@jbrowse/plugin-wiggle 2.1.7 → 2.2.1

package/src/BigWigAdapter/__snapshots__/BigWigAdapter.test.ts.snap

@@ -1,7 +1,7 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
 exports[`adapter can fetch features from volvox.bw adapter can fetch stats from volvox.bw 1`] = `
-Object {
+{
   "basesCovered": 49984,
   "featureDensity": 0.00002000640204865557,
   "scoreMax": 38,
@@ -14,7 +14,7 @@ Object {
 `;
 
 exports[`adapter can fetch features from volvox.bw get local stats 1`] = `
-Object {
+{
   "basesCovered": 30100,
   "featureCount": 30000,
   "featureDensity": 0.9966777408637874,
@@ -28,7 +28,7 @@ Object {
 `;
 
 exports[`adapter can fetch features from volvox.bw get region stats 1`] = `
-Object {
+{
   "basesCovered": 30001,
   "featureCount": 30001,
   "featureDensity": 1,
@@ -42,71 +42,71 @@ Object {
 `;
 
 exports[`adapter can fetch features from volvox.bw test basic aspects of getfeatures 1`] = `
-Array [
-  Object {
+[
+  {
     "end": 1003,
     "refName": "ctgA",
     "score": 18,
     "start": 1002,
     "uniqueId": ":ctgA:1002-1003",
   },
-  Object {
+  {
     "end": 1004,
     "refName": "ctgA",
     "score": 18,
     "start": 1003,
     "uniqueId": ":ctgA:1003-1004",
   },
-  Object {
+  {
     "end": 1005,
     "refName": "ctgA",
     "score": 18,
     "start": 1004,
     "uniqueId": ":ctgA:1004-1005",
   },
-  Object {
+  {
     "end": 1006,
     "refName": "ctgA",
     "score": 19,
     "start": 1005,
     "uniqueId": ":ctgA:1005-1006",
   },
-  Object {
+  {
     "end": 1007,
     "refName": "ctgA",
     "score": 20,
     "start": 1006,
     "uniqueId": ":ctgA:1006-1007",
   },
-  Object {
+  {
     "end": 1008,
     "refName": "ctgA",
     "score": 20,
     "start": 1007,
     "uniqueId": ":ctgA:1007-1008",
   },
-  Object {
+  {
     "end": 1009,
     "refName": "ctgA",
     "score": 20,
     "start": 1008,
     "uniqueId": ":ctgA:1008-1009",
   },
-  Object {
+  {
     "end": 1010,
     "refName": "ctgA",
     "score": 20,
     "start": 1009,
     "uniqueId": ":ctgA:1009-1010",
   },
-  Object {
+  {
     "end": 1011,
     "refName": "ctgA",
     "score": 20,
     "start": 1010,
     "uniqueId": ":ctgA:1010-1011",
   },
-  Object {
+  {
     "end": 1012,
     "refName": "ctgA",
     "score": 19,

package/src/BigWigAdapter/configSchema.ts

@@ -1,8 +1,16 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 
-export default ConfigurationSchema(
+/**
+ * #config BigWigAdapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const BigWigAdapter = ConfigurationSchema(
   'BigWigAdapter',
   {
+    /**
+     * #slot
+     */
     bigWigLocation: {
       type: 'fileLocation',
       defaultValue: {
@@ -10,6 +18,10 @@ export default ConfigurationSchema(
         locationType: 'UriLocation',
       },
     },
+
+    /**
+     * #slot
+     */
     source: {
       type: 'string',
       defaultValue: '',
@@ -18,3 +30,5 @@ export default ConfigurationSchema(
   },
   { explicitlyTyped: true },
 )
+
+export default BigWigAdapter

package/src/DensityRenderer/__snapshots__/DensityRenderer.test.js.snap

@@ -1,10 +1,16 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
 exports[`inverted mode and reversed 1`] = `
-Object {
+{
   "imageData": Any<Object>,
-  "reducedFeatures": Array [
-    Object {
+  "reducedFeatures": [
+    {
+      "end": 100,
+      "score": 1,
+      "start": 1,
+      "uniqueId": "t1",
+    },
+    {
       "end": 200,
       "score": 2,
       "start": 101,

package/src/DensityRenderer/configSchema.ts

@@ -1,11 +1,22 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 
-import ConfigSchema from '../configSchema'
+import baseWiggleRendererConfigSchema from '../configSchema'
+
+/**
+ * #config DensityRenderer
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
 
 const configSchema = ConfigurationSchema(
   'DensityRenderer',
   {},
-  { baseConfiguration: ConfigSchema, explicitlyTyped: true },
+  {
+    /**
+     * #baseConfiguration
+     */
+    baseConfiguration: baseWiggleRendererConfigSchema,
+    explicitlyTyped: true,
+  },
 )
 
 export default configSchema

package/src/LinePlotRenderer/configSchema.ts

@@ -1,16 +1,30 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import ConfigSchema from '../configSchema'
+import baseWiggleRendererConfigSchema from '../configSchema'
+
+/**
+ * #config LinePlotRenderer
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
 
 const configSchema = ConfigurationSchema(
   'LinePlotRenderer',
   {
+    /**
+     * #slot
+     */
     displayCrossHatches: {
       type: 'boolean',
       description: 'choose to draw cross hatches (sideways lines)',
       defaultValue: false,
     },
   },
-  { baseConfiguration: ConfigSchema, explicitlyTyped: true },
+  {
+    /**
+     * #baseConfiguration
+     */
+    baseConfiguration: baseWiggleRendererConfigSchema,
+    explicitlyTyped: true,
+  },
 )
 
 export default configSchema

package/src/LinearWiggleDisplay/models/configSchema.ts

@@ -3,6 +3,11 @@ import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-vie
 import { types } from 'mobx-state-tree'
 import PluginManager from '@jbrowse/core/PluginManager'
 
+/**
+ * #config LinearWiggleDisplay
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
 export default function WiggleConfigFactory(pluginManager: PluginManager) {
   const XYPlotRendererConfigSchema =
     pluginManager.getRendererType('XYPlotRenderer').configSchema
@@ -14,6 +19,9 @@ export default function WiggleConfigFactory(pluginManager: PluginManager) {
   return ConfigurationSchema(
     'LinearWiggleDisplay',
     {
+      /**
+       * #slot
+       */
       autoscale: {
         type: 'stringEnum',
         defaultValue: 'local',
@@ -27,52 +35,82 @@ export default function WiggleConfigFactory(pluginManager: PluginManager) {
         description:
           'global/local using their min/max values or w/ standard deviations (globalsd/localsd)',
       },
+
+      /**
+       * #slot
+       */
       minimalTicks: {
         type: 'boolean',
         defaultValue: false,
         description: 'use the minimal amount of ticks',
       },
 
+      /**
+       * #slot
+       */
       minScore: {
         type: 'number',
         defaultValue: Number.MIN_VALUE,
         description: 'minimum value for the y-scale',
       },
+      /**
+       * #slot
+       */
       maxScore: {
         type: 'number',
         description: 'maximum value for the y-scale',
         defaultValue: Number.MAX_VALUE,
       },
+      /**
+       * #slot
+       */
       numStdDev: {
         type: 'number',
         description:
           'number of standard deviations to use for autoscale types globalsd or localsd',
         defaultValue: 3,
       },
+      /**
+       * #slot
+       */
       scaleType: {
         type: 'stringEnum',
         model: types.enumeration('Scale type', ['linear', 'log']), // todo zscale
         description: 'The type of scale to use',
         defaultValue: 'linear',
       },
+      /**
+       * #slot
+       */
       inverted: {
         type: 'boolean',
         description: 'draw upside down',
         defaultValue: false,
       },
 
+      /**
+       * #slot
+       */
       defaultRendering: {
         type: 'stringEnum',
         model: types.enumeration('Rendering', ['density', 'xyplot', 'line']),
         defaultValue: 'xyplot',
       },
-
+      /**
+       * #slot
+       */
       renderers: ConfigurationSchema('RenderersConfiguration', {
         DensityRenderer: DensityRendererConfigSchema,
         XYPlotRenderer: XYPlotRendererConfigSchema,
         LinePlotRenderer: LinePlotRendererConfigSchema,
       }),
     },
-    { baseConfiguration: baseLinearDisplayConfigSchema, explicitlyTyped: true },
+    {
+      /**
+       * #baseConfiguration
+       */
+      baseConfiguration: baseLinearDisplayConfigSchema,
+      explicitlyTyped: true,
+    },
   )
 }