sliceIsVisible } from './slices'
@@ -33,10 +34,10 @@ function stateModelFactory(pluginManager: PluginManager) {
   const minHeight = 40
   const minWidth = 100
   const defaultHeight = 400
-  return types.compose(
-    BaseViewModel,
-    types
-      .model('CircularView', {
+  return types
+    .compose(
+      BaseViewModel,
+      types.model('CircularView', {
         /**
          * #property
          */
@@ -49,7 +50,7 @@ function stateModelFactory(pluginManager: PluginManager) {
         /**
          * #property
          */
-        bpPerPx: 2000000,
+        bpPerPx: 200,
         /**
          * #property
          */
@@ -102,449 +103,464 @@ function stateModelFactory(pluginManager: PluginManager) {
         minimumBlockWidth: 20,
 
         trackSelectorType: 'hierarchical',
-      })
-      .volatile(() => ({
-        width: 0,
-      }))
-      .views(self => ({
-        /**
-         * #getter
-         */
-        get staticSlices() {
-          return calculateStaticSlices(self)
-        },
-
-        /**
-         * #getter
-         */
-        get visibleSection() {
-          return viewportVisibleSection(
-            [
-              self.scrollX,
-              self.scrollX + self.width,
-              self.scrollY,
-              self.scrollY + self.height,
-            ],
-            this.centerXY,
-            this.radiusPx,
-          )
-        },
-        /**
-         * #getter
-         */
-        get circumferencePx() {
-          let elidedBp = 0
-          for (const r of this.elidedRegions) {
-            elidedBp += r.widthBp
-          }
-          return (
-            elidedBp / self.bpPerPx + self.spacingPx * this.elidedRegions.length
-          )
-        },
-        /**
-         * #getter
-         */
-        get radiusPx() {
-          return this.circumferencePx / (2 * Math.PI)
-        },
-        /**
-         * #getter
-         */
-        get bpPerRadian() {
-          return self.bpPerPx * this.radiusPx
-        },
-        /**
-         * #getter
-         */
-        get pxPerRadian() {
-          return this.radiusPx
-        },
-        /**
-         * #getter
-         */
-        get centerXY(): [number, number] {
-          return [
-            this.radiusPx + self.paddingPx,
-            this.radiusPx + self.paddingPx,
-          ]
-        },
-        /**
-         * #getter
-         */
-        get totalBp() {
-          let total = 0
-          for (const region of self.displayedRegions) {
-            total += region.end - region.start
-          }
-          return total
-        },
-        /**
-         * #getter
-         */
-        get maximumRadiusPx() {
-          return self.lockedFitToWindow
-            ? Math.min(self.width, self.height) / 2 - self.lockedPaddingPx
-            : 1000000
-        },
-        /**
-         * #getter
-         */
-        get maxBpPerPx() {
-          const minCircumferencePx = 2 * Math.PI * self.minimumRadiusPx
-          return this.totalBp / minCircumferencePx
-        },
-        /**
-         * #getter
-         */
-        get minBpPerPx() {
-          // min depends on window dimensions, clamp between old min(0.01) and max
-          const maxCircumferencePx = 2 * Math.PI * this.maximumRadiusPx
-          return clamp(
-            this.totalBp / maxCircumferencePx,
-            0.0000000001,
-            this.maxBpPerPx,
+      }),
+    )
+    .volatile(() => ({
+      volatileWidth: undefined as number | undefined,
+      error: undefined as unknown,
+    }))
+    .views(self => ({
+      /**
+       * #getter
+       */
+      get width() {
+        if (self.volatileWidth === undefined) {
+          throw new Error(
+            'wait for view to be initialized first before accessing width',
           )
-        },
-        /**
-         * #getter
-         */
-        get atMaxBpPerPx() {
-          return self.bpPerPx >= this.maxBpPerPx
-        },
-        /**
-         * #getter
-         */
-        get atMinBpPerPx() {
-          return self.bpPerPx <= this.minBpPerPx
-        },
-        /**
-         * #getter
-         */
-        get tooSmallToLock() {
-          return this.minBpPerPx <= 0.0000000001
-        },
-        /**
-         * #getter
-         */
-        get figureDimensions(): [number, number] {
-          return [
-            this.radiusPx * 2 + 2 * self.paddingPx,
-            this.radiusPx * 2 + 2 * self.paddingPx,
-          ]
-        },
-        /**
-         * #getter
-         */
-        get figureWidth() {
-          return this.figureDimensions[0]
-        },
-        /**
-         * #getter
-         */
-        get figureHeight() {
-          return this.figureDimensions[1]
-        },
-        /**
-         * #getter
-         * this is displayedRegions, post-processed to
-         * elide regions that are too small to see reasonably
-         */
-        get elidedRegions() {
-          // eslint-disable-next-line @typescript-eslint/no-explicit-any
-          const visible: any[] = []
-          self.displayedRegions.forEach(region => {
-            const widthBp = region.end - region.start
-            const widthPx = widthBp / self.bpPerPx
-            if (widthPx < self.minVisibleWidth) {
-              // too small to see, collapse into a single elision region
-              const lastVisible = visible[visible.length - 1]
-              if (lastVisible && lastVisible.elided) {
-                lastVisible.regions.push({ ...region })
-                lastVisible.widthBp += widthBp
-              } else {
-                visible.push({
-                  elided: true,
-                  widthBp,
-                  regions: [{ ...region }],
-                })
-              }
-            } else {
-              // big enough to see, display it
-              visible.push({ ...region, widthBp })
+        }
+        return self.volatileWidth
+      },
+      /**
+       * #getter
+       */
+      get staticSlices() {
+        return calculateStaticSlices(self)
+      },
+
+      /**
+       * #getter
+       */
+      get visibleSection() {
+        return viewportVisibleSection(
+          [
+            self.scrollX,
+            self.scrollX + self.width,
+            self.scrollY,
+            self.scrollY + self.height,
+          ],
+          this.centerXY,
+          this.radiusPx,
+        )
+      },
+      /**
+       * #getter
+       */
+      get circumferencePx() {
+        let elidedBp = 0
+
+        for (const r of this.elidedRegions) {
+          elidedBp += r.widthBp
+        }
+        return (
+          elidedBp / self.bpPerPx + self.spacingPx * this.elidedRegions.length
+        )
+      },
+      /**
+       * #getter
+       */
+      get radiusPx() {
+        return this.circumferencePx / (2 * Math.PI)
+      },
+      /**
+       * #getter
+       */
+      get bpPerRadian() {
+        return self.bpPerPx * this.radiusPx
+      },
+      /**
+       * #getter
+       */
+      get pxPerRadian() {
+        return this.radiusPx
+      },
+      /**
+       * #getter
+       */
+      get centerXY(): [number, number] {
+        return [this.radiusPx + self.paddingPx, this.radiusPx + self.paddingPx]
+      },
+      /**
+       * #getter
+       */
+      get totalBp() {
+        let total = 0
+        for (const region of self.displayedRegions) {
+          total += region.end - region.start
+        }
+        return total
+      },
+      /**
+       * #getter
+       */
+      get maximumRadiusPx() {
+        return self.lockedFitToWindow
+          ? Math.min(self.width, self.height) / 2 - self.lockedPaddingPx
+          : 1000000
+      },
+      /**
+       * #getter
+       */
+      get maxBpPerPx() {
+        const minCircumferencePx = 2 * Math.PI * self.minimumRadiusPx
+        return this.totalBp / minCircumferencePx
+      },
+      /**
+       * #getter
+       */
+      get minBpPerPx() {
+        // min depends on window dimensions, clamp between old min(0.01) and max
+        const maxCircumferencePx = 2 * Math.PI * this.maximumRadiusPx
+        return clamp(
+          this.totalBp / maxCircumferencePx,
+          0.0000000001,
+          this.maxBpPerPx,
+        )
+      },
+      /**
+       * #getter
+       */
+      get atMaxBpPerPx() {
+        return self.bpPerPx >= this.maxBpPerPx
+      },
+      /**
+       * #getter
+       */
+      get atMinBpPerPx() {
+        return self.bpPerPx <= this.minBpPerPx
+      },
+      /**
+       * #getter
+       */
+      get tooSmallToLock() {
+        return this.minBpPerPx <= 0.0000000001
+      },
+      /**
+       * #getter
+       */
+      get figureDimensions(): [number, number] {
+        return [
+          this.radiusPx * 2 + 2 * self.paddingPx,
+          this.radiusPx * 2 + 2 * self.paddingPx,
+        ]
+      },
+      /**
+       * #getter
+       */
+      get figureWidth() {
+        return this.figureDimensions[0]
+      },
+      /**
+       * #getter
+       */
+      get figureHeight() {
+        return this.figureDimensions[1]
+      },
+      /**
+       * #getter
+       * this is displayedRegions, post-processed to
+       * elide regions that are too small to see reasonably
+       */
+      get elidedRegions() {
+        const visible: (
+          | {
+              elided: true
+              widthBp: number
+              regions: IRegion[]
             }
-          })
-
-          // remove any single-region elisions
-          for (let i = 0; i < visible.length; i += 1) {
-            const v = visible[i]
-            if (v.elided && v.regions.length === 1) {
-              delete v.elided
-              visible[i] = { ...v, ...v.regions[0] }
+          | {
+              elided: false
+              widthBp: number
+              start: number
+              end: number
+              refName: string
             }
-          }
-          return visible
-        },
-        /**
-         * #getter
-         */
-        get assemblyNames() {
-          const assemblyNames: string[] = []
-          self.displayedRegions.forEach(displayedRegion => {
-            if (!assemblyNames.includes(displayedRegion.assemblyName)) {
-              assemblyNames.push(displayedRegion.assemblyName)
+        )[] = []
+        self.displayedRegions.forEach(region => {
+          const widthBp = region.end - region.start
+          const widthPx = widthBp / self.bpPerPx
+          if (widthPx < self.minVisibleWidth) {
+            // too small to see, collapse into a single elision region
+            const lastVisible = visible[visible.length - 1]
+            if (lastVisible?.elided) {
+              lastVisible.regions.push({ ...region })
+              lastVisible.widthBp += widthBp
+            } else {
+              visible.push({
+                elided: true,
+                widthBp,
+                regions: [{ ...region }],
+              })
             }
-          })
-          return assemblyNames
-        },
-        /**
-         * #getter
-         */
-        get initialized() {
-          const { assemblyManager } = getSession(self)
-          return this.assemblyNames.every(
-            a => assemblyManager.get(a)?.initialized,
-          )
-        },
-      }))
-      .views(self => ({
-        /**
-         * #getter
-         */
-        get visibleStaticSlices() {
-          return self.staticSlices.filter(s => sliceIsVisible(self, s))
-        },
-      }))
-      .volatile(() => ({
-        error: undefined as unknown,
-      }))
-      .actions(self => ({
-        /**
-         * #action
-         */
-        setWidth(newWidth: number) {
-          self.width = Math.max(newWidth, minWidth)
-          return self.width
-        },
-        /**
-         * #action
-         */
-        setHeight(newHeight: number) {
-          self.height = Math.max(newHeight, minHeight)
-          return self.height
-        },
-        /**
-         * #action
-         */
-        resizeHeight(distance: number) {
-          const oldHeight = self.height
-          const newHeight = this.setHeight(self.height + distance)
-          this.setModelViewWhenAdjust(!self.tooSmallToLock)
-          return newHeight - oldHeight
-        },
-        /**
-         * #action
-         */
-        resizeWidth(distance: number) {
-          const oldWidth = self.width
-          const newWidth = this.setWidth(self.width + distance)
-          this.setModelViewWhenAdjust(!self.tooSmallToLock)
-          return newWidth - oldWidth
-        },
-        /**
-         * #action
-         */
-        rotateClockwiseButton() {
-          this.rotateClockwise(Math.PI / 6)
-        },
+          } else {
+            // big enough to see, display it
+            visible.push({ ...region, widthBp, elided: false })
+          }
+        })
 
-        /**
-         * #action
-         */
-        rotateCounterClockwiseButton() {
-          this.rotateCounterClockwise(Math.PI / 6)
-        },
+        // remove any single-region elisions
+        for (let i = 0; i < visible.length; i += 1) {
+          const v = visible[i]
+          if (v.elided && v.regions.length === 1) {
+            visible[i] = { ...v, ...v.regions[0], elided: false }
+          }
+        }
+        return visible
+      },
+      /**
+       * #getter
+       */
+      get assemblyNames() {
+        const assemblyNames: string[] = []
+        self.displayedRegions.forEach(displayedRegion => {
+          if (!assemblyNames.includes(displayedRegion.assemblyName)) {
+            assemblyNames.push(displayedRegion.assemblyName)
+          }
+        })
+        return assemblyNames
+      },
+      /**
+       * #getter
+       */
+      get initialized() {
+        const { assemblyManager } = getSession(self)
+        return (
+          self.volatileWidth !== undefined &&
+          this.assemblyNames.every(a => assemblyManager.get(a)?.initialized)
+        )
+      },
+    }))
+    .views(self => ({
+      /**
+       * #getter
+       */
+      get visibleStaticSlices() {
+        return self.staticSlices.filter(s => sliceIsVisible(self, s))
+      },
+    }))
 
-        /**
-         * #action
-         */
-        rotateClockwise(distance = 0.17) {
-          self.offsetRadians += distance
-        },
+    .actions(self => ({
+      /**
+       * #action
+       */
+      setWidth(newWidth: number) {
+        self.volatileWidth = Math.max(newWidth, minWidth)
+        return self.volatileWidth
+      },
+      /**
+       * #action
+       */
+      setHeight(newHeight: number) {
+        self.height = Math.max(newHeight, minHeight)
+        return self.height
+      },
+      /**
+       * #action
+       */
+      resizeHeight(distance: number) {
+        const oldHeight = self.height
+        const newHeight = this.setHeight(self.height + distance)
+        this.setModelViewWhenAdjust(!self.tooSmallToLock)
+        return newHeight - oldHeight
+      },
+      /**
+       * #action
+       */
+      resizeWidth(distance: number) {
+        const oldWidth = self.width
+        const newWidth = this.setWidth(self.width + distance)
+        this.setModelViewWhenAdjust(!self.tooSmallToLock)
+        return newWidth - oldWidth
+      },
+      /**
+       * #action
+       */
+      rotateClockwiseButton() {
+        this.rotateClockwise(Math.PI / 6)
+      },
 
-        /**
-         * #action
-         */
-        rotateCounterClockwise(distance = 0.17) {
-          self.offsetRadians -= distance
-        },
+      /**
+       * #action
+       */
+      rotateCounterClockwiseButton() {
+        this.rotateCounterClockwise(Math.PI / 6)
+      },
 
-        /**
-         * #action
-         */
-        zoomInButton() {
-          this.setBpPerPx(self.bpPerPx / 1.4)
-        },
+      /**
+       * #action
+       */
+      rotateClockwise(distance = 0.17) {
+        self.offsetRadians += distance
+      },
 
-        /**
-         * #action
-         */
-        zoomOutButton() {
-          this.setBpPerPx(self.bpPerPx * 1.4)
-        },
+      /**
+       * #action
+       */
+      rotateCounterClockwise(distance = 0.17) {
+        self.offsetRadians -= distance
+      },
 
-        /**
-         * #action
-         */
-        setBpPerPx(newVal: number) {
-          self.bpPerPx = clamp(newVal, self.minBpPerPx, self.maxBpPerPx)
-        },
+      /**
+       * #action
+       */
+      zoomInButton() {
+        this.setBpPerPx(self.bpPerPx / 1.4)
+      },
 
-        /**
-         * #action
-         */
-        setModelViewWhenAdjust(secondCondition: boolean) {
-          if (self.lockedFitToWindow && secondCondition) {
-            this.setBpPerPx(self.minBpPerPx)
-          }
-        },
+      /**
+       * #action
+       */
+      zoomOutButton() {
+        this.setBpPerPx(self.bpPerPx * 1.4)
+      },
 
-        /**
-         * #action
-         */
-        closeView() {
-          // eslint-disable-next-line @typescript-eslint/no-explicit-any
-          getParent<any>(self, 2).removeView(self)
-        },
+      /**
+       * #action
+       */
+      setBpPerPx(newVal: number) {
+        self.bpPerPx = clamp(newVal, self.minBpPerPx, self.maxBpPerPx)
+      },
 
-        /**
-         * #action
-         */
-        setDisplayedRegions(regions: SnapshotOrInstance<typeof Region>[]) {
-          const previouslyEmpty = self.displayedRegions.length === 0
-          self.displayedRegions = cast(regions)
+      /**
+       * #action
+       */
+      setModelViewWhenAdjust(secondCondition: boolean) {
+        if (self.lockedFitToWindow && secondCondition) {
+          this.setBpPerPx(self.minBpPerPx)
+        }
+      },
 
-          if (previouslyEmpty) {
-            this.setBpPerPx(self.minBpPerPx)
-          } else {
-            this.setBpPerPx(self.bpPerPx)
-          }
-        },
+      /**
+       * #action
+       */
+      closeView() {
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        getParent<any>(self, 2).removeView(self)
+      },
 
-        /**
-         * #action
-         */
-        activateTrackSelector() {
-          if (self.trackSelectorType === 'hierarchical') {
-            const session = getSession(self)
-            if (isSessionModelWithWidgets(session)) {
-              const selector = session.addWidget(
-                'HierarchicalTrackSelectorWidget',
-                'hierarchicalTrackSelector',
-                { view: self },
-              )
-              session.showWidget(selector)
-              return selector
-            }
-          }
-          throw new Error(
-            `invalid track selector type ${self.trackSelectorType}`,
-          )
-        },
+      /**
+       * #action
+       */
+      setDisplayedRegions(regions: SnapshotOrInstance<typeof Region>[]) {
+        const previouslyEmpty = self.displayedRegions.length === 0
+        self.displayedRegions = cast(regions)
 
-        /**
-         * #action
-         */
-        toggleTrack(trackId: string) {
-          // if we have any tracks with that configuration, turn them off
-          const hiddenCount = this.hideTrack(trackId)
-          // if none had that configuration, turn one on
-          if (!hiddenCount) {
-            this.showTrack(trackId)
+        if (previouslyEmpty) {
+          this.setBpPerPx(self.minBpPerPx)
+        } else {
+          this.setBpPerPx(self.bpPerPx)
+        }
+      },
+
+      /**
+       * #action
+       */
+      activateTrackSelector() {
+        if (self.trackSelectorType === 'hierarchical') {
+          const session = getSession(self)
+          if (isSessionModelWithWidgets(session)) {
+            const selector = session.addWidget(
+              'HierarchicalTrackSelectorWidget',
+              'hierarchicalTrackSelector',
+              { view: self },
+            )
+            session.showWidget(selector)
+            return selector
           }
-        },
+        }
+        throw new Error(`invalid track selector type ${self.trackSelectorType}`)
+      },
 
-        /**
-         * #action
-         */
-        setError(error: unknown) {
-          console.error(error)
-          self.error = error
-        },
+      /**
+       * #action
+       */
+      toggleTrack(trackId: string) {
+        // if we have any tracks with that configuration, turn them off
+        const hiddenCount = this.hideTrack(trackId)
+        // if none had that configuration, turn one on
+        if (!hiddenCount) {
+          this.showTrack(trackId)
+        }
+      },
 
-        /**
-         * #action
-         */
-        showTrack(trackId: string, initialSnapshot = {}) {
-          const schema = pluginManager.pluggableConfigSchemaType('track')
-          const conf = resolveIdentifier(schema, getRoot(self), trackId)
-          const trackType = pluginManager.getTrackType(conf.type)
-          if (!trackType) {
-            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: AnyConfigurationModel) =>
-            supportedDisplays.includes(d.type),
-          )
-          const track = trackType.stateModel.create({
-            ...initialSnapshot,
-            type: conf.type,
-            configuration: conf,
-            displays: [{ type: displayConf.type, configuration: displayConf }],
-          })
-          self.tracks.push(track)
-        },
+      /**
+       * #action
+       */
+      setError(error: unknown) {
+        self.error = error
+      },
 
-        /**
-         * #action
-         */
-        addTrackConf(
-          configuration: AnyConfigurationModel,
-          initialSnapshot = {},
-        ) {
-          const { type } = configuration
-          const name = readConfObject(configuration, 'name')
-          const trackType = pluginManager.getTrackType(type)
-          if (!trackType) {
-            throw new Error(`unknown track type ${configuration.type}`)
-          }
-          const viewType = pluginManager.getViewType(self.type)
-          const supportedDisplays = viewType.displayTypes.map(d => d.name)
-          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)
-        },
+      /**
+       * #action
+       */
+      showTrack(trackId: string, initialSnapshot = {}) {
+        const schema = pluginManager.pluggableConfigSchemaType('track')
+        const conf = resolveIdentifier(schema, getRoot(self), trackId)
+        const trackType = pluginManager.getTrackType(conf.type)
+        if (!trackType) {
+          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: AnyConfigurationModel) =>
+          supportedDisplays.includes(d.type),
+        )
+        const track = trackType.stateModel.create({
+          ...initialSnapshot,
+          type: conf.type,
+          configuration: conf,
+          displays: [{ type: displayConf.type, configuration: displayConf }],
+        })
+        self.tracks.push(track)
+      },
 
-        /**
-         * #action
-         */
-        hideTrack(trackId: string) {
-          const schema = pluginManager.pluggableConfigSchemaType('track')
-          const conf = resolveIdentifier(schema, getRoot(self), trackId)
-          const t = self.tracks.filter(t => t.configuration === conf)
-          transaction(() => t.forEach(t => self.tracks.remove(t)))
-          return t.length
-        },
+      /**
+       * #action
+       */
+      addTrackConf(configuration: AnyConfigurationModel, initialSnapshot = {}) {
+        const { type } = configuration
+        const name = readConfObject(configuration, 'name')
+        const trackType = pluginManager.getTrackType(type)
+        if (!trackType) {
+          throw new Error(`unknown track type ${configuration.type}`)
+        }
+        const viewType = pluginManager.getViewType(self.type)
+        const supportedDisplays = viewType.displayTypes.map(d => d.name)
+        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)
+      },
 
-        /**
-         * #action
-         */
-        toggleFitToWindowLock() {
-          // when going unlocked -> locked and circle is cut off, set to the locked minBpPerPx
-          self.lockedFitToWindow = !self.lockedFitToWindow
-          this.setModelViewWhenAdjust(self.atMinBpPerPx)
-          return self.lockedFitToWindow
-        },
-      })),
-  )
+      /**
+       * #action
+       */
+      hideTrack(trackId: string) {
+        const schema = pluginManager.pluggableConfigSchemaType('track')
+        const conf = resolveIdentifier(schema, getRoot(self), trackId)
+        const t = self.tracks.filter(t => t.configuration === conf)
+        transaction(() => t.forEach(t => self.tracks.remove(t)))
+        return t.length
+      },
+
+      /**
+       * #action
+       */
+      toggleFitToWindowLock() {
+        // when going unlocked -> locked and circle is cut off, set to the
+        // locked minBpPerPx
+        self.lockedFitToWindow = !self.lockedFitToWindow
+        this.setModelViewWhenAdjust(self.atMinBpPerPx)
+        return self.lockedFitToWindow
+      },
+    }))
 }
 
 export type CircularViewStateModel = ReturnType<typeof stateModelFactory>