react-msaview 4.1.1 → 4.3.0

package/dist/components/header/ZoomMenu.js

@@ -0,0 +1,33 @@
+import React from 'react';
+import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
+import MoreVert from '@mui/icons-material/MoreVert';
+import RestartAlt from '@mui/icons-material/RestartAlt';
+import { observer } from 'mobx-react';
+const ZoomMenu = observer(function ({ model }) {
+    return (React.createElement(CascadingMenuButton, { menuItems: [
+            {
+                label: 'Fit to view',
+                onClick: () => {
+                    model.showEntire();
+                },
+            },
+            {
+                label: 'Reset zoom to default',
+                icon: RestartAlt,
+                onClick: () => {
+                    model.resetZoom();
+                },
+            },
+            {
+                label: 'Show extra zoom options',
+                checked: model.showZoomStar,
+                type: 'checkbox',
+                onClick: () => {
+                    model.setShowZoomStar(!model.showZoomStar);
+                },
+            },
+        ] },
+        React.createElement(MoreVert, null)));
+});
+export default ZoomMenu;
+//# sourceMappingURL=ZoomMenu.js.map

package/dist/components/header/ZoomMenu.js.map

@@ -0,0 +1 @@
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package/dist/components/header/ZoomStar.d.ts

@@ -0,0 +1,6 @@
+import React from 'react';
+import type { MsaViewModel } from '../../model';
+declare const ZoomStar: ({ model }: {
+    model: MsaViewModel;
+}) => React.JSX.Element;
+export default ZoomStar;

package/dist/components/header/ZoomStar.js

@@ -0,0 +1,40 @@
+import React from 'react';
+import RestartAlt from '@mui/icons-material/RestartAlt';
+import { IconButton } from '@mui/material';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+const useStyles = makeStyles()(theme => ({
+    dpad: {
+        display: 'grid',
+        gridTemplateColumns: 'repeat(3, 1fr)',
+    },
+    icon: {
+        padding: theme.spacing(0.5),
+    },
+}));
+const ZoomStar = observer(function ({ model }) {
+    const { classes } = useStyles();
+    return (React.createElement("div", { className: classes.dpad },
+        React.createElement("div", null),
+        React.createElement(IconButton, { className: classes.icon, onClick: () => {
+                model.zoomInVertical();
+            } }, "Y+"),
+        React.createElement("div", null),
+        React.createElement(IconButton, { className: classes.icon, onClick: () => {
+                model.zoomOutHorizontal();
+            } }, "X-"),
+        React.createElement(IconButton, { className: classes.icon, onClick: () => {
+                model.resetZoom();
+            } },
+            React.createElement(RestartAlt, null)),
+        React.createElement(IconButton, { className: classes.icon, onClick: () => {
+                model.zoomInHorizontal();
+            } }, "X+"),
+        React.createElement("div", null),
+        React.createElement(IconButton, { className: classes.icon, onClick: () => {
+                model.zoomOutVertical();
+            } }, "Y-"),
+        React.createElement("div", null)));
+});
+export default ZoomStar;
+//# sourceMappingURL=ZoomStar.js.map

package/dist/components/header/ZoomStar.js.map

@@ -0,0 +1 @@
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package/dist/components/tree/renderTreeCanvas.js

@@ -3,9 +3,10 @@ const extendBounds = 5;
 const radius = 2.5;
 const d = radius * 2;
 export function renderTree({ offsetY, ctx, model, theme, blockSizeYOverride, }) {
-    const { hierarchy, showBranchLen, blockSize } = model;
+    const { hierarchy, allBranchesLength0, showBranchLen: showBranchLenPre, blockSize, } = model;
     const by = blockSizeYOverride || blockSize;
     ctx.strokeStyle = theme.palette.text.primary;
+    const showBranchLen = allBranchesLength0 ? false : showBranchLenPre;
     for (const link of hierarchy.links()) {
         const { source, target } = link;
         if (target.height === 0 && !showBranchLen) {
@@ -32,8 +33,9 @@ export function renderTree({ offsetY, ctx, model, theme, blockSizeYOverride, })
     }
 }
 export function renderNodeBubbles({ ctx, clickMap, offsetY, model, blockSizeYOverride, }) {
-    const { hierarchy, showBranchLen, collapsed, blockSize, marginLeft: ml, } = model;
+    const { hierarchy, showBranchLen: showBranchLenPre, allBranchesLength0, collapsed, blockSize, marginLeft: ml, } = model;
     const by = blockSizeYOverride || blockSize;
+    const showBranchLen = allBranchesLength0 ? false : showBranchLenPre;
     for (const node of hierarchy.descendants()) {
         const val = showBranchLen ? 'len' : 'y';
         // @ts-expect-error
@@ -62,7 +64,7 @@ export function renderNodeBubbles({ ctx, clickMap, offsetY, model, blockSizeYOve
     }
 }
 export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSizeYOverride, }) {
-    const { fontSize, showBranchLen, treeMetadata, hierarchy, collapsed, collapsedLeaves, blockSize, labelsAlignRight, drawTree, treeAreaWidth, treeWidth, treeAreaWidthMinusMargin, marginLeft, leaves, noTree, } = model;
+    const { fontSize, showBranchLen: showBranchLenPre, allBranchesLength0, treeMetadata, hierarchy, collapsed, collapsedLeaves, blockSize, labelsAlignRight, drawTree, treeAreaWidth, treeWidth, treeAreaWidthMinusMargin, marginLeft, leaves, noTree, } = model;
     const by = blockSizeYOverride || blockSize;
     if (labelsAlignRight) {
         ctx.textAlign = 'right';
@@ -71,6 +73,7 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSi
     else {
         ctx.textAlign = 'start';
     }
+    const showBranchLen = allBranchesLength0 ? false : showBranchLenPre;
     for (const node of leaves) {
         const { data: { name, id }, 
         // @ts-expect-error

package/dist/components/tree/renderTreeCanvas.js.map

@@ -1 +1 @@
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package/dist/flatToTree.d.ts

@@ -0,0 +1,17 @@
+interface FlatItem {
+    id: number;
+    parent?: number;
+}
+interface TreeNode {
+    id: string;
+    name: string;
+    parent?: string;
+    children: TreeNode[];
+}
+/**
+ * Parses a flat list of items into a tree structure
+ * @param items - Array of flat items with id and optional parent
+ * @returns Array of root tree nodes
+ */
+export declare function flatToTree(items: FlatItem[]): TreeNode;
+export {};

package/dist/flatToTree.js

@@ -0,0 +1,41 @@
+/**
+ * Parses a flat list of items into a tree structure
+ * @param items - Array of flat items with id and optional parent
+ * @returns Array of root tree nodes
+ */
+export function flatToTree(items) {
+    // Create a map to store all nodes by their id for quick lookup
+    const nodeMap = new Map();
+    // First pass: Create all tree nodes
+    items.forEach(item => {
+        nodeMap.set(item.id, {
+            ...item,
+            id: `${item.id}`,
+            name: `${item.id}`,
+            parent: item.parent !== undefined ? `${item.parent}` : undefined,
+            children: [],
+        });
+    });
+    // Second pass: Build parent-child relationships
+    const roots = [];
+    items.forEach(item => {
+        const node = nodeMap.get(item.id);
+        if (item.parent !== undefined) {
+            // This item has a parent, add it to parent's children
+            const parentNode = nodeMap.get(item.parent);
+            if (parentNode) {
+                parentNode.children.push(node);
+            }
+            else {
+                // Parent doesn't exist, treat as root
+                roots.push(node);
+            }
+        }
+        else {
+            // This item has no parent, it's a root node
+            roots.push(node);
+        }
+    });
+    return roots[0];
+}
+//# sourceMappingURL=flatToTree.js.map

package/dist/flatToTree.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"flatToTree.js","sourceRoot":"","sources":["../src/flatToTree.ts"],"names":[],"mappings":"AAcA;;;;GAIG;AACH,MAAM,UAAU,UAAU,CAAC,KAAiB;IAC1C,+DAA+D;IAC/D,MAAM,OAAO,GAAG,IAAI,GAAG,EAAoB,CAAA;IAE3C,oCAAoC;IACpC,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;QACnB,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,EAAE;YACnB,GAAG,IAAI;YACP,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,EAAE;YAChB,IAAI,EAAE,GAAG,IAAI,CAAC,EAAE,EAAE;YAClB,MAAM,EAAE,IAAI,CAAC,MAAM,KAAK,SAAS,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,SAAS;YAChE,QAAQ,EAAE,EAAE;SACb,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;IAEF,gDAAgD;IAChD,MAAM,KAAK,GAAe,EAAE,CAAA;IAE5B,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;QACnB,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAE,CAAA;QAElC,IAAI,IAAI,CAAC,MAAM,KAAK,SAAS,EAAE,CAAC;YAC9B,sDAAsD;YACtD,MAAM,UAAU,GAAG,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;YAC3C,IAAI,UAAU,EAAE,CAAC;gBACf,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAChC,CAAC;iBAAM,CAAC;gBACN,sCAAsC;gBACtC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAClB,CAAC;QACH,CAAC;aAAM,CAAC;YACN,4CAA4C;YAC5C,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAClB,CAAC;IACH,CAAC,CAAC,CAAA;IAEF,OAAO,KAAK,CAAC,CAAC,CAAE,CAAA;AAClB,CAAC"}

package/dist/model.d.ts

@@ -1,35 +1,13 @@
-import React from 'react';
 import ClustalMSA from './parsers/ClustalMSA';
 import EmfMSA from './parsers/EmfMSA';
 import FastaMSA from './parsers/FastaMSA';
 import StockholmMSA from './parsers/StockholmMSA';
 import type { InterProScanResults } from './launchInterProScan';
-import type { NodeWithIds, NodeWithIdsAndLength } from './util';
+import type { Accession, BasicTrack, NodeWithIds, NodeWithIdsAndLength } from './types';
 import type { FileLocation as FileLocationType } from '@jbrowse/core/util/types';
 import type { Theme } from '@mui/material';
 import type { HierarchyNode } from 'd3-hierarchy';
 import type { Instance } from 'mobx-state-tree';
-export interface Accession {
-    accession: string;
-    name: string;
-    description: string;
-}
-export interface BasicTrackModel {
-    id: string;
-    name: string;
-    associatedRowName?: string;
-    height: number;
-}
-export interface TextTrackModel extends BasicTrackModel {
-    customColorScheme?: Record<string, string>;
-    data: string;
-}
-export interface ITextTrack {
-    ReactComponent: React.FC<any>;
-    model: TextTrackModel;
-}
-export type BasicTrack = ITextTrack;
-export declare function isGzip(buf: Uint8Array): boolean;
 /**
  * #stateModel MsaView
  * extends
@@ -52,13 +30,12 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
 } & {
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     showDomains: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    hideGaps: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     allowedGappyness: import("mobx-state-tree").IType<number | undefined, number, number>;
     contrastLettering: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     subFeatureRows: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     type: import("mobx-state-tree").ISimpleType<"MsaView">;
     drawMsaLetters: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    hideGaps: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    drawTreeText: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
     rowHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
     scrollY: import("mobx-state-tree").IType<number | undefined, number, number>;
@@ -275,6 +252,11 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * screens
      */
     highResScaleFactor: number;
+    /**
+     * #volatile
+     * obtained from localStorage
+     */
+    showZoomStar: boolean;
     /**
      * #volatile
      */
@@ -367,6 +349,10 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #action
      */
     setLoadingMSA(arg: boolean): void;
+    /**
+     * #volatile
+     */
+    setShowZoomStar(arg: boolean): void;
     /**
      * #action
      */
@@ -604,6 +590,10 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #getter
      */
     readonly leaves: HierarchyNode<NodeWithIdsAndLength>[];
+    /**
+     * #getter
+     */
+    readonly allBranchesLength0: boolean;
 } & {
     /**
      * #getter
@@ -648,6 +638,10 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #action
      */
     setDrawMsaLetters(arg: boolean): void;
+    /**
+     * #action
+     */
+    resetZoom(): void;
     /**
      * #action
      */
@@ -727,7 +721,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     /**
      * #getter
      */
-    readonly turnedOnTracks: ITextTrack[];
+    readonly turnedOnTracks: import("./types").ITextTrack[];
     /**
      * #getter
      */
@@ -880,12 +874,11 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     colorSchemeName: string;
     id: string;
     showDomains: boolean;
+    hideGaps: boolean;
     allowedGappyness: number;
     contrastLettering: boolean;
     subFeatureRows: boolean;
     drawMsaLetters: boolean;
-    hideGaps: boolean;
-    drawTreeText: boolean;
     rowHeight: number;
     scrollY: number;
     scrollX: number;

package/dist/model.js

@@ -4,6 +4,7 @@ import { ElementId, FileLocation } from '@jbrowse/core/util/types/mst';
 import { colord } from 'colord';
 import { ascending } from 'd3-array';
 import { cluster, hierarchy } from 'd3-hierarchy';
+import { parseEmfTree } from 'emf-js';
 import { saveAs } from 'file-saver';
 import { autorun, transaction } from 'mobx';
 import { addDisposer, cast, types } from 'mobx-state-tree';
@@ -12,24 +13,25 @@ import Stockholm from 'stockholm-js';
 import { blocksX, blocksY } from './calculateBlocks';
 import colorSchemes from './colorSchemes';
 import TextTrack from './components/TextTrack';
+import { flatToTree } from './flatToTree';
 import palettes from './ggplotPalettes';
 import { measureTextCanvas } from './measureTextCanvas';
 import { DataModelF } from './model/DataModel';
 import { DialogQueueSessionMixin } from './model/DialogQueue';
 import { MSAModelF } from './model/msaModel';
 import { TreeModelF } from './model/treeModel';
+import { parseAsn1 } from './parseAsn1';
 import parseNewick from './parseNewick';
 import ClustalMSA from './parsers/ClustalMSA';
 import EmfMSA from './parsers/EmfMSA';
-import EmfTree from './parsers/EmfTree';
 import FastaMSA from './parsers/FastaMSA';
 import StockholmMSA from './parsers/StockholmMSA';
 import { reparseTree } from './reparseTree';
 import { globalCoordToRowSpecificCoord, mouseOverCoordToGlobalCoord, } from './rowCoordinateCalculations';
-import { clamp, collapse, generateNodeIds, len, maxLength, setBrLength, skipBlanks, } from './util';
-export function isGzip(buf) {
-    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
-}
+import { clamp, collapse, generateNodeIds, isGzip, len, localStorageGetBoolean, localStorageSetBoolean, maxLength, setBrLength, skipBlanks, } from './util';
+const defaultRowHeight = 16;
+const defaultColWidth = 12;
+const showZoomStarKey = 'msa-showZoomStar';
 /**
  * #stateModel MsaView
  * extends
@@ -49,6 +51,10 @@ function stateModelFactory() {
          * #property
          */
         showDomains: false,
+        /**
+         * #property
+         */
+        hideGaps: true,
         /**
          * #property
          */
@@ -70,14 +76,6 @@ function stateModelFactory() {
          * #property
          */
         drawMsaLetters: true,
-        /**
-         * #property
-         */
-        hideGaps: false,
-        /**
-         * #property
-         */
-        drawTreeText: true,
         /**
          * #property
          * height of the div containing the view, px
@@ -87,7 +85,7 @@ function stateModelFactory() {
          * #property
          * height of each row, px
          */
-        rowHeight: 18,
+        rowHeight: defaultRowHeight,
         /**
          * #property
          * scroll position, Y-offset, px
@@ -102,7 +100,7 @@ function stateModelFactory() {
          * #property
          * width of columns, px
          */
-        colWidth: 14,
+        colWidth: defaultColWidth,
         /**
          * #property
          * filehandle object for the tree
@@ -180,6 +178,11 @@ function stateModelFactory() {
          * screens
          */
         highResScaleFactor: 2,
+        /**
+         * #volatile
+         * obtained from localStorage
+         */
+        showZoomStar: localStorageGetBoolean(showZoomStarKey, false),
         /**
          * #volatile
          */
@@ -280,6 +283,12 @@ function stateModelFactory() {
         setLoadingMSA(arg) {
             self.loadingMSA = arg;
         },
+        /**
+         * #volatile
+         */
+        setShowZoomStar(arg) {
+            self.showZoomStar = arg;
+        },
         /**
          * #action
          */
@@ -538,27 +547,16 @@ function stateModelFactory() {
          */
         get tree() {
             const text = self.data.tree;
-            let ret;
-            if (text) {
-                let t;
-                if (text.startsWith('SEQ')) {
-                    const r = new EmfTree(text);
-                    t = r.data.tree;
-                }
-                else {
-                    t = text;
-                }
-                ret = generateNodeIds(parseNewick(t));
-            }
-            else {
-                ret = this.MSA?.getTree() || {
+            return text
+                ? reparseTree(generateNodeIds(text.startsWith('BioTreeContainer')
+                    ? flatToTree(parseAsn1(text))
+                    : parseNewick(text.startsWith('SEQ') ? parseEmfTree(text).tree : text)))
+                : reparseTree(this.MSA?.getTree() || {
                     noTree: true,
                     children: [],
                     id: 'empty',
                     name: 'empty',
-                };
-            }
-            return reparseTree(ret);
+                });
         },
         /**
          * #getter
@@ -736,6 +734,12 @@ function stateModelFactory() {
         get leaves() {
             return this.hierarchy.leaves();
         },
+        /**
+         * #getter
+         */
+        get allBranchesLength0() {
+            return this.hierarchy.links().every(s => !s.source.data.length);
+        },
     }))
         .views(self => ({
         /**
@@ -822,6 +826,13 @@ function stateModelFactory() {
         setDrawMsaLetters(arg) {
             self.drawMsaLetters = arg;
         },
+        /**
+         * #action
+         */
+        resetZoom() {
+            self.setColWidth(defaultColWidth);
+            self.setRowHeight(defaultRowHeight);
+        },
         /**
          * #action
          */
@@ -1223,6 +1234,10 @@ function stateModelFactory() {
                     this.initFilter(key);
                 }
             }));
+            // autorun saves local settings
+            addDisposer(self, autorun(() => {
+                localStorageSetBoolean(showZoomStarKey, self.showZoomStar);
+            }));
             // autorun opens treeFilehandle
             addDisposer(self, autorun(async () => {
                 const { treeFilehandle } = self;