@jbrowse/plugin-linear-comparative-view 2.6.1

package/dist/LinearComparativeView/components/LinearComparativeView.js

@@ -0,0 +1,99 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const mui_1 = require("tss-react/mui");
+const mobx_react_1 = require("mobx-react");
+const configuration_1 = require("@jbrowse/core/configuration");
+const util_1 = require("@jbrowse/core/util");
+const ui_1 = require("@jbrowse/core/ui");
+const Rubberband_1 = __importDefault(require("./Rubberband"));
+const Header_1 = __importDefault(require("./Header"));
+const useStyles = (0, mui_1.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 = (0, mobx_react_1.observer)(({ model }) => {
+    const { classes } = useStyles();
+    return (react_1.default.createElement(react_1.default.Fragment, null, model.tracks.map(track => {
+        const [display] = track.displays;
+        const { RenderingComponent } = display;
+        const trackId = (0, configuration_1.getConf)(track, 'trackId');
+        return RenderingComponent ? (react_1.default.createElement("div", { className: classes.overlay, key: trackId, style: {
+                height: model.middleComparativeHeight,
+                overflow: 'hidden',
+            } },
+            react_1.default.createElement(RenderingComponent, { model: display }))) : null;
+    })));
+});
+// The comparative is in the middle of the views
+const MiddleComparativeView = (0, mobx_react_1.observer)(({ model }) => {
+    const { classes } = useStyles();
+    const { views } = model;
+    const { pluginManager } = (0, util_1.getEnv)(model);
+    const { ReactComponent } = pluginManager.getViewType(views[0].type);
+    return (react_1.default.createElement("div", { className: classes.rubberbandContainer },
+        react_1.default.createElement(Header_1.default, { model: model }),
+        react_1.default.createElement(Rubberband_1.default, { model: model, ControlComponent: react_1.default.createElement("div", { className: classes.rubberbandDiv }) }),
+        react_1.default.createElement("div", { className: classes.container },
+            react_1.default.createElement(ReactComponent, { model: views[0] }),
+            react_1.default.createElement("div", { className: classes.grid },
+                react_1.default.createElement(Overlays, { model: model })),
+            react_1.default.createElement(ui_1.ResizeHandle, { onDrag: n => model.setMiddleComparativeHeight(model.middleComparativeHeight + n), style: {
+                    height: 4,
+                    background: '#ccc',
+                } }),
+            react_1.default.createElement(ReactComponent, { model: views[1] }))));
+});
+const OverlayComparativeView = (0, mobx_react_1.observer)(({ model }) => {
+    const { classes } = useStyles();
+    const { views } = model;
+    const { pluginManager } = (0, util_1.getEnv)(model);
+    return (react_1.default.createElement("div", { className: classes.rubberbandContainer },
+        react_1.default.createElement(Header_1.default, { model: model }),
+        react_1.default.createElement(Rubberband_1.default, { model: model, ControlComponent: react_1.default.createElement("div", { className: classes.rubberbandDiv }) }),
+        react_1.default.createElement("div", { className: classes.container },
+            react_1.default.createElement("div", { className: classes.content },
+                react_1.default.createElement("div", { className: classes.relative }, views.map(view => {
+                    const { ReactComponent } = pluginManager.getViewType(view.type);
+                    return react_1.default.createElement(ReactComponent, { key: view.id, model: view });
+                })),
+                react_1.default.createElement(Overlays, { model: model })))));
+});
+exports.default = (0, mobx_react_1.observer)(function (props) {
+    const { model } = props;
+    const middle = model.tracks.some(({ displays }) => displays.some((d) => (0, configuration_1.getConf)(d, 'middle')));
+    return middle ? (react_1.default.createElement(MiddleComparativeView, { ...props })) : (react_1.default.createElement(OverlayComparativeView, { ...props }));
+});
+//# sourceMappingURL=LinearComparativeView.js.map

package/dist/LinearComparativeView/components/LinearComparativeView.js.map

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

@@ -0,0 +1,225 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importStar(require("react"));
+const mobx_react_1 = require("mobx-react");
+const material_1 = require("@mui/material");
+const mui_1 = require("tss-react/mui");
+const util_1 = require("@jbrowse/core/util");
+const ui_1 = require("@jbrowse/core/ui");
+const useStyles = (0, mui_1.makeStyles)()(theme => {
+    const { tertiary, primary } = theme.palette;
+    const background = tertiary
+        ? (0, material_1.alpha)(tertiary.main, 0.7)
+        : (0, material_1.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 = (0, mobx_react_1.observer)(({ model, coordX }) => {
+    const { classes } = useStyles();
+    return (react_1.default.createElement(material_1.Tooltip, { open: true, placement: "top", title: model.views
+            .map(view => view.pxToBp(coordX))
+            .map(elt => (react_1.default.createElement(material_1.Typography, { className: classes.sm, key: JSON.stringify(elt) }, (0, util_1.stringify)(elt)))), arrow: true },
+        react_1.default.createElement("div", { className: classes.guide, style: {
+                left: coordX,
+                background: 'red',
+            } })));
+});
+function Rubberband({ model, ControlComponent = react_1.default.createElement("div", null), }) {
+    const [startX, setStartX] = (0, react_1.useState)();
+    const [currentX, setCurrentX] = (0, react_1.useState)();
+    // clientX and clientY used for anchorPosition for menu
+    // offsetX used for calculations about width of selection
+    const [anchorPosition, setAnchorPosition] = (0, react_1.useState)();
+    const [guideX, setGuideX] = (0, react_1.useState)();
+    const controlsRef = (0, react_1.useRef)(null);
+    const rubberbandRef = (0, react_1.useRef)(null);
+    const { classes } = useStyles();
+    const mouseDragging = startX !== undefined && anchorPosition === undefined;
+    (0, react_1.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]);
+    (0, react_1.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_1.default.createElement(react_1.default.Fragment, null,
+            guideX !== undefined ? (react_1.default.createElement(VerticalGuide, { model: model, coordX: guideX })) : null,
+            react_1.default.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_1.default.createElement(react_1.default.Fragment, null,
+        rubberbandRef.current ? (react_1.default.createElement(react_1.default.Fragment, null,
+            react_1.default.createElement(material_1.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_1.default.createElement(material_1.Typography, { key: JSON.stringify(l) }, (0, util_1.stringify)(l))))),
+            react_1.default.createElement(material_1.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_1.default.createElement(material_1.Typography, { key: JSON.stringify(l) }, (0, util_1.stringify)(l))))))) : null,
+        react_1.default.createElement("div", { ref: rubberbandRef, className: classes.rubberband, style: { left, width } },
+            react_1.default.createElement(material_1.Typography, { variant: "h6", className: classes.rubberbandText }, numOfBpSelected.map((n, i) => (react_1.default.createElement(material_1.Typography, { key: `${n}_${i}` }, `${n.toLocaleString('en-US')}bp`))))),
+        react_1.default.createElement("div", { "data-testid": "rubberband_controls", className: classes.rubberbandControl, role: "presentation", ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove }, ControlComponent),
+        anchorPosition ? (react_1.default.createElement(ui_1.Menu, { anchorReference: "anchorPosition", anchorPosition: {
+                left: anchorPosition.clientX,
+                top: anchorPosition.clientY,
+            }, onMenuItemClick: handleMenuItemClick, open: open, onClose: handleClose, menuItems: model.rubberBandMenuItems() })) : null));
+}
+exports.default = (0, mobx_react_1.observer)(Rubberband);
+//# sourceMappingURL=Rubberband.js.map

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

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

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

package/dist/LinearComparativeView/index.js

@@ -0,0 +1,42 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = require("react");
+const ViewType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/ViewType"));
+const model_1 = __importDefault(require("./model"));
+exports.default = (pluginManager) => {
+    pluginManager.addViewType(() => {
+        return new ViewType_1.default({
+            name: 'LinearComparativeView',
+            displayName: 'Linear comparative view',
+            stateModel: (0, model_1.default)(pluginManager),
+            ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/LinearComparativeView')))),
+        });
+    });
+};
+//# sourceMappingURL=index.js.map

package/dist/LinearComparativeView/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearComparativeView/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,iCAA4B;AAE5B,4FAAmE;AACnE,oDAAkC;AAElC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,WAAW,CAAC,GAAG,EAAE;QAC7B,OAAO,IAAI,kBAAQ,CAAC;YAClB,IAAI,EAAE,uBAAuB;YAC7B,WAAW,EAAE,yBAAyB;YACtC,UAAU,EAAE,IAAA,eAAY,EAAC,aAAa,CAAC;YACvC,cAAc,EAAE,IAAA,YAAI,EAAC,GAAG,EAAE,mDAAQ,oCAAoC,GAAC,CAAC;SACzE,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}