react-msaview 4.4.4 → 4.4.5

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/version.ts

@@ -1 +1 @@
-export const version = '4.4.4'
+export const version = '4.4.5'

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 @@
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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>;

package/dist/StructureModel.js

@@ -1,11 +0,0 @@
-import { types } from 'mobx-state-tree';
-export const StructureModel = types.model({
-    id: types.identifier,
-    structure: types.model({
-        pdb: types.string,
-        startPos: types.number,
-        endPos: types.number,
-    }),
-    range: types.maybe(types.string),
-});
-//# sourceMappingURL=StructureModel.js.map

package/dist/StructureModel.js.map

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

@@ -1,27 +0,0 @@
-export declare const UniprotTrack: import("mobx-state-tree").IModelType<{
-    id: import("mobx-state-tree").ISimpleType<string>;
-    accession: import("mobx-state-tree").ISimpleType<string>;
-    name: import("mobx-state-tree").ISimpleType<string>;
-    associatedRowName: import("mobx-state-tree").ISimpleType<string>;
-    height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-}, {
-    error: unknown;
-    data: string | undefined;
-} & {
-    setError(error: unknown): void;
-    setData(data: string): void;
-} & {
-    afterCreate(): void;
-} & {
-    readonly loading: boolean;
-    readonly features: {
-        seq_id: string;
-        source: string;
-        type: string;
-        start: number;
-        end: number;
-        score: number;
-        strand: string;
-        phase: string;
-    }[] | undefined;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/dist/UniprotTrack.js

@@ -1,53 +0,0 @@
-import { types, addDisposer } from 'mobx-state-tree';
-import { autorun } from 'mobx';
-// locals
-import { parseGFF } from './util';
-export const UniprotTrack = types
-    .model({
-    id: types.string,
-    accession: types.string,
-    name: types.string,
-    associatedRowName: types.string,
-    height: types.optional(types.number, 100),
-})
-    .volatile(() => ({
-    error: undefined,
-    data: undefined,
-}))
-    .actions(self => ({
-    setError(error) {
-        self.error = error;
-    },
-    setData(data) {
-        self.data = data;
-    },
-}))
-    .actions(self => ({
-    afterCreate() {
-        addDisposer(self, autorun(async () => {
-            try {
-                const { accession } = self;
-                const accessionSansVersion = accession?.replace(/\.[^/.]+$/, '');
-                const url = `https://rest.uniprot.org/uniprotkb/${accessionSansVersion}.gff`;
-                const res = await fetch(url);
-                if (!res.ok) {
-                    throw new Error(`HTTP ${res.status} fetching ${url}: ${await res.text()}`);
-                }
-                self.setData(await res.text());
-            }
-            catch (e) {
-                console.error(e);
-                self.setError(e);
-            }
-        }));
-    },
-}))
-    .views(self => ({
-    get loading() {
-        return !self.data;
-    },
-    get features() {
-        return parseGFF(self.data);
-    },
-}));
-//# sourceMappingURL=UniprotTrack.js.map

package/dist/UniprotTrack.js.map

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package/dist/components/BoxTrack.d.ts

@@ -1,7 +0,0 @@
-import React from 'react';
-import { IBoxTrack, MsaViewModel } from '../model';
-declare const BoxTrack: ({ model, track, }: {
-    model: MsaViewModel;
-    track: IBoxTrack;
-}) => React.JSX.Element;
-export default BoxTrack;

package/dist/components/BoxTrack.js

@@ -1,15 +0,0 @@
-import React from 'react';
-import { observer } from 'mobx-react';
-import BoxTrackBlock from './BoxTrackBlock';
-const BoxTrack = observer(function ({ model, track, }) {
-    const { blocksX, msaAreaWidth } = model;
-    const { height } = track.model;
-    return (React.createElement("div", { style: {
-            position: 'relative',
-            height,
-            width: msaAreaWidth,
-            overflow: 'hidden',
-        } }, blocksX.map(bx => (React.createElement(BoxTrackBlock, { track: track, key: bx, model: model, offsetX: bx })))));
-});
-export default BoxTrack;
-//# sourceMappingURL=BoxTrack.js.map

package/dist/components/BoxTrack.js.map

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package/dist/components/BoxTrackBlock.d.ts

@@ -1,8 +0,0 @@
-import React from 'react';
-import { IBoxTrack, MsaViewModel } from '../model';
-declare const BoxTrackBlock: ({ track, model, offsetX, }: {
-    track: IBoxTrack;
-    model: MsaViewModel;
-    offsetX: number;
-}) => React.JSX.Element | null;
-export default BoxTrackBlock;