Rename some variables

GMOD · Jan 28, 2025 · 085d5d1 · 085d5d1
1 parent 33330c9
commit 085d5d1
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Showing 11 changed files with 289 additions and 311 deletions.
diff --git a/plugins/alignments/src/LinearSNPCoverageDisplay/model.ts b/plugins/alignments/src/LinearSNPCoverageDisplay/model.ts
@@ -57,7 +57,7 @@ function stateModelFactory(
         /**
          * #property
          */
-        showIndicators: types.maybe(types.boolean),
+        showInterbaseIndicators: types.maybe(types.boolean),
         /**
          * #property
          */
@@ -159,17 +159,15 @@ function stateModelFactory(
           const configBlob =
             getConf(self, ['renderers', self.rendererTypeName]) || {}
 
-          const {
-            showArcs: showArcs,
-            showInterbaseCounts,
-            showIndicators: showIndicators,
-          } = self
+          const { showArcs, showInterbaseCounts, showInterbaseIndicators } =
+            self
           return self.rendererType.configSchema.create(
             {
               ...configBlob,
               showInterbaseCounts:
                 showInterbaseCounts ?? configBlob.showInterbaseCounts,
-              showIndicators: showIndicators ?? configBlob.showIndicators,
+              showInterbaseIndicators:
+                showInterbaseIndicators ?? configBlob.showInterbaseIndicators,
               showArcs: showArcs ?? configBlob.showArcs,
             },
             getEnv(self),
@@ -195,10 +193,10 @@ function stateModelFactory(
         /**
          * #getter
          */
-        get showIndicatorsSetting() {
+        get showInterbaseIndicatorsSetting() {
           return (
-            self.showIndicators ??
-            readConfObject(this.rendererConfig, 'showIndicators')
+            self.showInterbaseIndicators ??
+            readConfObject(this.rendererConfig, 'showInterbaseIndicators')
           )
         },
 
@@ -238,8 +236,8 @@ function stateModelFactory(
       /**
        * #action
        */
-      setShowIndicators(arg: boolean) {
-        self.showIndicators = arg
+      setShowInterbaseIndicators(arg: boolean) {
+        self.showInterbaseIndicators = arg
       },
       /**
        * #action
@@ -368,9 +366,11 @@ function stateModelFactory(
               label: 'Show insertion/clipping indicators',
               icon: VisibilityIcon,
               type: 'checkbox',
-              checked: self.showIndicatorsSetting,
+              checked: self.showInterbaseIndicatorsSetting,
               onClick: () => {
-                self.setShowIndicators(!self.showIndicatorsSetting)
+                self.setShowInterbaseIndicators(
+                  !self.showInterbaseIndicatorsSetting,
+                )
               },
             },
             {

diff --git a/plugins/variants/src/MultiLinearVariantDisplay/components/Crosshair.tsx b/plugins/variants/src/MultiLinearVariantDisplay/components/Crosshair.tsx
@@ -35,7 +35,7 @@ const Crosshair = observer(function ({
   const { hoveredGenotype, height, scrollTop, rowHeight, sources } = model
   const { width } = getContainingView(model) as LinearGenomeViewModel
   const source = sources?.[Math.floor(mouseY / rowHeight)]
-  const y = mouseY - lineZoneHeight - scrollTop
+  const y = mouseY - scrollTop
   return source ? (
     <div className={classes.rel}>
       <svg

diff --git a/plugins/variants/src/MultiLinearVariantDisplay/model.ts b/plugins/variants/src/MultiLinearVariantDisplay/model.ts
@@ -31,6 +31,10 @@ export function stateModelFactory(configSchema: AnyConfigurationSchemaType) {
          * #property
          */
         minorAlleleFrequencyFilter: types.optional(types.number, 0),
+        /**
+         * #property
+         */
+        autoHeight: false,
       }),
     )
     .views(() => ({

diff --git a/plugins/variants/src/shared/MultiVariantBaseModel.tsx b/plugins/variants/src/shared/MultiVariantBaseModel.tsx
@@ -68,7 +68,7 @@ export default function MultiVariantBaseModelF(
          * #property
          * used only if autoHeight is false
          */
-        rowHeightSetting: types.optional(types.number, 1),
+        rowHeightSetting: types.optional(types.number, 8),
 
         /**
          * #property

diff --git a/website/docs/models/BaseWebSession.md b/website/docs/models/BaseWebSession.md
@@ -165,7 +165,7 @@ renderProps: () => {
 
 ```js
 // type signature
-getTrackActionMenuItems: (config: { [x: string]: any; } & NonEmptyObject & { setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({ [x: string]: any; } & NonEmptyObject & { ...; } & IStateTreeNode<...>); } & IStateTreeNode<...>) => ({ ...; } | { ...; })[]
+getTrackActionMenuItems: (config: { [x: string]: any; } & NonEmptyObject & { setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({ [x: string]: any; } & NonEmptyObject & { ...; } & IStateTreeNode<...>); } & IStateTreeNode<...>) => ({ ...; } | ... 1 more ... | { ...; })[]
 ```
 
 #### method: menus

diff --git a/website/docs/models/DesktopSessionTrackMenuMixin.md b/website/docs/models/DesktopSessionTrackMenuMixin.md
@@ -26,5 +26,5 @@ reference the markdown files in our repo of the checked out git tag
 
 ```js
 // type signature
-getTrackActionMenuItems: (trackConfig: { [x: string]: any; } & NonEmptyObject & { setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({ [x: string]: any; } & NonEmptyObject & { ...; } & IStateTreeNode<...>); } & IStateTreeNode<...>) => { ...; }[]
+getTrackActionMenuItems: (trackConfig: { [x: string]: any; } & NonEmptyObject & { setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({ [x: string]: any; } & NonEmptyObject & { ...; } & IStateTreeNode<...>); } & IStateTreeNode<...>) => ({ ...; } | { ...; })[]
 ```
diff --git a/website/docs/models/LinearSNPCoverageDisplay.md b/website/docs/models/LinearSNPCoverageDisplay.md
@@ -35,31 +35,31 @@ ISimpleType<"LinearSNPCoverageDisplay">
 type: types.literal('LinearSNPCoverageDisplay')
 ```
 
-#### property: drawInterbaseCounts
+#### property: showInterbaseCounts
 
 ```js
 // type signature
 IMaybe<ISimpleType<boolean>>
 // code
-drawInterbaseCounts: types.maybe(types.boolean)
+showInterbaseCounts: types.maybe(types.boolean)
 ```
 
-#### property: drawIndicators
+#### property: showIndicators
 
 ```js
 // type signature
 IMaybe<ISimpleType<boolean>>
 // code
-drawIndicators: types.maybe(types.boolean)
+showIndicators: types.maybe(types.boolean)
 ```
 
-#### property: drawArcs
+#### property: showArcs
 
 ```js
 // type signature
 IMaybe<ISimpleType<boolean>>
 // code
-drawArcs: types.maybe(types.boolean)
+showArcs: types.maybe(types.boolean)
 ```
 
 #### property: filterBySetting
@@ -112,21 +112,21 @@ any
 { [x: string]: any; } & NonEmptyObject & { setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({ [x: string]: any; } & NonEmptyObject & ... & IStateTreeNode<...>); } & IStateTreeNode<...>
 ```
 
-#### getter: drawArcsSetting
+#### getter: showArcsSetting
 
 ```js
 // type
 any
 ```
 
-#### getter: drawInterbaseCountsSetting
+#### getter: showInterbaseCountsSetting
 
 ```js
 // type
 any
 ```
 
-#### getter: drawIndicatorsSetting
+#### getter: showIndicatorsSetting
 
 ```js
 // type
@@ -266,23 +266,23 @@ updateVisibleModifications: (uniqueModifications: ModificationType[]) => void
 setModificationsReady: (flag: boolean) => void
 ```
 
-#### action: toggleDrawIndicators
+#### action: setShowIndicators
 
 ```js
 // type signature
-toggleDrawIndicators: () => void
+setShowIndicators: (arg: boolean) => void
 ```
 
-#### action: toggleDrawInterbaseCounts
+#### action: setShowInterbaseCounts
 
 ```js
 // type signature
-toggleDrawInterbaseCounts: () => void
+setShowInterbaseCounts: (arg: boolean) => void
 ```
 
-#### action: toggleDrawArcs
+#### action: setShowArcs
 
 ```js
 // type signature
-toggleDrawArcs: () => void
+setShowArcs: (arg: boolean) => void
 ```
diff --git a/website/docs/models/LinearVariantMatrixDisplay.md b/website/docs/models/LinearVariantMatrixDisplay.md
@@ -22,7 +22,7 @@ reference the markdown files in our repo of the checked out git tag
 
 extends
 
-- [LinearBareDisplay](../linearbaredisplay)
+- [MultiVariantBaseModel](../multivariantbasemodel)
 
 ### LinearVariantMatrixDisplay - Properties
 
@@ -35,67 +35,17 @@ ISimpleType<"LinearVariantMatrixDisplay">
 type: types.literal('LinearVariantMatrixDisplay')
 ```
 
-#### property: layout
-
-```js
-// type signature
-IOptionalIType<IType<Source[], Source[], Source[]>, [undefined]>
-// code
-layout: types.optional(types.frozen<Source[]>(), [])
-```
-
-#### property: configuration
-
-```js
-// type signature
-AnyConfigurationSchemaType
-// code
-configuration: ConfigurationReference(configSchema)
-```
-
-#### property: minorAlleleFrequencyFilter
+#### property: rowHeightSetting
 
 ```js
 // type signature
 IOptionalIType<ISimpleType<number>, [undefined]>
 // code
-minorAlleleFrequencyFilter: types.optional(types.number, 0.1)
-```
-
-#### property: showSidebarLabelsSetting
-
-```js
-// type signature
-true
-// code
-showSidebarLabelsSetting: true
-```
-
-#### property: phasedMode
-
-```js
-// type signature
-IOptionalIType<ISimpleType<string>, [undefined]>
-// code
-phasedMode: types.optional(types.string, 'none')
+rowHeightSetting: types.optional(types.number, 1)
 ```
 
 ### LinearVariantMatrixDisplay - Getters
 
-#### getter: preSources
-
-```js
-// type
-Source[]
-```
-
-#### getter: sources
-
-```js
-// type
-any[]
-```
-
 #### getter: blockType
 
 ```js
@@ -126,20 +76,6 @@ boolean
 
 ### LinearVariantMatrixDisplay - Methods
 
-#### method: adapterProps
-
-```js
-// type signature
-adapterProps: () => any
-```
-
-#### method: trackMenuItems
-
-```js
-// type signature
-trackMenuItems: () => (MenuDivider | MenuSubHeader | NormalMenuItem | CheckboxMenuItem | RadioMenuItem | SubMenuItem | { ...; } | { ...; })[]
-```
-
 #### method: renderProps
 
 ```js
@@ -149,76 +85,6 @@ renderProps: () => any
 
 ### LinearVariantMatrixDisplay - Actions
 
-#### action: setFeatures
-
-```js
-// type signature
-setFeatures: (f: Feature[]) => void
-```
-
-#### action: setLayout
-
-```js
-// type signature
-setLayout: (layout: Source[]) => void
-```
-
-#### action: clearLayout
-
-```js
-// type signature
-clearLayout: () => void
-```
-
-#### action: setSourcesLoading
-
-```js
-// type signature
-setSourcesLoading: (str: string) => void
-```
-
-#### action: setSources
-
-```js
-// type signature
-setSources: (sources: Source[]) => void
-```
-
-#### action: setMafFilter
-
-```js
-// type signature
-setMafFilter: (arg: number) => void
-```
-
-#### action: setShowSidebarLabels
-
-```js
-// type signature
-setShowSidebarLabels: (arg: boolean) => void
-```
-
-#### action: setPhasedMode
-
-```js
-// type signature
-setPhasedMode: (arg: string) => void
-```
-
-#### action: setHasPhased
-
-```js
-// type signature
-setHasPhased: (arg: boolean) => void
-```
-
-#### action: setSamplePloidy
-
-```js
-// type signature
-setSamplePloidy: (arg: Record<string, number>) => void
-```
-
 #### action: renderSvg
 
 ```js

diff --git a/website/docs/models/LinearWiggleDisplay.md b/website/docs/models/LinearWiggleDisplay.md
@@ -108,7 +108,7 @@ renderProps: () => any
 
 ```js
 // type signature
-trackMenuItems: () => (MenuDivider | MenuSubHeader | NormalMenuItem | CheckboxMenuItem | RadioMenuItem | SubMenuItem | { ...; } | { ...; } | { ...; })[]
+trackMenuItems: () => (MenuDivider | MenuSubHeader | NormalMenuItem | CheckboxMenuItem | RadioMenuItem | SubMenuItem | ... 4 more ... | { ...; })[]
 ```
 
 ### LinearWiggleDisplay - Actions