@jbrowse/plugin-linear-comparative-view 2.6.1

package/esm/LinearComparativeDisplay/stateModelFactory.js

@@ -0,0 +1,170 @@
+import { readConfObject, ConfigurationReference, } from '@jbrowse/core/configuration';
+import { types, getSnapshot } from 'mobx-state-tree';
+import { dedupe, getContainingView, getSession, makeAbortableReaction, } from '@jbrowse/core/util';
+import { getRpcSessionId } from '@jbrowse/core/util/tracks';
+import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes/models';
+/**
+ * #stateModel LinearComparativeDisplay
+ */
+function stateModelFactory(configSchema) {
+    return types
+        .compose('LinearComparativeDisplay', BaseDisplay, types.model({
+        /**
+         * #property
+         */
+        type: types.literal('LinearComparativeDisplay'),
+        /**
+         * #property
+         */
+        configuration: ConfigurationReference(configSchema),
+        /**
+         * #property
+         */
+        height: 100,
+    }))
+        .volatile(( /* self */) => ({
+        renderInProgress: undefined,
+        features: undefined,
+        message: undefined,
+    }))
+        .views(self => ({
+        /**
+         * #getter
+         */
+        renderProps() {
+            return {
+                rpcDriverName: self.rpcDriverName,
+                displayModel: self,
+                highResolutionScaling: 2,
+            };
+        },
+    }))
+        .actions(self => {
+        let renderInProgress;
+        return {
+            /**
+             * #action
+             * controlled by a reaction
+             */
+            setLoading(abortController) {
+                self.message = undefined;
+                self.error = undefined;
+                renderInProgress = abortController;
+            },
+            /**
+             * #action
+             * controlled by a reaction
+             */
+            setMessage(messageText) {
+                if (renderInProgress && !renderInProgress.signal.aborted) {
+                    renderInProgress.abort();
+                }
+                self.message = messageText;
+                self.error = undefined;
+                renderInProgress = undefined;
+            },
+            /**
+             * #action
+             * controlled by a reaction
+             */
+            setRendered(args) {
+                if (!args) {
+                    return;
+                }
+                const { features } = args;
+                const existingFeatures = self.features || [];
+                const featIds = new Set(existingFeatures.map(f => f.id()) || []);
+                const newFeatIds = new Set((features === null || features === void 0 ? void 0 : features.map(f => f.id())) || []);
+                let foundNewFeatureNotInExistingMap = false;
+                let foundExistingFeatureNotInNewMap = false;
+                for (let i = 0; i < features.length; i++) {
+                    if (!featIds.has(features[i].id())) {
+                        foundNewFeatureNotInExistingMap = true;
+                        break;
+                    }
+                }
+                for (let i = 0; i < existingFeatures.length; i++) {
+                    if (!newFeatIds.has(existingFeatures[i].id())) {
+                        foundExistingFeatureNotInNewMap = true;
+                        break;
+                    }
+                }
+                self.message = undefined;
+                self.error = undefined;
+                renderInProgress = undefined;
+                if (foundNewFeatureNotInExistingMap ||
+                    foundExistingFeatureNotInNewMap ||
+                    !self.features) {
+                    self.features = features;
+                }
+            },
+            /**
+             * #action
+             * controlled by a reaction
+             */
+            setError(error) {
+                console.error(error);
+                if (renderInProgress && !renderInProgress.signal.aborted) {
+                    renderInProgress.abort();
+                }
+                // the rendering failed for some reason
+                self.message = undefined;
+                self.error = error;
+                renderInProgress = undefined;
+            },
+        };
+    })
+        .actions(self => ({
+        afterAttach() {
+            makeAbortableReaction(
+            // @ts-expect-error
+            self, renderBlockData, renderBlockEffect, {
+                name: `${self.type} ${self.id} rendering`,
+                delay: 1000,
+                fireImmediately: true,
+            }, self.setLoading, self.setRendered, self.setError);
+        },
+    }));
+}
+function renderBlockData(self) {
+    const { rpcManager } = getSession(self);
+    const display = self;
+    // Alternative to readConfObject(config) is below used because renderProps is
+    // something under our control.  Compare to serverSideRenderedBlock
+    readConfObject(self.configuration);
+    const { adapterConfig } = self;
+    const parent = getContainingView(self);
+    const sessionId = getRpcSessionId(self);
+    getSnapshot(parent);
+    return parent.initialized
+        ? {
+            rpcManager,
+            renderProps: {
+                ...display.renderProps(),
+                view: parent,
+                adapterConfig,
+                sessionId,
+                timeout: 1000000,
+                self,
+            },
+        }
+        : undefined;
+}
+async function renderBlockEffect(props) {
+    if (!props) {
+        return;
+    }
+    const { rpcManager, renderProps } = props;
+    const { adapterConfig } = renderProps;
+    const view0 = renderProps.view.views[0];
+    const features = (await rpcManager.call('getFeats', 'CoreGetFeatures', {
+        regions: view0.staticBlocks.contentBlocks,
+        sessionId: 'getFeats',
+        adapterConfig,
+    }));
+    return {
+        features: dedupe(features, f => f.id()),
+    };
+}
+export default stateModelFactory;
+//# sourceMappingURL=stateModelFactory.js.map

package/esm/LinearComparativeDisplay/stateModelFactory.js.map

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package/esm/LinearComparativeView/components/Header.d.ts

@@ -0,0 +1,7 @@
+import React from 'react';
+import { LinearComparativeViewModel } from '../model';
+type LCV = LinearComparativeViewModel;
+declare const Header: ({ model }: {
+    model: LCV;
+}) => React.JSX.Element;
+export default Header;

package/esm/LinearComparativeView/components/Header.js

@@ -0,0 +1,61 @@
+import React, { useState } from 'react';
+import { IconButton, Typography } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import { SearchBox } from '@jbrowse/plugin-linear-genome-view';
+import { observer } from 'mobx-react';
+import { Menu } from '@jbrowse/core/ui';
+// icons
+import MoreVertIcon from '@mui/icons-material/MoreVert';
+import { TrackSelector as TrackSelectorIcon } from '@jbrowse/core/ui/Icons';
+const useStyles = makeStyles()(() => ({
+    headerBar: {
+        gridArea: '1/1/auto/span 2',
+        display: 'flex',
+    },
+    spacer: {
+        flexGrow: 1,
+    },
+    iconButton: {
+        margin: 5,
+    },
+    bp: {
+        display: 'flex',
+        alignItems: 'center',
+        marginLeft: 10,
+    },
+    searchContainer: {
+        marginLeft: 5,
+    },
+    searchBox: {
+        display: 'flex',
+    },
+}));
+const TrackSelector = observer(({ model }) => {
+    return (React.createElement(IconButton, { onClick: model.activateTrackSelector, title: "Open track selector" },
+        React.createElement(TrackSelectorIcon, null)));
+});
+const Header = observer(function ({ model }) {
+    const { classes } = useStyles();
+    const [menuAnchorEl, setMenuAnchorEl] = useState();
+    const anyShowHeaders = model.views.some(view => !view.hideHeader);
+    return (React.createElement("div", { className: classes.headerBar },
+        React.createElement(TrackSelector, { model: model }),
+        React.createElement(IconButton, { onClick: event => setMenuAnchorEl(event.currentTarget), className: classes.iconButton },
+            React.createElement(MoreVertIcon, null)),
+        !anyShowHeaders
+            ? model.views.map(view => (React.createElement("div", { key: view.id, className: classes.searchBox },
+                React.createElement("div", { className: classes.searchContainer },
+                    React.createElement(SearchBox, { model: view, showHelp: false })),
+                React.createElement("div", { className: classes.bp },
+                    React.createElement(Typography, { variant: "body2", color: "textSecondary", className: classes.bp },
+                        Math.round(view.coarseTotalBp).toLocaleString('en-US'),
+                        " bp")))))
+            : null,
+        React.createElement("div", { className: classes.spacer }),
+        menuAnchorEl ? (React.createElement(Menu, { anchorEl: menuAnchorEl, open: true, onMenuItemClick: (_event, callback) => {
+                callback();
+                setMenuAnchorEl(undefined);
+            }, menuItems: model.headerMenuItems(), onClose: () => setMenuAnchorEl(undefined) })) : null));
+});
+export default Header;
+//# sourceMappingURL=Header.js.map

package/esm/LinearComparativeView/components/Header.js.map

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package/esm/LinearComparativeView/components/LinearComparativeView.d.ts

@@ -0,0 +1,8 @@
+import React from 'react';
+import { LinearComparativeViewModel } from '../model';
+type LCV = LinearComparativeViewModel;
+declare const _default: (props: {
+    ExtraButtons?: React.ReactNode;
+    model: LCV;
+}) => React.JSX.Element;
+export default _default;

package/esm/LinearComparativeView/components/LinearComparativeView.js

@@ -0,0 +1,94 @@
+import React from 'react';
+import { makeStyles } from 'tss-react/mui';
+import { observer } from 'mobx-react';
+import { getConf } from '@jbrowse/core/configuration';
+import { getEnv } from '@jbrowse/core/util';
+import { ResizeHandle } from '@jbrowse/core/ui';
+import Rubberband from './Rubberband';
+import Header from './Header';
+const useStyles = makeStyles()(theme => ({
+    container: {
+        display: 'grid',
+    },
+    overlay: {
+        zIndex: 100,
+        gridArea: '1/1',
+    },
+    content: {
+        gridArea: '1/1',
+        position: 'relative',
+    },
+    grid: {
+        display: 'grid',
+    },
+    relative: {
+        position: 'relative',
+    },
+    // this helps keep the vertical guide inside the parent view container,
+    // similar style exists in the single LGV's trackscontainer
+    rubberbandContainer: {
+        position: 'relative',
+        overflow: 'hidden',
+    },
+    rubberbandDiv: {
+        width: '100%',
+        background: theme.palette.action.disabledBackground,
+        height: 15,
+        '&:hover': {
+            background: theme.palette.action.selected,
+        },
+    },
+}));
+const Overlays = observer(({ model }) => {
+    const { classes } = useStyles();
+    return (React.createElement(React.Fragment, null, model.tracks.map(track => {
+        const [display] = track.displays;
+        const { RenderingComponent } = display;
+        const trackId = getConf(track, 'trackId');
+        return RenderingComponent ? (React.createElement("div", { className: classes.overlay, key: trackId, style: {
+                height: model.middleComparativeHeight,
+                overflow: 'hidden',
+            } },
+            React.createElement(RenderingComponent, { model: display }))) : null;
+    })));
+});
+// The comparative is in the middle of the views
+const MiddleComparativeView = observer(({ model }) => {
+    const { classes } = useStyles();
+    const { views } = model;
+    const { pluginManager } = getEnv(model);
+    const { ReactComponent } = pluginManager.getViewType(views[0].type);
+    return (React.createElement("div", { className: classes.rubberbandContainer },
+        React.createElement(Header, { model: model }),
+        React.createElement(Rubberband, { model: model, ControlComponent: React.createElement("div", { className: classes.rubberbandDiv }) }),
+        React.createElement("div", { className: classes.container },
+            React.createElement(ReactComponent, { model: views[0] }),
+            React.createElement("div", { className: classes.grid },
+                React.createElement(Overlays, { model: model })),
+            React.createElement(ResizeHandle, { onDrag: n => model.setMiddleComparativeHeight(model.middleComparativeHeight + n), style: {
+                    height: 4,
+                    background: '#ccc',
+                } }),
+            React.createElement(ReactComponent, { model: views[1] }))));
+});
+const OverlayComparativeView = observer(({ model }) => {
+    const { classes } = useStyles();
+    const { views } = model;
+    const { pluginManager } = getEnv(model);
+    return (React.createElement("div", { className: classes.rubberbandContainer },
+        React.createElement(Header, { model: model }),
+        React.createElement(Rubberband, { model: model, ControlComponent: React.createElement("div", { className: classes.rubberbandDiv }) }),
+        React.createElement("div", { className: classes.container },
+            React.createElement("div", { className: classes.content },
+                React.createElement("div", { className: classes.relative }, views.map(view => {
+                    const { ReactComponent } = pluginManager.getViewType(view.type);
+                    return React.createElement(ReactComponent, { key: view.id, model: view });
+                })),
+                React.createElement(Overlays, { model: model })))));
+});
+export default observer(function (props) {
+    const { model } = props;
+    const middle = model.tracks.some(({ displays }) => displays.some((d) => getConf(d, 'middle')));
+    return middle ? (React.createElement(MiddleComparativeView, { ...props })) : (React.createElement(OverlayComparativeView, { ...props }));
+});
+//# sourceMappingURL=LinearComparativeView.js.map

package/esm/LinearComparativeView/components/LinearComparativeView.js.map

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package/esm/LinearComparativeView/components/Rubberband.d.ts

@@ -0,0 +1,9 @@
+import React from 'react';
+import { LinearComparativeViewModel } from '../model';
+type LCV = LinearComparativeViewModel;
+declare function Rubberband({ model, ControlComponent, }: {
+    model: LCV;
+    ControlComponent?: React.ReactElement;
+}): React.JSX.Element;
+declare const _default: typeof Rubberband;
+export default _default;

package/esm/LinearComparativeView/components/Rubberband.js

@@ -0,0 +1,200 @@
+import React, { useRef, useEffect, useState } from 'react';
+import { observer } from 'mobx-react';
+import { Popover, Tooltip, Typography, alpha } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import { stringify } from '@jbrowse/core/util';
+import { Menu } from '@jbrowse/core/ui';
+const useStyles = makeStyles()(theme => {
+    const { tertiary, primary } = theme.palette;
+    const background = tertiary
+        ? alpha(tertiary.main, 0.7)
+        : alpha(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: tertiary ? tertiary.contrastText : primary.contrastText,
+        },
+        popover: {
+            mouseEvents: 'none',
+            cursor: 'crosshair',
+        },
+        paper: {
+            paddingLeft: theme.spacing(1),
+            paddingRight: theme.spacing(1),
+        },
+        guide: {
+            pointerEvents: 'none',
+            height: '100%',
+            width: 1,
+            position: 'absolute',
+            zIndex: 10,
+        },
+        sm: {
+            fontSize: 10,
+        },
+    };
+});
+const VerticalGuide = observer(({ model, coordX }) => {
+    const { classes } = useStyles();
+    return (React.createElement(Tooltip, { open: true, placement: "top", title: model.views
+            .map(view => view.pxToBp(coordX))
+            .map(elt => (React.createElement(Typography, { className: classes.sm, key: JSON.stringify(elt) }, stringify(elt)))), arrow: true },
+        React.createElement("div", { className: classes.guide, style: {
+                left: coordX,
+                background: 'red',
+            } })));
+});
+function Rubberband({ model, ControlComponent = React.createElement("div", null), }) {
+    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 computeOffsets(offsetX, view) {
+            if (startX === undefined) {
+                return;
+            }
+            let leftPx = startX;
+            let rightPx = offsetX;
+            // handles clicking and dragging to the left
+            if (rightPx < leftPx) {
+                ;
+                [leftPx, rightPx] = [rightPx, leftPx];
+            }
+            const leftOffset = view.pxToBp(leftPx);
+            const rightOffset = view.pxToBp(rightPx);
+            return { leftOffset, rightOffset };
+        }
+        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,
+                });
+                model.views.forEach(view => {
+                    const args = computeOffsets(offsetX, view);
+                    if (args) {
+                        const { leftOffset, rightOffset } = args;
+                        view.setOffsets(leftOffset, rightOffset);
+                    }
+                });
+                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, model]);
+    useEffect(() => {
+        if (!mouseDragging &&
+            currentX !== undefined &&
+            startX !== undefined &&
+            Math.abs(currentX - startX) <= 3) {
+            handleClose();
+        }
+    }, [mouseDragging, currentX, startX]);
+    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.views.forEach(view => view.setOffsets(undefined, undefined));
+    }
+    function handleClose() {
+        setAnchorPosition(undefined);
+        setStartX(undefined);
+        setCurrentX(undefined);
+    }
+    const open = Boolean(anchorPosition);
+    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)));
+    }
+    /* Calculating Pixels for Mouse Dragging */
+    const right = anchorPosition ? anchorPosition.offsetX : currentX || 0;
+    const left = right < startX ? right : startX;
+    const width = Math.abs(right - startX);
+    const { views } = model;
+    const leftBpOffset = views.map(view => view.pxToBp(left));
+    const rightBpOffset = views.map(view => view.pxToBp(left + width));
+    const numOfBpSelected = views.map(view => Math.ceil(width * view.bpPerPx));
+    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 }, leftBpOffset.map(l => (React.createElement(Typography, { key: JSON.stringify(l) }, stringify(l))))),
+            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 }, rightBpOffset.map(l => (React.createElement(Typography, { key: JSON.stringify(l) }, stringify(l))))))) : null,
+        React.createElement("div", { ref: rubberbandRef, className: classes.rubberband, style: { left, width } },
+            React.createElement(Typography, { variant: "h6", className: classes.rubberbandText }, numOfBpSelected.map((n, i) => (React.createElement(Typography, { key: `${n}_${i}` }, `${n.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: open, onClose: handleClose, menuItems: model.rubberBandMenuItems() })) : null));
+}
+export default observer(Rubberband);
+//# sourceMappingURL=Rubberband.js.map

package/esm/LinearComparativeView/components/Rubberband.js.map

@@ -0,0 +1 @@
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package/esm/LinearComparativeView/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/esm/LinearComparativeView/index.js

@@ -0,0 +1,14 @@
+import { lazy } from 'react';
+import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType';
+import modelFactory from './model';
+export default (pluginManager) => {
+    pluginManager.addViewType(() => {
+        return new ViewType({
+            name: 'LinearComparativeView',
+            displayName: 'Linear comparative view',
+            stateModel: modelFactory(pluginManager),
+            ReactComponent: lazy(() => import('./components/LinearComparativeView')),
+        });
+    });
+};
+//# sourceMappingURL=index.js.map

package/esm/LinearComparativeView/index.js.map

@@ -0,0 +1 @@
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