Update autogen

docs/generateConfigDocs.ts

@@ -8,7 +8,7 @@ import {
   getAllFiles,
   removeComments,
   rm,
-} from './util'
+} from './util.ts'
 
 interface Derives {
   name: string

docs/generateStateModelDocs.ts

@@ -8,7 +8,7 @@ import {
   getAllFiles,
   removeComments,
   rm,
-} from './util'
+} from './util.ts'
 
 interface Action {
   name: string

docs/tsconfig.json

@@ -10,6 +10,7 @@
     "strict": true,
     "declaration": true,
     "module": "commonjs",
+    "allowImportingTsExtensions": true,
     "moduleResolution": "node"
   },
   "include": ["generateConfigDocs.ts", "generateStateModelDocs.ts", "util.ts"]

website/docs/config/BigBedAdapter.md

@@ -45,6 +45,6 @@ scoreColumn: {
 aggregateField: {
       type: 'string',
       description: 'An attribute to aggregate features with',
-      defaultValue: 'geneName',
+      defaultValue: 'geneName2',
     }
 ```

website/docs/config/VcfAdapter.md

@@ -25,6 +25,23 @@ reference the markdown files in our repo of the checked out git tag
 ```js
 vcfLocation: {
       type: 'fileLocation',
-      defaultValue: { uri: '/path/to/my.vcf', locationType: 'UriLocation' },
+      defaultValue: {
+        uri: '/path/to/my.vcf',
+        locationType: 'UriLocation',
+      },
+    }
+```
+
+#### slot: samplesTsvLocation
+
+```js
+samplesTsvLocation: {
+      type: 'fileLocation',
+      defaultValue: {
+        uri: '/path/to/samples.tsv',
+        description:
+          'tsv with header like name\tpopulation\tetc. where the first column is required, and is the sample names',
+        locationType: 'UriLocation',
+      },
     }
 ```

website/docs/config/VcfTabixAdapter.md

@@ -50,3 +50,17 @@ location: {
         },
       }
 ```
+
+#### slot: samplesTsvLocation
+
+```js
+samplesTsvLocation: {
+      type: 'fileLocation',
+      defaultValue: {
+        uri: '/path/to/samples.tsv',
+        description:
+          'tsv with header like name\tpopulation\tetc. where the first column is required, and is the sample names',
+        locationType: 'UriLocation',
+      },
+    }
+```

website/docs/models/AddTrackModel.md

@@ -130,13 +130,27 @@ boolean
 any
 ```
 
+#### getter: trackAdapterType
+
+```js
+// type
+any
+```
+
 #### getter: trackType
 
 ```js
 // type
 string
 ```
 
+#### getter: trackConfig
+
+```js
+// type
+any
+```
+
 #### getter: warningMessage
 
 ```js

website/docs/models/DotplotView.md

@@ -258,11 +258,32 @@ renderProps: () => any
 
 ```js
 // type signature
-menuItems: () => ({ label: string; onClick: () => void; icon: OverridableComponent<SvgIconTypeMap<{}, "svg">> & { muiName: string; }; } | { label: string; onClick: () => void; icon?: undefined; } | { ...; })[]
+menuItems: () => ({ label: string; icon: OverridableComponent<SvgIconTypeMap<{}, "svg">> & { muiName: string; }; onClick: () => void; } | { label: string; onClick: () => Widget; icon: (props: SvgIconProps) => Element; })[]
 ```
 
 ### DotplotView - Actions
 
+#### action: importFormRemoveRow
+
+```js
+// type signature
+importFormRemoveRow: (idx: number) => void
+```
+
+#### action: clearImportFormSyntenyTracks
+
+```js
+// type signature
+clearImportFormSyntenyTracks: () => void
+```
+
+#### action: setImportFormSyntenyTrack
+
+```js
+// type signature
+setImportFormSyntenyTrack: (arg: number, val: ImportFormSyntenyTrack) => void
+```
+
 #### action: setShowPanButtons
 
 ```js

website/docs/models/FacetedModel.md

@@ -38,7 +38,7 @@ filterText: types.optional(types.string, '')
 IOptionalIType<ISimpleType<boolean>, [undefined]>
 // code
 showSparse: types.optional(types.boolean, () =>
-        JSON.parse(localStorageGetItem('facet-showSparse') || 'false'),
+        localStorageGetBoolean('facet-showSparse', false),
       )
 ```
 
@@ -49,7 +49,7 @@ showSparse: types.optional(types.boolean, () =>
 IOptionalIType<ISimpleType<boolean>, [undefined]>
 // code
 showFilters: types.optional(types.boolean, () =>
-        JSON.parse(localStorageGetItem('facet-showFilters') || 'true'),
+        localStorageGetBoolean('facet-showFilters', true),
       )
 ```
 
@@ -60,7 +60,7 @@ showFilters: types.optional(types.boolean, () =>
 IOptionalIType<ISimpleType<boolean>, [undefined]>
 // code
 showOptions: types.optional(types.boolean, () =>
-        JSON.parse(localStorageGetItem('facet-showTableOptions') || 'false'),
+        localStorageGetBoolean('facet-showTableOptions', false),
       )
 ```
 
@@ -71,7 +71,7 @@ showOptions: types.optional(types.boolean, () =>
 IOptionalIType<ISimpleType<number>, [undefined]>
 // code
 panelWidth: types.optional(types.number, () =>
-        JSON.parse(localStorageGetItem('facet-panelWidth') || '400'),
+        localStorageGetNumber('facet-panelWidth', 400),
       )
 ```
 
@@ -105,6 +105,13 @@ string[] | readonly ["category", "adapter", "description"]
 any[]
 ```
 
+#### getter: filteredMetadataKeys
+
+```js
+// type
+any
+```
+
 #### getter: fields
 
 ```js

website/docs/models/LinearComparativeView.md

@@ -62,6 +62,15 @@ true
 showIntraviewLinks: true
 ```
 
+#### property: linkViews
+
+```js
+// type signature
+false
+// code
+linkViews: false
+```
+
 #### property: interactiveOverlay
 
 ```js
@@ -187,6 +196,13 @@ removeView: (view: { id: string; displayName: string; minimized: boolean; type:
 setLevelHeight: (newHeight: number, level?: number) => number
 ```
 
+#### action: setLinkViews
+
+```js
+// type signature
+setLinkViews: (arg: boolean) => void
+```
+
 #### action: activateTrackSelector
 
 ```js

website/docs/models/LinearGenomeView.md

@@ -144,9 +144,7 @@ show the "center line"
 IOptionalIType<ISimpleType<boolean>, [undefined]>
 // code
 showCenterLine: types.optional(types.boolean, () =>
-          Boolean(
-            JSON.parse(localStorageGetItem('lgv-showCenterLine') || 'false'),
-          ),
+          localStorageGetBoolean('lgv-showCenterLine', false),
         )
 ```
 
@@ -159,9 +157,7 @@ show the "cytobands" in the overview scale bar
 IOptionalIType<ISimpleType<boolean>, [undefined]>
 // code
 showCytobandsSetting: types.optional(types.boolean, () =>
-          Boolean(
-            JSON.parse(localStorageGetItem('lgv-showCytobands') || 'true'),
-          ),
+          localStorageGetBoolean('lgv-showCytobands', true),
         )
 ```
 
@@ -216,7 +212,7 @@ color by CDS
 IOptionalIType<ISimpleType<boolean>, [undefined]>
 // code
 colorByCDS: types.optional(types.boolean, () =>
-          Boolean(JSON.parse(localStorageGetItem('lgv-colorByCDS') || 'false')),
+          localStorageGetBoolean('lgv-colorByCDS', false),
         )
 ```
 
@@ -229,9 +225,7 @@ color by CDS
 IOptionalIType<ISimpleType<boolean>, [undefined]>
 // code
 showTrackOutlines: types.optional(types.boolean, () =>
-          Boolean(
-            JSON.parse(localStorageGetItem('lgv-showTrackOutlines') || 'true'),
-          ),
+          localStorageGetBoolean('lgv-showTrackOutlines', true),
         )
 ```
 

website/docs/models/LinearSyntenyView.md

@@ -74,18 +74,39 @@ menuItems: () => (MenuDivider | MenuSubHeader | NormalMenuItem | CheckboxMenuIte
 
 ### LinearSyntenyView - Actions
 
-#### action: toggleCurves
+#### action: importFormRemoveRow
 
 ```js
 // type signature
-toggleCurves: () => void
+importFormRemoveRow: (idx: number) => void
 ```
 
-#### action: toggleCIGAR
+#### action: clearImportFormSyntenyTracks
 
 ```js
 // type signature
-toggleCIGAR: () => void
+clearImportFormSyntenyTracks: () => void
+```
+
+#### action: setImportFormSyntenyTrack
+
+```js
+// type signature
+setImportFormSyntenyTrack: (arg: number, val: ImportFormSyntenyTrack) => void
+```
+
+#### action: setDrawCurves
+
+```js
+// type signature
+setDrawCurves: (arg: boolean) => void
+```
+
+#### action: setDrawCIGAR
+
+```js
+// type signature
+setDrawCIGAR: (arg: boolean) => void
 ```
 
 #### action: showAllRegions

website/docs/models/LinearVariantMatrixDisplay.md

@@ -22,7 +22,7 @@ reference the markdown files in our repo of the checked out git tag
 
 extends
 
-- [LinearBasicDisplay](../linearbasicdisplay)
+- [LinearBareDisplay](../linearbaredisplay)
 
 ### LinearVariantMatrixDisplay - Properties
 
@@ -53,13 +53,13 @@ AnyConfigurationSchemaType
 configuration: ConfigurationReference(configSchema)
 ```
 
-#### property: mafFilter
+#### property: minorAlleleFrequencyFilter
 
 ```js
 // type signature
 IOptionalIType<ISimpleType<number>, [undefined]>
 // code
-mafFilter: types.optional(types.number, 0.1)
+minorAlleleFrequencyFilter: types.optional(types.number, 0.1)
 ```
 
 #### property: showSidebarLabelsSetting
@@ -71,13 +71,29 @@ true
 showSidebarLabelsSetting: true
 ```
 
+#### property: phasedMode
+
+```js
+// type signature
+IOptionalIType<ISimpleType<string>, [undefined]>
+// code
+phasedMode: types.optional(types.string, 'none')
+```
+
 ### LinearVariantMatrixDisplay - Getters
 
+#### getter: preSources
+
+```js
+// type
+Source[]
+```
+
 #### getter: sources
 
 ```js
 // type
-any
+any[]
 ```
 
 #### getter: blockType
@@ -121,7 +137,7 @@ adapterProps: () => any
 
 ```js
 // type signature
-trackMenuItems: () => (MenuDivider | MenuSubHeader | NormalMenuItem | CheckboxMenuItem | RadioMenuItem | SubMenuItem | { ...; })[]
+trackMenuItems: () => (MenuDivider | MenuSubHeader | NormalMenuItem | CheckboxMenuItem | RadioMenuItem | SubMenuItem | { ...; } | { ...; })[]
 ```
 
 #### method: renderProps
@@ -182,6 +198,27 @@ setMafFilter: (arg: number) => void
 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