react-msaview 2.1.4 → 3.0.0

package/dist/components/Ruler.js

@@ -1,52 +0,0 @@
-import React, { useRef } from 'react';
-import { makeStyles } from 'tss-react/mui';
-import { observer } from 'mobx-react';
-import { makeTicks, mathPower } from './util';
-const useStyles = makeStyles()({
-    majorTickLabel: {
-        fontSize: '11px',
-    },
-    majorTick: {
-        stroke: '#555',
-    },
-    minorTick: {
-        stroke: '#999',
-    },
-});
-function RulerBlock({ start, end, bpPerPx, reversed, major, minor, }) {
-    const { classes } = useStyles();
-    const ticks = makeTicks(start, end, bpPerPx, major, minor);
-    return (React.createElement(React.Fragment, null,
-        ticks.map(tick => {
-            const x = (reversed ? end - tick.base : tick.base - start) / bpPerPx;
-            return (React.createElement("line", { key: tick.base, x1: x, x2: x, y1: 11, y2: tick.type === 'major' ? 11 + 6 : 11 + 4, strokeWidth: 1, stroke: tick.type === 'major' ? '#555' : '#999', className: tick.type === 'major' ? classes.majorTick : classes.minorTick, "data-bp": tick.base }));
-        }),
-        ticks
-            .filter(tick => tick.type === 'major')
-            .map(tick => {
-            const x = (reversed ? end - tick.base : tick.base - start) / bpPerPx;
-            return (React.createElement("text", { x: x, y: 10, key: `label-${tick.base}`, textAnchor: "middle", style: { fontSize: '11px' }, className: classes.majorTickLabel }, mathPower(tick.base + 1)));
-        })));
-}
-const Ruler = observer(function ({ model }) {
-    const { MSA, colWidth, msaAreaWidth, rulerHeight, resizeHandleWidth, scrollX, blocksX, blockSize, } = model;
-    const ref = useRef(null);
-    const offsetX = blocksX[0];
-    return !MSA ? null : (React.createElement("div", { ref: ref, style: {
-            position: 'relative',
-            width: msaAreaWidth,
-            cursor: 'crosshair',
-            overflow: 'hidden',
-            height: rulerHeight,
-            background: '#ccc',
-        } },
-        React.createElement("svg", { style: {
-                width: blocksX.length * blockSize,
-                position: 'absolute',
-                left: scrollX + offsetX + resizeHandleWidth,
-                pointerEvents: 'none',
-            } },
-            React.createElement(RulerBlock, { key: offsetX, start: offsetX / colWidth, end: offsetX / colWidth + (blockSize * blocksX.length) / colWidth, bpPerPx: 1 / colWidth }))));
-});
-export default Ruler;
-//# sourceMappingURL=Ruler.js.map

package/dist/components/Ruler.js.map

@@ -1 +0,0 @@
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package/dist/components/TreeBranchMenu.js.map

@@ -1 +0,0 @@
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package/dist/components/TreeCanvas.js.map

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

@@ -1,255 +0,0 @@
-import React, { useEffect, useRef, useState } from 'react';
-import { observer } from 'mobx-react';
-import RBush from 'rbush';
-import TreeMenu from './TreeMenu';
-import TreeBranchMenu from './TreeBranchMenu';
-const extendBounds = 5;
-const radius = 3.5;
-const d = radius * 2;
-const padding = 600;
-const TreeCanvasBlock = observer(function ({ model, offsetY, }) {
-    const ref = useRef(null);
-    const clickMap = useRef(new RBush());
-    const mouseoverRef = useRef(null);
-    const [branchMenu, setBranchMenu] = useState();
-    const [toggleNodeMenu, setToggleNodeMenu] = useState();
-    const [hoverElt, setHoverElt] = useState();
-    const { hierarchy, rowHeight, scrollY, treeWidth, treeMetadata, showBranchLen, collapsed, margin, labelsAlignRight, noTree, blockSize, drawNodeBubbles, drawTree, treeAreaWidth, structures, highResScaleFactor, } = model;
-    useEffect(() => {
-        var _a;
-        clickMap.current.clear();
-        if (!ref.current) {
-            return;
-        }
-        const ctx = ref.current.getContext('2d');
-        if (!ctx) {
-            return;
-        }
-        ctx.resetTransform();
-        ctx.scale(highResScaleFactor, highResScaleFactor);
-        ctx.clearRect(0, 0, treeWidth + padding, blockSize);
-        ctx.translate(margin.left, -offsetY);
-        const font = ctx.font;
-        ctx.font = font.replace(/\d+px/, `${Math.max(8, rowHeight - 8)}px`);
-        if (!noTree && drawTree) {
-            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 + blockSize >= y1 && y2 >= offsetY) {
-                    ctx.beginPath();
-                    ctx.moveTo(sx, sy);
-                    ctx.lineTo(sx, ty);
-                    ctx.lineTo(tx, ty);
-                    ctx.stroke();
-                }
-            }
-            if (drawNodeBubbles) {
-                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 { id = '', name = '' } = data;
-                    if (y > offsetY - extendBounds &&
-                        y < offsetY + blockSize + 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.current.insert({
-                            minX: x - radius,
-                            maxX: x - radius + d,
-                            minY: y - radius,
-                            maxY: y - radius + d,
-                            branch: true,
-                            id,
-                            name,
-                        });
-                    }
-                }
-            }
-        }
-        if (rowHeight >= 5) {
-            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 = ((_a = treeMetadata[name]) === null || _a === void 0 ? void 0 : _a.genome) || name;
-                if (y > offsetY - extendBounds &&
-                    y < offsetY + blockSize + 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' : 'black';
-                    if (!drawTree && !labelsAlignRight) {
-                        ctx.fillText(displayName, 0, yp);
-                        clickMap.current.insert({
-                            minX: 0,
-                            maxX: width,
-                            minY: yp - height,
-                            maxY: yp,
-                            name,
-                            id,
-                        });
-                    }
-                    else if (labelsAlignRight) {
-                        const smallPadding = 2;
-                        const offset = treeAreaWidth - smallPadding - margin.left;
-                        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.current.insert({
-                            minX: treeAreaWidth - margin.left - width,
-                            maxX: treeAreaWidth - margin.left,
-                            minY: yp - height,
-                            maxY: yp,
-                            name,
-                            id,
-                        });
-                    }
-                    else {
-                        ctx.fillText(displayName, xp + d, yp);
-                        clickMap.current.insert({
-                            minX: xp + d,
-                            maxX: xp + d + width,
-                            minY: yp - height,
-                            maxY: yp,
-                            name,
-                            id,
-                        });
-                    }
-                }
-            }
-            ctx.setLineDash([]);
-        }
-    }, [
-        collapsed,
-        rowHeight,
-        margin.left,
-        hierarchy,
-        offsetY,
-        treeWidth,
-        showBranchLen,
-        noTree,
-        blockSize,
-        drawNodeBubbles,
-        drawTree,
-        labelsAlignRight,
-        treeAreaWidth,
-        structures,
-        highResScaleFactor,
-        treeMetadata,
-    ]);
-    useEffect(() => {
-        const canvas = mouseoverRef.current;
-        if (!canvas) {
-            return;
-        }
-        const ctx = canvas.getContext('2d');
-        if (!ctx) {
-            return;
-        }
-        ctx.resetTransform();
-        ctx.clearRect(0, 0, treeWidth + padding, blockSize);
-        ctx.translate(margin.left, -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, margin.left, offsetY, blockSize, treeWidth]);
-    function hoverBranchClickMap(event) {
-        const x = event.nativeEvent.offsetX - margin.left;
-        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 - margin.left;
-        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;
-    }
-    return (React.createElement(React.Fragment, null,
-        (branchMenu === null || branchMenu === void 0 ? void 0 : branchMenu.id) ? (React.createElement(TreeBranchMenu, { node: branchMenu, model: model, onClose: () => setBranchMenu(undefined) })) : null,
-        (toggleNodeMenu === null || toggleNodeMenu === void 0 ? void 0 : toggleNodeMenu.id) ? (React.createElement(TreeMenu, { node: toggleNodeMenu, model: model, onClose: () => setToggleNodeMenu(undefined) })) : null,
-        React.createElement("canvas", { width: (treeWidth + padding) * highResScaleFactor, height: blockSize * highResScaleFactor, style: {
-                width: treeWidth + padding,
-                height: blockSize,
-                top: scrollY + offsetY,
-                left: 0,
-                position: 'absolute',
-            }, 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 === null || data === void 0 ? void 0 : data.id) {
-                    setBranchMenu({ ...data, x, y });
-                }
-                const data2 = hoverNameClickMap(event);
-                if (data2 === null || data2 === void 0 ? void 0 : data2.id) {
-                    setToggleNodeMenu({ ...data2, x, y });
-                }
-            }, ref: ref }),
-        React.createElement("canvas", { style: {
-                width: treeWidth + padding,
-                height: blockSize,
-                top: scrollY + offsetY,
-                left: 0,
-                position: 'absolute',
-                pointerEvents: 'none',
-                zIndex: 100,
-            }, width: treeWidth + padding, height: blockSize, ref: mouseoverRef })));
-});
-export default TreeCanvasBlock;
-//# sourceMappingURL=TreeCanvasBlock.js.map

package/dist/components/TreeCanvasBlock.js.map

@@ -1 +0,0 @@
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package/dist/components/TreeMenu.js.map

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

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

package/dist/components/TreeRuler.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"TreeRuler.js","sourceRoot":"","sources":["../../src/components/TreeRuler.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAKrC,MAAM,SAAS,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAA2B,EAAE,EAAE;IAChE,MAAM,EAAE,SAAS,EAAE,GAAG,KAAK,CAAA;IAC3B,OAAO,6BAAK,KAAK,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,GAAI,CAAA;AAC7C,CAAC,CAAC,CAAA;AAEF,eAAe,SAAS,CAAA"}

package/dist/components/data/seq2.js.map

@@ -1 +0,0 @@
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package/dist/components/dialogs/AboutDlg.js.map

@@ -1 +0,0 @@
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package/dist/components/dialogs/AddTrackDlg.js.map

@@ -1 +0,0 @@
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package/dist/components/dialogs/AnnotationDlg.js.map

@@ -1 +0,0 @@
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package/dist/components/dialogs/MetadataDlg.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"MetadataDlg.js","sourceRoot":"","sources":["../../../src/components/dialogs/MetadataDlg.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,aAAa,EAAE,MAAM,eAAe,CAAA;AAC7C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAE,MAAM,mDAAmD,CAAA;AAK9E,MAAM,cAAc,GAAG,QAAQ,CAAC,UAAU,EACxC,KAAK,EACL,OAAO,GAIR;IACC,MAAM,EAAE,MAAM,EAAE,GAAG,KAAK,CAAA;IAExB,OAAO,CACL,oBAAC,MAAM,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,OAAO,EAAE,EAAE,IAAI,QAAC,KAAK,EAAC,UAAU;QACrD,oBAAC,aAAa;YACZ,oBAAC,UAAU,IAAC,UAAU,EAAE,MAAM,GAAI,CACpB,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,cAAc,CAAA"}

package/dist/components/dialogs/SettingsDlg.js

@@ -1,48 +0,0 @@
-import React, { useState } from 'react';
-import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
-import { Dialog } from '@jbrowse/core/ui';
-import { Button, Checkbox, DialogActions, DialogContent, FormControlLabel, MenuItem, TextField, } from '@mui/material';
-import colorSchemes from '../../colorSchemes';
-const useStyles = makeStyles()(theme => ({
-    field: {
-        margin: theme.spacing(4),
-    },
-}));
-const SettingsDialog = observer(function ({ model, onClose, }) {
-    const { classes } = useStyles();
-    const { colorSchemeName, noTree } = model;
-    const [rowHeight, setRowHeight] = useState(`${model.rowHeight}`);
-    const [colWidth, setColWidth] = useState(`${model.colWidth}`);
-    const [treeWidth, setTreeWidth] = useState(`${model.treeWidth}`);
-    function error(n) {
-        return Number.isNaN(+n) || +n < 0;
-    }
-    const rowHeightError = error(rowHeight);
-    const colWidthError = error(colWidth);
-    const treeWidthError = error(treeWidth);
-    return (React.createElement(Dialog, { open: true, onClose: () => onClose(), title: "Settings" },
-        React.createElement(DialogContent, null,
-            React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: model.showBranchLen, onChange: () => model.toggleBranchLen() }), label: "Show branch length" }),
-            React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: model.bgColor, onChange: () => model.toggleBgColor() }), label: "Color background" }),
-            React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: model.drawNodeBubbles, onChange: () => model.toggleNodeBubbles() }), label: "Draw node bubbles" }),
-            React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: model.drawTree, onChange: () => model.toggleDrawTree() }), label: "Draw tree (if available)" }),
-            React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: model.labelsAlignRight, onChange: () => model.toggleLabelsAlignRight() }), label: "Labels align right (note: labels may draw over tree, but can adjust tree width or tree area width in UI)" }),
-            React.createElement(TextField, { className: classes.field, label: "Row height (px)", value: rowHeight, error: rowHeightError, onChange: event => setRowHeight(event.target.value) }),
-            React.createElement(TextField, { className: classes.field, label: "Column width (px)", value: colWidth, error: colWidthError, onChange: event => setColWidth(event.target.value) }),
-            React.createElement("br", null),
-            !noTree ? (React.createElement(TextField, { className: classes.field, label: "Tree width (px)", value: treeWidth, error: treeWidthError, onChange: event => setTreeWidth(event.target.value) })) : null,
-            React.createElement("br", null),
-            React.createElement(TextField, { select: true, label: "Color scheme", value: colorSchemeName, onChange: event => model.setColorSchemeName(event.target.value) }, Object.keys(colorSchemes).map(option => (React.createElement(MenuItem, { key: option, value: option }, option)))),
-            React.createElement(DialogActions, null,
-                React.createElement(Button, { disabled: rowHeightError || colWidthError || treeWidthError, onClick: () => {
-                        model.setRowHeight(+rowHeight);
-                        model.setColWidth(+colWidth);
-                        if (!noTree) {
-                            model.setTreeWidth(+treeWidth);
-                        }
-                        onClose();
-                    }, variant: "contained", color: "primary" }, "Submit")))));
-});
-export default SettingsDialog;
-//# sourceMappingURL=SettingsDlg.js.map

package/dist/components/dialogs/SettingsDlg.js.map

@@ -1 +0,0 @@
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package/dist/components/dialogs/TrackInfoDlg.js.map

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package/dist/components/dialogs/TracklistDlg.js.map

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package/dist/components/dialogs/TreeNodeInfoDlg.js.map

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