@jbrowse/plugin-linear-genome-view 2.2.1 → 2.3.0

package/dist/LinearGenomeView/components/LinearGenomeViewSvg.js.map

@@ -1 +1 @@
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package/{esm/LinearGenomeView/components/OverviewRubberBand.d.ts → dist/LinearGenomeView/components/OverviewRubberband.d.ts}

@@ -2,10 +2,10 @@ import React from 'react';
 import { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel';
 import { LinearGenomeViewModel } from '..';
 type LGV = LinearGenomeViewModel;
-declare function OverviewRubberBand({ model, overview, ControlComponent, }: {
+declare function OverviewRubberband({ model, overview, ControlComponent, }: {
     model: LGV;
     overview: Base1DViewModel;
     ControlComponent?: React.ReactElement;
 }): JSX.Element;
-declare const _default: typeof OverviewRubberBand;
+declare const _default: typeof OverviewRubberband;
 export default _default;

package/dist/LinearGenomeView/components/{OverviewRubberBand.js → OverviewRubberband.js}

@@ -22,51 +22,30 @@ var __importStar = (this && this.__importStar) || function (mod) {
     __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 = __importStar(require("react"));
 const material_1 = require("@mui/material");
 const mui_1 = require("tss-react/mui");
 const util_1 = require("@jbrowse/core/util");
 const mobx_react_1 = require("mobx-react");
-const __1 = require("..");
-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,
-        },
-    };
+const RubberbandSpan_1 = __importDefault(require("./RubberbandSpan"));
+const util_2 = require("./util");
+const useStyles = (0, mui_1.makeStyles)()({
+    rubberbandControl: {
+        cursor: 'crosshair',
+        width: '100%',
+        minHeight: 8,
+    },
+    guide: {
+        pointerEvents: 'none',
+        height: '100%',
+        width: 1,
+        position: 'absolute',
+        zIndex: 10,
+    },
 });
 const HoverTooltip = (0, mobx_react_1.observer)(({ model, open, guideX, overview, }) => {
     var _a;
@@ -83,21 +62,19 @@ const HoverTooltip = (0, mobx_react_1.observer)(({ model, open, guideX, overview
                 left: guideX,
             } })));
 });
-function OverviewRubberBand({ model, overview, ControlComponent = react_1.default.createElement("div", null), }) {
+function OverviewRubberband({ model, overview, ControlComponent = react_1.default.createElement("div", null), }) {
     const { cytobandOffset } = model;
     const [startX, setStartX] = (0, react_1.useState)();
     const [currentX, setCurrentX] = (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;
     (0, react_1.useEffect)(() => {
         function globalMouseMove(event) {
             const ref = controlsRef.current;
             if (ref && mouseDragging) {
-                const relativeX = event.clientX - ref.getBoundingClientRect().left;
-                setCurrentX(relativeX);
+                setCurrentX((0, util_2.getRelativeX)(event, ref));
             }
         }
         function globalMouseUp() {
@@ -147,14 +124,10 @@ function OverviewRubberBand({ model, overview, ControlComponent = react_1.defaul
     function mouseDown(event) {
         event.preventDefault();
         event.stopPropagation();
-        if (controlsRef.current) {
-            setStartX(event.clientX - controlsRef.current.getBoundingClientRect().left);
-        }
+        setStartX((0, util_2.getRelativeX)(event, controlsRef.current));
     }
     function mouseMove(event) {
-        if (controlsRef.current) {
-            setGuideX(event.clientX - controlsRef.current.getBoundingClientRect().left);
-        }
+        setGuideX((0, util_2.getRelativeX)(event, controlsRef.current));
     }
     function mouseOut() {
         setGuideX(undefined);
@@ -162,7 +135,7 @@ function OverviewRubberBand({ model, overview, ControlComponent = react_1.defaul
     if (startX === undefined) {
         return (react_1.default.createElement("div", { style: { position: 'relative' } },
             guideX !== undefined ? (react_1.default.createElement(HoverTooltip, { model: model, open: !mouseDragging, overview: overview, guideX: guideX })) : null,
-            react_1.default.createElement("div", { className: classes.rubberBandControl, role: "presentation", ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove }, ControlComponent)));
+            react_1.default.createElement("div", { className: classes.rubberbandControl, role: "presentation", ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove }, ControlComponent)));
     }
     let left = startX || 0;
     let width = 0;
@@ -182,33 +155,8 @@ function OverviewRubberBand({ model, overview, ControlComponent = react_1.defaul
         }
     }
     return (react_1.default.createElement("div", { style: { position: 'relative' } },
-        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 },
-                react_1.default.createElement(material_1.Typography, null, leftBpOffset ? (0, util_1.stringify)(leftBpOffset) : '')),
-            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 },
-                react_1.default.createElement(material_1.Typography, null, rightBpOffset ? (0, util_1.stringify)(rightBpOffset) : '')))) : null,
-        react_1.default.createElement("div", { ref: rubberBandRef, className: classes.rubberBand, style: {
-                left,
-                width: Math.abs(width),
-                height: __1.HEADER_OVERVIEW_HEIGHT,
-            } }),
-        react_1.default.createElement("div", { "data-testid": "rubberBand_controls", className: classes.rubberBandControl, role: "presentation", ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove }, ControlComponent)));
+        leftBpOffset && rightBpOffset ? (react_1.default.createElement(RubberbandSpan_1.default, { leftBpOffset: leftBpOffset, rightBpOffset: rightBpOffset, width: width, left: left })) : null,
+        react_1.default.createElement("div", { "data-testid": "rubberband_controls", className: classes.rubberbandControl, role: "presentation", ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove }, ControlComponent)));
 }
-exports.default = (0, mobx_react_1.observer)(OverviewRubberBand);
-//# sourceMappingURL=OverviewRubberBand.js.map
+exports.default = (0, mobx_react_1.observer)(OverviewRubberband);
+//# sourceMappingURL=OverviewRubberband.js.map

package/dist/LinearGenomeView/components/OverviewRubberband.js.map

@@ -0,0 +1 @@
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package/dist/LinearGenomeView/components/{OverviewScaleBar.d.ts → OverviewScalebar.d.ts}

@@ -122,10 +122,10 @@ declare const Cytobands: ({ overview, block, assembly, }: {
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
     block: ContentBlock;
 }) => JSX.Element;
-declare function OverviewScaleBar({ model, children, }: {
+declare function OverviewScalebar({ model, children, }: {
     model: LGV;
     children: React.ReactNode;
 }): JSX.Element;
-declare const _default: typeof OverviewScaleBar;
+declare const _default: typeof OverviewScalebar;
 export default _default;
 export { Cytobands, Polygon };

package/dist/LinearGenomeView/components/{OverviewScaleBar.js → OverviewScalebar.js}

@@ -8,49 +8,50 @@ const react_1 = __importDefault(require("react"));
 const material_1 = require("@mui/material");
 const mui_1 = require("tss-react/mui");
 const mobx_react_1 = require("mobx-react");
+// core
 const Base1DViewModel_1 = __importDefault(require("@jbrowse/core/util/Base1DViewModel"));
 const util_1 = require("@jbrowse/core/util");
 const blockTypes_1 = require("@jbrowse/core/util/blockTypes");
 // locals
 const __1 = require("..");
 const util_2 = require("../util");
-const OverviewRubberBand_1 = __importDefault(require("./OverviewRubberBand"));
+const OverviewRubberband_1 = __importDefault(require("./OverviewRubberband"));
 const wholeSeqSpacer = 2;
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    scaleBar: {
+    scalebar: {
         height: __1.HEADER_OVERVIEW_HEIGHT,
     },
-    scaleBarBorder: {
+    scalebarBorder: {
         border: '1px solid',
     },
-    scaleBarContig: {
+    scalebarContig: {
         backgroundColor: theme.palette.background.default,
         position: 'absolute',
         top: 0,
         height: __1.HEADER_OVERVIEW_HEIGHT,
     },
-    scaleBarContigForward: {
+    scalebarContigForward: {
         backgroundImage: `url("data:image/svg+xml,%3Csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 15 9'%3E%3Cpath d='M-.1 0L6 4.5L-.1 9' fill='none' stroke='%23ddd'/%3E%3C/svg%3E")`,
         backgroundRepeat: 'repeat',
     },
-    scaleBarContigReverse: {
+    scalebarContigReverse: {
         backgroundImage: `url("data:image/svg+xml,%3Csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 15 9'%3E%3Cpath d='M6 0L0 4.5L6 9' fill='none' stroke='%23ddd'/%3E%3C/svg%3E")`,
         backgroundRepeat: 'repeat',
     },
-    scaleBarRefName: {
+    scalebarRefName: {
         position: 'absolute',
         fontWeight: 'bold',
         pointerEvents: 'none',
         zIndex: 100,
     },
-    scaleBarLabel: {
+    scalebarLabel: {
         height: __1.HEADER_OVERVIEW_HEIGHT,
         position: 'absolute',
         display: 'flex',
         justifyContent: 'center',
         pointerEvents: 'none',
     },
-    scaleBarVisibleRegion: {
+    scalebarVisibleRegion: {
         position: 'absolute',
         height: __1.HEADER_OVERVIEW_HEIGHT,
         pointerEvents: 'none',
@@ -210,18 +211,18 @@ const OverviewBox = (0, mobx_react_1.observer)(({ scale, model, block, overview,
         react_1.default.createElement(material_1.Typography, { style: {
                 left: block.offsetPx + 3,
                 color: canDisplayCytobands ? 'black' : refNameColor,
-            }, className: classes.scaleBarRefName }, refName),
-        react_1.default.createElement("div", { className: cx(classes.scaleBarContig, canDisplayCytobands
+            }, className: classes.scalebarRefName }, refName),
+        react_1.default.createElement("div", { className: cx(classes.scalebarContig, canDisplayCytobands
                 ? undefined
                 : reversed
-                    ? classes.scaleBarContigReverse
-                    : classes.scaleBarContigForward, !canDisplayCytobands ? classes.scaleBarBorder : undefined), style: {
+                    ? classes.scalebarContigReverse
+                    : classes.scalebarContigForward, !canDisplayCytobands ? classes.scalebarBorder : undefined), style: {
                 left: block.offsetPx + cytobandOffset,
                 width: block.widthPx,
                 borderColor: refNameColor,
             } },
             !canDisplayCytobands
-                ? tickLabels.map((tickLabel, labelIdx) => (react_1.default.createElement(material_1.Typography, { key: `${JSON.stringify(block)}-${tickLabel}-${labelIdx}`, className: classes.scaleBarLabel, variant: "body2", style: {
+                ? tickLabels.map((tickLabel, labelIdx) => (react_1.default.createElement(material_1.Typography, { key: `${JSON.stringify(block)}-${tickLabel}-${labelIdx}`, className: classes.scalebarLabel, variant: "body2", style: {
                         left: ((labelIdx + 1) * majorPitch) / scale,
                         pointerEvents: 'none',
                         color: refNameColor,
@@ -230,14 +231,14 @@ const OverviewBox = (0, mobx_react_1.observer)(({ scale, model, block, overview,
             canDisplayCytobands ? (react_1.default.createElement("svg", { style: { width: '100%' } },
                 react_1.default.createElement(Cytobands, { overview: overview, assembly: assembly, block: block }))) : null)));
 });
-const ScaleBar = (0, mobx_react_1.observer)(({ model, scale, overview, }) => {
+const Scalebar = (0, mobx_react_1.observer)(({ model, scale, overview, }) => {
     const { classes } = useStyles();
     const theme = (0, material_1.useTheme)();
     const { dynamicBlocks, showCytobands, cytobandOffset } = model;
     const visibleRegions = dynamicBlocks.contentBlocks;
     const overviewVisibleRegions = overview.dynamicBlocks;
     const { tertiary, primary } = theme.palette;
-    const scaleBarColor = tertiary ? tertiary.light : primary.light;
+    const scalebarColor = tertiary ? tertiary.light : primary.light;
     if (!visibleRegions.length) {
         return null;
     }
@@ -251,17 +252,17 @@ const ScaleBar = (0, mobx_react_1.observer)(({ model, scale, overview, }) => {
         ...last,
         coord: last.reversed ? last.start : last.end,
     }) || 0;
-    const color = showCytobands ? '#f00' : scaleBarColor;
+    const color = showCytobands ? '#f00' : scalebarColor;
     const transparency = showCytobands ? 0.1 : 0.3;
-    return (react_1.default.createElement("div", { className: classes.scaleBar },
-        react_1.default.createElement("div", { className: classes.scaleBarVisibleRegion, style: {
+    return (react_1.default.createElement("div", { className: classes.scalebar },
+        react_1.default.createElement("div", { className: classes.scalebarVisibleRegion, style: {
                 width: lastOverviewPx - firstOverviewPx,
                 left: firstOverviewPx + cytobandOffset,
                 background: (0, material_1.alpha)(color, transparency),
                 borderColor: color,
             } }),
         overviewVisibleRegions.map((block, idx) => {
-            return !(block instanceof blockTypes_1.ContentBlock) ? (react_1.default.createElement("div", { key: `${JSON.stringify(block)}-${idx}`, className: classes.scaleBarContig, style: {
+            return !(block instanceof blockTypes_1.ContentBlock) ? (react_1.default.createElement("div", { key: `${JSON.stringify(block)}-${idx}`, className: classes.scalebarContig, style: {
                     width: block.widthPx,
                     left: block.offsetPx,
                     backgroundColor: '#999',
@@ -269,7 +270,7 @@ const ScaleBar = (0, mobx_react_1.observer)(({ model, scale, overview, }) => {
                 } })) : (react_1.default.createElement(OverviewBox, { scale: scale, block: block, model: model, overview: overview, key: `${JSON.stringify(block)}-${idx}` }));
         })));
 });
-function OverviewScaleBar({ model, children, }) {
+function OverviewScalebar({ model, children, }) {
     const { classes } = useStyles();
     const { totalBp, width, cytobandOffset, displayedRegions } = model;
     const overview = Base1DViewModel_1.default.create({
@@ -282,11 +283,11 @@ function OverviewScaleBar({ model, children, }) {
     overview.showAllRegions();
     const scale = totalBp / (modWidth - (displayedRegions.length - 1) * wholeSeqSpacer);
     return (react_1.default.createElement("div", null,
-        react_1.default.createElement(OverviewRubberBand_1.default, { model: model, overview: overview, ControlComponent: react_1.default.createElement(ScaleBar, { model: model, overview: overview, scale: scale }) }),
+        react_1.default.createElement(OverviewRubberband_1.default, { model: model, overview: overview, ControlComponent: react_1.default.createElement(Scalebar, { model: model, overview: overview, scale: scale }) }),
         react_1.default.createElement("div", { className: classes.overview },
             react_1.default.createElement("svg", { height: __1.HEADER_BAR_HEIGHT, className: classes.overviewSvg },
                 react_1.default.createElement(Polygon, { model: model, overview: overview })),
             children)));
 }
-exports.default = (0, mobx_react_1.observer)(OverviewScaleBar);
-//# sourceMappingURL=OverviewScaleBar.js.map
+exports.default = (0, mobx_react_1.observer)(OverviewScalebar);
+//# sourceMappingURL=OverviewScalebar.js.map

package/dist/LinearGenomeView/components/OverviewScalebar.js.map

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

@@ -117,7 +117,7 @@ function RefNameAutocomplete({ model, onSelect, assemblyName, style, fetchResult
     }, [assemblyName, fetchResults, debouncedSearch, session, model]);
     const inputBoxVal = coarseVisibleLocStrings || value || '';
     // heuristic, text width + icon width
-    // + 45 accomodates help icon and search icon
+    // + 45 accommodates help icon and search icon
     const width = Math.min(Math.max((0, util_1.measureText)(inputBoxVal, 16) + 45, minWidth), 550);
     // notes on implementation:
     // The selectOnFocus setting helps highlight the field when clicked

package/dist/LinearGenomeView/components/RefNameAutocomplete.js.map

@@ -1 +1 @@
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package/dist/LinearGenomeView/components/{RubberBand.d.ts → Rubberband.d.ts}

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

package/dist/LinearGenomeView/components/Rubberband.js

@@ -0,0 +1,57 @@
+"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 = __importStar(require("react"));
+const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
+const ui_1 = require("@jbrowse/core/ui");
+// locals
+const VerticalGuide_1 = __importDefault(require("./VerticalGuide"));
+const RubberbandSpan_1 = __importDefault(require("./RubberbandSpan"));
+const hooks_1 = require("./hooks");
+const useStyles = (0, mui_1.makeStyles)()({
+    rubberbandControl: {
+        cursor: 'crosshair',
+        width: '100%',
+        minHeight: 8,
+    },
+});
+function Rubberband({ model, ControlComponent = react_1.default.createElement("div", null), }) {
+    const ref = (0, react_1.useRef)(null);
+    const { classes } = useStyles();
+    const { guideX, rubberbandOn, leftBpOffset, rightBpOffset, numOfBpSelected, width, left, anchorPosition, handleMenuItemClick, open, handleClose, mouseMove, mouseDown, mouseOut, } = (0, hooks_1.useRangeSelect)(ref, model);
+    return (react_1.default.createElement(react_1.default.Fragment, null,
+        guideX !== undefined ? (react_1.default.createElement(VerticalGuide_1.default, { model: model, coordX: guideX })) : rubberbandOn ? (react_1.default.createElement(RubberbandSpan_1.default, { leftBpOffset: leftBpOffset, rightBpOffset: rightBpOffset, numOfBpSelected: numOfBpSelected, width: width, left: left })) : null,
+        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,
+        react_1.default.createElement("div", { "data-testid": "rubberband_controls", className: classes.rubberbandControl, ref: ref, onMouseDown: mouseDown, onMouseMove: mouseMove, onMouseOut: mouseOut }, ControlComponent)));
+}
+exports.default = (0, mobx_react_1.observer)(Rubberband);
+//# sourceMappingURL=Rubberband.js.map

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

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

@@ -0,0 +1,14 @@
+/// <reference types="react" />
+interface Offset {
+    coord: number;
+    refName?: string;
+    oob?: boolean;
+}
+declare function RubberbandSpan({ leftBpOffset, rightBpOffset, numOfBpSelected, left, width, }: {
+    leftBpOffset: Offset;
+    rightBpOffset: Offset;
+    numOfBpSelected?: number;
+    left: number;
+    width: number;
+}): JSX.Element;
+export default RubberbandSpan;