@jbrowse/plugin-wiggle 2.1.7 → 2.2.0

package/src/MultiLinearWiggleDisplay/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 MultiLinearWiggleDisplay
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
 export default function WiggleConfigFactory(pluginManager: PluginManager) {
   const MultiXYPlotRendererConfigSchema = pluginManager.getRendererType(
     'MultiXYPlotRenderer',
@@ -22,6 +27,9 @@ export default function WiggleConfigFactory(pluginManager: PluginManager) {
   return ConfigurationSchema(
     'MultiLinearWiggleDisplay',
     {
+      /**
+       * #slot
+       */
       autoscale: {
         type: 'stringEnum',
         defaultValue: 'local',
@@ -35,40 +43,63 @@ 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', [
@@ -81,6 +112,9 @@ export default function WiggleConfigFactory(pluginManager: PluginManager) {
         defaultValue: 'multirowxy',
       },
 
+      /**
+       * #slot
+       */
       renderers: ConfigurationSchema('RenderersConfiguration', {
         MultiXYPlotRenderer: MultiXYPlotRendererConfigSchema,
         MultiDensityRenderer: MultiDensityRendererConfigSchema,
@@ -89,6 +123,12 @@ export default function WiggleConfigFactory(pluginManager: PluginManager) {
         MultiRowLineRenderer: MultiRowLineRendererConfigSchema,
       }),
     },
-    { baseConfiguration: baseLinearDisplayConfigSchema, explicitlyTyped: true },
+    {
+      /**
+       * #baseConfiguration
+       */
+      baseConfiguration: baseLinearDisplayConfigSchema,
+      explicitlyTyped: true,
+    },
   )
 }

package/src/MultiQuantitativeTrack/configSchema.ts

@@ -0,0 +1,23 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+import { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes/models'
+import PluginManager from '@jbrowse/core/PluginManager'
+
+/**
+ * #config MultiQuantitativeTrack
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const configSchema = (pluginManager: PluginManager) => {
+  return ConfigurationSchema(
+    'MultiQuantitativeTrack',
+    {},
+    {
+      /**
+       * #baseConfiguration
+       */
+      baseConfiguration: createBaseTrackConfig(pluginManager),
+    },
+  )
+}
+
+export default configSchema

package/src/MultiQuantitativeTrack/index.ts

@@ -1,18 +1,11 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import {
-  createBaseTrackConfig,
-  createBaseTrackModel,
-} from '@jbrowse/core/pluggableElementTypes/models'
+import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models'
 import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType'
 import PluginManager from '@jbrowse/core/PluginManager'
+import configSchemaF from './configSchema'
 
 export default (pluginManager: PluginManager) => {
   pluginManager.addTrackType(() => {
-    const configSchema = ConfigurationSchema(
-      'MultiQuantitativeTrack',
-      {},
-      { baseConfiguration: createBaseTrackConfig(pluginManager) },
-    )
+    const configSchema = configSchemaF(pluginManager)
     return new TrackType({
       name: 'MultiQuantitativeTrack',
       configSchema,

package/src/MultiRowLineRenderer/configSchema.ts

@@ -1,16 +1,27 @@
 import { types } from 'mobx-state-tree'
 
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import ConfigSchema from '../configSchema'
+import baseWiggleRendererConfigSchema from '../configSchema'
+
+/**
+ * #config MultiRowLineRenderer
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
 
 const configSchema = ConfigurationSchema(
   'MultiRowLineRenderer',
   {
+    /**
+     * #slot
+     */
     displayCrossHatches: {
       type: 'boolean',
       description: 'choose to draw cross hatches (sideways lines)',
       defaultValue: false,
     },
+    /**
+     * #slot
+     */
     summaryScoreMode: {
       type: 'stringEnum',
       model: types.enumeration('Score type', ['max', 'min', 'avg', 'whiskers']),
@@ -19,7 +30,13 @@ const configSchema = ConfigurationSchema(
       defaultValue: 'avg',
     },
   },
-  { baseConfiguration: ConfigSchema, explicitlyTyped: true },
+  {
+    /**
+     * #baseConfiguration
+     */
+    baseConfiguration: baseWiggleRendererConfigSchema,
+    explicitlyTyped: true,
+  },
 )
 
 export default configSchema

package/src/MultiRowXYPlotRenderer/configSchema.ts

@@ -1,20 +1,34 @@
 import { types } from 'mobx-state-tree'
 
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import ConfigSchema from '../configSchema'
+import baseWiggleRendererConfigSchema from '../configSchema'
+
+/**
+ * #config MultiRowXYPlotRenderer
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
 
 const configSchema = ConfigurationSchema(
   'MultiRowXYPlotRenderer',
   {
+    /**
+     * #slot
+     */
     filled: {
       type: 'boolean',
       defaultValue: true,
     },
+    /**
+     * #slot
+     */
     displayCrossHatches: {
       type: 'boolean',
       description: 'choose to draw cross hatches (sideways lines)',
       defaultValue: false,
     },
+    /**
+     * #slot
+     */
     summaryScoreMode: {
       type: 'stringEnum',
       model: types.enumeration('Score type', ['max', 'min', 'avg', 'whiskers']),
@@ -22,12 +36,21 @@ const configSchema = ConfigurationSchema(
         'choose whether to use max/min/average or whiskers which combines all three into the same rendering',
       defaultValue: 'whiskers',
     },
+    /**
+     * #slot
+     */
     minSize: {
       type: 'number',
       defaultValue: 0,
     },
   },
-  { baseConfiguration: ConfigSchema, explicitlyTyped: true },
+  {
+    /**
+     * #baseConfiguration
+     */
+    baseConfiguration: baseWiggleRendererConfigSchema,
+    explicitlyTyped: true,
+  },
 )
 
 export default configSchema

package/src/MultiWiggleAdapter/configSchema.ts

@@ -1,16 +1,32 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 
-export default ConfigurationSchema(
+/**
+ * #config MultiWiggleAdapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const MultiWiggleAdapter = ConfigurationSchema(
   'MultiWiggleAdapter',
   {
+    /**
+     * #slot
+     */
     subadapters: {
       type: 'frozen',
       defaultValue: [],
+      description: 'array of subadapter JSON objects',
     },
+    /**
+     * #slot
+     */
     bigWigs: {
       type: 'frozen',
+      description:
+        'array of bigwig filenames, alternative to the subadapters slot',
       defaultValue: [],
     },
   },
   { explicitlyTyped: true },
 )
+
+export default MultiWiggleAdapter

package/src/MultiXYPlotRenderer/configSchema.ts

@@ -1,19 +1,33 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 import { types } from 'mobx-state-tree'
-import ConfigSchema from '../configSchema'
+import baseWiggleRendererConfigSchema from '../configSchema'
+
+/**
+ * #config MultiXYPlotRenderer
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
 
 const configSchema = ConfigurationSchema(
   'MultiXYPlotRenderer',
   {
+    /**
+     * #slot
+     */
     filled: {
       type: 'boolean',
       defaultValue: true,
     },
+    /**
+     * #slot
+     */
     displayCrossHatches: {
       type: 'boolean',
       description: 'choose to draw cross hatches (sideways lines)',
       defaultValue: false,
     },
+    /**
+     * #slot
+     */
     summaryScoreMode: {
       type: 'stringEnum',
       model: types.enumeration('Score type', ['max', 'min', 'avg', 'whiskers']),
@@ -21,11 +35,20 @@ const configSchema = ConfigurationSchema(
         'choose whether to use max/min/average or whiskers which combines all three into the same rendering',
       defaultValue: 'avg',
     },
+    /**
+     * #slot
+     */
     minSize: {
       type: 'number',
       defaultValue: 0,
     },
   },
-  { baseConfiguration: ConfigSchema, explicitlyTyped: true },
+  {
+    /**
+     * #baseConfiguration
+     */
+    baseConfiguration: baseWiggleRendererConfigSchema,
+    explicitlyTyped: true,
+  },
 )
 export default configSchema

package/src/QuantitativeTrack/configSchema.ts

@@ -0,0 +1,23 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+import { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes/models'
+import PluginManager from '@jbrowse/core/PluginManager'
+
+/**
+ * #config QuantitativeTrack
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+function configSchemaFactory(pluginManager: PluginManager) {
+  return ConfigurationSchema(
+    'QuantitativeTrack',
+    {},
+    {
+      /**
+       * #baseConfiguration
+       */
+      baseConfiguration: createBaseTrackConfig(pluginManager),
+    },
+  )
+}
+
+export default configSchemaFactory

package/src/QuantitativeTrack/index.ts

@@ -1,18 +1,11 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import {
-  createBaseTrackConfig,
-  createBaseTrackModel,
-} from '@jbrowse/core/pluggableElementTypes/models'
+import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models'
 import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType'
 import PluginManager from '@jbrowse/core/PluginManager'
+import configSchemaF from './configSchema'
 
 export default (pluginManager: PluginManager) => {
   pluginManager.addTrackType(() => {
-    const configSchema = ConfigurationSchema(
-      'QuantitativeTrack',
-      {},
-      { baseConfiguration: createBaseTrackConfig(pluginManager) },
-    )
+    const configSchema = configSchemaF(pluginManager)
     return new TrackType({
       name: 'QuantitativeTrack',
       configSchema,

package/src/WiggleBaseRenderer.tsx

@@ -82,7 +82,7 @@ export default abstract class WiggleBaseRenderer extends FeatureRendererType {
     }
   }
 
-  /*
+  /**
    * draw features to context given props, to be used by derived renderer
    * classes
    */

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

@@ -4,6 +4,12 @@ exports[`several features 1`] = `
 Object {
   "imageData": Any<Object>,
   "reducedFeatures": Array [
+    Object {
+      "end": 100,
+      "score": 1,
+      "start": 1,
+      "uniqueId": "t1",
+    },
     Object {
       "end": 200,
       "score": 2,

package/src/XYPlotRenderer/configSchema.ts

@@ -1,19 +1,33 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import ConfigSchema from '../configSchema'
+import baseWiggleRendererConfigSchema from '../configSchema'
 import { types } from 'mobx-state-tree'
 
+/**
+ * #config XYPlotRenderer
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
 const configSchema = ConfigurationSchema(
   'XYPlotRenderer',
   {
+    /**
+     * #slot
+     */
     filled: {
       type: 'boolean',
       defaultValue: true,
     },
+    /**
+     * #slot
+     */
     displayCrossHatches: {
       type: 'boolean',
       description: 'choose to draw cross hatches (sideways lines)',
       defaultValue: false,
     },
+    /**
+     * #slot
+     */
     summaryScoreMode: {
       type: 'stringEnum',
       model: types.enumeration('Score type', ['max', 'min', 'avg', 'whiskers']),
@@ -21,12 +35,21 @@ const configSchema = ConfigurationSchema(
         'choose whether to use max/min/average or whiskers which combines all three into the same rendering',
       defaultValue: 'whiskers',
     },
+    /**
+     * #slot
+     */
     minSize: {
       type: 'number',
       defaultValue: 0,
     },
   },
-  { baseConfiguration: ConfigSchema, explicitlyTyped: true },
+  {
+    /**
+     * #baseConfiguration
+     */
+    baseConfiguration: baseWiggleRendererConfigSchema,
+    explicitlyTyped: true,
+  },
 )
 
 export default configSchema

package/src/configSchema.ts

@@ -1,29 +1,50 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 import { types } from 'mobx-state-tree'
 
-export default ConfigurationSchema(
+/**
+ * #config WiggleRenderer
+ * this is the "base wiggle renderer config schema"
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const WiggleRenderer = ConfigurationSchema(
   'WiggleRenderer',
   {
+    /**
+     * #slot
+     */
     color: {
       type: 'color',
       description: 'the color of track, overrides posColor and negColor',
       defaultValue: '#f0f',
     },
+    /**
+     * #slot
+     */
     posColor: {
       type: 'color',
       description: 'the color to use when the score is positive',
       defaultValue: 'blue',
     },
+    /**
+     * #slot
+     */
     negColor: {
       type: 'color',
       description: 'the color to use when the score is negative',
       defaultValue: 'red',
     },
+    /**
+     * #slot
+     */
     clipColor: {
       type: 'color',
       description: 'the color of the clipping marker',
       defaultValue: 'red',
     },
+    /**
+     * #slot
+     */
     bicolorPivot: {
       type: 'stringEnum',
       model: types.enumeration('Scale type', [
@@ -35,6 +56,9 @@ export default ConfigurationSchema(
       description: 'type of bicolor pivot',
       defaultValue: 'numeric',
     },
+    /**
+     * #slot
+     */
     bicolorPivotValue: {
       type: 'number',
       defaultValue: 0,
@@ -43,3 +67,4 @@ export default ConfigurationSchema(
   },
   { explicitlyTyped: true },
 )
+export default WiggleRenderer

package/src/drawxy.ts

@@ -83,7 +83,7 @@ export function drawXY(
   const getHeight = (n: number) => (filled ? toOrigin(n) : Math.max(minSize, 1))
   let hasClipping = false
 
-  let prevLeftPx = 0
+  let prevLeftPx = -Infinity
   const reducedFeatures = []
   const crossingOrigin = niceMin < pivotValue && niceMax > pivotValue
 
@@ -96,7 +96,7 @@ export function drawXY(
     for (const feature of features.values()) {
       const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx)
       if (feature.get('summary')) {
-        const w = rightPx - leftPx + fudgeFactor
+        const w = Math.max(rightPx - leftPx + fudgeFactor, minSize)
         const max = feature.get('maxScore')
         const c = colorCallback(feature, max)
         const effectiveC = crossingOrigin
@@ -255,7 +255,7 @@ export function drawLine(
 
   let lastVal
 
-  let prevLeftPx = 0
+  let prevLeftPx = -Infinity
   const reducedFeatures = []
   for (const feature of features.values()) {
     const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx)
@@ -347,7 +347,7 @@ export function drawDensity(
   }
   const [niceMin, niceMax] = scale2.domain()
 
-  let prevLeftPx = 0
+  let prevLeftPx = -Infinity
   let hasClipping = false
   const reducedFeatures = []
   for (const feature of features.values()) {