react-msaview 3.1.7 → 3.1.8

package/src/parseGFF.ts

@@ -0,0 +1,32 @@
+export function parseGFF(str?: string) {
+  return str
+    ?.split('\n')
+    .map(f => f.trim())
+    .filter(f => !!f && !f.startsWith('#'))
+    .map(f => {
+      const [seq_id, source, type, start, end, score, strand, phase, col9] =
+        f.split('\t')
+
+      return {
+        seq_id,
+        source,
+        type,
+        start: +start,
+        end: +end,
+        score: +score,
+        strand,
+        phase,
+        ...Object.fromEntries(
+          col9
+            .split(';')
+            .map(f => f.trim())
+            .filter(f => !!f)
+            .map(f => f.split('='))
+            .map(([key, val]) => [
+              key.trim(),
+              decodeURIComponent(val).trim().split(',').join(' '),
+            ]),
+        ),
+      }
+    })
+}

package/src/renderToSvg.tsx

@@ -6,10 +6,12 @@ import { Theme } from '@mui/material'
 
 // locals
 import { MsaViewModel } from './model'
-import { renderTreeCanvas } from './components/TreePanel/renderTreeCanvas'
-import { renderMSABlock } from './components/MSAPanel/renderMSABlock'
+import { renderTreeCanvas } from './components/tree/renderTreeCanvas'
+import { renderMSABlock } from './components/msa/renderMSABlock'
 import { colorContrast } from './util'
-import MinimapSVG from './components/MinimapSVG'
+
+import MinimapSVG from './components/minimap/MinimapSVG'
+import { renderBoxFeatureCanvasBlock } from './components/msa/renderBoxFeatureCanvasBlock'
 
 export async function renderToSvg(
   model: MsaViewModel,
@@ -126,11 +128,21 @@ function CoreRendering({
     height: number,
   ) => CanvasRenderingContext2D & { getSvg: () => { innerHTML: string } }
 }) {
-  const clipId = 'tree'
+  const clipId1 = 'tree'
+  const clipId2 = 'msa'
   const { treeAreaWidth, colorScheme } = model
   const contrastScheme = colorContrast(colorScheme, theme)
   const ctx1 = Context(width, height)
   const ctx2 = Context(width, height)
+  renderBoxFeatureCanvasBlock({
+    ctx: ctx2,
+    offsetX,
+    offsetY,
+    model,
+    blockSizeYOverride: height,
+    highResScaleFactorOverride: 1,
+  })
+  const msaAreaWidth = width - treeAreaWidth
   renderTreeCanvas({
     model,
     offsetY,
@@ -146,23 +158,30 @@ function CoreRendering({
     offsetX,
     contrastScheme,
     ctx: ctx2,
-    blockSizeXOverride: width - treeAreaWidth,
+    blockSizeXOverride: msaAreaWidth,
     blockSizeYOverride: height,
     highResScaleFactorOverride: 1,
   })
   return (
     <>
       <defs>
-        <clipPath id={clipId}>
+        <clipPath id={clipId1}>
           <rect x={0} y={0} width={treeAreaWidth} height={height} />
         </clipPath>
       </defs>
+      <defs>
+        <clipPath id={clipId2}>
+          <rect x={0} y={0} width={msaAreaWidth} height={height} />
+        </clipPath>
+      </defs>
+
       <g
-        clipPath={`url(#${clipId})`}
+        clipPath={`url(#${clipId1})`}
         /* eslint-disable-next-line react/no-danger */
         dangerouslySetInnerHTML={{ __html: ctx1.getSvg().innerHTML }}
       />
       <g
+        clipPath={`url(#${clipId2})`}
         transform={`translate(${treeAreaWidth} 0)`}
         /* eslint-disable-next-line react/no-danger */
         dangerouslySetInnerHTML={{ __html: ctx2.getSvg().innerHTML }}
@@ -214,5 +233,5 @@ function SvgWrapper({
 }
 
 function NullWrapper({ children }: { children: React.ReactNode }) {
-  return <>{children}</>
+  return children
 }

package/src/reparseTree.ts

@@ -0,0 +1,16 @@
+import { NodeWithIds } from './util'
+
+export function reparseTree(tree: NodeWithIds): NodeWithIds {
+  return {
+    ...tree,
+    branchset: tree.branchset.map(r =>
+      r.branchset.length
+        ? reparseTree(r)
+        : {
+            branchset: [r],
+            id: `${r.id}-leafnode`,
+            name: `${r.name}-hidden`,
+          },
+    ),
+  }
+}

package/src/util.ts

@@ -63,39 +63,6 @@ export function colorContrast(
   ])
 }
 
-export function parseGFF(str?: string) {
-  return str
-    ?.split('\n')
-    .map(f => f.trim())
-    .filter(f => !!f && !f.startsWith('#'))
-    .map(f => {
-      const [seq_id, source, type, start, end, score, strand, phase, col9] =
-        f.split('\t')
-
-      return {
-        seq_id,
-        source,
-        type,
-        start: +start,
-        end: +end,
-        score: +score,
-        strand,
-        phase,
-        ...Object.fromEntries(
-          col9
-            .split(';')
-            .map(f => f.trim())
-            .filter(f => !!f)
-            .map(f => f.split('='))
-            .map(([key, val]) => [
-              key.trim(),
-              decodeURIComponent(val).trim().split(',').join(' '),
-            ]),
-        ),
-      }
-    })
-}
-
 export function skipBlanks(blanks: number[], arg: string | string[]) {
   let s = ''
   let b = 0
@@ -148,3 +115,7 @@ export function collapse(d: HierarchyNode<NodeWithIds>) {
 export function clamp(min: number, num: number, max: number) {
   return Math.min(Math.max(num, min), max)
 }
+
+export function len(a: { end: number; start: number }) {
+  return a.end - a.start
+}

package/src/version.ts

@@ -1 +1 @@
-export const version = '3.1.7'
+export const version = '3.1.8'

package/dist/DataModel.js.map

@@ -1 +0,0 @@
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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

@@ -1 +0,0 @@
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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

@@ -1 +0,0 @@
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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;

package/dist/components/BoxTrackBlock.js

@@ -1,136 +0,0 @@
-import React, { useRef, useMemo, useEffect } from 'react';
-import { observer } from 'mobx-react';
-import { getSnapshot, isStateTreeNode } from 'mobx-state-tree';
-import Layout from '../layout';
-const BoxTrackBlock = observer(function ({ track, model, offsetX, }) {
-    const { blockSize, colWidth, blanks, rowHeight, highResScaleFactor, fontSize, scrollX, } = model;
-    const { height, features, associatedRowName } = track.model;
-    const feats = isStateTreeNode(features)
-        ? // @ts-expect-error
-            getSnapshot(features)
-        : features;
-    const layout = useMemo(() => {
-        const temp = new Layout();
-        feats?.forEach((feature, index) => {
-            const { start, end } = feature;
-            if (associatedRowName) {
-                const s = model.rowSpecificBpToPx(associatedRowName, start - 1);
-                const e = model.rowSpecificBpToPx(associatedRowName, end);
-                temp.addRect(`${index}`, s, e, rowHeight, feature);
-            }
-            else {
-                const s = model.globalBpToPx(start - 1);
-                const e = model.globalBpToPx(end);
-                temp.addRect(`${index}`, s, e, rowHeight, feature);
-            }
-        });
-        return temp;
-        // might convert to autorun based drawing
-        // eslint-disable-next-line react-hooks/exhaustive-deps
-    }, [rowHeight, feats, associatedRowName, model, blanks]);
-    const ref = useRef(null);
-    const labelRef = useRef(null);
-    const mouseoverRef = useRef(null);
-    useEffect(() => {
-        if (!ref.current) {
-            return;
-        }
-        const ctx = ref.current.getContext('2d');
-        if (!ctx) {
-            return;
-        }
-        ctx.resetTransform();
-        ctx.scale(highResScaleFactor, highResScaleFactor);
-        ctx.clearRect(0, 0, blockSize, height);
-        ctx.translate(-offsetX, 0);
-        ctx.textAlign = 'center';
-        ctx.font = ctx.font.replace(/\d+px/, `${fontSize}px`);
-        const xStart = Math.max(0, Math.floor(offsetX / colWidth));
-        ctx.fillStyle = 'goldenrod';
-        layout.rectangles.forEach(value => {
-            const { minX, maxX, minY, maxY } = value;
-            const x1 = (minX - xStart) * colWidth + offsetX - (offsetX % colWidth);
-            const x2 = (maxX - xStart) * colWidth + offsetX - (offsetX % colWidth);
-            if (x2 - x1 > 0) {
-                ctx.fillRect(x1, minY, x2 - x1, (maxY - minY) / 2);
-            }
-        });
-    }, [
-        associatedRowName,
-        fontSize,
-        blockSize,
-        colWidth,
-        layout.rectangles,
-        model,
-        rowHeight,
-        height,
-        offsetX,
-        highResScaleFactor,
-        features,
-        blanks,
-    ]);
-    useEffect(() => {
-        if (!labelRef.current) {
-            return;
-        }
-        const ctx = labelRef.current.getContext('2d');
-        if (!ctx) {
-            return;
-        }
-        // this logic is very similar to MSACanvas
-        ctx.resetTransform();
-        ctx.scale(highResScaleFactor, highResScaleFactor);
-        ctx.clearRect(0, 0, blockSize, height);
-        ctx.translate(-offsetX, 0);
-        ctx.textAlign = 'center';
-        ctx.font = ctx.font.replace(/\d+px/, `${Math.max(8, rowHeight - 8)}px`);
-        ctx.fillStyle = 'black';
-        ctx.textAlign = 'left';
-        for (const value of layout.rectangles.values()) {
-            const { minX, maxX, maxY, minY, data } = value;
-            const x1 = minX * colWidth;
-            const x2 = maxX * colWidth;
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any
-            const feature = data;
-            if (x2 - x1 > 0) {
-                const note = feature.attributes?.Note?.[0];
-                const name = feature.attributes?.Name?.[0];
-                const type = feature.type;
-                ctx.fillText([type, name, note].filter(f => !!f).join(' - '), Math.max(Math.min(-scrollX, x2), x1), minY + (maxY - minY));
-            }
-        }
-    }, [
-        blockSize,
-        colWidth,
-        scrollX,
-        highResScaleFactor,
-        height,
-        layout.rectangles,
-        offsetX,
-        features,
-        model,
-        rowHeight,
-        blanks,
-    ]);
-    return !features ? null : (React.createElement(React.Fragment, null,
-        React.createElement("canvas", { ref: ref, height: height * highResScaleFactor, width: blockSize * highResScaleFactor, style: {
-                position: 'absolute',
-                left: scrollX + offsetX,
-                width: blockSize,
-                height,
-            } }),
-        React.createElement("canvas", { ref: labelRef, height: height * highResScaleFactor, width: blockSize * highResScaleFactor, style: {
-                position: 'absolute',
-                left: scrollX + offsetX,
-                width: blockSize,
-                height,
-            } }),
-        React.createElement("canvas", { ref: mouseoverRef, height: height * highResScaleFactor, width: blockSize * highResScaleFactor, style: {
-                position: 'absolute',
-                left: scrollX + offsetX,
-                width: blockSize,
-                height,
-            } })));
-});
-export default BoxTrackBlock;
-//# sourceMappingURL=BoxTrackBlock.js.map

package/dist/components/BoxTrackBlock.js.map

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package/dist/components/ExportSVGDialog.js.map

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