@jbrowse/plugin-linear-genome-view 2.13.0 → 2.14.0

package/esm/LinearGenomeView/model.js

@@ -2,12 +2,12 @@ import { lazy } from 'react';
 import { getConf } from '@jbrowse/core/configuration';
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models';
 import { ElementId } from '@jbrowse/core/util/types/mst';
-import { assembleLocString, clamp, findLast, getContainingView, getSession, isViewContainer, isSessionModelWithWidgets, isSessionWithAddTracks, localStorageGetItem, localStorageSetItem, measureText, springAnimate, sum, } from '@jbrowse/core/util';
+import { assembleLocString, clamp, findLast, getSession, isSessionModelWithWidgets, isSessionWithAddTracks, localStorageGetItem, localStorageSetItem, measureText, springAnimate, sum, } from '@jbrowse/core/util';
 import calculateDynamicBlocks from '@jbrowse/core/util/calculateDynamicBlocks';
 import calculateStaticBlocks from '@jbrowse/core/util/calculateStaticBlocks';
 import { getParentRenderProps } from '@jbrowse/core/util/tracks';
 import { when, transaction, autorun } from 'mobx';
-import { addDisposer, cast, getSnapshot, getRoot, resolveIdentifier, types, } from 'mobx-state-tree';
+import { addDisposer, cast, getSnapshot, getRoot, resolveIdentifier, types, getParent, } from 'mobx-state-tree';
 import Base1DView from '@jbrowse/core/util/Base1DViewModel';
 import { moveTo, pxToBp, bpToPx } from '@jbrowse/core/util/Base1DUtils';
 import { saveAs } from 'file-saver';
@@ -147,6 +147,11 @@ export function stateModelFactory(pluginManager) {
          * color by CDS
          */
         colorByCDS: types.optional(types.boolean, () => Boolean(JSON.parse(localStorageGetItem('lgv-colorByCDS') || 'false'))),
+        /**
+         * #property
+         * color by CDS
+         */
+        showTrackOutlines: types.optional(types.boolean, () => Boolean(JSON.parse(localStorageGetItem('lgv-showTrackOutlines') || 'true'))),
     }))
         .volatile(() => ({
         volatileWidth: undefined,
@@ -164,9 +169,6 @@ export function stateModelFactory(pluginManager) {
         rightOffset: undefined,
     }))
         .views(self => ({
-        scaleBarDisplayPrefix() {
-            return '';
-        },
         /**
          * #getter
          * this is the effective value of the track labels setting, incorporating
@@ -207,14 +209,20 @@ export function stateModelFactory(pluginManager) {
         /**
          * #method
          */
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        scaleBarDisplayPrefix() {
+            return getParent(self, 2).type === 'LinearSyntenyView'
+                ? self.assemblyNames[0]
+                : '';
+        },
+        /**
+         * #method
+         */
         MiniControlsComponent() {
             return MiniControls;
         },
         /**
          * #method
          */
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         HeaderComponent() {
             return Header;
         },
@@ -223,8 +231,7 @@ export function stateModelFactory(pluginManager) {
          */
         get assemblyErrors() {
             const { assemblyManager } = getSession(self);
-            const { assemblyNames } = self;
-            return assemblyNames
+            return self.assemblyNames
                 .map(a => { var _a; return (_a = assemblyManager.get(a)) === null || _a === void 0 ? void 0 : _a.error; })
                 .filter(f => !!f)
                 .join(', ');
@@ -411,6 +418,12 @@ export function stateModelFactory(pluginManager) {
         },
     }))
         .actions(self => ({
+        /**
+         * #action
+         */
+        setShowTrackOutlines(arg) {
+            self.showTrackOutlines = arg;
+        },
         /**
          * #action
          */
@@ -463,8 +476,7 @@ export function stateModelFactory(pluginManager) {
          * #action
          */
         addToHighlights(highlight) {
-            var _a;
-            (_a = self.highlight) === null || _a === void 0 ? void 0 : _a.push(highlight);
+            self.highlight.push(highlight);
         },
         /**
          * #action
@@ -592,7 +604,9 @@ export function stateModelFactory(pluginManager) {
             const schema = pluginManager.pluggableConfigSchemaType('track');
             const conf = resolveIdentifier(schema, getRoot(self), trackId);
             const t = self.tracks.filter(t => t.configuration === conf);
-            transaction(() => t.forEach(t => self.tracks.remove(t)));
+            transaction(() => {
+                t.forEach(t => self.tracks.remove(t));
+            });
             return t.length;
         },
     }))
@@ -654,22 +668,6 @@ export function stateModelFactory(pluginManager) {
             tracks.splice(newIndex, 0, self.tracks[oldIndex]);
             self.tracks = cast(tracks);
         },
-        /**
-         * #action
-         */
-        closeView() {
-            const parent = getContainingView(self);
-            if (parent) {
-                // I am embedded in a some other view
-                if (isViewContainer(parent)) {
-                    parent.removeView(self);
-                }
-            }
-            else {
-                // I am part of a session
-                getSession(self).removeView(self);
-            }
-        },
         /**
          * #action
          */
@@ -902,8 +900,9 @@ export function stateModelFactory(pluginManager) {
          * that offset is calculated manually with this method
          */
         get cytobandOffset() {
+            var _a;
             return this.showCytobands
-                ? measureText(self.displayedRegions[0].refName, 12) + 15
+                ? measureText(((_a = self.displayedRegions[0]) === null || _a === void 0 ? void 0 : _a.refName) || '', 12) + 15
                 : 0;
         },
     }))
@@ -965,7 +964,9 @@ export function stateModelFactory(pluginManager) {
                     type: 'checkbox',
                     checked: self.colorByCDS,
                     icon: PaletteIcon,
-                    onClick: () => self.setColorByCDS(!self.colorByCDS),
+                    onClick: () => {
+                        self.setColorByCDS(!self.colorByCDS);
+                    },
                 },
                 {
                     label: 'Show...',
@@ -979,32 +980,50 @@ export function stateModelFactory(pluginManager) {
                             label: 'Show center line',
                             type: 'checkbox',
                             checked: self.showCenterLine,
-                            onClick: () => self.setShowCenterLine(!self.showCenterLine),
+                            onClick: () => {
+                                self.setShowCenterLine(!self.showCenterLine);
+                            },
                         },
                         {
                             label: 'Show header',
                             type: 'checkbox',
                             checked: !self.hideHeader,
-                            onClick: () => self.setHideHeader(!self.hideHeader),
+                            onClick: () => {
+                                self.setHideHeader(!self.hideHeader);
+                            },
+                        },
+                        {
+                            label: 'Show track outlines',
+                            type: 'checkbox',
+                            checked: self.showTrackOutlines,
+                            onClick: () => {
+                                self.setShowTrackOutlines(!self.showTrackOutlines);
+                            },
                         },
                         {
                             label: 'Show header overview',
                             type: 'checkbox',
                             checked: !self.hideHeaderOverview,
-                            onClick: () => self.setHideHeaderOverview(!self.hideHeaderOverview),
+                            onClick: () => {
+                                self.setHideHeaderOverview(!self.hideHeaderOverview);
+                            },
                             disabled: self.hideHeader,
                         },
                         {
                             label: 'Show no tracks active button',
                             type: 'checkbox',
                             checked: !self.hideNoTracksActive,
-                            onClick: () => self.setHideNoTracksActive(!self.hideNoTracksActive),
+                            onClick: () => {
+                                self.setHideNoTracksActive(!self.hideNoTracksActive);
+                            },
                         },
                         {
                             label: 'Show guidelines',
                             type: 'checkbox',
                             checked: self.showGridlines,
-                            onClick: () => self.setShowGridlines(!self.showGridlines),
+                            onClick: () => {
+                                self.setShowGridlines(!self.showGridlines);
+                            },
                         },
                         ...(canShowCytobands
                             ? [
@@ -1012,7 +1031,9 @@ export function stateModelFactory(pluginManager) {
                                     label: 'Show ideogram',
                                     type: 'checkbox',
                                     checked: self.showCytobands,
-                                    onClick: () => self.setShowCytobands(!showCytobands),
+                                    onClick: () => {
+                                        self.setShowCytobands(!showCytobands);
+                                    },
                                 },
                             ]
                             : []),
@@ -1027,21 +1048,27 @@ export function stateModelFactory(pluginManager) {
                             icon: VisibilityIcon,
                             type: 'radio',
                             checked: self.trackLabelsSetting === 'overlapping',
-                            onClick: () => self.setTrackLabels('overlapping'),
+                            onClick: () => {
+                                self.setTrackLabels('overlapping');
+                            },
                         },
                         {
                             label: 'Offset',
                             icon: VisibilityIcon,
                             type: 'radio',
                             checked: self.trackLabelsSetting === 'offset',
-                            onClick: () => self.setTrackLabels('offset'),
+                            onClick: () => {
+                                self.setTrackLabels('offset');
+                            },
                         },
                         {
                             label: 'Hidden',
                             icon: VisibilityIcon,
                             type: 'radio',
                             checked: self.trackLabelsSetting === 'hidden',
-                            onClick: () => self.setTrackLabels('hidden'),
+                            onClick: () => {
+                                self.setTrackLabels('hidden');
+                            },
                         },
                     ],
                 },
@@ -1162,13 +1189,11 @@ export function stateModelFactory(pluginManager) {
         async navToLocString(input, optAssemblyName) {
             const { assemblyNames } = self;
             const { assemblyManager } = getSession(self);
-            const { isValidRefName } = assemblyManager;
             const assemblyName = optAssemblyName || assemblyNames[0];
             if (assemblyName) {
-                // wait before isValidRefName can be called
                 await assemblyManager.waitForAssembly(assemblyName);
             }
-            return this.navToLocations(parseLocStrings(input, assemblyName, isValidRefName), assemblyName);
+            return this.navToLocations(parseLocStrings(input, assemblyName, (ref, asm) => assemblyManager.isValidRefName(ref, asm)), assemblyName);
         },
         /**
          * #action
@@ -1297,16 +1322,19 @@ export function stateModelFactory(pluginManager) {
                 {
                     label: 'Zoom to region',
                     icon: ZoomInIcon,
-                    onClick: () => self.moveTo(self.leftOffset, self.rightOffset),
+                    onClick: () => {
+                        self.moveTo(self.leftOffset, self.rightOffset);
+                    },
                 },
                 {
                     label: 'Get sequence',
                     icon: MenuOpenIcon,
-                    onClick: () => getSession(self).queueDialog(handleClose => [
-                        GetSequenceDialog,
-                        // eslint-disable-next-line @typescript-eslint/no-explicit-any
-                        { model: self, handleClose },
-                    ]),
+                    onClick: () => {
+                        getSession(self).queueDialog(handleClose => [
+                            GetSequenceDialog,
+                            { model: self, handleClose },
+                        ]);
+                    },
                 },
             ];
         },
@@ -1380,6 +1408,7 @@ export function stateModelFactory(pluginManager) {
         },
     }))
         .preProcessSnapshot(snap => {
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         if (!snap) {
             return snap;
         }

package/esm/LinearGenomeView/svgcomponents/SVGLinearGenomeView.js

@@ -16,7 +16,6 @@ export async function renderToSvg(model, opts) {
     const { textHeight = 18, headerHeight = 40, rulerHeight = 50, fontSize = 13, cytobandHeight = 100, trackLabels = 'offset', themeName = 'default', Wrapper = ({ children }) => children, } = opts;
     const session = getSession(model);
     const { allThemes } = session;
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     const { createRootFn } = getRoot(model);
     const theme = allThemes === null || allThemes === void 0 ? void 0 : allThemes()[themeName];
     const { width, tracks, showCytobands } = model;

package/esm/LinearGenomeView/svgcomponents/SVGRuler.js

@@ -11,7 +11,7 @@ function Ruler({ start, end, bpPerPx, reversed = false, major = true, minor = tr
     return (React.createElement(React.Fragment, null,
         ticks.map(tick => {
             const x = (reversed ? end - tick.base : tick.base - start) / bpPerPx;
-            return (React.createElement("line", { key: 'tick-' + tick.base, x1: x, x2: x, y1: 0, y2: tick.type === 'major' ? 6 : 4, strokeWidth: 1, stroke: c }));
+            return (React.createElement("line", { key: `tick-${tick.base}`, x1: x, x2: x, y1: 0, y2: tick.type === 'major' ? 6 : 4, strokeWidth: 1, stroke: c }));
         }),
         !hideText
             ? ticks

package/esm/LinearGenomeView/util.d.ts

@@ -20,7 +20,7 @@ export declare function makeTicks(start: number, end: number, bpPerPx: number, e
  *
  * Used by navToLocations and navToLocString
  */
-export declare function generateLocations(regions: ParsedLocString[] | undefined, assemblyManager: AssemblyManager, assemblyName?: string): Promise<{
+export declare function generateLocations(regions: ParsedLocString[], assemblyManager: AssemblyManager, assemblyName?: string): Promise<{
     assemblyName: string;
     parentRegion: import("@jbrowse/core/assemblyManager/assembly").BasicRegion;
     end?: number | undefined;

package/esm/LinearGenomeView/util.js

@@ -34,9 +34,6 @@ export function makeTicks(start, end, bpPerPx, emitMajor = true, emitMinor = tru
     const gridPitch = chooseGridPitch(bpPerPx, 60, 15);
     let minBase = start;
     let maxBase = end;
-    if (minBase === null || maxBase === null) {
-        return [];
-    }
     if (bpPerPx < 0) {
         ;
         [minBase, maxBase] = [maxBase, minBase];
@@ -67,7 +64,7 @@ export function makeTicks(start, end, bpPerPx, emitMajor = true, emitMinor = tru
  *
  * Used by navToLocations and navToLocString
  */
-export async function generateLocations(regions = [], assemblyManager, assemblyName) {
+export async function generateLocations(regions, assemblyManager, assemblyName) {
     return Promise.all(regions.map(async (region) => {
         const asmName = region.assemblyName || assemblyName;
         if (!asmName) {
@@ -123,15 +120,13 @@ export function parseLocStrings(input, assemblyName, isValidRefName) {
         // if this fails, try interpreting as a whitespace-separated refname,
         // start, end if start and end are integer inputs
         const [refName, start, end] = inputs;
-        if (`${e}`.match(/Unknown reference sequence/) &&
+        if (/Unknown reference sequence/.exec(`${e}`) &&
             Number.isInteger(+start) &&
             Number.isInteger(+end)) {
             return [
-                parseLocString(refName + ':' + start + '..' + end, ref => isValidRefName(ref, assemblyName)),
+                parseLocString(`${refName}:${start}..${end}`, ref => isValidRefName(ref, assemblyName)),
             ];
         }
-        else {
-            throw e;
-        }
+        throw e;
     }
 }