move options to track menu, add first_render functionality

plugins/linear-genome-view/src/BaseLinearDisplay/components/LinearBlocks.tsx

@@ -52,6 +52,7 @@ const RenderedBlocks = observer(function ({
       {blockDefinitions.map(block => {
         if (block instanceof ContentBlock) {
           const state = blockState.get(block.key)
+
           return (
             <ContentBlockComponent
               block={block}

plugins/linear-genome-view/src/BaseLinearDisplay/models/BaseLinearDisplayModel.tsx

@@ -105,7 +105,7 @@ function stateModelFactory() {
       /**
        * #getter
        * max height determined by the blockState
-       * configurable to default track height to this to show all features
+       * configurable to default the track height to this to show all features
        */
       get layoutMaxHeight() {
         const { blockDefinitions, blockState } = self
@@ -118,6 +118,7 @@ function stateModelFactory() {
         )
         return maxHeight
       },
+
       /**
        * #getter
        * how many milliseconds to wait for the display to

plugins/linear-genome-view/src/BaseLinearDisplay/models/TrackHeightMixin.tsx

@@ -1,5 +1,8 @@
-import { getConf } from '@jbrowse/core/configuration'
 import { types } from 'mobx-state-tree'
+import { getConf } from '@jbrowse/core/configuration'
+import { getContainingView } from '@jbrowse/core/util'
+
+import { LinearGenomeViewModel } from '../../LinearGenomeView'
 
 const minDisplayHeight = 20
 
@@ -26,24 +29,48 @@ export default function TrackHeightMixin() {
        * #property
        */
       scrollTop: 0,
+      /**
+       * #property
+       */
+      firstRenderHeight: 100,
+    }))
+    .actions(self => ({
+      /**
+       * #action
+       */
+      setFirstRenderHeight(val: number) {
+        self.firstRenderHeight = val
+        return val
+      },
     }))
     .views(self => ({
+      /**
+       * #getter
+       * returns the height value as determined by the trackHeightSetting
+       */
       get adjustLayout() {
-        return (
-          // @ts-expect-error
-          self.trackHeightSetting === 'on' ||
-          // @ts-expect-error
-          self.trackHeightSetting === 'first_render'
-        )
+        const { trackHeightSetting } = getContainingView(
+          self,
+        ) as LinearGenomeViewModel
+
+        // @ts-expect-error
+        const height = self.layoutMaxHeight
+
+        return trackHeightSetting === 'on'
+          ? height
+          : trackHeightSetting === 'first_render' &&
+              self.firstRenderHeight === 100
+            ? self.setFirstRenderHeight(height)
+            : trackHeightSetting === 'first_render'
+              ? self.firstRenderHeight
+              : undefined
       },
       get height() {
         return (
           self.heightPreConfig ??
-          (this.adjustLayout
-            ? // @ts-expect-error
-              self.layoutMaxHeight
-            : // @ts-expect-error
-              (getConf(self, 'height') as number))
+          this.adjustLayout ??
+          // @ts-expect-error
+          (getConf(self, 'height') as number)
         )
       },
     }))

plugins/linear-genome-view/src/LinearBasicDisplay/model.ts

@@ -4,7 +4,7 @@ import {
   ConfigurationReference,
   AnyConfigurationSchemaType,
 } from '@jbrowse/core/configuration'
-import { getSession, localStorageGetItem } from '@jbrowse/core/util'
+import { getSession } from '@jbrowse/core/util'
 import { MenuItem } from '@jbrowse/core/ui'
 import { types, getEnv, Instance } from 'mobx-state-tree'
 
@@ -55,13 +55,6 @@ function stateModelFactory(configSchema: AnyConfigurationSchemaType) {
          * #property
          */
         configuration: ConfigurationReference(configSchema),
-        /**
-         * #property
-         */
-        adjustLayoutHeight: types.optional(
-          types.string,
-          () => localStorageGetItem('lgv-adjustLayoutHeight') || 'off',
-        ),
       }),
     )
     .views(self => ({
@@ -124,16 +117,6 @@ function stateModelFactory(configSchema: AnyConfigurationSchemaType) {
           getEnv(self),
         )
       },
-      /**
-       * #getter
-       */
-      get trackHeightSetting() {
-        const sessionSetting = getConf(getSession(self), [
-          'renderer',
-          'trackHeight',
-        ])
-        return self.adjustLayoutHeight || sessionSetting
-      },
     }))
 
     .actions(self => ({
@@ -161,13 +144,6 @@ function stateModelFactory(configSchema: AnyConfigurationSchemaType) {
       setMaxHeight(val?: number) {
         self.trackMaxHeight = val
       },
-      /**
-       * #action
-       */
-      setAdjustLayoutHeight(setting: 'on' | 'off' | 'first_render') {
-        localStorage.setItem('lgv-adjustLayoutHeight', setting)
-        self.adjustLayoutHeight = setting
-      },
     }))
     .views(self => {
       const {
@@ -230,29 +206,6 @@ function stateModelFactory(configSchema: AnyConfigurationSchemaType) {
                 ])
               },
             },
-            {
-              label: 'Auto-adjust track height',
-              subMenu: [
-                {
-                  label: 'Off (use trackHeight from config)',
-                  type: 'radio',
-                  checked: self.trackHeightSetting === 'off',
-                  onClick: () => self.setAdjustLayoutHeight('off'),
-                },
-                {
-                  label: 'On (auto-adjust to show all features)',
-                  type: 'radio',
-                  checked: self.trackHeightSetting === 'on',
-                  onClick: () => self.setAdjustLayoutHeight('on'),
-                },
-                {
-                  label: 'On first render (auto-adjust to show all features)',
-                  type: 'radio',
-                  checked: self.trackHeightSetting === 'first_render',
-                  onClick: () => self.setAdjustLayoutHeight('first_render'),
-                },
-              ],
-            },
           ]
         },
       }

plugins/linear-genome-view/src/LinearGenomeView/model.ts

@@ -238,6 +238,15 @@ export function stateModelFactory(pluginManager: PluginManager) {
           () => localStorageGetItem('lgv-trackLabels') || '',
         ),
 
+        /**
+         * #property
+         * setting to auto-adjust the layout height of tracks
+         */
+        adjustLayoutHeight: types.optional(
+          types.string,
+          () => localStorageGetItem('lgv-adjustLayoutHeight') || 'off',
+        ),
+
         /**
          * #property
          * show the "gridlines" in the track area
@@ -280,6 +289,16 @@ export function stateModelFactory(pluginManager: PluginManager) {
         ])
         return self.trackLabels || sessionSetting
       },
+      /**
+       * #getter
+       */
+      get trackHeightSetting() {
+        const sessionSetting = getConf(getSession(self), [
+          'LinearGenomeViewPlugin',
+          'trackHeight',
+        ])
+        return self.adjustLayoutHeight || sessionSetting
+      },
       /**
        * #getter
        */
@@ -796,6 +815,14 @@ export function stateModelFactory(pluginManager: PluginManager) {
         self.trackLabels = setting
       },
 
+      /**
+       * #action
+       */
+      setAdjustLayoutHeight(setting: 'on' | 'off' | 'first_render') {
+        localStorage.setItem('lgv-adjustLayoutHeight', setting)
+        self.adjustLayoutHeight = setting
+      },
+
       /**
        * #action
        */
@@ -1182,6 +1209,29 @@ export function stateModelFactory(pluginManager: PluginManager) {
               },
             ],
           },
+          {
+            label: 'Track height',
+            subMenu: [
+              {
+                label: 'Use default (from config)',
+                type: 'radio',
+                checked: self.trackHeightSetting === 'off',
+                onClick: () => self.setAdjustLayoutHeight('off'),
+              },
+              {
+                label: 'Auto-adjust to show all features on track',
+                type: 'radio',
+                checked: self.trackHeightSetting === 'on',
+                onClick: () => self.setAdjustLayoutHeight('on'),
+              },
+              {
+                label: 'Auto-adjust to show height of initial features',
+                type: 'radio',
+                checked: self.trackHeightSetting === 'first_render',
+                onClick: () => self.setAdjustLayoutHeight('first_render'),
+              },
+            ],
+          },
         ]
 
         // add track's view level menu options

plugins/linear-genome-view/src/index.ts

@@ -53,6 +53,18 @@ export default class LinearGenomeViewPlugin extends Plugin {
         'hidden',
       ]),
     },
+    /**
+     * #slot configuration.LinearGenomeViewPlugin.trackLabels
+     */
+    trackHeight: {
+      type: 'string',
+      defaultValue: 'off',
+      model: types.enumeration('trackHeightOptions', [
+        'off',
+        'on',
+        'first_render',
+      ]),
+    },
   })
 
   install(pluginManager: PluginManager) {