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

package/src/LinearGenomeView/{index.tsx → model.ts}

@@ -22,7 +22,7 @@ import { BlockSet, BaseBlock } from '@jbrowse/core/util/blockTypes'
 import calculateDynamicBlocks from '@jbrowse/core/util/calculateDynamicBlocks'
 import calculateStaticBlocks from '@jbrowse/core/util/calculateStaticBlocks'
 import { getParentRenderProps } from '@jbrowse/core/util/tracks'
-import { transaction, autorun } from 'mobx'
+import { when, transaction, autorun } from 'mobx'
 import {
   addDisposer,
   cast,
@@ -902,7 +902,7 @@ export function stateModelFactory(pluginManager: PluginManager) {
        * this "clears the view" and makes the view return to the import form
        */
       clearView() {
-        self.displayedRegions.clear()
+        this.setDisplayedRegions([])
         self.tracks.clear()
         // it is necessary to run these after setting displayed regions empty
         // or else model.offsetPx gets set to Infinity and breaks
@@ -1267,6 +1267,7 @@ export function stateModelFactory(pluginManager: PluginManager) {
         const { assemblyNames } = self
         const { assemblyManager } = getSession(self)
         const { isValidRefName } = assemblyManager
+        await when(() => self.volatileWidth !== undefined)
         const assemblyName = optAssemblyName || assemblyNames[0]
         let parsedLocStrings
         const inputs = locString
@@ -1281,8 +1282,8 @@ export function stateModelFactory(pluginManager: PluginManager) {
         // first try interpreting as a whitespace-separated sequence of
         // multiple locstrings
         try {
-          parsedLocStrings = inputs.map(l =>
-            parseLocString(l, ref => isValidRefName(ref, assemblyName)),
+          parsedLocStrings = inputs.map(loc =>
+            parseLocString(loc, ref => isValidRefName(ref, assemblyName)),
           )
         } catch (e) {
           // if this fails, try interpreting as a whitespace-separated refname,
@@ -1584,6 +1585,8 @@ export {
   ZoomControls,
   LinearGenomeView,
 }
+
 export type LinearGenomeViewStateModel = ReturnType<typeof stateModelFactory>
 export type LinearGenomeViewModel = Instance<LinearGenomeViewStateModel>
+
 export { default as ReactComponent } from './components/LinearGenomeView'

package/src/index.ts

@@ -1,42 +1,38 @@
-import { lazy } from 'react'
-import { when } from 'mobx'
-
-import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
-import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType'
 import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { AbstractSessionModel, isAbstractMenuManager } from '@jbrowse/core/util'
+
+// icons
 import LineStyleIcon from '@mui/icons-material/LineStyle'
+
+// locals
 import {
   BaseLinearDisplay,
   BaseLinearDisplayComponent,
-  baseLinearDisplayConfigSchema,
   BlockModel,
+  BlockMsg,
+  baseLinearDisplayConfigSchema,
 } from './BaseLinearDisplay'
-import {
+import LinearBareDisplayF, {
   configSchemaFactory as linearBareDisplayConfigSchemaFactory,
-  stateModelFactory as LinearBareDisplayStateModelFactory,
 } from './LinearBareDisplay'
-import {
+import LinearGenomeViewF, {
+  renderToSvg,
   LinearGenomeViewModel,
   LinearGenomeViewStateModel,
-  stateModelFactory as linearGenomeViewStateModelFactory,
-  renderToSvg,
   RefNameAutocomplete,
   SearchBox,
   ZoomControls,
   LinearGenomeView,
 } from './LinearGenomeView'
-
-import {
+import LinearBasicDisplayF, {
   configSchema as linearBasicDisplayConfigSchemaFactory,
   modelFactory as linearBasicDisplayModelFactory,
 } from './LinearBasicDisplay'
 
 import FeatureTrackF from './FeatureTrack'
 import BasicTrackF from './BasicTrack'
-
-type LGV = LinearGenomeViewModel
+import LaunchLinearGenomeViewF from './LaunchLinearGenomeView'
 
 export default class LinearGenomeViewPlugin extends Plugin {
   name = 'LinearGenomeViewPlugin'
@@ -53,99 +49,10 @@ export default class LinearGenomeViewPlugin extends Plugin {
   install(pluginManager: PluginManager) {
     FeatureTrackF(pluginManager)
     BasicTrackF(pluginManager)
-    pluginManager.addDisplayType(() => {
-      const configSchema = linearBareDisplayConfigSchemaFactory(pluginManager)
-      return new DisplayType({
-        name: 'LinearBareDisplay',
-        configSchema,
-        stateModel: LinearBareDisplayStateModelFactory(configSchema),
-        trackType: 'BasicTrack',
-        viewType: 'LinearGenomeView',
-        ReactComponent: BaseLinearDisplayComponent,
-      })
-    })
-
-    pluginManager.addDisplayType(() => {
-      const configSchema = linearBasicDisplayConfigSchemaFactory(pluginManager)
-      return new DisplayType({
-        name: 'LinearBasicDisplay',
-        configSchema,
-        stateModel: linearBasicDisplayModelFactory(configSchema),
-        trackType: 'FeatureTrack',
-        viewType: 'LinearGenomeView',
-        ReactComponent: BaseLinearDisplayComponent,
-      })
-    })
-
-    pluginManager.addViewType(
-      () =>
-        new ViewType({
-          name: 'LinearGenomeView',
-          stateModel: linearGenomeViewStateModelFactory(pluginManager),
-          ReactComponent: lazy(
-            () => import('./LinearGenomeView/components/LinearGenomeView'),
-          ),
-        }),
-    )
-
-    pluginManager.addToExtensionPoint(
-      'LaunchView-LinearGenomeView',
-      // @ts-ignore
-      async ({
-        session,
-        assembly,
-        loc,
-        tracks = [],
-      }: {
-        session: AbstractSessionModel
-        assembly?: string
-        loc: string
-        tracks?: string[]
-      }) => {
-        try {
-          const { assemblyManager } = session
-          const view = session.addView('LinearGenomeView', {}) as LGV
-
-          await when(() => !!view.volatileWidth)
-
-          if (!assembly) {
-            throw new Error(
-              'No assembly provided when launching linear genome view',
-            )
-          }
-
-          const asm = await assemblyManager.waitForAssembly(assembly)
-          if (!asm) {
-            throw new Error(
-              `Assembly "${assembly}" not found when launching linear genome view`,
-            )
-          }
-
-          view.navToLocString(loc, assembly)
-
-          const idsNotFound = [] as string[]
-          tracks.forEach(track => {
-            try {
-              view.showTrack(track)
-            } catch (e) {
-              if (`${e}`.match('Could not resolve identifier')) {
-                idsNotFound.push(track)
-              } else {
-                throw e
-              }
-            }
-          })
-          if (idsNotFound.length) {
-            throw new Error(
-              `Could not resolve identifiers: ${idsNotFound.join(',')}`,
-            )
-          }
-        } catch (e) {
-          session.notify(`${e}`, 'error')
-          throw e
-        }
-      },
-    )
+    LinearBasicDisplayF(pluginManager)
+    LinearGenomeViewF(pluginManager)
+    LinearBareDisplayF(pluginManager)
+    LaunchLinearGenomeViewF(pluginManager)
   }
 
   configure(pluginManager: PluginManager) {
@@ -171,6 +78,7 @@ export {
   BaseLinearDisplay,
   RefNameAutocomplete,
   SearchBox,
+  BlockMsg,
 }
 
 export type { LinearGenomeViewModel, LinearGenomeViewStateModel, BlockModel }

package/dist/BaseLinearDisplay/models/TooLargeMessage.js.map

@@ -1 +0,0 @@
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package/dist/BaseLinearDisplay/models/baseLinearDisplayConfigSchema.d.ts

@@ -1 +0,0 @@
-export declare const baseLinearDisplayConfigSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/dist/BaseLinearDisplay/models/baseLinearDisplayConfigSchema.js.map

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

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

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

@@ -1,221 +0,0 @@
-"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 { primary, tertiary } = 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 VerticalGuide = (0, mobx_react_1.observer)(({ model, coordX }) => {
-    const { classes } = useStyles();
-    return (react_1.default.createElement(material_1.Tooltip, { open: true, placement: "top", title: (0, util_1.stringify)(model.pxToBp(coordX)), 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;
-    const { setOffsets, pxToBp } = model;
-    (0, react_1.useEffect)(() => {
-        function computeOffsets(offsetX) {
-            if (startX === undefined) {
-                return;
-            }
-            let leftPx = startX;
-            let rightPx = offsetX;
-            if (rightPx < leftPx) {
-                ;
-                [leftPx, rightPx] = [rightPx, leftPx];
-            }
-            const leftOffset = pxToBp(leftPx);
-            const rightOffset = 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,
-                });
-                const args = computeOffsets(offsetX);
-                if (args) {
-                    const { leftOffset, rightOffset } = args;
-                    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, setOffsets, pxToBp]);
-    (0, react_1.useEffect)(() => {
-        if (!mouseDragging &&
-            currentX !== undefined &&
-            startX !== undefined &&
-            Math.abs(currentX - startX) <= 3) {
-            handleClose();
-        }
-    }, [mouseDragging, currentX, startX, model.bpPerPx]);
-    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.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 leftBpOffset = model.pxToBp(left);
-    const rightBpOffset = model.pxToBp(left + width);
-    const numOfBpSelected = Math.ceil(width * model.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 },
-                react_1.default.createElement(material_1.Typography, null, (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, (0, util_1.stringify)(rightBpOffset))))) : 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.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/LinearGenomeView/components/RubberBand.js.map

@@ -1 +0,0 @@
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package/esm/BaseLinearDisplay/models/TooLargeMessage.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"TooLargeMessage.js","sourceRoot":"","sources":["../../../src/BaseLinearDisplay/models/TooLargeMessage.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,QAAQ,MAAM,wBAAwB,CAAA;AAG7C,SAAS,eAAe,CAAC,EACvB,KAAK,GAQN;IACC,MAAM,EAAE,oBAAoB,EAAE,GAAG,KAAK,CAAA;IACtC,OAAO,CACL,oBAAC,QAAQ,IACP,QAAQ,EAAC,SAAS,EAClB,MAAM,EAAE,GAAG,EAAE;YACX,IAAI,CAAC,KAAK,CAAC,oBAAoB,EAAE;gBAC/B,OAAO,CAAC,KAAK,CAAC,kBAAkB,CAAC,CAAA;aAClC;iBAAM;gBACL,KAAK,CAAC,gBAAgB,CAAC,KAAK,CAAC,oBAAoB,CAAC,CAAA;gBAClD,KAAK,CAAC,MAAM,EAAE,CAAA;aACf;QACH,CAAC,EACD,UAAU,EAAC,YAAY,EACvB,OAAO,EAAE,GAAG,oBAAoB,CAAC,CAAC,CAAC,oBAAoB,GAAG,IAAI,CAAC,CAAC,CAAC,EAAE;2DACd,GACrD,CACH,CAAA;AACH,CAAC;AAED,eAAe,eAAe,CAAA"}

package/esm/BaseLinearDisplay/models/baseLinearDisplayConfigSchema.d.ts

@@ -1 +0,0 @@
-export declare const baseLinearDisplayConfigSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/esm/BaseLinearDisplay/models/baseLinearDisplayConfigSchema.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"baseLinearDisplayConfigSchema.js","sourceRoot":"","sources":["../../../src/BaseLinearDisplay/models/baseLinearDisplayConfigSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;;;;GAKG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,CAAC,MAAM,6BAA6B,GAAG,mBAAmB,CAC9D,mBAAmB,EACnB;IACE;;OAEG;IACH,uBAAuB,EAAE;QACvB,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,qGAAqG;QACvG,YAAY,EAAE,GAAG;KAClB;IACD;;OAEG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,OAAS;QACvB,WAAW,EACT,4FAA4F;KAC/F;CACF,EACD;IACE;;OAEG;IACH,kBAAkB,EAAE,WAAW;CAChC,CACF,CAAA"}

package/esm/LinearGenomeView/components/OverviewRubberBand.js.map

@@ -1 +0,0 @@
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package/esm/LinearGenomeView/components/OverviewScaleBar.js.map

@@ -1 +0,0 @@
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