react-msaview 4.4.4 → 4.4.6

package/dist/components/MSAPanel/renderMSABlock_BACKUP_139826.js.map

@@ -1 +0,0 @@
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package/dist/components/MSAPanel/renderMSABlock_BASE_139826.d.ts

@@ -1,13 +0,0 @@
-import { MsaViewModel } from '../../model';
-import { Theme } from '@mui/material';
-export declare function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, theme, highResScaleFactorOverride, blockSizeXOverride, blockSizeYOverride, }: {
-    offsetX: number;
-    offsetY: number;
-    theme: Theme;
-    model: MsaViewModel;
-    contrastScheme: Record<string, string>;
-    ctx: CanvasRenderingContext2D;
-    highResScaleFactorOverride?: number;
-    blockSizeXOverride?: number;
-    blockSizeYOverride?: number;
-}): void;

package/dist/components/MSAPanel/renderMSABlock_BASE_139826.js

@@ -1,82 +0,0 @@
-import { getClustalXColor, getPercentIdentityColor } from '../../colorSchemes';
-export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, theme, highResScaleFactorOverride, blockSizeXOverride, blockSizeYOverride, }) {
-    const { hierarchy, colWidth, blockSize, rowHeight, fontSize, highResScaleFactor, } = model;
-    const k = highResScaleFactorOverride || highResScaleFactor;
-    const bx = blockSizeXOverride || blockSize;
-    const by = blockSizeYOverride || blockSize;
-    ctx.resetTransform();
-    ctx.scale(k, k);
-    ctx.clearRect(0, 0, bx, by);
-    ctx.translate(-offsetX, rowHeight / 2 - offsetY);
-    ctx.textAlign = 'center';
-    ctx.font = ctx.font.replace(/\d+px/, `${fontSize}px`);
-    const leaves = hierarchy.leaves();
-    const yStart = Math.max(0, Math.floor((offsetY - rowHeight) / rowHeight));
-    const yEnd = Math.max(0, Math.ceil((offsetY + by + rowHeight) / rowHeight));
-    const xStart = Math.max(0, Math.floor(offsetX / colWidth));
-    const xEnd = Math.max(0, Math.ceil((offsetX + bx) / colWidth));
-    const visibleLeaves = leaves.slice(yStart, yEnd);
-    drawTiles({
-        model,
-        ctx,
-        theme,
-        offsetX,
-        offsetY,
-        xStart,
-        xEnd,
-        visibleLeaves,
-    });
-    drawText({
-        model,
-        ctx,
-        offsetX,
-        contrastScheme,
-        theme,
-        xStart,
-        xEnd,
-        visibleLeaves,
-    });
-}
-function drawTiles({ model, offsetX, ctx, visibleLeaves, theme, xStart, xEnd, }) {
-    const { bgColor, colorSchemeName, colorScheme, colStats, columns, colWidth, rowHeight, } = model;
-    for (const node of visibleLeaves) {
-        const { 
-        // @ts-expect-error
-        x: y, data: { name }, } = node;
-        const str = columns[name]?.slice(xStart, xEnd);
-        for (let i = 0; i < str?.length; i++) {
-            const letter = str[i];
-            const color = colorSchemeName === 'clustalx_protein_dynamic'
-                ? getClustalXColor(colStats[xStart + i], model, name, xStart + i)
-                : colorSchemeName === 'percent_identity_dynamic'
-                    ? getPercentIdentityColor(colStats[xStart + i], model, name, xStart + i)
-                    : colorScheme[letter.toUpperCase()];
-            if (bgColor) {
-                const x = i * colWidth + offsetX - (offsetX % colWidth);
-                ctx.fillStyle = color || theme.palette.background.default;
-                ctx.fillRect(x, y - rowHeight, colWidth, rowHeight);
-            }
-        }
-    }
-}
-function drawText({ model, offsetX, contrastScheme, ctx, visibleLeaves, xStart, xEnd, }) {
-    const { bgColor, colorScheme, columns, colWidth, rowHeight } = model;
-    if (rowHeight >= 5 && colWidth > rowHeight / 2) {
-        for (const node of visibleLeaves) {
-            const { 
-            // @ts-expect-error
-            x: y, data: { name }, } = node;
-            const str = columns[name]?.slice(xStart, xEnd);
-            for (let i = 0; i < str?.length; i++) {
-                const letter = str[i];
-                const color = colorScheme[letter.toUpperCase()];
-                const contrast = contrastScheme[letter.toUpperCase()] || 'black';
-                const x = i * colWidth + offsetX - (offsetX % colWidth);
-                // note: -rowHeight/4 matches +rowHeight/4 in tree
-                ctx.fillStyle = bgColor ? contrast : color || 'black';
-                ctx.fillText(letter, x + colWidth / 2, y - rowHeight / 4);
-            }
-        }
-    }
-}
-//# sourceMappingURL=renderMSABlock_BASE_139826.js.map

package/dist/components/MSAPanel/renderMSABlock_BASE_139826.js.map

@@ -1 +0,0 @@
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package/dist/components/MSAPanel/renderMSABlock_LOCAL_139826.d.ts

@@ -1,9 +0,0 @@
-import { MsaViewModel } from '../../model';
-import { Theme } from '@mui/material';
-import { Application } from 'pixi.js';
-export declare function renderMSABlock({ model, app, contrastScheme, theme, }: {
-    theme: Theme;
-    model: MsaViewModel;
-    contrastScheme: Record<string, string>;
-    app: Application;
-}): void;

package/dist/components/MSAPanel/renderMSABlock_LOCAL_139826.js

@@ -1,89 +0,0 @@
-import { getClustalXColor, getPercentIdentityColor } from '../../colorSchemes';
-import { BitmapText } from 'pixi.js';
-export function renderMSABlock({ model, app, contrastScheme, theme, }) {
-    const { hierarchy, msaAreaWidth, scrollX, scrollY, colWidth, blockSize, height, rowHeight, highResScaleFactor, } = model;
-    const offsetX = scrollX;
-    const offsetY = scrollY;
-    const k = highResScaleFactor;
-    const bx = msaAreaWidth;
-    const by = height;
-    const leaves = hierarchy.leaves();
-    const yStart = Math.max(0, Math.floor((offsetY - rowHeight) / rowHeight));
-    const yEnd = Math.max(0, Math.ceil((offsetY + by + rowHeight) / rowHeight));
-    const xStart = Math.max(0, Math.floor(offsetX / colWidth));
-    const xEnd = Math.max(0, Math.ceil((offsetX + bx) / colWidth));
-    const visibleLeaves = leaves.slice(yStart, yEnd);
-    drawTiles({
-        model,
-        app,
-        theme,
-        offsetX,
-        offsetY,
-        xStart,
-        xEnd,
-        visibleLeaves,
-    });
-    drawText({
-        model,
-        app,
-        offsetX,
-        contrastScheme,
-        theme,
-        xStart,
-        xEnd,
-        visibleLeaves,
-    });
-}
-function drawTiles({ model, offsetX, app, visibleLeaves, theme, xStart, xEnd, }) {
-    const { bgColor, colorSchemeName, colorScheme, colStats, columns, colWidth, rowHeight, } = model;
-    for (const node of visibleLeaves) {
-        const { 
-        // @ts-expect-error
-        x: y, data: { name }, } = node;
-        const str = columns[name]?.slice(xStart, xEnd);
-        for (let i = 0; i < str?.length; i++) {
-            const letter = str[i];
-            const color = colorSchemeName === 'clustalx_protein_dynamic'
-                ? getClustalXColor(colStats[xStart + i], model, name, xStart + i)
-                : colorSchemeName === 'percent_identity_dynamic'
-                    ? getPercentIdentityColor(colStats[xStart + i], model, name, xStart + i)
-                    : colorScheme[letter.toUpperCase()];
-            if (bgColor) {
-                const x = i * colWidth + offsetX - (offsetX % colWidth);
-                // ctx.fillStyle = color || theme.palette.background.default
-                // ctx.fillRect(x, y - rowHeight, colWidth, rowHeight)
-            }
-        }
-    }
-}
-function drawText({ model, offsetX, contrastScheme, app, visibleLeaves, xStart, xEnd, }) {
-    const { bgColor, colorScheme, columns, colWidth, rowHeight } = model;
-    if (rowHeight >= 5 && colWidth > rowHeight / 2) {
-        for (const node of visibleLeaves) {
-            const { 
-            // @ts-expect-error
-            x: y, data: { name }, } = node;
-            const str = columns[name]?.slice(xStart, xEnd);
-            for (let i = 0; i < str?.length; i++) {
-                const letter = str[i];
-                const color = colorScheme[letter.toUpperCase()];
-                const contrast = contrastScheme[letter.toUpperCase()] || 'black';
-                const x = i * colWidth + offsetX - (offsetX % colWidth);
-                // note: -rowHeight/4 matches +rowHeight/4 in tree
-                // ctx.fillStyle = bgColor ? contrast : color || 'black'
-                // ctx.fillText(letter, x + colWidth / 2, y - rowHeight / 4)
-                const t = new BitmapText({
-                    text: letter,
-                    x,
-                    y,
-                    style: {
-                        fontFamily: 'Arial',
-                        fontSize: 20,
-                    },
-                });
-                app.stage.addChild(t);
-            }
-        }
-    }
-}
-//# sourceMappingURL=renderMSABlock_LOCAL_139826.js.map

package/dist/components/MSAPanel/renderMSABlock_LOCAL_139826.js.map

@@ -1 +0,0 @@
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package/dist/components/MSAPanel/renderMSABlock_REMOTE_139826.js

@@ -1,2 +0,0 @@
-"use strict";
-//# sourceMappingURL=renderMSABlock_REMOTE_139826.js.map

package/dist/components/MSAPanel/renderMSABlock_REMOTE_139826.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"renderMSABlock_REMOTE_139826.js","sourceRoot":"","sources":["../../../src/components/MSAPanel/renderMSABlock_REMOTE_139826.ts"],"names":[],"mappings":""}

package/dist/components/MSAPanel/renderMSAMouseover.d.ts

@@ -1,5 +0,0 @@
-import { MsaViewModel } from '../../model';
-export declare function renderMouseover({ ctx, model, }: {
-    ctx: CanvasRenderingContext2D;
-    model: MsaViewModel;
-}): void;

package/dist/components/MSAPanel/renderMSAMouseover.js

@@ -1,30 +0,0 @@
-const hoverColor = 'rgba(0,0,0,0.15)';
-const highlightColor = 'rgba(128,128,0,0.2)';
-export function renderMouseover({ ctx, model, }) {
-    const { mouseCol, colWidth, width, height, rowHeight, scrollX, scrollY, mouseRow, 
-    // @ts-expect-error
-    mouseCol2, mouseClickRow, mouseClickCol, } = model;
-    ctx.resetTransform();
-    ctx.clearRect(0, 0, width, height);
-    if (mouseCol !== undefined) {
-        ctx.fillStyle = hoverColor;
-        ctx.fillRect((mouseCol - 1) * colWidth + scrollX, 0, colWidth, height);
-    }
-    if (mouseRow !== undefined) {
-        ctx.fillStyle = hoverColor;
-        ctx.fillRect(0, mouseRow * rowHeight + scrollY, width, rowHeight);
-    }
-    if (mouseClickCol !== undefined) {
-        ctx.fillStyle = highlightColor;
-        ctx.fillRect((mouseClickCol - 1) * colWidth + scrollX, 0, colWidth, height);
-    }
-    if (mouseClickRow !== undefined) {
-        ctx.fillStyle = highlightColor;
-        ctx.fillRect(0, mouseClickRow * rowHeight + scrollY, width, rowHeight);
-    }
-    if (mouseCol2 !== undefined) {
-        ctx.fillStyle = highlightColor;
-        ctx.fillRect((mouseCol2 - 1) * colWidth + scrollX, 0, colWidth, height);
-    }
-}
-//# sourceMappingURL=renderMSAMouseover.js.map

package/dist/components/MSAPanel/renderMSAMouseover.js.map

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package/dist/components/Minimap.d.ts

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

package/dist/components/Minimap.js

@@ -1,72 +0,0 @@
-import React, { useEffect, useRef, useState } from 'react';
-import { observer } from 'mobx-react';
-const Minimap = observer(function ({ model }) {
-    const [mouseDown, setMouseDown] = useState();
-    const scheduled = useRef(false);
-    const [hovered, setHovered] = useState(false);
-    const { scrollX, msaAreaWidth: W, minimapHeight: H, colWidth, numColumns, } = model;
-    const unit = W / numColumns / colWidth;
-    const left = -scrollX;
-    const right = left + W;
-    const s = left * unit;
-    const e = right * unit;
-    const fill = 'rgba(66, 119, 127, 0.3)';
-    useEffect(() => {
-        function fn(event) {
-            if (mouseDown !== undefined) {
-                if (!scheduled.current) {
-                    scheduled.current = true;
-                    window.requestAnimationFrame(() => {
-                        model.setScrollX(mouseDown.scrollX - (event.clientX - mouseDown.clientX) / unit);
-                        scheduled.current = false;
-                    });
-                }
-            }
-        }
-        function fn2() {
-            setMouseDown(undefined);
-        }
-        if (mouseDown !== undefined) {
-            document.addEventListener('mousemove', fn);
-            document.addEventListener('mouseup', fn2);
-            return () => {
-                document.removeEventListener('mousemove', fn);
-                document.removeEventListener('mousemove', fn2);
-            };
-        }
-    }, [model, unit, mouseDown]);
-    const BAR_HEIGHT = 12;
-    const H2 = H - 12;
-    return (React.createElement("div", { style: { position: 'relative', height: H, width: '100%' } },
-        React.createElement("div", { style: {
-                boxSizing: 'border-box',
-                height: BAR_HEIGHT,
-                border: '1px solid #555',
-            } }),
-        React.createElement("div", { style: {
-                position: 'absolute',
-                top: 0,
-                left: Math.max(0, s),
-                background: hovered ? 'rgba(66,119,127,0.6)' : fill,
-                cursor: 'pointer',
-                border: '1px solid #555',
-                boxSizing: 'border-box',
-                height: BAR_HEIGHT,
-                width: e - s,
-                zIndex: 100,
-            }, onMouseOver: () => setHovered(true), onMouseOut: () => setHovered(false), onMouseDown: event => {
-                setMouseDown({
-                    clientX: event.clientX,
-                    scrollX: model.scrollX,
-                });
-            } }),
-        React.createElement("svg", { height: H2, style: { width: '100%' } },
-            React.createElement("polygon", { fill: fill, points: [
-                    [e, 0],
-                    [s, 0],
-                    [0, H2],
-                    [W, H2],
-                ].toString() }))));
-});
-export default Minimap;
-//# sourceMappingURL=Minimap.js.map

package/dist/components/Minimap.js.map

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package/dist/components/MinimapSVG.d.ts

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

package/dist/components/MinimapSVG.js

@@ -1,25 +0,0 @@
-import React from 'react';
-import { observer } from 'mobx-react';
-const MinimapSVG = observer(function ({ model }) {
-    const { scrollX, msaAreaWidth: W, minimapHeight: H, colWidth, numColumns, } = model;
-    const BAR_HEIGHT = 12;
-    const H2 = H - 12;
-    const unit = W / numColumns / colWidth;
-    const left = -scrollX;
-    const right = left + W;
-    const s = left * unit;
-    const e = right * unit;
-    const fill = 'rgba(66, 119, 127, 0.3)';
-    return (React.createElement(React.Fragment, null,
-        React.createElement("rect", { x: 0, y: 0, width: W, height: BAR_HEIGHT, stroke: "#555", fill: "none" }),
-        React.createElement("rect", { x: Math.max(0, s), y: 0, width: e - s, height: BAR_HEIGHT, fill: fill, stroke: "#555" }),
-        React.createElement("g", { transform: `translate(0 ${BAR_HEIGHT})` },
-            React.createElement("polygon", { fill: fill, points: [
-                    [e, 0],
-                    [s, 0],
-                    [0, H2],
-                    [W, H2],
-                ].toString() }))));
-});
-export default MinimapSVG;
-//# sourceMappingURL=MinimapSVG.js.map

package/dist/components/MinimapSVG.js.map

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

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

package/dist/components/MultiAlignmentSelector.js

@@ -1,13 +0,0 @@
-import React from 'react';
-import { observer } from 'mobx-react';
-import { Select } from '@mui/material';
-const MultiAlignmentSelector = observer(function ({ model, }) {
-    const { currentAlignment, alignmentNames } = model;
-    return alignmentNames.length > 0 ? (React.createElement(Select, { native: true, value: currentAlignment, size: "small", onChange: event => {
-            model.setCurrentAlignment(+event.target.value);
-            model.setScrollX(0);
-            model.setScrollY(0);
-        } }, alignmentNames.map((option, index) => (React.createElement("option", { key: `${option}-${index}`, value: index }, option))))) : null;
-});
-export default MultiAlignmentSelector;
-//# sourceMappingURL=MultiAlignmentSelector.js.map

package/dist/components/MultiAlignmentSelector.js.map

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package/dist/components/TreePanel/TreeBranchMenu.d.ts

@@ -1,14 +0,0 @@
-import React from 'react';
-import { MsaViewModel } from '../../model';
-interface Node {
-    x: number;
-    y: number;
-    name: string;
-    id: string;
-}
-declare const TreeBranchMenu: ({ node, model, onClose, }: {
-    node: Node;
-    model: MsaViewModel;
-    onClose: () => void;
-}) => React.JSX.Element;
-export default TreeBranchMenu;

package/dist/components/TreePanel/TreeBranchMenu.js

@@ -1,26 +0,0 @@
-import React from 'react';
-import { Menu, MenuItem } from '@mui/material';
-import { observer } from 'mobx-react';
-const TreeBranchMenu = observer(function ({ node, model, onClose, }) {
-    return (React.createElement(Menu, { anchorReference: "anchorPosition", anchorPosition: {
-            left: node.x,
-            top: node.y,
-        }, transitionDuration: 0, keepMounted: true, open: Boolean(node), onClose: onClose },
-        React.createElement(MenuItem, { dense: true, disabled: true }, node.name),
-        React.createElement(MenuItem, { dense: true, onClick: () => {
-                model.toggleCollapsed(node.id);
-                onClose();
-            } }, model.collapsed.includes(node.id)
-            ? 'Expand this node'
-            : 'Collapse this node'),
-        React.createElement(MenuItem, { dense: true, onClick: () => {
-                model.showOnly === node.id
-                    ? model.setShowOnly(undefined)
-                    : model.setShowOnly(node.id);
-                onClose();
-            } }, model.showOnly === node.id
-            ? 'Disable show only this node'
-            : 'Show only this node')));
-});
-export default TreeBranchMenu;
-//# sourceMappingURL=TreeBranchMenu.js.map

package/dist/components/TreePanel/TreeBranchMenu.js.map

@@ -1 +0,0 @@
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package/dist/components/TreePanel/TreeCanvas.d.ts

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

package/dist/components/TreePanel/TreeCanvas.js

@@ -1,100 +0,0 @@
-import React, { useEffect, useRef, useState } from 'react';
-import normalizeWheel from 'normalize-wheel';
-import { observer } from 'mobx-react';
-import TreeCanvasBlock from './TreeCanvasBlock';
-import { padding } from './renderTreeCanvas';
-const TreeCanvas = observer(function ({ model }) {
-    const ref = useRef(null);
-    const scheduled = useRef(false);
-    const deltaY = useRef(0);
-    const prevY = useRef(0);
-    const { treeWidth, height, blocksY } = model;
-    const [mouseDragging, setMouseDragging] = useState(false);
-    useEffect(() => {
-        const curr = ref.current;
-        if (!curr) {
-            return;
-        }
-        function onWheel(origEvent) {
-            const event = normalizeWheel(origEvent);
-            deltaY.current += event.pixelY;
-            if (!scheduled.current) {
-                scheduled.current = true;
-                requestAnimationFrame(() => {
-                    model.doScrollY(-deltaY.current);
-                    deltaY.current = 0;
-                    scheduled.current = false;
-                });
-            }
-            origEvent.preventDefault();
-        }
-        curr.addEventListener('wheel', onWheel);
-        return () => {
-            curr.removeEventListener('wheel', onWheel);
-        };
-    }, [model]);
-    useEffect(() => {
-        let cleanup = () => { };
-        function globalMouseMove(event) {
-            event.preventDefault();
-            const currY = event.clientY;
-            const distanceY = currY - prevY.current;
-            if (distanceY) {
-                // use rAF to make it so multiple event handlers aren't fired per-frame
-                // see https://calendar.perfplanet.com/2013/the-runtime-performance-checklist/
-                if (!scheduled.current) {
-                    scheduled.current = true;
-                    window.requestAnimationFrame(() => {
-                        model.doScrollY(distanceY);
-                        scheduled.current = false;
-                        prevY.current = event.clientY;
-                    });
-                }
-            }
-        }
-        function globalMouseUp() {
-            prevY.current = 0;
-            if (mouseDragging) {
-                setMouseDragging(false);
-            }
-        }
-        if (mouseDragging) {
-            window.addEventListener('mousemove', globalMouseMove, true);
-            window.addEventListener('mouseup', globalMouseUp, true);
-            cleanup = () => {
-                window.removeEventListener('mousemove', globalMouseMove, true);
-                window.removeEventListener('mouseup', globalMouseUp, true);
-            };
-        }
-        return cleanup;
-    }, [model, mouseDragging]);
-    function mouseDown(event) {
-        // check if clicking a draggable element or a resize handle
-        const target = event.target;
-        if (target.draggable || target.dataset.resizer) {
-            return;
-        }
-        // otherwise do click and drag scroll
-        if (event.button === 0) {
-            prevY.current = event.clientY;
-            setMouseDragging(true);
-        }
-    }
-    // this local mouseup is used in addition to the global because sometimes
-    // the global add/remove are not called in time, resulting in issue #533
-    function mouseUp(event) {
-        event.preventDefault();
-        setMouseDragging(false);
-    }
-    function mouseLeave(event) {
-        event.preventDefault();
-    }
-    return (React.createElement("div", { ref: ref, onMouseDown: mouseDown, onMouseUp: mouseUp, onMouseLeave: mouseLeave, style: {
-            height,
-            position: 'relative',
-            overflow: 'hidden',
-            width: treeWidth + padding,
-        } }, blocksY.map(block => (React.createElement(TreeCanvasBlock, { key: block, model: model, offsetY: block })))));
-});
-export default TreeCanvas;
-//# sourceMappingURL=TreeCanvas.js.map

package/dist/components/TreePanel/TreeCanvas.js.map

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package/dist/components/TreePanel/TreeCanvasBlock.d.ts

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