@jbrowse/plugin-alignments 2.1.7 → 2.2.1

package/src/LinearSNPCoverageDisplay/models/model.ts

@@ -8,7 +8,6 @@ import {
 } from '@jbrowse/core/configuration'
 import { linearWiggleDisplayModelFactory } from '@jbrowse/plugin-wiggle'
 import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
-
 import PluginManager from '@jbrowse/core/PluginManager'
 import { getContainingView } from '@jbrowse/core/util'
 
@@ -21,19 +20,38 @@ const rendererTypes = new Map([['snpcoverage', 'SNPCoverageRenderer']])
 
 type LGV = LinearGenomeViewModel
 
-const stateModelFactory = (
+/**
+ * #stateModel LinearSNPCoverageDisplay
+ * extends `LinearWiggleDisplay`
+ */
+function stateModelFactory(
   pluginManager: PluginManager,
   configSchema: AnyConfigurationSchemaType,
-) =>
-  types
+) {
+  return types
     .compose(
       'LinearSNPCoverageDisplay',
       linearWiggleDisplayModelFactory(pluginManager, configSchema),
       types.model({
+        /**
+         * #property
+         */
         type: types.literal('LinearSNPCoverageDisplay'),
+        /**
+         * #property
+         */
         drawInterbaseCounts: types.maybe(types.boolean),
+        /**
+         * #property
+         */
         drawIndicators: types.maybe(types.boolean),
+        /**
+         * #property
+         */
         drawArcs: types.maybe(types.boolean),
+        /**
+         * #property
+         */
         filterBy: types.optional(
           types.model({
             flagInclude: types.optional(types.number, 0),
@@ -45,6 +63,9 @@ const stateModelFactory = (
           }),
           {},
         ),
+        /**
+         * #property
+         */
         colorBy: types.maybe(
           types.model({
             type: types.string,
@@ -57,9 +78,15 @@ const stateModelFactory = (
       modificationTagMap: observable.map({}),
     }))
     .actions(self => ({
+      /**
+       * #action
+       */
       setConfig(configuration: AnyConfigurationModel) {
         self.configuration = configuration
       },
+      /**
+       * #action
+       */
       setFilterBy(filter: {
         flagInclude: number
         flagExclude: number
@@ -68,10 +95,16 @@ const stateModelFactory = (
       }) {
         self.filterBy = cast(filter)
       },
+      /**
+       * #action
+       */
       setColorBy(colorBy?: { type: string; tag?: string }) {
         self.colorBy = cast(colorBy)
       },
 
+      /**
+       * #action
+       */
       updateModificationColorMap(uniqueModifications: string[]) {
         const colorPalette = ['red', 'blue', 'green', 'orange', 'purple']
         let i = 0
@@ -87,6 +120,9 @@ const stateModelFactory = (
     .views(self => {
       const { renderProps: superRenderProps } = self
       return {
+        /**
+         * #getter
+         */
         get rendererConfig() {
           const configBlob =
             getConf(self, ['renderers', self.rendererTypeName]) || {}
@@ -102,17 +138,26 @@ const stateModelFactory = (
             getEnv(self),
           )
         },
+        /**
+         * #getter
+         */
         get drawArcsSetting() {
           return (
             self.drawArcs ?? readConfObject(this.rendererConfig, 'drawArcs')
           )
         },
+        /**
+         * #getter
+         */
         get drawInterbaseCountsSetting() {
           return (
             self.drawInterbaseCounts ??
             readConfObject(this.rendererConfig, 'drawInterbaseCounts')
           )
         },
+        /**
+         * #getter
+         */
         get drawIndicatorsSetting() {
           return (
             self.drawIndicators ??
@@ -120,6 +165,9 @@ const stateModelFactory = (
           )
         },
 
+        /**
+         * #getter
+         */
         get modificationsReady() {
           return self.colorBy?.type === 'modifications'
             ? Object.keys(JSON.parse(JSON.stringify(self.modificationTagMap)))
@@ -127,6 +175,9 @@ const stateModelFactory = (
             : true
         },
 
+        /**
+         * #method
+         */
         renderProps() {
           const superProps = superRenderProps()
           const { colorBy, filterBy, modificationTagMap } = self
@@ -144,12 +195,21 @@ const stateModelFactory = (
       }
     })
     .actions(self => ({
+      /**
+       * #action
+       */
       toggleDrawIndicators() {
         self.drawIndicators = !self.drawIndicatorsSetting
       },
+      /**
+       * #action
+       */
       toggleDrawInterbaseCounts() {
         self.drawInterbaseCounts = !self.drawInterbaseCountsSetting
       },
+      /**
+       * #action
+       */
       toggleDrawArcs() {
         self.drawArcs = !self.drawArcsSetting
       },
@@ -195,10 +255,16 @@ const stateModelFactory = (
     .views(self => {
       const { trackMenuItems: superTrackMenuItems } = self
       return {
+        /**
+         * #getter
+         */
         get TooltipComponent() {
           return Tooltip
         },
 
+        /**
+         * #getter
+         */
         get adapterConfig() {
           const subadapter = getConf(self.parentTrack, 'adapter')
           return {
@@ -207,18 +273,30 @@ const stateModelFactory = (
           }
         },
 
+        /**
+         * #getter
+         */
         get rendererTypeName() {
           return rendererTypes.get('snpcoverage')
         },
 
+        /**
+         * #getter
+         */
         get needsScalebar() {
           return true
         },
 
+        /**
+         * #method
+         */
         contextMenuItems() {
           return []
         },
 
+        /**
+         * #method
+         */
         trackMenuItems() {
           return [
             ...superTrackMenuItems(),
@@ -244,6 +322,7 @@ const stateModelFactory = (
         },
       }
     })
+}
 
 export type SNPCoverageDisplayModel = ReturnType<typeof stateModelFactory>
 

package/src/PileupRPC/rpcMethods.ts

@@ -1,11 +1,12 @@
-import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'
 import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType'
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'
+import { renameRegionsIfNeeded, Region } from '@jbrowse/core/util'
 import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods'
-import { renameRegionsIfNeeded } from '@jbrowse/core/util'
-import { Region } from '@jbrowse/core/util/types'
 import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals'
-import { toArray } from 'rxjs/operators'
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
+import { toArray } from 'rxjs/operators'
+
+// locals
 import { getTagAlt } from '../util'
 import { getModificationTypes } from '../BamAdapter/MismatchParser'
 
@@ -41,14 +42,11 @@ export class PileupGetGlobalValueForTag extends RpcMethodType {
     },
     rpcDriverClassName: string,
   ) {
-    const deserializedArgs = await this.deserializeArguments(
-      args,
-      rpcDriverClassName,
-    )
-    const { adapterConfig, sessionId, regions, tag } = deserializedArgs
-    const dataAdapter = (
-      await getAdapter(this.pluginManager, sessionId, adapterConfig)
-    ).dataAdapter as BaseFeatureDataAdapter
+    const pm = this.pluginManager
+    const deArgs = await this.deserializeArguments(args, rpcDriverClassName)
+    const { adapterConfig, sessionId, regions, tag } = deArgs
+    const dataAdapter = (await getAdapter(pm, sessionId, adapterConfig))
+      .dataAdapter as BaseFeatureDataAdapter
 
     const features = dataAdapter.getFeaturesInMultipleRegions(regions)
     const featuresArray = await features.pipe(toArray()).toPromise()
@@ -96,14 +94,11 @@ export class PileupGetVisibleModifications extends RpcMethodType {
     },
     rpcDriverClassName: string,
   ) {
-    const deserializedArgs = await this.deserializeArguments(
-      args,
-      rpcDriverClassName,
-    )
-    const { adapterConfig, sessionId, regions } = deserializedArgs
-    const dataAdapter = (
-      await getAdapter(this.pluginManager, sessionId, adapterConfig)
-    ).dataAdapter as BaseFeatureDataAdapter
+    const pm = this.pluginManager
+    const deArgs = await this.deserializeArguments(args, rpcDriverClassName)
+    const { adapterConfig, sessionId, regions } = deArgs
+    const dataAdapter = (await getAdapter(pm, sessionId, adapterConfig))
+      .dataAdapter as BaseFeatureDataAdapter
 
     const features = dataAdapter.getFeaturesInMultipleRegions(regions)
     const featuresArray = await features.pipe(toArray()).toPromise()

package/src/PileupRenderer/{PileupRenderer.tsx → PileupRenderer.ts}

@@ -150,7 +150,7 @@ export default class PileupRenderer extends BoxRendererType {
 
   // get width and height of chars the height is an approximation: width
   // letter M is approximately the height
-  getCharWidthHeight(ctx: CanvasRenderingContext2D) {
+  getCharWidthHeight() {
     const charWidth = measureText('A')
     const charHeight = measureText('M') - 2
     return { charWidth, charHeight }
@@ -178,9 +178,9 @@ export default class PileupRenderer extends BoxRendererType {
 
     // Expand the start and end of feature when softclipping enabled
     if (showSoftClip) {
-      const mismatches = feature.get('mismatches') as Mismatch[]
+      const mismatches = feature.get('mismatches') as Mismatch[] | undefined
       const seq = feature.get('seq') as string
-      if (seq) {
+      if (seq && mismatches) {
         for (let i = 0; i < mismatches.length; i += 1) {
           const { type, start, cliplen = 0 } = mismatches[i]
           if (type === 'softclip') {
@@ -237,11 +237,7 @@ export default class PileupRenderer extends BoxRendererType {
 
     const maxClippingSize = readConfObject(config, 'maxClippingSize')
     const { start, end } = region
-    const len = end - start
-    const bpExpansion = Math.max(
-      len,
-      showSoftClip ? Math.round(maxClippingSize) : 0,
-    )
+    const bpExpansion = showSoftClip ? Math.round(maxClippingSize) : 0
 
     return {
       // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
@@ -853,7 +849,7 @@ export default class PileupRenderer extends BoxRendererType {
 
     const pxPerBp = Math.min(1 / bpPerPx, 2)
     const w = Math.max(minSubfeatureWidth, pxPerBp)
-    const mismatches: Mismatch[] = feature.get('mismatches')
+    const mismatches = feature.get('mismatches') as Mismatch[] | undefined
     const heightLim = charHeight - 2
 
     // extraHorizontallyFlippedOffset is used to draw interbase items, which
@@ -862,6 +858,10 @@ export default class PileupRenderer extends BoxRendererType {
       ? 1 / bpPerPx + 1
       : -1
 
+    if (!mismatches) {
+      return
+    }
+
     // two pass rendering: first pass, draw all the mismatches except wide
     // insertion markers
     for (let i = 0; i < mismatches.length; i += 1) {
@@ -1056,9 +1056,9 @@ export default class PileupRenderer extends BoxRendererType {
     const { regions, bpPerPx } = renderArgs
     const [region] = regions
     const minFeatWidth = readConfObject(config, 'minSubfeatureWidth')
-    const mismatches: Mismatch[] = feature.get('mismatches')
+    const mismatches = feature.get('mismatches') as Mismatch[] | undefined
     const seq = feature.get('seq')
-    const { charWidth, charHeight } = this.getCharWidthHeight(ctx)
+    const { charWidth, charHeight } = this.getCharWidthHeight()
     const { bases } = theme.palette
     const colorForBase: { [key: string]: string } = {
       A: bases.A.main,
@@ -1069,59 +1069,49 @@ export default class PileupRenderer extends BoxRendererType {
     }
 
     // Display all bases softclipped off in lightened colors
-    if (seq) {
-      mismatches
-        .filter(mismatch => mismatch.type === 'softclip')
-        .forEach(mismatch => {
-          const softClipLength = mismatch.cliplen || 0
-          const s = feature.get('start')
-          const softClipStart =
-            mismatch.start === 0 ? s - softClipLength : s + mismatch.start
-
-          for (let k = 0; k < softClipLength; k += 1) {
-            const base = seq.charAt(k + mismatch.start)
-
-            // If softclip length+start is longer than sequence, no need to
-            // continue showing base
-            if (!base) {
-              return
-            }
-
-            const [softClipLeftPx, softClipRightPx] = bpSpanPx(
-              softClipStart + k,
-              softClipStart + k + 1,
-              region,
-              bpPerPx,
-            )
-            const softClipWidthPx = Math.max(
-              minFeatWidth,
-              Math.abs(softClipLeftPx - softClipRightPx),
-            )
+    if (!(seq && mismatches)) {
+      return
+    }
+    mismatches
+      .filter(mismatch => mismatch.type === 'softclip')
+      .forEach(mismatch => {
+        const len = mismatch.cliplen || 0
+        const s = feature.get('start')
+        const start = mismatch.start === 0 ? s - len : s + mismatch.start
+
+        for (let k = 0; k < len; k += 1) {
+          const base = seq.charAt(k + mismatch.start)
+
+          // If softclip length+start is longer than sequence, no need to
+          // continue showing base
+          if (!base) {
+            return
+          }
 
-            // Black accounts for IUPAC ambiguity code bases such as N that
-            // show in soft clipping
-            const baseColor = colorForBase[base] || '#000000'
-            ctx.fillStyle = baseColor
-            fillRect(
-              ctx,
-              softClipLeftPx,
-              topPx,
-              softClipWidthPx,
-              heightPx,
-              canvasWidth,
-            )
+          const [leftPx, rightPx] = bpSpanPx(
+            start + k,
+            start + k + 1,
+            region,
+            bpPerPx,
+          )
+          const widthPx = Math.max(minFeatWidth, rightPx - leftPx)
+
+          // Black accounts for IUPAC ambiguity code bases such as N that
+          // show in soft clipping
+          const baseColor = colorForBase[base] || '#000000'
+          ctx.fillStyle = baseColor
+          fillRect(ctx, leftPx, topPx, widthPx, heightPx, canvasWidth)
 
-            if (softClipWidthPx >= charWidth && heightPx >= charHeight - 5) {
-              ctx.fillStyle = theme.palette.getContrastText(baseColor)
-              ctx.fillText(
-                base,
-                softClipLeftPx + (softClipWidthPx - charWidth) / 2 + 1,
-                topPx + heightPx,
-              )
-            }
+          if (widthPx >= charWidth && heightPx >= charHeight - 5) {
+            ctx.fillStyle = theme.palette.getContrastText(baseColor)
+            ctx.fillText(
+              base,
+              leftPx + (widthPx - charWidth) / 2 + 1,
+              topPx + heightPx,
+            )
           }
-        })
-    }
+        }
+      })
   }
 
   makeImageData({
@@ -1161,7 +1151,7 @@ export default class PileupRenderer extends BoxRendererType {
     }
     ctx.font = 'bold 10px Courier New,monospace'
 
-    const { charWidth, charHeight } = this.getCharWidthHeight(ctx)
+    const { charWidth, charHeight } = this.getCharWidthHeight()
     const drawSNPsMuted = shouldDrawSNPsMuted(colorBy?.type)
     const drawIndels = shouldDrawIndels(colorBy?.type)
     for (let i = 0; i < layoutRecords.length; i++) {
@@ -1271,13 +1261,13 @@ export default class PileupRenderer extends BoxRendererType {
     const features = await this.getFeatures(renderProps)
     const layout = this.createLayoutInWorker(renderProps)
     const { regions, bpPerPx } = renderProps
+    const [region] = regions
 
     const layoutRecords = this.layoutFeats({
       ...renderProps,
       features,
       layout,
     })
-    const [region] = regions
 
     // only need reference sequence if there are features and only for some
     // cases

package/src/PileupRenderer/configSchema.ts

@@ -1,16 +1,28 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 import { types } from 'mobx-state-tree'
 
-export default ConfigurationSchema(
+/**
+ * #config PileupRenderer
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const PileupRenderer = ConfigurationSchema(
   'PileupRenderer',
   {
-    // default magenta here is used to detect the user has not customized this
+    /**
+     * #slot
+     * default magenta here is used to detect the user has not customized this
+     */
     color: {
       type: 'color',
       description: 'the color of each feature in a pileup alignment',
       defaultValue: '#f0f',
       contextVariable: ['feature'],
     },
+
+    /**
+     * #slot
+     */
     orientationType: {
       type: 'stringEnum',
       model: types.enumeration('orientationType', ['fr', 'rf', 'ff']),
@@ -18,6 +30,9 @@ export default ConfigurationSchema(
       description:
         'read sequencer orienation. fr is normal "reads pointing at each other ---> <--- while some other sequencers can use other options',
     },
+    /**
+     * #slot
+     */
     displayMode: {
       type: 'stringEnum',
       model: types.enumeration('displayMode', [
@@ -28,39 +43,60 @@ export default ConfigurationSchema(
       description: 'Alternative display modes',
       defaultValue: 'normal',
     },
+    /**
+     * #slot
+     */
     minSubfeatureWidth: {
       type: 'number',
       description:
         'the minimum width in px for a pileup mismatch feature. use for increasing/decreasing mismatch marker widths when zoomed out, e.g. 0 or 1',
       defaultValue: 0.7,
     },
+    /**
+     * #slot
+     */
     maxHeight: {
       type: 'integer',
       description: 'the maximum height to be used in a pileup rendering',
       defaultValue: 1200,
     },
+    /**
+     * #slot
+     */
     maxClippingSize: {
       type: 'integer',
       description: 'the max clip size to be used in a pileup rendering',
       defaultValue: 10000,
     },
+    /**
+     * #slot
+     */
     height: {
       type: 'number',
       description: 'the height of each feature in a pileup alignment',
       defaultValue: 7,
       contextVariable: ['feature'],
     },
+    /**
+     * #slot
+     */
     noSpacing: {
       type: 'boolean',
       description: 'remove spacing between features',
       defaultValue: false,
     },
+    /**
+     * #slot
+     */
     largeInsertionIndicatorScale: {
       type: 'number',
       description:
         'scale at which to draw the large insertion indicators (bp/pixel)',
       defaultValue: 10,
     },
+    /**
+     * #slot
+     */
     mismatchAlpha: {
       type: 'boolean',
       defaultValue: false,
@@ -69,3 +105,4 @@ export default ConfigurationSchema(
   },
   { explicitlyTyped: true },
 )
+export default PileupRenderer

package/src/PileupRenderer/index.ts

@@ -4,13 +4,12 @@ import ReactComponent from './components/PileupRendering'
 import configSchema from './configSchema'
 
 export default function register(pluginManager: PluginManager) {
-  pluginManager.addRendererType(
-    () =>
-      new PileupRenderer({
-        name: 'PileupRenderer',
-        ReactComponent,
-        configSchema,
-        pluginManager,
-      }),
-  )
+  pluginManager.addRendererType(() => {
+    return new PileupRenderer({
+      name: 'PileupRenderer',
+      ReactComponent,
+      configSchema,
+      pluginManager,
+    })
+  })
 }

package/src/SNPCoverageAdapter/configSchema.ts

@@ -1,14 +1,23 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { types } from 'mobx-state-tree'
 
-export default (pluginManager: PluginManager) =>
-  types.late(() =>
-    ConfigurationSchema(
-      'SNPCoverageAdapter',
-      {
-        subadapter: pluginManager.pluggableConfigSchemaType('adapter'),
-      },
-      { explicitlyTyped: true },
-    ),
-  )
+/**
+ * #config SNPCoverageAdapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const configSchema = ConfigurationSchema(
+  'SNPCoverageAdapter',
+  {
+    /**
+     * #slot
+     * normally refers to a BAM or CRAM adapter
+     */
+    subadapter: {
+      type: 'frozen',
+      defaultValue: null,
+    },
+  },
+  { explicitlyTyped: true },
+)
+
+export default configSchema

package/src/SNPCoverageAdapter/index.ts

@@ -1,23 +1,22 @@
 import PluginManager from '@jbrowse/core/PluginManager'
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-import configSchemaFactory from './configSchema'
+import configSchema from './configSchema'
 import { capabilities } from './SNPCoverageAdapter'
 
-export default (pluginManager: PluginManager) => {
-  pluginManager.addAdapterType(
-    () =>
-      new AdapterType({
-        name: 'SNPCoverageAdapter',
-        adapterMetadata: {
-          category: null,
-          displayName: null,
-          hiddenFromGUI: true,
-          description: null,
-        },
-        getAdapterClass: () =>
-          import('./SNPCoverageAdapter').then(r => r.default),
-        configSchema: configSchemaFactory(pluginManager),
-        adapterCapabilities: capabilities,
-      }),
-  )
+export default function (pluginManager: PluginManager) {
+  pluginManager.addAdapterType(() => {
+    return new AdapterType({
+      name: 'SNPCoverageAdapter',
+      adapterMetadata: {
+        category: null,
+        displayName: null,
+        hiddenFromGUI: true,
+        description: null,
+      },
+      getAdapterClass: () =>
+        import('./SNPCoverageAdapter').then(r => r.default),
+      configSchema,
+      adapterCapabilities: capabilities,
+    })
+  })
 }