@jbrowse/plugin-linear-genome-view 1.7.11 → 2.1.0

package/dist/LinearGenomeView/components/OverviewRubberBand.js

@@ -1,310 +1,246 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _typeof = require("@babel/runtime/helpers/typeof");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
-
-var _react = _interopRequireWildcard(require("react"));
-
-var _core = require("@material-ui/core");
-
-var _util = require("@jbrowse/core/util");
-
-var _mobxReact = require("mobx-react");
-
-var _propTypes = _interopRequireDefault(require("prop-types"));
-
-var _ = require("..");
-
-function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
-
-function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
-
-var useStyles = (0, _core.makeStyles)(function (theme) {
-  var _theme$palette = theme.palette,
-      tertiary = _theme$palette.tertiary,
-      primary = _theme$palette.primary;
-  var background = tertiary ? (0, _core.alpha)(tertiary.main, 0.7) : (0, _core.alpha)(primary.main, 0.7);
-  return {
-    rubberBand: {
-      height: '100%',
-      background: background,
-      position: 'absolute',
-      zIndex: 10,
-      textAlign: 'center',
-      overflow: 'hidden'
-    },
-    rubberBandControl: {
-      cursor: 'crosshair',
-      width: '100%',
-      minHeight: 8
-    },
-    rubberBandText: {
-      color: tertiary ? tertiary.contrastText : primary.contrastText
-    },
-    popover: {
-      mouseEvents: 'none',
-      cursor: 'crosshair'
-    },
-    paper: {
-      paddingLeft: theme.spacing(1),
-      paddingRight: theme.spacing(1)
-    },
-    guide: {
-      pointerEvents: 'none',
-      height: '100%',
-      width: 1,
-      position: 'absolute',
-      zIndex: 10
-    }
-  };
-});
-var HoverTooltip = (0, _mobxReact.observer)(function (_ref) {
-  var _assembly$cytobands;
-
-  var model = _ref.model,
-      open = _ref.open,
-      guideX = _ref.guideX,
-      overview = _ref.overview;
-  var classes = useStyles();
-  var cytobandOffset = model.cytobandOffset;
-
-  var _getSession = (0, _util.getSession)(model),
-      assemblyManager = _getSession.assemblyManager;
-
-  var px = overview.pxToBp(guideX - cytobandOffset);
-  var assembly = assemblyManager.get(px.assemblyName);
-  var cytoband = assembly === null || assembly === void 0 ? void 0 : (_assembly$cytobands = assembly.cytobands) === null || _assembly$cytobands === void 0 ? void 0 : _assembly$cytobands.find(function (f) {
-    return px.coord > f.get('start') && px.coord < f.get('end') && px.refName === assembly.getCanonicalRefName(f.get('refName'));
-  });
-  return /*#__PURE__*/_react.default.createElement(_core.Tooltip, {
-    open: open,
-    placement: "top",
-    title: [(0, _util.stringify)(px), cytoband === null || cytoband === void 0 ? void 0 : cytoband.get('name')].join(' '),
-    arrow: true
-  }, /*#__PURE__*/_react.default.createElement("div", {
-    className: classes.guide,
-    style: {
-      left: guideX
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
     }
-  }));
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
 });
-
-function OverviewRubberBand(_ref2) {
-  var model = _ref2.model,
-      overview = _ref2.overview,
-      _ref2$ControlComponen = _ref2.ControlComponent,
-      ControlComponent = _ref2$ControlComponen === void 0 ? /*#__PURE__*/_react.default.createElement("div", null) : _ref2$ControlComponen;
-  var cytobandOffset = model.cytobandOffset;
-
-  var _useState = (0, _react.useState)(),
-      _useState2 = (0, _slicedToArray2.default)(_useState, 2),
-      startX = _useState2[0],
-      setStartX = _useState2[1];
-
-  var _useState3 = (0, _react.useState)(),
-      _useState4 = (0, _slicedToArray2.default)(_useState3, 2),
-      currentX = _useState4[0],
-      setCurrentX = _useState4[1];
-
-  var _useState5 = (0, _react.useState)(),
-      _useState6 = (0, _slicedToArray2.default)(_useState5, 2),
-      guideX = _useState6[0],
-      setGuideX = _useState6[1];
-
-  var controlsRef = (0, _react.useRef)(null);
-  var rubberBandRef = (0, _react.useRef)(null);
-  var classes = useStyles();
-  var mouseDragging = startX !== undefined;
-  (0, _react.useEffect)(function () {
-    function globalMouseMove(event) {
-      var ref = controlsRef.current;
-
-      if (ref && mouseDragging) {
-        var relativeX = event.clientX - ref.getBoundingClientRect().left;
-        setCurrentX(relativeX);
-      }
+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 __read = (this && this.__read) || function (o, n) {
+    var m = typeof Symbol === "function" && o[Symbol.iterator];
+    if (!m) return o;
+    var i = m.call(o), r, ar = [], e;
+    try {
+        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
     }
-
-    function globalMouseUp() {
-      if (controlsRef.current && startX !== undefined && currentX !== undefined) {
-        if (Math.abs(currentX - startX) > 3) {
-          model.zoomToDisplayedRegions(overview.pxToBp(startX - cytobandOffset), overview.pxToBp(currentX - cytobandOffset));
+    catch (error) { e = { error: error }; }
+    finally {
+        try {
+            if (r && !r.done && (m = i["return"])) m.call(i);
         }
-      }
-      /* handling clicking and centering at a specific Bp */
-
-
-      if (controlsRef.current && startX !== undefined && currentX === undefined) {
-        var clickedAt = overview.pxToBp(startX - cytobandOffset);
-        model.centerAt(Math.round(clickedAt.coord), clickedAt.refName, clickedAt.index);
-      }
-
-      setStartX(undefined);
-      setCurrentX(undefined);
-
-      if (startX !== undefined) {
-        setGuideX(undefined);
-      }
+        finally { if (e) throw e.error; }
     }
-
-    function globalKeyDown(event) {
-      if (event.key === 'Escape') {
-        setStartX(undefined);
-        setCurrentX(undefined);
-      }
-    }
-
-    if (mouseDragging) {
-      window.addEventListener('mousemove', globalMouseMove, true);
-      window.addEventListener('mouseup', globalMouseUp, true);
-      window.addEventListener('keydown', globalKeyDown, true);
-      return function () {
-        window.removeEventListener('mousemove', globalMouseMove, true);
-        window.removeEventListener('mouseup', globalMouseUp, true);
-        window.removeEventListener('keydown', globalKeyDown, true);
-      };
+    return ar;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var react_1 = __importStar(require("react"));
+var material_1 = require("@mui/material");
+var mui_1 = require("tss-react/mui");
+var util_1 = require("@jbrowse/core/util");
+var mobx_react_1 = require("mobx-react");
+var prop_types_1 = __importDefault(require("prop-types"));
+var __1 = require("..");
+var useStyles = (0, mui_1.makeStyles)()(function (theme) {
+    // @ts-ignore
+    var _a = theme.palette, tertiary = _a.tertiary, primary = _a.primary;
+    var background = tertiary
+        ? (0, material_1.alpha)(tertiary.main, 0.7)
+        : (0, material_1.alpha)(primary.main, 0.7);
+    return {
+        rubberBand: {
+            height: '100%',
+            background: 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,
+        },
+    };
+});
+var HoverTooltip = (0, mobx_react_1.observer)(function (_a) {
+    var _b;
+    var model = _a.model, open = _a.open, guideX = _a.guideX, overview = _a.overview;
+    var classes = useStyles().classes;
+    var cytobandOffset = model.cytobandOffset;
+    var assemblyManager = (0, util_1.getSession)(model).assemblyManager;
+    var px = overview.pxToBp(guideX - cytobandOffset);
+    var assembly = assemblyManager.get(px.assemblyName);
+    var cytoband = (_b = assembly === null || assembly === void 0 ? void 0 : assembly.cytobands) === null || _b === void 0 ? void 0 : _b.find(function (f) {
+        return px.coord > f.get('start') &&
+            px.coord < f.get('end') &&
+            px.refName === assembly.getCanonicalRefName(f.get('refName'));
+    });
+    return (react_1.default.createElement(material_1.Tooltip, { open: open, placement: "top", title: [(0, util_1.stringify)(px), cytoband === null || cytoband === void 0 ? void 0 : cytoband.get('name')].join(' '), arrow: true },
+        react_1.default.createElement("div", { className: classes.guide, style: {
+                left: guideX,
+            } })));
+});
+function OverviewRubberBand(_a) {
+    var _b;
+    var model = _a.model, overview = _a.overview, _c = _a.ControlComponent, ControlComponent = _c === void 0 ? react_1.default.createElement("div", null) : _c;
+    var cytobandOffset = model.cytobandOffset;
+    var _d = __read((0, react_1.useState)(), 2), startX = _d[0], setStartX = _d[1];
+    var _e = __read((0, react_1.useState)(), 2), currentX = _e[0], setCurrentX = _e[1];
+    var _f = __read((0, react_1.useState)(), 2), guideX = _f[0], setGuideX = _f[1];
+    var controlsRef = (0, react_1.useRef)(null);
+    var rubberBandRef = (0, react_1.useRef)(null);
+    var classes = useStyles().classes;
+    var mouseDragging = startX !== undefined;
+    (0, react_1.useEffect)(function () {
+        function globalMouseMove(event) {
+            var ref = controlsRef.current;
+            if (ref && mouseDragging) {
+                var relativeX = event.clientX - ref.getBoundingClientRect().left;
+                setCurrentX(relativeX);
+            }
+        }
+        function globalMouseUp() {
+            // click and drag
+            if (startX !== undefined && currentX !== undefined) {
+                if (Math.abs(currentX - startX) > 3) {
+                    model.moveTo(overview.pxToBp(startX - cytobandOffset), overview.pxToBp(currentX - cytobandOffset));
+                }
+            }
+            // just a click
+            if (startX !== undefined && currentX === undefined) {
+                var click = overview.pxToBp(startX - cytobandOffset);
+                if (!click.refName) {
+                    (0, util_1.getSession)(model).notify('unknown position clicked');
+                    console.error('unknown position clicked', click);
+                }
+                else {
+                    model.centerAt(Math.round(click.coord), click.refName, click.index);
+                }
+            }
+            setStartX(undefined);
+            setCurrentX(undefined);
+            if (startX !== undefined) {
+                setGuideX(undefined);
+            }
+        }
+        function globalKeyDown(event) {
+            if (event.key === 'Escape') {
+                setStartX(undefined);
+                setCurrentX(undefined);
+            }
+        }
+        if (mouseDragging) {
+            window.addEventListener('mousemove', globalMouseMove, true);
+            window.addEventListener('mouseup', globalMouseUp, true);
+            window.addEventListener('keydown', globalKeyDown, true);
+            return function () {
+                window.removeEventListener('mousemove', globalMouseMove, true);
+                window.removeEventListener('mouseup', globalMouseUp, true);
+                window.removeEventListener('keydown', globalKeyDown, true);
+            };
+        }
+        return function () { };
+    }, [mouseDragging, currentX, startX, model, overview, cytobandOffset]);
+    function mouseDown(event) {
+        event.preventDefault();
+        event.stopPropagation();
+        if (controlsRef.current) {
+            setStartX(event.clientX - controlsRef.current.getBoundingClientRect().left);
+        }
     }
-
-    return function () {};
-  }, [mouseDragging, currentX, startX, model, overview, cytobandOffset]);
-
-  function mouseDown(event) {
-    event.preventDefault();
-    event.stopPropagation();
-
-    if (controlsRef.current) {
-      setStartX(event.clientX - controlsRef.current.getBoundingClientRect().left);
+    function mouseMove(event) {
+        if (controlsRef.current) {
+            setGuideX(event.clientX - controlsRef.current.getBoundingClientRect().left);
+        }
     }
-  }
-
-  function mouseMove(event) {
-    if (controlsRef.current) {
-      setGuideX(event.clientX - controlsRef.current.getBoundingClientRect().left);
+    function mouseOut() {
+        setGuideX(undefined);
     }
-  }
-
-  function mouseOut() {
-    setGuideX(undefined);
-  }
-
-  if (startX === undefined) {
-    return /*#__PURE__*/_react.default.createElement("div", {
-      style: {
-        position: 'relative'
-      }
-    }, guideX !== undefined ? /*#__PURE__*/_react.default.createElement(HoverTooltip, {
-      model: model,
-      open: !mouseDragging,
-      overview: overview,
-      guideX: guideX
-    }) : null, /*#__PURE__*/_react.default.createElement("div", {
-      className: classes.rubberBandControl,
-      role: "presentation",
-      ref: controlsRef,
-      onMouseDown: mouseDown,
-      onMouseOut: mouseOut,
-      onMouseMove: mouseMove
-    }, ControlComponent));
-  }
-
-  var left = startX || 0;
-  var width = 0;
-
-  if (startX !== undefined && currentX !== undefined) {
-    left = currentX < startX ? currentX : startX;
-    width = currentX - startX;
-  } // calculate the start and end bp of drag
-
-
-  var leftBpOffset;
-  var rightBpOffset;
-
-  if (startX) {
-    leftBpOffset = overview.pxToBp(startX - cytobandOffset);
-    rightBpOffset = overview.pxToBp(startX + width - cytobandOffset);
-
-    if (currentX && currentX < startX) {
-      ;
-      var _ref3 = [rightBpOffset, leftBpOffset];
-      leftBpOffset = _ref3[0];
-      rightBpOffset = _ref3[1];
+    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)));
     }
-  }
-
-  return /*#__PURE__*/_react.default.createElement("div", {
-    style: {
-      position: 'relative'
+    var left = startX || 0;
+    var width = 0;
+    if (startX !== undefined && currentX !== undefined) {
+        left = currentX < startX ? currentX : startX;
+        width = currentX - startX;
     }
-  }, rubberBandRef.current ? /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, /*#__PURE__*/_react.default.createElement(_core.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
-  }, /*#__PURE__*/_react.default.createElement(_core.Typography, null, leftBpOffset ? (0, _util.stringify)(leftBpOffset) : '')), /*#__PURE__*/_react.default.createElement(_core.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
-  }, /*#__PURE__*/_react.default.createElement(_core.Typography, null, rightBpOffset ? (0, _util.stringify)(rightBpOffset) : ''))) : null, /*#__PURE__*/_react.default.createElement("div", {
-    ref: rubberBandRef,
-    className: classes.rubberBand,
-    style: {
-      left: left,
-      width: Math.abs(width),
-      height: _.HEADER_OVERVIEW_HEIGHT
+    // calculate the start and end bp of drag
+    var leftBpOffset;
+    var rightBpOffset;
+    if (startX) {
+        leftBpOffset = overview.pxToBp(startX - cytobandOffset);
+        rightBpOffset = overview.pxToBp(startX + width - cytobandOffset);
+        if (currentX && currentX < startX) {
+            ;
+            _b = __read([rightBpOffset, leftBpOffset], 2), leftBpOffset = _b[0], rightBpOffset = _b[1];
+        }
     }
-  }), /*#__PURE__*/_react.default.createElement("div", {
-    "data-testid": "rubberBand_controls",
-    className: classes.rubberBandControl,
-    role: "presentation",
-    ref: controlsRef,
-    onMouseDown: mouseDown,
-    onMouseOut: mouseOut,
-    onMouseMove: mouseMove
-  }, ControlComponent));
+    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: 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)));
 }
-
 OverviewRubberBand.propTypes = {
-  model: _mobxReact.PropTypes.objectOrObservableObject.isRequired,
-  overview: _mobxReact.PropTypes.objectOrObservableObject.isRequired,
-  ControlComponent: _propTypes.default.node
+    model: mobx_react_1.PropTypes.objectOrObservableObject.isRequired,
+    overview: mobx_react_1.PropTypes.objectOrObservableObject.isRequired,
+    ControlComponent: prop_types_1.default.node,
 };
 OverviewRubberBand.defaultProps = {
-  ControlComponent: /*#__PURE__*/_react.default.createElement("div", null)
+    ControlComponent: react_1.default.createElement("div", null),
 };
-
-var _default = (0, _mobxReact.observer)(OverviewRubberBand);
-
-exports.default = _default;
+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

@@ -12,9 +12,9 @@ declare const Polygon: ({ model, overview, useOffset, }: {
 declare type LGV = LinearGenomeViewModel;
 declare const Cytobands: ({ overview, block, assembly, }: {
     overview: Base1DViewModel;
-    assembly?: (import("mobx-state-tree").ModelInstanceTypeProps<{
-        configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    }> & {
+    assembly?: ({
+        configuration: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         error: Error | undefined;
         regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
         refNameAliases: {