@jbrowse/plugin-alignments 2.1.6 → 2.2.0

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/PileupRenderer/PileupRenderer.tsx

@@ -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 }
@@ -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
@@ -1058,7 +1054,7 @@ export default class PileupRenderer extends BoxRendererType {
     const minFeatWidth = readConfObject(config, 'minSubfeatureWidth')
     const mismatches: Mismatch[] = feature.get('mismatches')
     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,
@@ -1161,7 +1157,7 @@ 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 +1267,13 @@ 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/SNPCoverageAdapter/configSchema.ts

@@ -1,14 +1,22 @@
 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 SNPCoverageAdapter = (pluginManager: PluginManager) =>
+  ConfigurationSchema(
+    'SNPCoverageAdapter',
+    {
+      /**
+       * #slot
+       * normally refers to a BAM or CRAM adapter
+       */
+      subadapter: pluginManager.pluggableConfigSchemaType('adapter'),
+    },
+    { explicitlyTyped: true },
   )
+
+export default SNPCoverageAdapter

package/src/SNPCoverageRenderer/configSchema.ts

@@ -1,30 +1,50 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 
-export default ConfigurationSchema(
+/**
+ * #config SNPCoverageRenderer
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const SNPCoverageRenderer = ConfigurationSchema(
   'SNPCoverageRenderer',
   {
+    /**
+     * #slot
+     */
     clipColor: {
       type: 'color',
       description: 'the color of the clipping marker',
       defaultValue: 'red',
     },
+    /**
+     * #slot
+     */
     indicatorThreshold: {
       type: 'number',
       description:
         'the proportion of reads containing a insertion/clip indicator',
       defaultValue: 0.4,
     },
+    /**
+     * #slot
+     */
     drawArcs: {
       type: 'boolean',
       description: 'Draw sashimi-style arcs for intron features',
       defaultValue: true,
     },
+    /**
+     * #slot
+     */
     drawInterbaseCounts: {
       type: 'boolean',
       description:
         'draw count "upsidedown histogram" of the interbase events that don\'t contribute to the coverage count so are not drawn in the normal histogram',
       defaultValue: true,
     },
+    /**
+     * #slot
+     */
     drawIndicators: {
       type: 'boolean',
       description:
@@ -34,3 +54,5 @@ export default ConfigurationSchema(
   },
   { explicitlyTyped: true },
 )
+
+export default SNPCoverageRenderer

package/src/SNPCoverageRenderer/index.ts

@@ -1,16 +1,9 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import ConfigSchema from './configSchema'
+import configSchema from './configSchema'
 import PluginManager from '@jbrowse/core/PluginManager'
 import SNPCoverageRenderer from './SNPCoverageRenderer'
 
 import { WiggleRendering } from '@jbrowse/plugin-wiggle'
 
-export const configSchema = ConfigurationSchema(
-  'SNPCoverageRenderer',
-  {},
-  { baseConfiguration: ConfigSchema, explicitlyTyped: true },
-)
-
 export default function register(pluginManager: PluginManager) {
   pluginManager.addRendererType(
     () =>

package/src/declare.d.ts

@@ -1 +0,0 @@
-declare module '@gmod/cram'