Update auto-generated docs

plugins/linear-comparative-view/src/LinearSyntenyView/model.ts

@@ -6,11 +6,11 @@ import PluginManager from '@jbrowse/core/PluginManager'
 import CropFreeIcon from '@mui/icons-material/CropFree'
 import LinkIcon from '@mui/icons-material/Link'
 import LinkOffIcon from '@mui/icons-material/LinkOff'
+import VisibilityIcon from '@mui/icons-material/Visibility'
 import { Curves } from './components/Icons'
 
 // locals
 import baseModel from '../LinearComparativeView/model'
-import VisibilityIcon from '@mui/icons-material/Visibility'
 
 /**
  * #stateModel LinearSyntenyView

website/docs/config/LinearComparativeDisplay.md

@@ -9,16 +9,6 @@ source code. See [Config guide](/docs/config_guide) for more info
 
 ## Docs
 
-### LinearComparativeDisplay - Slots
+### LinearComparativeDisplay - Identifier
 
-#### slot: renderer
-
-```js
-renderer: pluginManager.pluggableConfigSchemaType('renderer')
-```
-
-## LinearComparativeDisplay - Derives from
-
-```js
-baseConfiguration: baseLinearDisplayConfigSchema
-```
+#### slot: explicitIdentifier

website/docs/config/LinearSyntenyDisplay.md

@@ -22,14 +22,6 @@ trackIds: {
       }
 ```
 
-#### slot: renderer
-
-```js
-renderer: types.optional(pluginManager.pluggableConfigSchemaType('renderer'), {
-  type: 'LinearSyntenyRenderer',
-})
-```
-
 #### slot: middle
 
 currently unused
@@ -40,7 +32,7 @@ middle: { type: 'boolean', defaultValue: true }
 
 ## LinearSyntenyDisplay - Derives from
 
-this refers to the base linear comparative display
+this refers to the LinearComparativeDisplay
 
 ```js
 baseConfiguration: baseConfigFactory(pluginManager)

website/docs/models/DotplotView.md

@@ -421,3 +421,10 @@ squareView: () => void
 // type signature
 squareViewProportional: () => void
 ```
+
+#### action: showAllRegions
+
+```js
+// type signature
+showAllRegions: () => void
+```

website/docs/models/JBrowseReactCGVSessionModel.md

@@ -262,8 +262,6 @@ removeView: () => void
 
 #### action: addWidget
 
-does nothing
-
 ```js
 // type signature
 addWidget: (
@@ -276,8 +274,6 @@ addWidget: (
 
 #### action: showWidget
 
-does nothing
-
 ```js
 // type signature
 showWidget: (widget: any) => void

website/docs/models/LinearComparativeDisplay.md

@@ -42,13 +42,6 @@ height: 100
 
 ### LinearComparativeDisplay - Getters
 
-#### getter: rendererTypeName
-
-```js
-// type
-any
-```
-
 #### getter: renderProps
 
 ```js
@@ -82,7 +75,7 @@ controlled by a reaction
 
 ```js
 // type signature
-setRendered: (args?: { data: unknown; reactElement: React.ReactElement; renderingComponent: React.Component; }) => void
+setRendered: (args?: { features: Feature[]; }) => void
 ```
 
 #### action: setError

website/docs/models/LinearComparativeView.md

@@ -31,15 +31,6 @@ ISimpleType<"LinearComparativeView">
 type: types.literal('LinearComparativeView')
 ```
 
-#### property: height
-
-```js
-// type signature
-number
-// code
-height: defaultHeight
-```
-
 #### property: trackSelectorType
 
 ```js
@@ -156,6 +147,16 @@ any[]
 
 ### LinearComparativeView - Methods
 
+#### method: headerMenuItems
+
+includes a subset of view menu options because the full list is a little
+overwhelming. overridden by subclasses
+
+```js
+// type signature
+headerMenuItems: () => MenuItem[]
+```
+
 #### method: menuItems
 
 ```js
@@ -179,13 +180,6 @@ rubberBandMenuItems: () => { label: string; onClick: () => void; }[]
 setWidth: (newWidth: number) => void
 ```
 
-#### action: setHeight
-
-```js
-// type signature
-setHeight: (newHeight: number) => void
-```
-
 #### action: setViews
 
 ```js

website/docs/models/LinearSyntenyDisplay.md

@@ -35,34 +35,88 @@ configuration: ConfigurationReference(configSchema)
 
 ### LinearSyntenyDisplay - Getters
 
-#### getter: rendererTypeName
+#### getter: adapterConfig
 
 ```js
 // type
 any
 ```
 
-#### getter: adapterConfig
+#### getter: trackIds
 
 ```js
 // type
-any
+string[]
 ```
 
-#### getter: trackIds
+#### getter: numFeats
 
-unused
+```js
+// type
+number
+```
+
+#### getter: featMap
 
 ```js
 // type
-string[]
+{ [k: string]: FeatPos; }
+```
+
+### LinearSyntenyDisplay - Actions
+
+#### action: setFeatPositions
+
+```js
+// type signature
+setFeatPositions: (arg: FeatPos[]) => void
+```
+
+#### action: setMainCanvasRef
+
+```js
+// type signature
+setMainCanvasRef: (ref: HTMLCanvasElement) => void
+```
+
+#### action: setClickMapCanvasRef
+
+```js
+// type signature
+setClickMapCanvasRef: (ref: HTMLCanvasElement) => void
+```
+
+#### action: setCigarClickMapCanvasRef
+
+```js
+// type signature
+setCigarClickMapCanvasRef: (ref: HTMLCanvasElement) => void
 ```
 
-### LinearSyntenyDisplay - Methods
+#### action: setMouseoverCanvasRef
+
+```js
+// type signature
+setMouseoverCanvasRef: (ref: HTMLCanvasElement) => void
+```
+
+#### action: setMouseoverId
+
+```js
+// type signature
+setMouseoverId: (arg: number) => void
+```
+
+#### action: setCigarMouseoverId
+
+```js
+// type signature
+setCigarMouseoverId: (arg: number) => void
+```
 
-#### method: renderProps
+#### action: setClickId
 
 ```js
 // type signature
-renderProps: () => { rpcDriverName: string; displayModel: { id: string; type: never; rpcDriverName: string; configuration: any; height: number; } & NonEmptyObject & { rendererTypeName: string; error: unknown; } & ... 6 more ... & IStateTreeNode<...>; config: any; width: number; height: number; }
+setClickId: (arg: number) => void
 ```

website/docs/models/LinearSyntenyView.md

@@ -24,6 +24,15 @@ ISimpleType<"LinearSyntenyView">
 type: types.literal('LinearSyntenyView')
 ```
 
+#### property: /
+
+```js
+// type signature
+true
+// code
+drawCIGAR: true
+```
+
 #### property: drawCurves
 
 ```js
@@ -35,13 +44,14 @@ drawCurves: false
 
 ### LinearSyntenyView - Methods
 
-#### method: menuItems
+#### method: headerMenuItems
 
-adds functions to draw curves and square the view
+includes a subset of view menu options because the full list is a little
+overwhelming
 
 ```js
 // type signature
-menuItems: () => (MenuDivider | MenuSubHeader | NormalMenuItem | CheckboxMenuItem | RadioMenuItem | SubMenuItem | { ...; })[]
+headerMenuItems: () => (MenuDivider | MenuSubHeader | NormalMenuItem | CheckboxMenuItem | RadioMenuItem | SubMenuItem | { ...; } | { ...; } | { ...; })[]
 ```
 
 ### LinearSyntenyView - Actions
@@ -52,3 +62,17 @@ menuItems: () => (MenuDivider | MenuSubHeader | NormalMenuItem | CheckboxMenuIte
 // type signature
 toggleCurves: () => void
 ```
+
+#### action: toggleCIGAR
+
+```js
+// type signature
+toggleCIGAR: () => void
+```
+
+#### action: showAllRegions
+
+```js
+// type signature
+showAllRegions: () => void
+```