react-msaview 4.4.4 → 4.4.6

package/dist/components/TreePanel/TreeCanvasBlock.js

@@ -1,118 +0,0 @@
-import React, { useCallback, useEffect, useRef, useState } from 'react';
-import { autorun } from 'mobx';
-import { observer } from 'mobx-react';
-import { useTheme } from '@mui/material';
-import RBush from 'rbush';
-import TreeNodeMenu from './TreeNodeMenu';
-import TreeBranchMenu from './TreeBranchMenu';
-import { padding, renderTreeCanvas } from './renderTreeCanvas';
-const TreeCanvasBlock = observer(function ({ model, offsetY, }) {
-    const theme = useTheme();
-    const ref = useRef();
-    const clickMap = useRef(new RBush());
-    const mouseoverRef = useRef(null);
-    const [branchMenu, setBranchMenu] = useState();
-    const [toggleNodeMenu, setToggleNodeMenu] = useState();
-    const [hoverElt, setHoverElt] = useState();
-    const { scrollY, treeAreaWidth, blockSize, highResScaleFactor } = model;
-    const width = treeAreaWidth + padding;
-    const height = blockSize;
-    const w2 = width * highResScaleFactor;
-    const h2 = height * highResScaleFactor;
-    const vref = useCallback((arg) => {
-        model.incrementRef();
-        ref.current = arg;
-    }, 
-    // eslint-disable-next-line react-hooks/exhaustive-deps
-    [model, height, width]);
-    useEffect(() => {
-        const ctx = ref.current?.getContext('2d');
-        if (!ctx) {
-            return;
-        }
-        return autorun(() => {
-            renderTreeCanvas({
-                ctx,
-                model,
-                offsetY,
-                clickMap: clickMap.current,
-                theme,
-            });
-        });
-    }, [model, offsetY, theme]);
-    useEffect(() => {
-        const ctx = mouseoverRef.current?.getContext('2d');
-        if (!ctx) {
-            return;
-        }
-        ctx.resetTransform();
-        ctx.clearRect(0, 0, treeAreaWidth + padding, blockSize);
-        ctx.translate(0, -offsetY);
-        if (hoverElt) {
-            const { minX, maxX, minY, maxY } = hoverElt;
-            ctx.fillStyle = 'rgba(0,0,0,0.1)';
-            ctx.fillRect(minX, minY, maxX - minX, maxY - minY);
-        }
-    }, [hoverElt, offsetY, blockSize, treeAreaWidth]);
-    function hoverBranchClickMap(event) {
-        const x = event.nativeEvent.offsetX;
-        const y = event.nativeEvent.offsetY;
-        const [entry] = clickMap.current.search({
-            minX: x,
-            maxX: x + 1,
-            minY: y + offsetY,
-            maxY: y + 1 + offsetY,
-        });
-        return entry && entry.branch
-            ? { ...entry, x: event.clientX, y: event.clientY }
-            : undefined;
-    }
-    function hoverNameClickMap(event) {
-        const x = event.nativeEvent.offsetX;
-        const y = event.nativeEvent.offsetY;
-        const [entry] = clickMap.current.search({
-            minX: x,
-            maxX: x + 1,
-            minY: y + offsetY,
-            maxY: y + 1 + offsetY,
-        });
-        return entry && !entry.branch
-            ? { ...entry, x: event.clientX, y: event.clientY }
-            : undefined;
-    }
-    const style = {
-        width,
-        height,
-        top: scrollY + offsetY,
-        left: 0,
-        position: 'absolute',
-    };
-    return (React.createElement(React.Fragment, null,
-        branchMenu?.id ? (React.createElement(TreeBranchMenu, { node: branchMenu, model: model, onClose: () => setBranchMenu(undefined) })) : null,
-        toggleNodeMenu?.id ? (React.createElement(TreeNodeMenu, { node: toggleNodeMenu, model: model, onClose: () => setToggleNodeMenu(undefined) })) : null,
-        React.createElement("canvas", { width: w2, height: h2, style: style, onMouseMove: event => {
-                if (!ref.current) {
-                    return;
-                }
-                const ret = hoverNameClickMap(event) || hoverBranchClickMap(event);
-                ref.current.style.cursor = ret ? 'pointer' : 'default';
-                setHoverElt(hoverNameClickMap(event));
-            }, onClick: event => {
-                const { clientX: x, clientY: y } = event;
-                const data = hoverBranchClickMap(event);
-                if (data?.id) {
-                    setBranchMenu({ ...data, x, y });
-                }
-                const data2 = hoverNameClickMap(event);
-                if (data2?.id) {
-                    setToggleNodeMenu({ ...data2, x, y });
-                }
-            }, onMouseLeave: () => setHoverElt(undefined), ref: vref }),
-        React.createElement("canvas", { style: {
-                ...style,
-                pointerEvents: 'none',
-                zIndex: 100,
-            }, width: width, height: height, ref: mouseoverRef })));
-});
-export default TreeCanvasBlock;
-//# sourceMappingURL=TreeCanvasBlock.js.map

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

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

@@ -1,13 +0,0 @@
-import React from 'react';
-import { MsaViewModel } from '../../model';
-declare const TreeMenu: ({ node, onClose, model, }: {
-    node: {
-        x: number;
-        y: number;
-        name: string;
-        id: string;
-    };
-    model: MsaViewModel;
-    onClose: () => void;
-}) => React.JSX.Element;
-export default TreeMenu;

package/dist/components/TreePanel/TreeNodeMenu.js

@@ -1,74 +0,0 @@
-import React, { lazy } from 'react';
-import { Menu, MenuItem } from '@mui/material';
-import { observer } from 'mobx-react';
-// lazies
-const TreeNodeInfoDialog = lazy(() => import('./dialogs/TreeNodeInfoDialog'));
-const TreeMenu = observer(function ({ node, onClose, model, }) {
-    const { selectedStructures, collapsed, collapsed2, structures } = model;
-    const nodeDetails = node ? model.getRowData(node.name) : undefined;
-    return (React.createElement(Menu, { anchorReference: "anchorPosition", anchorPosition: {
-            top: node.y,
-            left: node.x,
-        }, 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.queueDialog(onClose => [
-                    TreeNodeInfoDialog,
-                    {
-                        info: model.getRowData(node.name),
-                        model,
-                        nodeName: node.name,
-                        onClose,
-                    },
-                ]);
-                onClose();
-            } }, "More info..."),
-        React.createElement(MenuItem, { dense: true, onClick: () => {
-                if (collapsed.includes(node.id)) {
-                    model.toggleCollapsed(node.id);
-                }
-                else {
-                    if (node.id.endsWith('-leafnode')) {
-                        model.toggleCollapsed2(`${node.id}`);
-                    }
-                    else {
-                        model.toggleCollapsed2(`${node.id}-leafnode`);
-                    }
-                }
-                onClose();
-            } }, collapsed.includes(node.id) || collapsed2.includes(node.id)
-            ? 'Show node'
-            : 'Hide node'),
-        structures[node.name]?.map(entry => !selectedStructures.some(n => n.id === node.name) ? (React.createElement(MenuItem, { key: JSON.stringify(entry), dense: true, onClick: () => {
-                model.addStructureToSelection({
-                    structure: entry,
-                    id: node.name,
-                });
-                onClose();
-            } },
-            "Add PDB to selection (",
-            entry.pdb,
-            ")")) : (React.createElement(MenuItem, { key: JSON.stringify(entry), dense: true, onClick: () => {
-                model.removeStructureFromSelection({
-                    structure: entry,
-                    id: node.name,
-                });
-                onClose();
-            } },
-            "Remove PDB from selection (",
-            entry.pdb,
-            ")"))), // @ts-expect-error
-        nodeDetails?.data.accession?.map(accession => (React.createElement(MenuItem, { dense: true, key: accession, onClick: () => {
-                model.addUniprotTrack({
-                    // @ts-expect-error
-                    name: nodeDetails?.data.name,
-                    accession,
-                });
-                onClose();
-            } },
-            "Open UniProt track (",
-            accession,
-            ")")))));
-});
-export default TreeMenu;
-//# sourceMappingURL=TreeNodeMenu.js.map

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

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

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

package/dist/components/TreePanel/TreeRuler.js

@@ -1,8 +0,0 @@
-import React from 'react';
-import { observer } from 'mobx-react';
-const TreeRuler = observer(({ model }) => {
-    const { treeAreaWidth } = model;
-    return React.createElement("div", { style: { flexShrink: 0, width: treeAreaWidth } });
-});
-export default TreeRuler;
-//# sourceMappingURL=TreeRuler.js.map

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

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

@@ -1,9 +0,0 @@
-import React from 'react';
-import { MsaViewModel } from '../../../model';
-declare const _default: ({ info, model, nodeName, onClose, }: {
-    info: Record<string, unknown>;
-    model: MsaViewModel;
-    nodeName: string;
-    onClose: () => void;
-}) => React.JSX.Element;
-export default _default;

package/dist/components/TreePanel/dialogs/TreeNodeInfoDialog.js

@@ -1,16 +0,0 @@
-import React from 'react';
-import { Dialog } from '@jbrowse/core/ui';
-import { DialogContent } from '@mui/material';
-import { observer } from 'mobx-react';
-import { Attributes, BaseCard, } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
-export default observer(function ({ info, model, nodeName, onClose, }) {
-    const { treeMetadata } = model;
-    const metadata = treeMetadata[nodeName];
-    return (React.createElement(Dialog, { onClose: () => onClose(), open: true, title: "Tree node info" },
-        React.createElement(DialogContent, null,
-            React.createElement(BaseCard, { title: "Attributes" },
-                React.createElement(Attributes, { attributes: { nodeName, ...info } })),
-            metadata ? (React.createElement(BaseCard, { title: "Extra metadata" },
-                React.createElement(Attributes, { attributes: metadata }))) : null)));
-});
-//# sourceMappingURL=TreeNodeInfoDialog.js.map

package/dist/components/TreePanel/dialogs/TreeNodeInfoDialog.js.map

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

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

package/dist/components/TreePanel/index.js

@@ -1,10 +0,0 @@
-import React from 'react';
-import { observer } from 'mobx-react';
-import TreeCanvas from './TreeCanvas';
-const TreePanel = observer(function ({ model }) {
-    const { treeAreaWidth } = model;
-    return (React.createElement("div", { style: { flexShrink: 0, width: treeAreaWidth } },
-        React.createElement(TreeCanvas, { model: model })));
-});
-export default TreePanel;
-//# sourceMappingURL=index.js.map

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

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

@@ -1,46 +0,0 @@
-import RBush from 'rbush';
-import { Theme } from '@mui/material';
-import { MsaViewModel } from '../../model';
-export declare const padding = 600;
-interface ClickEntry {
-    name: string;
-    id: string;
-    branch?: boolean;
-    minX: number;
-    maxX: number;
-    minY: number;
-    maxY: number;
-}
-export declare function renderTree({ offsetY, ctx, model, theme, blockSizeYOverride, }: {
-    offsetY: number;
-    ctx: CanvasRenderingContext2D;
-    model: MsaViewModel;
-    theme: Theme;
-    blockSizeYOverride?: number;
-}): void;
-export declare function renderNodeBubbles({ ctx, clickMap, offsetY, model, blockSizeYOverride, }: {
-    ctx: CanvasRenderingContext2D;
-    clickMap?: RBush<ClickEntry>;
-    offsetY: number;
-    model: MsaViewModel;
-    theme: Theme;
-    blockSizeYOverride?: number;
-}): void;
-export declare function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSizeYOverride, }: {
-    model: MsaViewModel;
-    offsetY: number;
-    ctx: CanvasRenderingContext2D;
-    clickMap?: RBush<ClickEntry>;
-    theme: Theme;
-    blockSizeYOverride?: number;
-}): void;
-export declare function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highResScaleFactorOverride, blockSizeYOverride, }: {
-    model: MsaViewModel;
-    offsetY: number;
-    ctx: CanvasRenderingContext2D;
-    clickMap?: RBush<ClickEntry>;
-    theme: Theme;
-    highResScaleFactorOverride?: number;
-    blockSizeYOverride?: number;
-}): void;
-export {};

package/dist/components/TreePanel/renderTreeCanvas.js

@@ -1,180 +0,0 @@
-export const padding = 600;
-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 by = blockSizeYOverride || blockSize;
-    ctx.strokeStyle = theme.palette.text.primary;
-    for (const { source, target } of hierarchy.links()) {
-        const y = showBranchLen ? 'len' : 'y';
-        // @ts-expect-error
-        const { x: sy, [y]: sx } = source;
-        // @ts-expect-error
-        const { x: ty, [y]: tx } = target;
-        const y1 = Math.min(sy, ty);
-        const y2 = Math.max(sy, ty);
-        // 1d line intersection to check if line crosses block at all, this is
-        // an optimization that allows us to skip drawing most tree links
-        // outside the block
-        if (offsetY + by >= y1 && y2 >= offsetY) {
-            ctx.beginPath();
-            ctx.moveTo(sx, sy);
-            ctx.lineTo(sx, ty);
-            ctx.lineTo(tx, ty);
-            ctx.stroke();
-        }
-    }
-}
-export function renderNodeBubbles({ ctx, clickMap, offsetY, model, blockSizeYOverride, }) {
-    const { hierarchy, showBranchLen, collapsed, blockSize, marginLeft: ml, } = model;
-    const by = blockSizeYOverride || blockSize;
-    for (const node of hierarchy.descendants()) {
-        const val = showBranchLen ? 'len' : 'y';
-        const { 
-        // @ts-expect-error
-        x: y, 
-        // @ts-expect-error
-        [val]: x, data, } = node;
-        const { branchset, id = '', name = '' } = data;
-        if (!id.endsWith('-leafnode') &&
-            branchset.length &&
-            y > offsetY - extendBounds &&
-            y < offsetY + by + extendBounds) {
-            ctx.strokeStyle = 'black';
-            ctx.fillStyle = collapsed.includes(id) ? 'black' : 'white';
-            ctx.beginPath();
-            ctx.arc(x, y, radius, 0, 2 * Math.PI);
-            ctx.fill();
-            ctx.stroke();
-            clickMap?.insert({
-                minX: x - radius + ml,
-                maxX: x - radius + d + ml,
-                minY: y - radius,
-                maxY: y - radius + d,
-                branch: true,
-                id,
-                name,
-            });
-        }
-    }
-}
-export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSizeYOverride, }) {
-    const { rowHeight, showBranchLen, treeMetadata, hierarchy, blockSize, labelsAlignRight, drawTree, structures, treeAreaWidth, treeAreaWidthMinusMargin, marginLeft: ml, noTree, } = model;
-    const by = blockSizeYOverride || blockSize;
-    if (labelsAlignRight) {
-        ctx.textAlign = 'right';
-        ctx.setLineDash([1, 3]);
-    }
-    else {
-        ctx.textAlign = 'start';
-    }
-    for (const node of hierarchy.leaves()) {
-        const { 
-        // @ts-expect-error
-        x: y, 
-        // @ts-expect-error
-        y: x, data: { name, id }, 
-        // @ts-expect-error
-        len, } = node;
-        const displayName = treeMetadata[name]?.genome || name;
-        if (y > offsetY - extendBounds && y < offsetY + by + extendBounds) {
-            // note: +rowHeight/4 matches with -rowHeight/4 in msa
-            const yp = y + rowHeight / 4;
-            const xp = showBranchLen ? len : x;
-            const { width } = ctx.measureText(displayName);
-            const height = ctx.measureText('M').width; // use an 'em' for height
-            const hasStructure = structures[name];
-            ctx.fillStyle = hasStructure ? 'blue' : theme.palette.text.primary;
-            if (!drawTree && !labelsAlignRight) {
-                ctx.fillText(displayName, 0, yp);
-                clickMap?.insert({
-                    minX: 0 + ml,
-                    maxX: width + ml,
-                    minY: yp - height,
-                    maxY: yp,
-                    name,
-                    id,
-                });
-            }
-            else if (labelsAlignRight) {
-                const smallPadding = 2;
-                const offset = treeAreaWidthMinusMargin - smallPadding;
-                if (drawTree && !noTree) {
-                    const { width } = ctx.measureText(displayName);
-                    ctx.moveTo(xp + radius + 2, y);
-                    ctx.lineTo(offset - smallPadding - width, y);
-                    ctx.stroke();
-                }
-                ctx.fillText(displayName, offset, yp);
-                clickMap?.insert({
-                    minX: treeAreaWidth - width,
-                    maxX: treeAreaWidth,
-                    minY: yp - height,
-                    maxY: yp,
-                    name,
-                    id,
-                });
-            }
-            else {
-                ctx.fillText(displayName, xp + d, yp);
-                clickMap?.insert({
-                    minX: xp + d + ml,
-                    maxX: xp + d + width + ml,
-                    minY: yp - height,
-                    maxY: yp,
-                    name,
-                    id,
-                });
-            }
-        }
-    }
-    ctx.setLineDash([]);
-}
-export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highResScaleFactorOverride, blockSizeYOverride, }) {
-    clickMap?.clear();
-    const { noTree, drawTree, drawNodeBubbles, treeWidth, highResScaleFactor, blockSize, fontSize, rowHeight, marginLeft, nref, } = model;
-    const by = blockSizeYOverride || blockSize;
-    ctx.resetTransform();
-    // this is a bogus use of nref, it is never less than 0. we just are using it
-    // in this statement because otherwise it would be an unused variable, we
-    // just need to use nref to indicate a redraw in an autorun when canvas ref
-    // is updated and in order to convince bundlers like not to delete unused
-    // usage with propertyReadSideEffects
-    const k = nref < 0 ? -Infinity : highResScaleFactorOverride || highResScaleFactor;
-    ctx.scale(k, k);
-    ctx.clearRect(0, 0, treeWidth + padding, by);
-    ctx.translate(marginLeft, -offsetY);
-    const font = ctx.font;
-    ctx.font = font.replace(/\d+px/, `${fontSize}px`);
-    if (!noTree && drawTree) {
-        renderTree({
-            ctx,
-            offsetY,
-            model,
-            theme,
-            blockSizeYOverride,
-        });
-        if (drawNodeBubbles) {
-            renderNodeBubbles({
-                ctx,
-                offsetY,
-                clickMap,
-                model,
-                theme,
-                blockSizeYOverride,
-            });
-        }
-    }
-    if (rowHeight >= 5) {
-        renderTreeLabels({
-            ctx,
-            offsetY,
-            model,
-            clickMap,
-            theme,
-            blockSizeYOverride,
-        });
-    }
-}
-//# sourceMappingURL=renderTreeCanvas.js.map

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

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

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

package/dist/components/VerticalGuide.js

@@ -1,30 +0,0 @@
-import React from 'react';
-import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
-import { Tooltip } from '@mui/material';
-const useStyles = makeStyles()({
-    guide: {
-        pointerEvents: 'none',
-        height: '100%',
-        width: 1,
-        position: 'absolute',
-        zIndex: 10,
-    },
-});
-const VerticalGuide = observer(function ({ model, coordX, }) {
-    const { treeAreaWidth } = model;
-    const { classes } = useStyles();
-    return (React.createElement(React.Fragment, null,
-        React.createElement(Tooltip, { open: true, placement: "top", title: `${model.pxToBp(coordX) + 1}`, arrow: true },
-            React.createElement("div", { style: {
-                    left: coordX + treeAreaWidth,
-                    position: 'absolute',
-                    height: 1,
-                } })),
-        React.createElement("div", { className: classes.guide, style: {
-                left: coordX + treeAreaWidth,
-                background: 'red',
-            } })));
-});
-export default VerticalGuide;
-//# sourceMappingURL=VerticalGuide.js.map

package/dist/components/VerticalGuide.js.map

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

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