react-msaview 4.4.4 → 4.4.6

package/src/layout.ts

@@ -1,4 +1,4 @@
-import RBush from 'rbush'
+import Flatbush from 'flatbush'
 
 export default class Layout {
   public rectangles: Map<
@@ -13,11 +13,13 @@ export default class Layout {
     }
   >
 
-  public maxHeightReached: boolean
+  public maxHeightReached = false
 
   private maxHeight: number
 
-  private rbush: RBush<{ id: string }>
+  private flatbush: Flatbush | null = null
+
+  private indexToId: string[] = []
 
   private pTotalHeight: number
 
@@ -26,13 +28,51 @@ export default class Layout {
   }: {
     maxHeight?: number
   } = {}) {
-    this.maxHeightReached = false
-    this.rbush = new RBush()
     this.rectangles = new Map()
     this.maxHeight = Math.ceil(maxHeight)
     this.pTotalHeight = 0 // total height, in units of bitmap squares (px/pitchY)
   }
 
+  private rebuildIndex() {
+    // Rebuild the spatial index with current rectangles
+    const rects = Array.from(this.rectangles.values())
+    if (rects.length === 0) {
+      this.flatbush = null
+      this.indexToId = []
+      return
+    }
+
+    this.flatbush = new Flatbush(rects.length)
+    this.indexToId = []
+
+    for (const rect of rects) {
+      this.flatbush.add(rect.minX, rect.minY, rect.maxX, rect.maxY)
+      this.indexToId.push(rect.id)
+    }
+
+    this.flatbush.finish()
+  }
+
+  private collides(box: {
+    minX: number
+    minY: number
+    maxX: number
+    maxY: number
+  }): boolean {
+    if (!this.flatbush) {
+      return false
+    }
+
+    const results = this.flatbush.search(
+      box.minX,
+      box.minY,
+      box.maxX,
+      box.maxY,
+    )
+
+    return results.length > 0
+  }
+
   /**
    * @returns top position for the rect, or Null if laying
    *  out the rect would exceed maxHeighe
@@ -44,7 +84,7 @@ export default class Layout {
     height: number,
     data: unknown,
   ): number | null {
-    // add to rbush
+    // add to flatbush
     const existingRecord = this.rectangles.get(id)
     if (existingRecord) {
       return existingRecord.minY
@@ -52,7 +92,7 @@ export default class Layout {
 
     let currHeight = 0
     while (
-      this.rbush.collides({
+      this.collides({
         minX: left,
         minY: currHeight,
         maxX: right,
@@ -71,8 +111,8 @@ export default class Layout {
       id,
       data,
     }
-    this.rbush.insert(record)
     this.rectangles.set(id, record)
+    this.rebuildIndex()
     this.pTotalHeight = Math.max(this.pTotalHeight, currHeight)
     return currHeight
   }

package/src/model/treeModel.ts

@@ -70,14 +70,14 @@ export function TreeModelF() {
        * set tree area width (px)
        */
       setTreeAreaWidth(n: number) {
-        self.treeAreaWidth = n
+        self.treeAreaWidth = Math.round(n)
       },
       /**
        * #action
        * set tree width (px)
        */
       setTreeWidth(n: number) {
-        self.treeWidth = n
+        self.treeWidth = Math.round(n)
       },
 
       /**

package/src/model.ts

@@ -289,6 +289,14 @@ function stateModelFactory() {
        */
       mouseClickCol: undefined as number | undefined,
 
+      /**
+       * #volatile
+       * the currently hovered tree node ID and its descendant leaf names
+       */
+      hoveredTreeNode: undefined as
+        | { nodeId: string; descendantNames: string[] }
+        | undefined,
+
       /**
        * #volatile
        * a dummy variable that is incremented when ref changes so autorun for
@@ -327,7 +335,7 @@ function stateModelFactory() {
       /**
        * #action
        */
-      drawRelativeTo(id: string) {
+      drawRelativeTo(id: string | undefined) {
         self.relativeTo = id
       },
       /**
@@ -396,6 +404,31 @@ function stateModelFactory() {
         self.mouseCol = col
         self.mouseRow = row
       },
+
+      /**
+       * #action
+       * set hovered tree node and its descendants
+       */
+      setHoveredTreeNode(nodeId?: string) {
+        if (!nodeId) {
+          self.hoveredTreeNode = undefined
+          return
+        }
+
+        // Find the node in the hierarchy
+        const node = (self as any).hierarchy.find(
+          (n: any) => n.data.id === nodeId,
+        )
+        if (!node) {
+          self.hoveredTreeNode = undefined
+          return
+        }
+
+        // Get all descendant leaf names
+        const descendantNames = node.leaves().map((leaf: any) => leaf.data.name)
+
+        self.hoveredTreeNode = { nodeId, descendantNames }
+      },
       /**
        * #action
        */
@@ -673,6 +706,7 @@ function stateModelFactory() {
           // todo: investigate whether needed, typescript says children always true
           // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
           .sum(d => (d.children ? 0 : 1))
+          // eslint-disable-next-line unicorn/no-array-sort
           .sort((a, b) => ascending(a.data.length || 1, b.data.length || 1))
 
         if (self.showOnly) {
@@ -911,7 +945,7 @@ function stateModelFactory() {
        * #getter
        */
       get maxScrollX() {
-        return -self.totalWidth + (self.msaAreaWidth - 100)
+        return Math.min(-self.totalWidth + (self.msaAreaWidth - 100), 0)
       },
       /**
        * #getter
@@ -1009,7 +1043,7 @@ function stateModelFactory() {
        * #action
        */
       doScrollX(deltaX: number) {
-        self.scrollX = clamp(self.scrollX + deltaX, self.maxScrollX, 0)
+        this.setScrollX(self.scrollX + deltaX)
       },
 
       /**
@@ -1243,7 +1277,7 @@ function stateModelFactory() {
             }
           }
         }
-        return ret.sort((a, b) => len(b) - len(a))
+        return ret.toSorted((a, b) => len(b) - len(a))
       },
       /**
        * #getter
@@ -1525,6 +1559,75 @@ function stateModelFactory() {
         ...rest
       } = snap
 
+      // Default values to filter out
+      const defaults = {
+        // Main model defaults
+        showDomains: false,
+        hideGaps: true,
+        allowedGappyness: 100,
+        contrastLettering: true,
+        subFeatureRows: false,
+        drawMsaLetters: true,
+        height: 550,
+        rowHeight: defaultRowHeight,
+        scrollY: 0,
+        scrollX: 0,
+        colWidth: defaultColWidth,
+        currentAlignment: 0,
+        // MSA model defaults
+        bgColor: true,
+        colorSchemeName: 'maeditor',
+        // Tree model defaults
+        drawLabels: true,
+        labelsAlignRight: false,
+        treeAreaWidth: 400,
+        treeWidth: 300,
+        treeWidthMatchesArea: true,
+        showBranchLen: true,
+        drawTree: true,
+        drawNodeBubbles: true,
+      }
+
+      // Properties that should always be included even if they match defaults
+      const alwaysInclude = new Set(['id', 'type', 'relativeTo'])
+
+      // Filter out properties that match default values
+      function filterDefaults(obj: Record<string, any>): Record<string, any> {
+        const filtered: Record<string, any> = {}
+        for (const [key, value] of Object.entries(obj)) {
+          // Always include essential properties
+          if (alwaysInclude.has(key)) {
+            filtered[key] = value
+            continue
+          }
+
+          // Skip if value matches default
+          if (defaults[key as keyof typeof defaults] === value) {
+            continue
+          }
+
+          // Handle nested objects
+          if (value && typeof value === 'object' && !Array.isArray(value)) {
+            const filteredNested = filterDefaults(value)
+            // Only include nested object if it has non-default properties
+            if (Object.keys(filteredNested).length > 0) {
+              filtered[key] = filteredNested
+            }
+          } else if (Array.isArray(value)) {
+            // Only include arrays that aren't empty
+            if (value.length > 0) {
+              filtered[key] = value
+            }
+          } else {
+            // Include non-default primitives
+            filtered[key] = value
+          }
+        }
+        return filtered
+      }
+
+      const filteredRest = filterDefaults(rest)
+
       // remove the MSA/tree data from the tree if the filehandle available in
       // which case it can be reloaded on refresh
       return {
@@ -1533,7 +1636,7 @@ function stateModelFactory() {
           ...(result.msaFilehandle ? {} : { msa }),
           ...(result.treeMetadataFilehandle ? {} : { treeMetadata }),
         },
-        ...rest,
+        ...filteredRest,
       }
     })
 }

package/src/rowCoordinateCalculations.test.ts

@@ -90,11 +90,24 @@ test('with gaps in sequence', () => {
   expect(globalCoordToRowSpecificCoord(sequence, 0)).toBe(0)
   expect(globalCoordToRowSpecificCoord(sequence, 1)).toBe(1)
   expect(globalCoordToRowSpecificCoord(sequence, 2)).toBe(2)
-  // Position 3 in global coordinates is after the gap
+  // Position 2 is a gap, so count before it is 2
   expect(globalCoordToRowSpecificCoord(sequence, 3)).toBe(2)
   expect(globalCoordToRowSpecificCoord(sequence, 4)).toBe(3)
   expect(globalCoordToRowSpecificCoord(sequence, 5)).toBe(4)
-  // Position 6 in global coordinates is after the gap
+  // Position 5 is a gap, so count before it is 4
+  expect(globalCoordToRowSpecificCoord(sequence, 6)).toBe(4)
+})
+
+test('with mixed gap characters (- and .)', () => {
+  const sequence = 'AC.GT-A'
+  expect(globalCoordToRowSpecificCoord(sequence, 0)).toBe(0)
+  expect(globalCoordToRowSpecificCoord(sequence, 1)).toBe(1)
+  // Position 2 is a gap (.), so count before it is 2
+  expect(globalCoordToRowSpecificCoord(sequence, 2)).toBe(2)
+  expect(globalCoordToRowSpecificCoord(sequence, 3)).toBe(2)
+  expect(globalCoordToRowSpecificCoord(sequence, 4)).toBe(3)
+  // Position 5 is a gap (-), so count before it is 4
+  expect(globalCoordToRowSpecificCoord(sequence, 5)).toBe(4)
   expect(globalCoordToRowSpecificCoord(sequence, 6)).toBe(4)
 })
 

package/src/rowCoordinateCalculations.ts

@@ -38,13 +38,9 @@ export function globalCoordToRowSpecificCoord(seq: string, position: number) {
   // Iterate until we reach the target position or end of sequence
   while (currentPosition < position && currentPosition < sequenceLength) {
     // If current character is not a gap, increment the non-gap counter
-    if (seq[currentPosition] !== '-') {
+    if (!isBlank(seq[currentPosition])) {
       nonGapCount++
     }
-    // If we've reached the target position in non-gap coordinates, break
-    else if (nonGapCount >= position) {
-      break
-    }
     currentPosition++
   }
 

package/src/seqCoordToRowSpecificGlobalCoord.test.ts

@@ -19,13 +19,13 @@ describe('seqCoordToRowSpecificGlobalCoord', () => {
     expect(seqCoordToRowSpecificGlobalCoord({ row, position: 0 })).toBe(0)
 
     // Position 1 (T after first gap) -> Global index 2
-    expect(seqCoordToRowSpecificGlobalCoord({ row, position: 1 })).toBe(1)
+    expect(seqCoordToRowSpecificGlobalCoord({ row, position: 1 })).toBe(2)
 
     // Position 3 (C after second gap) -> Global index 5
-    expect(seqCoordToRowSpecificGlobalCoord({ row, position: 3 })).toBe(4)
+    expect(seqCoordToRowSpecificGlobalCoord({ row, position: 3 })).toBe(5)
 
     // Position 5 (T after third gap) -> Global index 8
-    expect(seqCoordToRowSpecificGlobalCoord({ row, position: 5 })).toBe(7)
+    expect(seqCoordToRowSpecificGlobalCoord({ row, position: 5 })).toBe(8)
 
     // Position 8 (end of sequence) -> Global index 11
     expect(seqCoordToRowSpecificGlobalCoord({ row, position: 8 })).toBe(11)
@@ -46,8 +46,8 @@ describe('seqCoordToRowSpecificGlobalCoord', () => {
     // Sequence positions: A(0) G(1) C(2)
 
     expect(seqCoordToRowSpecificGlobalCoord({ row, position: 0 })).toBe(0)
-    expect(seqCoordToRowSpecificGlobalCoord({ row, position: 1 })).toBe(1)
-    expect(seqCoordToRowSpecificGlobalCoord({ row, position: 2 })).toBe(4)
-    expect(seqCoordToRowSpecificGlobalCoord({ row, position: 3 })).toBe(6)
+    expect(seqCoordToRowSpecificGlobalCoord({ row, position: 1 })).toBe(3)
+    expect(seqCoordToRowSpecificGlobalCoord({ row, position: 2 })).toBe(5)
+    expect(seqCoordToRowSpecificGlobalCoord({ row, position: 3 })).toBe(7)
   })
 })

package/src/seqCoordToRowSpecificGlobalCoord.ts

@@ -9,12 +9,17 @@ export function seqCoordToRowSpecificGlobalCoord({
 }) {
   let k = 0
   let i = 0
-  for (; k < position; i++) {
+  // Find the position-th non-gap character
+  while (i < row.length) {
     if (!isBlank(row[i])) {
+      if (k === position) {
+        return i
+      }
       k++
-    } else if (k >= position) {
-      break
     }
+    i++
   }
-  return i
+  // If position is 0 and we didn't find any non-gap character, return 0
+  // Otherwise return i (which is row.length at this point)
+  return position === 0 ? 0 : i
 }

package/src/version.ts

@@ -1 +1 @@
-export const version = '4.4.4'
+export const version = '4.4.6'

package/dist/DataModel.d.ts

@@ -1,34 +0,0 @@
-/**
- * #stateModel DataModel
- * the data stored for the model. this is sometimes temporary in the case that
- * e.g. msaFilehandle is available on the parent model, because then the msa
- * data will not be persisted in saved session snapshots, it will be fetched
- * from msaFilehandle at startup
- */
-export declare function DataModelF(): import("mobx-state-tree").IModelType<{
-    /**
-     * #property
-     */
-    tree: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    /**
-     * #property
-     */
-    msa: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    /**
-     * #property
-     */
-    treeMetadata: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-}, {
-    /**
-     * #action
-     */
-    setTree(tree?: string): void;
-    /**
-     * #action
-     */
-    setMSA(msa?: string): void;
-    /**
-     * #action
-     */
-    setTreeMetadata(treeMetadata?: string): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/dist/DataModel.js

@@ -1,46 +0,0 @@
-import { types } from 'mobx-state-tree';
-/**
- * #stateModel DataModel
- * the data stored for the model. this is sometimes temporary in the case that
- * e.g. msaFilehandle is available on the parent model, because then the msa
- * data will not be persisted in saved session snapshots, it will be fetched
- * from msaFilehandle at startup
- */
-export function DataModelF() {
-    return types
-        .model({
-        /**
-         * #property
-         */
-        tree: types.maybe(types.string),
-        /**
-         * #property
-         */
-        msa: types.maybe(types.string),
-        /**
-         * #property
-         */
-        treeMetadata: types.maybe(types.string),
-    })
-        .actions(self => ({
-        /**
-         * #action
-         */
-        setTree(tree) {
-            self.tree = tree;
-        },
-        /**
-         * #action
-         */
-        setMSA(msa) {
-            self.msa = msa;
-        },
-        /**
-         * #action
-         */
-        setTreeMetadata(treeMetadata) {
-            self.treeMetadata = treeMetadata;
-        },
-    }));
-}
-//# sourceMappingURL=DataModel.js.map

package/dist/DataModel.js.map

@@ -1 +0,0 @@
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package/dist/DialogQueue.d.ts

@@ -1,25 +0,0 @@
-import { DialogComponentType } from '@jbrowse/core/util';
-/**
- * #stateModel DialogQueueSessionMixin
- */
-export declare function DialogQueueSessionMixin(): import("mobx-state-tree").IModelType<{}, {
-    queueOfDialogs: [DialogComponentType, any][];
-} & {
-    /**
-     * #getter
-     */
-    readonly DialogComponent: DialogComponentType;
-    /**
-     * #getter
-     */
-    readonly DialogProps: any;
-} & {
-    /**
-     * #action
-     */
-    removeActiveDialog(): void;
-    /**
-     * #action
-     */
-    queueDialog(cb: (doneCallback: () => void) => [DialogComponentType, unknown]): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/dist/DialogQueue.js

@@ -1,44 +0,0 @@
-import { types } from 'mobx-state-tree';
-/**
- * #stateModel DialogQueueSessionMixin
- */
-export function DialogQueueSessionMixin() {
-    return types
-        .model('DialogQueueSessionMixin', {})
-        .volatile(() => ({
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        queueOfDialogs: [],
-    }))
-        .views(self => ({
-        /**
-         * #getter
-         */
-        get DialogComponent() {
-            return self.queueOfDialogs[0]?.[0];
-        },
-        /**
-         * #getter
-         */
-        get DialogProps() {
-            return self.queueOfDialogs[0]?.[1];
-        },
-    }))
-        .actions(self => ({
-        /**
-         * #action
-         */
-        removeActiveDialog() {
-            self.queueOfDialogs = self.queueOfDialogs.slice(1);
-        },
-        /**
-         * #action
-         */
-        queueDialog(cb) {
-            const [component, props] = cb(() => {
-                this.removeActiveDialog();
-            });
-            self.queueOfDialogs = [...self.queueOfDialogs, [component, props]];
-        },
-    }));
-}
-//# sourceMappingURL=DialogQueue.js.map

package/dist/DialogQueue.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"DialogQueue.js","sourceRoot":"","sources":["../src/DialogQueue.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC;;GAEG;AACH,MAAM,UAAU,uBAAuB;IACrC,OAAO,KAAK;SACT,KAAK,CAAC,yBAAyB,EAAE,EAAE,CAAC;SACpC,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;QACf,8DAA8D;QAC9D,cAAc,EAAE,EAAkC;KACnD,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,eAAe;YACjB,OAAO,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;QACpC,CAAC;QACD;;WAEG;QACH,IAAI,WAAW;YACb,OAAO,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;QACpC,CAAC;KACF,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,kBAAkB;YAChB,IAAI,CAAC,cAAc,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QACpD,CAAC;QACD;;WAEG;QACH,WAAW,CACT,EAAgE;YAEhE,MAAM,CAAC,SAAS,EAAE,KAAK,CAAC,GAAG,EAAE,CAAC,GAAG,EAAE;gBACjC,IAAI,CAAC,kBAAkB,EAAE,CAAA;YAC3B,CAAC,CAAC,CAAA;YACF,IAAI,CAAC,cAAc,GAAG,CAAC,GAAG,IAAI,CAAC,cAAc,EAAE,CAAC,SAAS,EAAE,KAAK,CAAC,CAAC,CAAA;QACpE,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}

package/dist/SelectedStructuresMixin.d.ts

@@ -1,46 +0,0 @@
-import { SnapshotIn } from 'mobx-state-tree';
-import { StructureModel } from './StructureModel';
-export type StructureSnap = SnapshotIn<typeof StructureModel>;
-export declare function SelectedStructuresMixin(): import("mobx-state-tree").IModelType<{
-    /**
-     * #property
-     * currently "selected" structures, generally PDB 3-D protein structures
-     */
-    selectedStructures: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
-        id: import("mobx-state-tree").ISimpleType<string>;
-        structure: import("mobx-state-tree").IModelType<{
-            pdb: import("mobx-state-tree").ISimpleType<string>;
-            startPos: import("mobx-state-tree").ISimpleType<number>;
-            endPos: import("mobx-state-tree").ISimpleType<number>;
-        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-        range: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-}, {
-    /**
-     * #action
-     * add to the selected structures
-     */
-    addStructureToSelection(elt: StructureSnap): void;
-    /**
-     * #action
-     * remove from the selected structures
-     */
-    removeStructureFromSelection(elt: StructureSnap): void;
-    /**
-     * #action
-     * toggle a structure from the selected structures list
-     */
-    toggleStructureSelection(elt: {
-        id: string;
-        structure: {
-            startPos: number;
-            endPos: number;
-            pdb: string;
-        };
-    }): void;
-    /**
-     * #action
-     * clear all selected structures
-     */
-    clearSelectedStructures(): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/dist/SelectedStructuresMixin.js

@@ -1,52 +0,0 @@
-import { cast, types } from 'mobx-state-tree';
-import { StructureModel } from './StructureModel';
-export function SelectedStructuresMixin() {
-    return types
-        .model({
-        /**
-         * #property
-         * currently "selected" structures, generally PDB 3-D protein structures
-         */
-        selectedStructures: types.array(StructureModel),
-    })
-        .actions(self => ({
-        /**
-         * #action
-         * add to the selected structures
-         */
-        addStructureToSelection(elt) {
-            self.selectedStructures.push(elt);
-        },
-        /**
-         * #action
-         * remove from the selected structures
-         */
-        removeStructureFromSelection(elt) {
-            const r = self.selectedStructures.find(node => node.id === elt.id);
-            if (r) {
-                self.selectedStructures.remove(r);
-            }
-        },
-        /**
-         * #action
-         * toggle a structure from the selected structures list
-         */
-        toggleStructureSelection(elt) {
-            const r = self.selectedStructures.find(node => node.id === elt.id);
-            if (r) {
-                self.selectedStructures.remove(r);
-            }
-            else {
-                self.selectedStructures.push(elt);
-            }
-        },
-        /**
-         * #action
-         * clear all selected structures
-         */
-        clearSelectedStructures() {
-            self.selectedStructures = cast([]);
-        },
-    }));
-}
-//# sourceMappingURL=SelectedStructuresMixin.js.map

package/dist/SelectedStructuresMixin.js.map

@@ -1 +0,0 @@
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package/dist/StructureModel.d.ts

@@ -1,9 +0,0 @@
-export declare const StructureModel: import("mobx-state-tree").IModelType<{
-    id: import("mobx-state-tree").ISimpleType<string>;
-    structure: import("mobx-state-tree").IModelType<{
-        pdb: import("mobx-state-tree").ISimpleType<string>;
-        startPos: import("mobx-state-tree").ISimpleType<number>;
-        endPos: import("mobx-state-tree").ISimpleType<number>;
-    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-    range: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-}, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;