Add track menu items for the indicators/fuzz

GMOD · Feb 16, 2021 · 0b263b9 · 0b263b9
1 parent f41b301
commit 0b263b9
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Showing 3 changed files with 70 additions and 21 deletions.
diff --git a/plugins/alignments/src/LinearPileupDisplay/model.ts b/plugins/alignments/src/LinearPileupDisplay/model.ts
@@ -359,12 +359,14 @@ const stateModelFactory = (
           return filters
         },
 
+        get rendererConfig() {
+          const configBlob =
+            getConf(self, ['renderers', self.rendererTypeName]) || {}
+          return self.rendererType.configSchema.create(configBlob)
+        },
+
         get renderProps() {
           const view = getContainingView(self) as LGV
-          const config = self.rendererType.configSchema.create(
-            getConf(self, ['renderers', self.rendererTypeName]) || {},
-          )
-
           return {
             ...self.composedRenderProps,
             ...getParentRenderProps(self),
@@ -377,7 +379,7 @@ const stateModelFactory = (
             colorTagMap: JSON.parse(JSON.stringify(self.colorTagMap)),
             filters: this.filters,
             showSoftClip: self.showSoftClipping,
-            config,
+            config: this.rendererConfig,
           }
         },
 

diff --git a/plugins/alignments/src/LinearSNPCoverageDisplay/models/model.ts b/plugins/alignments/src/LinearSNPCoverageDisplay/models/model.ts
@@ -1,5 +1,5 @@
 import { types, cast } from 'mobx-state-tree'
-import { getConf } from '@jbrowse/core/configuration'
+import { getConf, readConfObject } from '@jbrowse/core/configuration'
 import { getParentRenderProps } from '@jbrowse/core/util/tracks'
 import {
   linearWiggleDisplayModelFactory,
@@ -25,6 +25,8 @@ const stateModelFactory = (
       linearWiggleDisplayModelFactory(pluginManager, configSchema),
       types.model({
         type: types.literal('LinearSNPCoverageDisplay'),
+        drawInterbaseFuzz: types.maybe(types.boolean),
+        drawIndicators: types.maybe(types.boolean),
         filterBy: types.optional(
           types.model({
             flagInclude: types.optional(types.number, 0),
@@ -51,6 +53,42 @@ const stateModelFactory = (
         self.filterBy = cast(filter)
       },
     }))
+    .views(self => ({
+      get rendererConfig() {
+        const configBlob =
+          getConf(self, ['renderers', self.rendererTypeName]) || {}
+
+        return self.rendererType.configSchema.create({
+          ...configBlob,
+          drawInterbaseFuzz:
+            self.drawInterbaseFuzz === undefined
+              ? configBlob.drawInterbaseFuzz
+              : self.drawInterbaseFuzz,
+          drawIndicators:
+            self.drawIndicators === undefined
+              ? configBlob.drawIndicators
+              : self.drawIndicators,
+        })
+      },
+      get drawInterbaseFuzzSetting() {
+        return self.drawInterbaseFuzz !== undefined
+          ? self.drawInterbaseFuzz
+          : readConfObject(this.rendererConfig, 'drawInterbaseFuzz')
+      },
+      get drawIndicatorsSetting() {
+        return self.drawIndicators !== undefined
+          ? self.drawIndicators
+          : readConfObject(this.rendererConfig, 'drawIndicators')
+      },
+    }))
+    .actions(self => ({
+      toggleDrawIndicators() {
+        self.drawIndicators = !self.drawIndicators
+      },
+      toggleDrawInterbaseFuzz() {
+        self.drawInterbaseFuzz = !self.drawInterbaseFuzz
+      },
+    }))
 
     .views(self => ({
       get TooltipComponent() {
@@ -77,6 +115,27 @@ const stateModelFactory = (
         return []
       },
 
+      get composedTrackMenuItems() {
+        return [
+          {
+            label: 'Draw indicators',
+            type: 'checkbox',
+            checked: self.drawIndicatorsSetting,
+            onClick: () => {
+              self.toggleDrawIndicators()
+            },
+          },
+          {
+            label: 'Draw interbase fuzz',
+            type: 'checkbox',
+            checked: self.drawInterbaseFuzzSetting,
+            onClick: () => {
+              self.toggleDrawInterbaseFuzz()
+            },
+          },
+        ]
+      },
+
       // The SNPCoverage filters are called twice because the BAM/CRAM features
       // pass filters and then the SNPCoverage score features pass through
       // here, and those have no name/flags/tags so those are passed thru
@@ -128,10 +187,6 @@ const stateModelFactory = (
       },
 
       get renderProps() {
-        const config = self.rendererType.configSchema.create(
-          getConf(self, ['renderers', self.rendererTypeName]) || {},
-        )
-
         return {
           ...self.composedRenderProps,
           ...getParentRenderProps(self),
@@ -141,7 +196,7 @@ const stateModelFactory = (
           displayModel: self,
           scaleOpts: this.scaleOpts,
           filters: self.filters,
-          config,
+          config: self.rendererConfig,
         }
       },
     }))

diff --git a/plugins/alignments/src/SNPCoverageRenderer/SNPCoverageRenderer.ts b/plugins/alignments/src/SNPCoverageRenderer/SNPCoverageRenderer.ts
@@ -104,17 +104,9 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
     for (const feature of features.values()) {
       const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx)
       const infoArray: BaseInfo[] = feature.get('snpinfo') || []
-      const total = infoArray.find(info => info.base === 'total')?.score || 0
-      const softclip =
-        infoArray.find(info => info.base === 'softclip')?.score || 0
-      const hardclip =
-        infoArray.find(info => info.base === 'hardclip')?.score || 0
-      const insertion =
-        infoArray.find(info => info.base === 'insertion')?.score || 0
-      const deletion =
-        infoArray.find(info => info.base === 'deletion')?.score || 0
+      const totalScore =
+        infoArray.find(info => info.base === 'total')?.score || 0
 
-      const totalScore = total - softclip - hardclip - insertion - deletion
       const w = Math.max(rightPx - leftPx + 0.3, 1)
       infoArray
         .filter(