react-msaview 2.1.5 → 3.0.0

package/dist/components/MSAPanel/renderMSABlock.js

@@ -0,0 +1,81 @@
+import { getClustalXColor, getPercentIdentityColor } from '../../colorSchemes';
+export function renderBlock({ model, offsetX, offsetY, contrastScheme, ctx, }) {
+    const { hierarchy, colWidth, blockSize, rowHeight, fontSize, highResScaleFactor, } = model;
+    ctx.resetTransform();
+    ctx.scale(highResScaleFactor, highResScaleFactor);
+    ctx.clearRect(0, 0, blockSize, blockSize);
+    ctx.translate(-offsetX, rowHeight / 2 - offsetY);
+    ctx.textAlign = 'center';
+    ctx.font = ctx.font.replace(/\d+px/, `${fontSize}px`);
+    const leaves = hierarchy.leaves();
+    const b = blockSize;
+    const yStart = Math.max(0, Math.floor((offsetY - rowHeight) / rowHeight));
+    const yEnd = Math.max(0, Math.ceil((offsetY + b + rowHeight) / rowHeight));
+    const xStart = Math.max(0, Math.floor(offsetX / colWidth));
+    const xEnd = Math.max(0, Math.ceil((offsetX + b) / colWidth));
+    const visibleLeaves = leaves.slice(yStart, yEnd);
+    drawTiles({
+        model,
+        ctx,
+        offsetX,
+        offsetY,
+        xStart,
+        xEnd,
+        visibleLeaves,
+    });
+    drawText({
+        model,
+        ctx,
+        offsetX,
+        contrastScheme,
+        xStart,
+        xEnd,
+        visibleLeaves,
+    });
+}
+function drawTiles({ model, offsetX, ctx, visibleLeaves, xStart, xEnd, }) {
+    var _a;
+    const { bgColor, colorSchemeName, colorScheme, colStats, columns, colWidth, rowHeight, } = model;
+    // eslint-disable-next-line @typescript-eslint/no-floating-promises
+    for (const node of visibleLeaves) {
+        const { 
+        // @ts-expect-error
+        x: y, data: { name }, } = node;
+        const str = (_a = columns[name]) === null || _a === void 0 ? void 0 : _a.slice(xStart, xEnd);
+        for (let i = 0; i < (str === null || str === void 0 ? void 0 : 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 || 'white';
+                ctx.fillRect(x, y - rowHeight, colWidth, rowHeight);
+            }
+        }
+    }
+}
+function drawText({ model, offsetX, contrastScheme, ctx, visibleLeaves, xStart, xEnd, }) {
+    var _a;
+    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 = (_a = columns[name]) === null || _a === void 0 ? void 0 : _a.slice(xStart, xEnd);
+            for (let i = 0; i < (str === null || str === void 0 ? void 0 : 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.js.map

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

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

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

package/dist/components/MSAView.js

@@ -1,41 +1,36 @@
-import React, { lazy, Suspense } from 'react';
+import React, { Suspense } from 'react';
 import { observer } from 'mobx-react';
 import { Typography } from '@mui/material';
 // locals
 import ImportForm from './ImportForm';
-import Rubberband from './Rubberband';
-import TreeCanvas from './TreeCanvas';
-import MSACanvas from './MSACanvas';
-import Ruler from './Ruler';
-import TreeRuler from './TreeRuler';
+import TreeRuler from './TreePanel/TreeRuler';
 import Header from './Header';
 import Track from './Track';
 import { HorizontalResizeHandle, VerticalResizeHandle } from './ResizeHandles';
-import MSAMouseoverCanvas from './MSAMouseoverCanvas';
-const AnnotationDialog = lazy(() => import('./dialogs/AnnotationDlg'));
-export default observer(function ({ model }) {
-    const { done, initialized, treeAreaWidth, height, turnedOnTracks } = model;
+import MSAPanel from './MSAPanel';
+import TreePanel from './TreePanel';
+import Minimap from './Minimap';
+const MSAView = observer(function ({ model }) {
+    const { done, initialized } = model;
+    return (React.createElement("div", null, !initialized ? (React.createElement(ImportForm, { model: model })) : !done ? (React.createElement(Typography, { variant: "h4" }, "Loading...")) : (React.createElement(MSAView2, { model: model }))));
+});
+const MSAView2 = observer(function ({ model }) {
+    const { height, turnedOnTracks, DialogComponent, DialogProps } = model;
     return (React.createElement("div", null,
-        !initialized ? (React.createElement(ImportForm, { model: model })) : !done ? (React.createElement(Typography, { variant: "h4" }, "Loading...")) : (React.createElement("div", null,
-            React.createElement("div", { style: { height, overflow: 'hidden' } },
-                React.createElement(Header, { model: model }),
-                React.createElement("div", null,
-                    React.createElement("div", { style: { position: 'relative' } },
-                        React.createElement("div", { style: { display: 'flex' } },
-                            React.createElement("div", { style: { flexShrink: 0, width: treeAreaWidth } },
-                                React.createElement(TreeRuler, { model: model })),
-                            React.createElement(Rubberband, { model: model, ControlComponent: React.createElement(Ruler, { model: model }) })), turnedOnTracks === null || turnedOnTracks === void 0 ? void 0 :
-                        turnedOnTracks.map(track => (React.createElement(Track, { key: track.model.id, model: model, track: track }))),
-                        React.createElement("div", { style: { display: 'flex' } },
-                            React.createElement("div", { style: { flexShrink: 0, width: treeAreaWidth } },
-                                React.createElement(TreeCanvas, { model: model })),
-                            React.createElement(VerticalResizeHandle, { model: model }),
-                            React.createElement(MSACanvas, { model: model }),
-                            React.createElement(MSAMouseoverCanvas, { model: model }))))),
-            React.createElement(HorizontalResizeHandle, { model: model }))),
-        model.DialogComponent ? (React.createElement(Suspense, { fallback: null },
-            React.createElement(model.DialogComponent, { ...(model.DialogProps || {}), onClose: () => model.setDialogComponent() }))) : null,
-        model.annotPos ? (React.createElement(Suspense, { fallback: null },
-            React.createElement(AnnotationDialog, { data: model.annotPos, model: model, onClose: () => model.clearAnnotationClickBoundaries() }))) : null));
+        React.createElement("div", { style: { height, overflow: 'hidden' } },
+            React.createElement(Header, { model: model }),
+            React.createElement("div", { style: { position: 'relative' } },
+                React.createElement("div", { style: { display: 'flex' } },
+                    React.createElement(TreeRuler, { model: model }),
+                    React.createElement(Minimap, { model: model })), turnedOnTracks === null || turnedOnTracks === void 0 ? void 0 :
+                turnedOnTracks.map(track => (React.createElement(Track, { key: track.model.id, model: model, track: track }))),
+                React.createElement("div", { style: { display: 'flex' } },
+                    React.createElement(TreePanel, { model: model }),
+                    React.createElement(VerticalResizeHandle, { model: model }),
+                    React.createElement(MSAPanel, { model: model })))),
+        React.createElement(HorizontalResizeHandle, { model: model }),
+        DialogComponent ? (React.createElement(Suspense, { fallback: null },
+            React.createElement(DialogComponent, { ...DialogProps }))) : null));
 });
+export default MSAView;
 //# sourceMappingURL=MSAView.js.map

package/dist/components/MSAView.js.map

@@ -1 +1 @@
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package/dist/components/Minimap.d.ts

@@ -0,0 +1,6 @@
+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

@@ -0,0 +1,72 @@
+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(() => {
+        if (mouseDown !== undefined) {
+            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);
+            }
+            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

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

@@ -0,0 +1,8 @@
+import React from 'react';
+import { MsaViewModel } from '../model';
+declare function OverviewRubberband({ model, ControlComponent, }: {
+    model: MsaViewModel;
+    ControlComponent?: React.ReactElement;
+}): React.JSX.Element;
+declare const _default: typeof OverviewRubberband;
+export default _default;

package/dist/components/OverviewRubberband.js

@@ -0,0 +1,185 @@
+import React, { useRef, useEffect, useState, lazy } from 'react';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+import { Popover, Typography, alpha } from '@mui/material';
+import { Menu } from '@jbrowse/core/ui';
+// icons
+import AssignmentIcon from '@mui/icons-material/Assignment';
+import VerticalGuide from './VerticalGuide';
+const AnnotationDialog = lazy(() => import('./dialogs/AnnotationDialog'));
+const useStyles = makeStyles()(theme => {
+    const background = 'tertiary' in theme.palette && theme.palette.tertiary
+        ? alpha(theme.palette.tertiary.main, 0.7)
+        : alpha(theme.palette.primary.main, 0.7);
+    return {
+        rubberband: {
+            height: '100%',
+            background,
+            position: 'absolute',
+            zIndex: 10,
+            textAlign: 'center',
+            overflow: 'hidden',
+        },
+        rubberbandControl: {
+            cursor: 'crosshair',
+            width: '100%',
+            minHeight: 8,
+        },
+        rubberbandText: {
+            color: theme.palette.tertiary
+                ? theme.palette.tertiary.contrastText
+                : theme.palette.primary.contrastText,
+        },
+        popover: {
+            mouseEvents: 'none',
+            cursor: 'crosshair',
+        },
+        paper: {
+            paddingLeft: theme.spacing(1),
+            paddingRight: theme.spacing(1),
+        },
+    };
+});
+function OverviewRubberband({ model, ControlComponent = React.createElement("div", null), }) {
+    const { treeAreaWidth } = model;
+    const [startX, setStartX] = useState();
+    const [currentX, setCurrentX] = useState();
+    // clientX and clientY used for anchorPosition for menu
+    // offsetX used for calculations about width of selection
+    const [anchorPosition, setAnchorPosition] = useState();
+    const [guideX, setGuideX] = useState();
+    const controlsRef = useRef(null);
+    const rubberbandRef = useRef(null);
+    const { classes } = useStyles();
+    const mouseDragging = startX !== undefined && anchorPosition === undefined;
+    useEffect(() => {
+        function globalMouseMove(event) {
+            if (controlsRef.current && mouseDragging) {
+                const relativeX = event.clientX - controlsRef.current.getBoundingClientRect().left;
+                setCurrentX(relativeX);
+            }
+        }
+        function globalMouseUp(event) {
+            if (startX !== undefined && controlsRef.current) {
+                const { clientX, clientY } = event;
+                const ref = controlsRef.current;
+                const offsetX = clientX - ref.getBoundingClientRect().left;
+                // as stated above, store both clientX/Y and offsetX for different
+                // purposes
+                setAnchorPosition({
+                    offsetX,
+                    clientX,
+                    clientY,
+                });
+                setGuideX(undefined);
+            }
+        }
+        if (mouseDragging) {
+            window.addEventListener('mousemove', globalMouseMove);
+            window.addEventListener('mouseup', globalMouseUp);
+            return () => {
+                window.removeEventListener('mousemove', globalMouseMove);
+                window.removeEventListener('mouseup', globalMouseUp);
+            };
+        }
+        return () => { };
+    }, [startX, mouseDragging, anchorPosition]);
+    useEffect(() => {
+        if (!mouseDragging &&
+            currentX !== undefined &&
+            startX !== undefined &&
+            Math.abs(currentX - startX) <= 3) {
+            handleClose();
+        }
+    }, [mouseDragging, currentX, startX, model.colWidth]);
+    function mouseDown(event) {
+        event.preventDefault();
+        event.stopPropagation();
+        const relativeX = event.clientX -
+            event.target.getBoundingClientRect().left;
+        setStartX(relativeX);
+        setCurrentX(relativeX);
+    }
+    function mouseMove(event) {
+        const target = event.target;
+        setGuideX(event.clientX - target.getBoundingClientRect().left);
+    }
+    function mouseOut() {
+        setGuideX(undefined);
+        model.clearAnnotationClickBoundaries();
+    }
+    function handleClose() {
+        setAnchorPosition(undefined);
+        setStartX(undefined);
+        setCurrentX(undefined);
+    }
+    function handleMenuItemClick(_, callback) {
+        callback();
+        handleClose();
+    }
+    if (startX === undefined) {
+        return (React.createElement(React.Fragment, null,
+            guideX !== undefined ? (React.createElement(VerticalGuide, { model: model, coordX: guideX })) : null,
+            React.createElement("div", { "data-testid": "rubberband_controls", className: classes.rubberbandControl, role: "presentation", ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove }, ControlComponent)));
+    }
+    const right = anchorPosition ? anchorPosition.offsetX : currentX || 0;
+    const left = right < startX ? right : startX;
+    const width = Math.abs(right - startX);
+    const leftBpOffset = model.pxToBp(left);
+    const rightBpOffset = model.pxToBp(left + width);
+    const numOfBpSelected = Math.ceil(width / model.colWidth);
+    const menuItems = [
+        {
+            label: 'Create annotation',
+            icon: AssignmentIcon,
+            onClick: () => {
+                model.setAnnotationClickBoundaries(leftBpOffset, rightBpOffset);
+                model.queueDialog(onClose => [
+                    AnnotationDialog,
+                    {
+                        data: model.annotPos,
+                        model,
+                        onClose: () => {
+                            model.clearAnnotationClickBoundaries();
+                            onClose();
+                        },
+                    },
+                ]);
+                handleClose();
+            },
+        },
+    ];
+    return (React.createElement(React.Fragment, null,
+        rubberbandRef.current ? (React.createElement(React.Fragment, null,
+            React.createElement(Popover, { className: classes.popover, classes: {
+                    paper: classes.paper,
+                }, open: true, anchorEl: rubberbandRef.current, anchorOrigin: {
+                    vertical: 'top',
+                    horizontal: 'left',
+                }, transformOrigin: {
+                    vertical: 'bottom',
+                    horizontal: 'right',
+                }, keepMounted: true, disableRestoreFocus: true },
+                React.createElement(Typography, null, leftBpOffset + 1)),
+            React.createElement(Popover, { className: classes.popover, classes: {
+                    paper: classes.paper,
+                }, open: true, anchorEl: rubberbandRef.current, anchorOrigin: {
+                    vertical: 'top',
+                    horizontal: 'right',
+                }, transformOrigin: {
+                    vertical: 'bottom',
+                    horizontal: 'left',
+                }, keepMounted: true, disableRestoreFocus: true },
+                React.createElement(Typography, null, rightBpOffset + 1)))) : null,
+        React.createElement("div", { ref: rubberbandRef, className: classes.rubberband, style: { left: left + treeAreaWidth, width } },
+            React.createElement(Typography, { variant: "h6", className: classes.rubberbandText },
+                numOfBpSelected.toLocaleString('en-US'),
+                " bp")),
+        React.createElement("div", { "data-testid": "rubberband_controls", className: classes.rubberbandControl, role: "presentation", ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove }, ControlComponent),
+        anchorPosition ? (React.createElement(Menu, { anchorReference: "anchorPosition", anchorPosition: {
+                left: anchorPosition.clientX,
+                top: anchorPosition.clientY,
+            }, onMenuItemClick: handleMenuItemClick, open: Boolean(anchorPosition), onClose: handleClose, menuItems: menuItems })) : null));
+}
+export default observer(OverviewRubberband);
+//# sourceMappingURL=OverviewRubberband.js.map

package/dist/components/OverviewRubberband.js.map

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

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package/dist/components/Rubberband.js

@@ -1,4 +1,4 @@
-import React, { useRef, useEffect, useState } from 'react';
+import React, { useRef, useEffect, useState, lazy } from 'react';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
 import { Popover, Typography, alpha } from '@mui/material';
@@ -6,6 +6,7 @@ import { Menu } from '@jbrowse/core/ui';
 // icons
 import AssignmentIcon from '@mui/icons-material/Assignment';
 import VerticalGuide from './VerticalGuide';
+const AnnotationDialog = lazy(() => import('./dialogs/AnnotationDialog'));
 const useStyles = makeStyles()(theme => {
     const background = 'tertiary' in theme.palette && theme.palette.tertiary
         ? alpha(theme.palette.tertiary.main, 0.7)
@@ -133,6 +134,17 @@ function Rubberband({ model, ControlComponent = React.createElement("div", null)
             icon: AssignmentIcon,
             onClick: () => {
                 model.setAnnotationClickBoundaries(leftBpOffset, rightBpOffset);
+                model.queueDialog(onClose => [
+                    AnnotationDialog,
+                    {
+                        data: model.annotPos,
+                        model,
+                        onClose: () => {
+                            model.clearAnnotationClickBoundaries();
+                            onClose();
+                        },
+                    },
+                ]);
                 handleClose();
             },
         },

package/dist/components/Rubberband.js.map

@@ -1 +1 @@
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package/dist/components/TextTrack.js

@@ -3,7 +3,7 @@ import { useTheme } from '@mui/material';
 import { observer } from 'mobx-react';
 import { colorContrast } from '../util';
 const AnnotationBlock = observer(function ({ track, model, offsetX, }) {
-    const { blockSize, scrollX, bgColor, colorScheme: modelColorScheme, colWidth, rowHeight, highResScaleFactor, } = model;
+    const { blockSize, scrollX, bgColor, colorScheme: modelColorScheme, colWidth, fontSize, rowHeight, highResScaleFactor, } = model;
     const { model: { customColorScheme, data }, } = track;
     const colorScheme = customColorScheme || modelColorScheme;
     const theme = useTheme();
@@ -23,7 +23,7 @@ const AnnotationBlock = observer(function ({ track, model, offsetX, }) {
         ctx.clearRect(0, 0, blockSize, rowHeight);
         ctx.translate(-offsetX, 0);
         ctx.textAlign = 'center';
-        ctx.font = ctx.font.replace(/\d+px/, `${Math.max(8, rowHeight - 8)}px`);
+        ctx.font = ctx.font.replace(/\d+px/, `${fontSize}px`);
         const xStart = Math.max(0, Math.floor(offsetX / colWidth));
         const xEnd = Math.max(0, Math.ceil((offsetX + blockSize) / colWidth));
         const str = data === null || data === void 0 ? void 0 : data.slice(xStart, xEnd);
@@ -41,6 +41,7 @@ const AnnotationBlock = observer(function ({ track, model, offsetX, }) {
             }
         }
     }, [
+        fontSize,
         bgColor,
         blockSize,
         colWidth,

package/dist/components/TextTrack.js.map

@@ -1 +1 @@
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