@jbrowse/plugin-dotplot-view 3.6.4 → 3.7.0

package/esm/DotplotView/components/DotplotControls.js

@@ -1,41 +1,62 @@
-import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
+import { lazy, useState } from 'react';
 import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
 import { TrackSelector as TrackSelectorIcon } from '@jbrowse/core/ui/Icons';
-import CropDinIcon from '@mui/icons-material/CropDin';
-import CropLandscapeIcon from '@mui/icons-material/CropLandscape';
+import { getSession } from '@jbrowse/core/util';
 import MoreVert from '@mui/icons-material/MoreVert';
-import SettingsOverscanIcon from '@mui/icons-material/SettingsOverscan';
+import ShuffleIcon from '@mui/icons-material/Shuffle';
 import ZoomIn from '@mui/icons-material/ZoomIn';
 import ZoomOut from '@mui/icons-material/ZoomOut';
 import { IconButton } from '@mui/material';
 import { observer } from 'mobx-react';
+import ColorBySelector from './ColorBySelector';
 import { CursorMouse, CursorMove } from './CursorIcon';
+import MinLengthSlider from './MinLengthSlider';
+import OpacitySlider from './OpacitySlider';
+const DiagonalizationProgressDialog = lazy(() => import('./DiagonalizationProgressDialog'));
 const DotplotControls = observer(function ({ model, }) {
-    return (_jsxs("div", { children: [_jsx(IconButton, { onClick: () => {
+    var _a;
+    const [showDynamicControls, setShowDynamicControls] = useState(true);
+    const hasDisplays = (_a = model.tracks[0]) === null || _a === void 0 ? void 0 : _a.displays[0];
+    return (_jsxs("div", { style: { display: 'flex', alignItems: 'center', gap: '4px' }, children: [_jsx(IconButton, { onClick: () => {
                     model.zoomOut();
                 }, children: _jsx(ZoomOut, {}) }), _jsx(IconButton, { onClick: () => {
                     model.zoomIn();
                 }, children: _jsx(ZoomIn, {}) }), _jsx(IconButton, { onClick: () => model.activateTrackSelector(), title: "Open track selector", children: _jsx(TrackSelectorIcon, {}) }), _jsx(CascadingMenuButton, { menuItems: [
                     {
                         label: 'Square view - same bp per pixel',
-                        icon: CropDinIcon,
                         onClick: () => {
                             model.squareView();
                         },
+                        helpText: 'Makes both views use the same zoom level (bp per pixel), adjusting to the average of each. This ensures features are displayed at comparable scales for easier visual comparison.',
                     },
                     {
                         label: 'Rectangular view - same total bp',
-                        icon: CropLandscapeIcon,
                         onClick: () => {
                             model.squareViewProportional();
                         },
+                        helpText: 'Adjusts zoom levels proportionally so both views show the same total number of base pairs. This accounts for different view widths while maintaining the same total genomic span.',
                     },
                     {
                         label: 'Show all regions',
-                        icon: SettingsOverscanIcon,
                         onClick: () => {
                             model.showAllRegions();
                         },
+                        helpText: 'Zooms out to display all genome assemblies in their entirety. Useful for getting a high-level overview or resetting the view after zooming into specific regions.',
+                    },
+                    {
+                        label: 'Re-order chromosomes',
+                        icon: ShuffleIcon,
+                        onClick: () => {
+                            getSession(model).queueDialog(handleClose => [
+                                DiagonalizationProgressDialog,
+                                {
+                                    handleClose,
+                                    model,
+                                },
+                            ]);
+                        },
+                        helpText: 'Diagonalization algorithmically reorders and reorients chromosomes to minimize crossing synteny lines, creating a more diagonal pattern. This makes it easier to identify large-scale genomic rearrangements, inversions, and translocations. The process runs on the webworker for better performance.',
                     },
                     {
                         type: 'checkbox',
@@ -44,6 +65,7 @@ const DotplotControls = observer(function ({ model, }) {
                         onClick: () => {
                             model.setDrawCigar(!model.drawCigar);
                         },
+                        helpText: 'Toggle detailed CIGAR string visualization showing matches, insertions, and deletions in alignments. Disable for a cleaner view that shows only broad syntenic blocks.',
                     },
                     {
                         label: 'Show pan buttons',
@@ -52,48 +74,64 @@ const DotplotControls = observer(function ({ model, }) {
                         onClick: () => {
                             model.setShowPanButtons(!model.showPanButtons);
                         },
+                        helpText: 'Show or hide directional pan buttons that allow you to navigate the dotplot view by clicking arrows. Useful for precise navigation without using mouse drag.',
+                    },
+                    {
+                        label: 'Show dynamic controls',
+                        type: 'checkbox',
+                        checked: showDynamicControls,
+                        onClick: () => {
+                            setShowDynamicControls(!showDynamicControls);
+                        },
+                        helpText: 'Toggle visibility of dynamic controls like opacity and minimum length sliders. These controls allow you to adjust dotplot visualization parameters in real-time.',
                     },
                     {
                         label: 'Click and drag mode',
+                        helpText: 'Configure how clicking and dragging behaves in the dotplot view. Choose between panning and region selection as the default action.',
                         subMenu: [
                             {
-                                label: 'Pan by default, select region when ctrl/cmd key is held',
+                                label: 'Pan by default',
                                 icon: CursorMove,
                                 type: 'radio',
                                 checked: model.cursorMode === 'move',
                                 onClick: () => {
                                     model.setCursorMode('move');
                                 },
+                                helpText: 'Click and drag to pan the view. Hold Ctrl/Cmd while dragging to select a region for zooming or creating a linear synteny view.',
                             },
                             {
-                                label: 'Select region by default, pan when ctrl/cmd key is held',
+                                label: 'Select region by default',
                                 icon: CursorMouse,
                                 type: 'radio',
                                 checked: model.cursorMode === 'crosshair',
                                 onClick: () => {
                                     model.setCursorMode('crosshair');
                                 },
+                                helpText: 'Click and drag to select a region for zooming or creating a linear synteny view. Hold Ctrl/Cmd while dragging to pan the view instead.',
                             },
                         ],
                     },
                     {
                         label: 'Wheel scroll mode',
+                        helpText: 'Configure how mouse wheel scrolling behaves in the dotplot view.',
                         subMenu: [
                             {
-                                label: 'Pans view',
+                                label: 'Pan view',
                                 type: 'radio',
                                 checked: model.wheelMode === 'pan',
                                 onClick: () => {
                                     model.setWheelMode('pan');
                                 },
+                                helpText: 'Mouse wheel scrolling will pan the view up/down. Useful for navigating through the genome without changing zoom level.',
                             },
                             {
-                                label: 'Zooms view',
+                                label: 'Zoom view',
                                 type: 'radio',
                                 checked: model.wheelMode === 'zoom',
                                 onClick: () => {
                                     model.setWheelMode('zoom');
                                 },
+                                helpText: 'Mouse wheel scrolling will zoom in/out of the view. Provides quick zoom control for detailed inspection of regions.',
                             },
                             {
                                 label: 'Disable',
@@ -102,9 +140,10 @@ const DotplotControls = observer(function ({ model, }) {
                                 onClick: () => {
                                     model.setWheelMode('none');
                                 },
+                                helpText: 'Mouse wheel scrolling will be disabled for the dotplot view. Use this to prevent accidental zoom or pan when scrolling the page.',
                             },
                         ],
                     },
-                ], children: _jsx(MoreVert, {}) })] }));
+                ], children: _jsx(MoreVert, {}) }), _jsx(ColorBySelector, { model: model }), hasDisplays && showDynamicControls ? (_jsxs(_Fragment, { children: [_jsx(OpacitySlider, { model: model }), _jsx(MinLengthSlider, { model: model })] })) : null] }));
 });
 export default DotplotControls;

package/esm/DotplotView/components/DotplotTooltips.d.ts

@@ -0,0 +1,15 @@
+import type { DotplotViewModel } from '../model';
+type Coord = [number, number] | undefined;
+interface DotplotTooltipsProps {
+    model: DotplotViewModel;
+    mouseOvered: boolean;
+    validSelect: boolean;
+    mouserect: Coord;
+    mouserectClient: Coord;
+    xdistance: number;
+    mousedown: Coord;
+    mousedownClient: Coord;
+    ydistance: number;
+}
+export default function DotplotTooltips({ model, mouseOvered, validSelect, mouserect, mouserectClient, xdistance, mousedown, mousedownClient, ydistance, }: DotplotTooltipsProps): import("react/jsx-runtime").JSX.Element;
+export {};

package/esm/DotplotView/components/DotplotTooltips.js

@@ -0,0 +1,7 @@
+import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
+import { Suspense, lazy } from 'react';
+const TooltipWhereClicked = lazy(() => import('./DotplotTooltipClick'));
+const TooltipWhereMouseovered = lazy(() => import('./DotplotTooltipMouseover'));
+export default function DotplotTooltips({ model, mouseOvered, validSelect, mouserect, mouserectClient, xdistance, mousedown, mousedownClient, ydistance, }) {
+    return (_jsxs(_Fragment, { children: [mouseOvered && validSelect ? (_jsx(Suspense, { fallback: null, children: _jsx(TooltipWhereMouseovered, { model: model, mouserect: mouserect, mouserectClient: mouserectClient, xdistance: xdistance }) })) : null, validSelect ? (_jsx(Suspense, { fallback: null, children: _jsx(TooltipWhereClicked, { model: model, mousedown: mousedown, mousedownClient: mousedownClient, xdistance: xdistance, ydistance: ydistance }) })) : null] }));
+}

package/esm/DotplotView/components/DotplotView.js

@@ -1,16 +1,19 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
-import { Suspense, lazy, useEffect, useRef, useState } from 'react';
-import { LoadingEllipses, Menu, ResizeHandle } from '@jbrowse/core/ui';
-import { transaction } from 'mobx';
+import { LoadingEllipses, ResizeHandle } from '@jbrowse/core/ui';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
 import { HorizontalAxis, VerticalAxis } from './Axes';
-import Grid from './Grid';
+import DotplotTooltips from './DotplotTooltips';
 import Header from './Header';
 import ImportForm from './ImportForm';
-const TooltipWhereClicked = lazy(() => import('./DotplotTooltipClick'));
-const TooltipWhereMouseovered = lazy(() => import('./DotplotTooltipMouseover'));
-const blank = { left: 0, top: 0, width: 0, height: 0 };
+import MouseInteractionLayer from './MouseInteractionLayer';
+import SelectionContextMenu from './SelectionContextMenu';
+import { useCtrlKeyTracking } from './hooks/useCtrlKeyTracking';
+import { useCursorMode } from './hooks/useCursorMode';
+import { useMouseCoordinates } from './hooks/useMouseCoordinates';
+import { useMouseMoveHandler } from './hooks/useMouseMoveHandler';
+import { useMouseUpHandler } from './hooks/useMouseUpHandler';
+import { useWheelHandler } from './hooks/useWheelHandler';
 const useStyles = makeStyles()(theme => ({
     spacer: {
         gridColumn: '1/2',
@@ -51,9 +54,6 @@ const useStyles = makeStyles()(theme => ({
         borderTop: '1px solid #fafafa',
     },
 }));
-function getOffset(coord, rect) {
-    return coord && [coord[0] - rect.left, coord[1] - rect.top];
-}
 const RenderedComponent = observer(({ model }) => {
     const { classes } = useStyles();
     return (_jsx("div", { className: classes.overlay, children: model.tracks.map(track => {
@@ -63,118 +63,14 @@ const RenderedComponent = observer(({ model }) => {
         }) }));
 });
 const DotplotViewInternal = observer(function ({ model, }) {
-    var _a, _b;
     const { classes } = useStyles();
-    const [mousecurrClient, setMouseCurrClient] = useState();
-    const [mousedownClient, setMouseDownClient] = useState();
-    const [mouseOvered, setMouseOvered] = useState(false);
-    const [mouseupClient, setMouseUpClient] = useState();
-    const ref = useRef(null);
-    const root = useRef(null);
-    const distanceX = useRef(0);
-    const distanceY = useRef(0);
-    const scheduled = useRef(false);
-    const [ctrlKeyWasUsed, setCtrlKeyWasUsed] = useState(false);
-    const [ctrlKeyDown, setCtrlKeyDown] = useState(false);
-    const svg = ((_a = ref.current) === null || _a === void 0 ? void 0 : _a.getBoundingClientRect()) || blank;
-    const rootRect = ((_b = ref.current) === null || _b === void 0 ? void 0 : _b.getBoundingClientRect()) || blank;
-    const mousedown = getOffset(mousedownClient, svg);
-    const mousecurr = getOffset(mousecurrClient, svg);
-    const mouseup = getOffset(mouseupClient, svg);
-    const mouserect = mouseup || mousecurr;
-    const mouserectClient = mouseupClient || mousecurrClient;
-    const xdistance = mousedown && mouserect ? mouserect[0] - mousedown[0] : 0;
-    const ydistance = mousedown && mouserect ? mouserect[1] - mousedown[1] : 0;
     const { hview, vview, wheelMode, cursorMode } = model;
-    const validPan = (cursorMode === 'move' && !ctrlKeyWasUsed) ||
-        (cursorMode === 'crosshair' && ctrlKeyWasUsed);
-    const validSelect = (cursorMode === 'move' && ctrlKeyWasUsed) ||
-        (cursorMode === 'crosshair' && !ctrlKeyWasUsed);
-    useEffect(() => {
-        function onWheel(event) {
-            event.preventDefault();
-            distanceX.current += event.deltaX;
-            distanceY.current -= event.deltaY;
-            if (!scheduled.current) {
-                scheduled.current = true;
-                window.requestAnimationFrame(() => {
-                    transaction(() => {
-                        if (wheelMode === 'pan') {
-                            hview.scroll(distanceX.current / 3);
-                            vview.scroll(distanceY.current / 10);
-                        }
-                        else if (wheelMode === 'zoom') {
-                            if (Math.abs(distanceY.current) > Math.abs(distanceX.current) * 2 &&
-                                mousecurr) {
-                                const val = distanceY.current < 0 ? 1.1 : 0.9;
-                                hview.zoomTo(hview.bpPerPx * val, mousecurr[0]);
-                                vview.zoomTo(vview.bpPerPx * val, rootRect.height - mousecurr[1]);
-                            }
-                        }
-                    });
-                    scheduled.current = false;
-                    distanceX.current = 0;
-                    distanceY.current = 0;
-                });
-            }
-        }
-        if (ref.current) {
-            const curr = ref.current;
-            curr.addEventListener('wheel', onWheel);
-            return () => {
-                curr.removeEventListener('wheel', onWheel);
-            };
-        }
-        return () => { };
-    }, [hview, vview, wheelMode, mousecurr, rootRect.height]);
-    useEffect(() => {
-        function globalMouseMove(event) {
-            setMouseCurrClient([event.clientX, event.clientY]);
-            if (mousecurrClient && mousedownClient && validPan && !mouseupClient) {
-                hview.scroll(-event.clientX + mousecurrClient[0]);
-                vview.scroll(event.clientY - mousecurrClient[1]);
-            }
-        }
-        window.addEventListener('mousemove', globalMouseMove);
-        return () => {
-            window.removeEventListener('mousemove', globalMouseMove);
-        };
-    }, [validPan, mousecurrClient, mousedownClient, mouseupClient, hview, vview]);
-    useEffect(() => {
-        function globalCtrlKeyDown(event) {
-            if (event.metaKey || event.ctrlKey) {
-                setCtrlKeyDown(true);
-            }
-        }
-        function globalCtrlKeyUp(event) {
-            if (!event.metaKey && !event.ctrlKey) {
-                setCtrlKeyDown(false);
-            }
-        }
-        window.addEventListener('keydown', globalCtrlKeyDown);
-        window.addEventListener('keyup', globalCtrlKeyUp);
-        return () => {
-            window.removeEventListener('keydown', globalCtrlKeyDown);
-            window.addEventListener('keyup', globalCtrlKeyUp);
-        };
-    }, []);
-    useEffect(() => {
-        function globalMouseUp(event) {
-            if (Math.abs(xdistance) > 3 && Math.abs(ydistance) > 3 && validSelect) {
-                setMouseUpClient([event.clientX, event.clientY]);
-            }
-            else {
-                setMouseDownClient(undefined);
-            }
-        }
-        if (mousedown && !mouseup) {
-            window.addEventListener('mouseup', globalMouseUp, true);
-            return () => {
-                window.removeEventListener('mouseup', globalMouseUp, true);
-            };
-        }
-        return () => { };
-    }, [validSelect, mousedown, mouseup, xdistance, ydistance]);
+    const { mousecurrClient, mousedownClient, mouseupClient, mouseOvered, setMouseCurrClient, setMouseDownClient, setMouseUpClient, setMouseOvered, ref, root, rootRect, mousedown, mousecurr, mouseup, mouserect, mouserectClient, xdistance, ydistance, } = useMouseCoordinates();
+    const { ctrlKeyDown, validPan, validSelect, setCtrlKeyWasUsed, setCtrlKeyDown, } = useCursorMode(cursorMode);
+    useWheelHandler(ref, wheelMode, hview, vview, mousecurr, rootRect.height);
+    useMouseMoveHandler(mousecurrClient, mousedownClient, mouseupClient, validPan, hview, vview, setMouseCurrClient);
+    useCtrlKeyTracking(setCtrlKeyDown);
+    useMouseUpHandler(mousedown, mouseup, xdistance, ydistance, validSelect, setMouseUpClient, setMouseDownClient);
     return (_jsxs("div", { children: [_jsx(Header, { model: model, selection: !validSelect || !(mousedown && mouserect)
                     ? undefined
                     : {
@@ -184,45 +80,7 @@ const DotplotViewInternal = observer(function ({ model, }) {
                     setMouseOvered(false);
                 }, onMouseEnter: () => {
                     setMouseOvered(true);
-                }, children: [_jsxs("div", { className: classes.container, children: [_jsx(VerticalAxis, { model: model }), _jsx(HorizontalAxis, { model: model }), _jsxs("div", { ref: ref, className: classes.content, children: [mouseOvered && validSelect ? (_jsx(Suspense, { fallback: null, children: _jsx(TooltipWhereMouseovered, { model: model, mouserect: mouserect, mouserectClient: mouserectClient, xdistance: xdistance }) })) : null, validSelect ? (_jsx(Suspense, { fallback: null, children: _jsx(TooltipWhereClicked, { model: model, mousedown: mousedown, mousedownClient: mousedownClient, xdistance: xdistance, ydistance: ydistance }) })) : null, _jsx("div", { style: { cursor: ctrlKeyDown ? 'pointer' : cursorMode }, onMouseDown: event => {
-                                            if (event.button === 0) {
-                                                const { clientX, clientY } = event;
-                                                setMouseDownClient([clientX, clientY]);
-                                                setMouseCurrClient([clientX, clientY]);
-                                                setCtrlKeyWasUsed(ctrlKeyDown);
-                                            }
-                                        }, children: _jsx(Grid, { model: model, children: validSelect && mousedown && mouserect ? (_jsx("rect", { fill: "rgba(255,0,0,0.3)", x: Math.min(mouserect[0], mousedown[0]), y: Math.min(mouserect[1], mousedown[1]), width: Math.abs(xdistance), height: Math.abs(ydistance) })) : null }) }), _jsx("div", { className: classes.spacer })] }), _jsx(RenderedComponent, { model: model }), _jsx(Menu, { open: Boolean(mouseup), onMenuItemClick: (_, callback) => {
-                                    callback();
-                                    setMouseUpClient(undefined);
-                                    setMouseDownClient(undefined);
-                                }, onClose: () => {
-                                    setMouseUpClient(undefined);
-                                    setMouseDownClient(undefined);
-                                }, anchorReference: "anchorPosition", anchorPosition: mouseupClient
-                                    ? {
-                                        top: mouseupClient[1] + 50,
-                                        left: mouseupClient[0] + 50,
-                                    }
-                                    : undefined, style: { zIndex: 800 }, menuItems: [
-                                    {
-                                        label: 'Zoom in',
-                                        onClick: () => {
-                                            if (mousedown && mouseup) {
-                                                model.zoomInToMouseCoords(mousedown, mouseup);
-                                            }
-                                            setMouseOvered(false);
-                                        },
-                                    },
-                                    {
-                                        label: 'Open linear synteny view',
-                                        onClick: () => {
-                                            if (mousedown && mouseup) {
-                                                model.onDotplotView(mousedown, mouseup);
-                                            }
-                                            setMouseOvered(false);
-                                        },
-                                    },
-                                ] })] }), _jsx(ResizeHandle, { onDrag: n => model.setHeight(model.height + n), className: classes.resizeHandle })] })] }));
+                }, children: [_jsxs("div", { className: classes.container, children: [_jsx(VerticalAxis, { model: model }), _jsx(HorizontalAxis, { model: model }), _jsxs("div", { ref: ref, className: classes.content, children: [_jsx(DotplotTooltips, { model: model, mouseOvered: mouseOvered, validSelect: validSelect, mouserect: mouserect, mouserectClient: mouserectClient, xdistance: xdistance, mousedown: mousedown, mousedownClient: mousedownClient, ydistance: ydistance }), _jsx(MouseInteractionLayer, { model: model, ctrlKeyDown: ctrlKeyDown, cursorMode: cursorMode, validSelect: validSelect, mousedown: mousedown, mouserect: mouserect, xdistance: xdistance, ydistance: ydistance, setMouseDownClient: setMouseDownClient, setMouseCurrClient: setMouseCurrClient, setCtrlKeyWasUsed: setCtrlKeyWasUsed }), _jsx("div", { className: classes.spacer })] }), _jsx(RenderedComponent, { model: model }), _jsx(SelectionContextMenu, { model: model, mouseup: mouseup, mouseupClient: mouseupClient, mousedown: mousedown, setMouseUpClient: setMouseUpClient, setMouseDownClient: setMouseDownClient, setMouseOvered: setMouseOvered })] }), _jsx(ResizeHandle, { onDrag: n => model.setHeight(model.height + n), className: classes.resizeHandle })] })] }));
 });
 const DotplotView = observer(function ({ model }) {
     const { initialized, loading, error } = model;

package/esm/DotplotView/components/DotplotWarnings.js

@@ -1,5 +1,5 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
-import { lazy, useState } from 'react';
+import { Suspense, lazy, useState } from 'react';
 import { Alert, Button } from '@mui/material';
 import { observer } from 'mobx-react';
 const WarningDialog = lazy(() => import('./WarningDialog'));
@@ -9,9 +9,9 @@ const DotplotWarnings = observer(function ({ model, }) {
     const [hide, setHide] = useState(false);
     return trackWarnings.length && !hide ? (_jsxs(Alert, { severity: "warning", children: ["Warnings during render", ' ', _jsx(Button, { onClick: () => {
                     setShown(true);
-                }, children: "More info" }), shown ? (_jsx(WarningDialog, { trackWarnings: trackWarnings, handleClose: () => {
-                    setShown(false);
-                } })) : null, _jsx(Button, { variant: "contained", onClick: () => {
+                }, children: "More info" }), shown ? (_jsx(Suspense, { fallback: null, children: _jsx(WarningDialog, { trackWarnings: trackWarnings, handleClose: () => {
+                        setShown(false);
+                    } }) })) : null, _jsx(Button, { variant: "contained", onClick: () => {
                     setHide(true);
                 }, children: "Dismiss" })] })) : null;
 });

package/esm/DotplotView/components/ImportForm/index.js

@@ -34,7 +34,6 @@ function doSubmit({ model, assembly1, assembly2, }) {
                 }
             });
         }
-        model.showAllRegions();
         model.setAssemblyNames(assembly2, assembly1);
     });
 }

package/esm/DotplotView/components/MinLengthSlider.d.ts

@@ -0,0 +1,5 @@
+import type { DotplotViewModel } from '../model';
+declare const MinLengthSlider: ({ model, }: {
+    model: DotplotViewModel;
+}) => import("react/jsx-runtime").JSX.Element;
+export default MinLengthSlider;

package/esm/DotplotView/components/MinLengthSlider.js

@@ -0,0 +1,39 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { useEffect, useState } from 'react';
+import { Slider, Typography } from '@mui/material';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+import SliderTooltip from './SliderTooltip';
+const useStyles = makeStyles()({
+    container: {
+        display: 'flex',
+        alignItems: 'center',
+        marginLeft: 16,
+        marginRight: 16,
+        minWidth: 150,
+    },
+});
+const MinLengthSlider = observer(function ({ model, }) {
+    var _a, _b;
+    const { classes } = useStyles();
+    const firstDisplay = (_a = model.tracks[0]) === null || _a === void 0 ? void 0 : _a.displays[0];
+    const minAlignmentLength = (_b = firstDisplay === null || firstDisplay === void 0 ? void 0 : firstDisplay.minAlignmentLength) !== null && _b !== void 0 ? _b : 0;
+    const [minLengthValue, setMinLengthValue] = useState(Math.log2(Math.max(1, minAlignmentLength)) * 100);
+    useEffect(() => {
+        setMinLengthValue(Math.log2(Math.max(1, minAlignmentLength)) * 100);
+    }, [minAlignmentLength]);
+    return (_jsxs("span", { className: classes.container, children: [_jsx(Typography, { variant: "body2", style: { marginRight: 8 }, children: "Min length:" }), _jsx(Slider, { value: minLengthValue, onChange: (_, val) => {
+                    setMinLengthValue(val);
+                }, onChangeCommitted: () => {
+                    const newMinLength = Math.round(2 ** (minLengthValue / 100));
+                    for (const track of model.tracks) {
+                        for (const display of track.displays) {
+                            ;
+                            display.setMinAlignmentLength(newMinLength);
+                        }
+                    }
+                }, min: 0, max: Math.log2(1000000) * 100, valueLabelDisplay: "auto", valueLabelFormat: newValue => Math.round(2 ** (newValue / 100)).toLocaleString(), size: "small", style: { minWidth: 100 }, slots: {
+                    valueLabel: SliderTooltip,
+                } })] }));
+});
+export default MinLengthSlider;

package/esm/DotplotView/components/MouseInteractionLayer.d.ts

@@ -0,0 +1,17 @@
+import type { DotplotViewModel } from '../model';
+type Coord = [number, number] | undefined;
+interface MouseInteractionLayerProps {
+    model: DotplotViewModel;
+    ctrlKeyDown: boolean;
+    cursorMode: string;
+    validSelect: boolean;
+    mousedown: Coord;
+    mouserect: Coord;
+    xdistance: number;
+    ydistance: number;
+    setMouseDownClient: (coord: Coord) => void;
+    setMouseCurrClient: (coord: Coord) => void;
+    setCtrlKeyWasUsed: (wasUsed: boolean) => void;
+}
+export default function MouseInteractionLayer({ model, ctrlKeyDown, cursorMode, validSelect, mousedown, mouserect, xdistance, ydistance, setMouseDownClient, setMouseCurrClient, setCtrlKeyWasUsed, }: MouseInteractionLayerProps): import("react/jsx-runtime").JSX.Element;
+export {};

package/esm/DotplotView/components/MouseInteractionLayer.js

@@ -0,0 +1,12 @@
+import { jsx as _jsx } from "react/jsx-runtime";
+import Grid from './Grid';
+export default function MouseInteractionLayer({ model, ctrlKeyDown, cursorMode, validSelect, mousedown, mouserect, xdistance, ydistance, setMouseDownClient, setMouseCurrClient, setCtrlKeyWasUsed, }) {
+    return (_jsx("div", { style: { cursor: ctrlKeyDown ? 'pointer' : cursorMode }, onMouseDown: event => {
+            if (event.button === 0) {
+                const { clientX, clientY } = event;
+                setMouseDownClient([clientX, clientY]);
+                setMouseCurrClient([clientX, clientY]);
+                setCtrlKeyWasUsed(ctrlKeyDown);
+            }
+        }, children: _jsx(Grid, { model: model, children: validSelect && mousedown && mouserect ? (_jsx("rect", { fill: "rgba(255,0,0,0.3)", x: Math.min(mouserect[0], mousedown[0]), y: Math.min(mouserect[1], mousedown[1]), width: Math.abs(xdistance), height: Math.abs(ydistance) })) : null }) }));
+}

package/esm/DotplotView/components/OpacitySlider.d.ts

@@ -0,0 +1,5 @@
+import type { DotplotViewModel } from '../model';
+declare const OpacitySlider: ({ model, }: {
+    model: DotplotViewModel;
+}) => import("react/jsx-runtime").JSX.Element;
+export default OpacitySlider;

package/esm/DotplotView/components/OpacitySlider.js

@@ -0,0 +1,38 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { Slider, Typography } from '@mui/material';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+import SliderTooltip from './SliderTooltip';
+const useStyles = makeStyles()({
+    container: {
+        display: 'flex',
+        alignItems: 'center',
+        marginLeft: 16,
+        marginRight: 16,
+        minWidth: 150,
+    },
+});
+const OpacitySlider = observer(function ({ model, }) {
+    var _a, _b;
+    const { classes } = useStyles();
+    const firstDisplay = (_a = model.tracks[0]) === null || _a === void 0 ? void 0 : _a.displays[0];
+    const alpha = (_b = firstDisplay === null || firstDisplay === void 0 ? void 0 : firstDisplay.alpha) !== null && _b !== void 0 ? _b : 1;
+    const exponent = 3;
+    const alphaToSlider = (a) => Math.pow(a, 1 / exponent);
+    const sliderToAlpha = (s) => Math.pow(s, exponent);
+    const sliderValue = alphaToSlider(alpha);
+    const handleAlphaChange = (_event, value) => {
+        const sliderVal = typeof value === 'number' ? value : value[0];
+        const newAlpha = sliderToAlpha(sliderVal);
+        for (const track of model.tracks) {
+            for (const display of track.displays) {
+                ;
+                display.setAlpha(newAlpha);
+            }
+        }
+    };
+    return (_jsxs("span", { className: classes.container, children: [_jsx(Typography, { variant: "body2", style: { marginRight: 8 }, children: "Opacity:" }), _jsx(Slider, { value: sliderValue, onChange: handleAlphaChange, min: 0, max: 1, step: 0.01, valueLabelDisplay: "auto", size: "small", style: { minWidth: 100 }, slots: {
+                    valueLabel: SliderTooltip,
+                }, valueLabelFormat: value => sliderToAlpha(value).toFixed(3) })] }));
+});
+export default OpacitySlider;

package/esm/DotplotView/components/SelectionContextMenu.d.ts

@@ -0,0 +1,13 @@
+import type { DotplotViewModel } from '../model';
+type Coord = [number, number] | undefined;
+interface SelectionContextMenuProps {
+    model: DotplotViewModel;
+    mouseup: Coord;
+    mouseupClient: Coord;
+    mousedown: Coord;
+    setMouseUpClient: (coord: Coord) => void;
+    setMouseDownClient: (coord: Coord) => void;
+    setMouseOvered: (isOvered: boolean) => void;
+}
+export default function SelectionContextMenu({ model, mouseup, mouseupClient, mousedown, setMouseUpClient, setMouseDownClient, setMouseOvered, }: SelectionContextMenuProps): import("react/jsx-runtime").JSX.Element;
+export {};

package/esm/DotplotView/components/SelectionContextMenu.js

@@ -0,0 +1,39 @@
+import { jsx as _jsx } from "react/jsx-runtime";
+import { Menu } from '@jbrowse/core/ui';
+function getSelectionMenuItems(model, mousedown, mouseup, setMouseOvered) {
+    return [
+        {
+            label: 'Zoom in',
+            onClick: () => {
+                if (mousedown && mouseup) {
+                    model.zoomInToMouseCoords(mousedown, mouseup);
+                }
+                setMouseOvered(false);
+            },
+        },
+        {
+            label: 'Open linear synteny view',
+            onClick: () => {
+                if (mousedown && mouseup) {
+                    model.onDotplotView(mousedown, mouseup);
+                }
+                setMouseOvered(false);
+            },
+        },
+    ];
+}
+export default function SelectionContextMenu({ model, mouseup, mouseupClient, mousedown, setMouseUpClient, setMouseDownClient, setMouseOvered, }) {
+    return (_jsx(Menu, { open: Boolean(mouseup), onMenuItemClick: (_, callback) => {
+            callback();
+            setMouseUpClient(undefined);
+            setMouseDownClient(undefined);
+        }, onClose: () => {
+            setMouseUpClient(undefined);
+            setMouseDownClient(undefined);
+        }, anchorReference: "anchorPosition", anchorPosition: mouseupClient
+            ? {
+                top: mouseupClient[1] + 50,
+                left: mouseupClient[0] + 50,
+            }
+            : undefined, style: { zIndex: 11000 }, menuItems: getSelectionMenuItems(model, mousedown, mouseup, setMouseOvered) }));
+}

package/esm/DotplotView/components/SliderTooltip.d.ts

@@ -0,0 +1,2 @@
+import type { SliderValueLabelProps } from '@mui/material';
+export default function SliderTooltip(props: SliderValueLabelProps): import("react/jsx-runtime").JSX.Element;

package/esm/DotplotView/components/SliderTooltip.js

@@ -0,0 +1,6 @@
+import { jsx as _jsx } from "react/jsx-runtime";
+import { Tooltip } from '@mui/material';
+export default function SliderTooltip(props) {
+    const { children, open, value } = props;
+    return (_jsx(Tooltip, { open: open, enterTouchDelay: 0, placement: "top", title: value, arrow: true, children: children }));
+}

package/esm/DotplotView/components/hooks/useCtrlKeyTracking.d.ts

@@ -0,0 +1 @@
+export declare function useCtrlKeyTracking(setCtrlKeyDown: (isDown: boolean) => void): void;