@jbrowse/plugin-linear-genome-view 2.7.0 → 2.7.2

package/esm/LinearGenomeView/model.js

@@ -56,7 +56,7 @@ export const WIDGET_HEIGHT = 32;
  */
 export function stateModelFactory(pluginManager) {
     return types
-        .compose(BaseViewModel, types.model('LinearGenomeView', {
+        .compose('LinearGenomeView', BaseViewModel, types.model({
         /**
          * #property
          */
@@ -108,12 +108,6 @@ export function stateModelFactory(pluginManager) {
          * #property
          */
         trackSelectorType: types.optional(types.enumeration(['hierarchical']), 'hierarchical'),
-        /**
-         * #property
-         * how to display the track labels, can be "overlapping", "offset", or
-         * "hidden"
-         */
-        trackLabels: types.optional(types.string, () => localStorageGetItem('lgv-trackLabels') || 'overlapping'),
         /**
          * #property
          * show the "center line"
@@ -124,6 +118,15 @@ export function stateModelFactory(pluginManager) {
          * show the "cytobands" in the overview scale bar
          */
         showCytobandsSetting: types.optional(types.boolean, () => Boolean(JSON.parse(localStorageGetItem('lgv-showCytobands') || 'true'))),
+        /**
+         * #property
+         * how to display the track labels, can be "overlapping", "offset", or
+         * "hidden", or empty string "" (which results in conf being used). see
+         * LinearGenomeViewPlugin
+         * https://jbrowse.org/jb2/docs/config/lineargenomeviewplugin/ docs for
+         * how conf is used
+         */
+        trackLabels: types.optional(types.string, () => localStorageGetItem('lgv-trackLabels') || ''),
         /**
          * #property
          * show the "gridlines" in the track area
@@ -146,6 +149,18 @@ export function stateModelFactory(pluginManager) {
         rightOffset: undefined,
     }))
         .views(self => ({
+        /**
+         * #getter
+         * this is the effective value of the track labels setting, incorporating
+         * both the config and view state. use this instead of view.trackLabels
+         */
+        get trackLabelsSetting() {
+            const sessionSetting = getConf(getSession(self), [
+                'LinearGenomeViewPlugin',
+                'trackLabels',
+            ]);
+            return self.trackLabels || sessionSetting;
+        },
         /**
          * #getter
          */
@@ -586,6 +601,7 @@ export function stateModelFactory(pluginManager) {
          * #action
          */
         setTrackLabels(setting) {
+            localStorage.setItem('lgv-trackLabels', setting);
             self.trackLabels = setting;
         },
         /**
@@ -916,21 +932,21 @@ export function stateModelFactory(pluginManager) {
                             label: 'Overlapping',
                             icon: VisibilityIcon,
                             type: 'radio',
-                            checked: self.trackLabels === 'overlapping',
+                            checked: self.trackLabelsSetting === 'overlapping',
                             onClick: () => self.setTrackLabels('overlapping'),
                         },
                         {
                             label: 'Offset',
                             icon: VisibilityIcon,
                             type: 'radio',
-                            checked: self.trackLabels === 'offset',
+                            checked: self.trackLabelsSetting === 'offset',
                             onClick: () => self.setTrackLabels('offset'),
                         },
                         {
                             label: 'Hidden',
                             icon: VisibilityIcon,
                             type: 'radio',
-                            checked: self.trackLabels === 'hidden',
+                            checked: self.trackLabelsSetting === 'hidden',
                             onClick: () => self.setTrackLabels('hidden'),
                         },
                     ],
@@ -1021,9 +1037,8 @@ export function stateModelFactory(pluginManager) {
             }, { delay: 150 }));
             addDisposer(self, autorun(() => {
                 const s = (s) => JSON.stringify(s);
-                const { trackLabels, showCytobandsSetting, showCenterLine } = self;
+                const { showCytobandsSetting, showCenterLine } = self;
                 if (typeof localStorage !== 'undefined') {
-                    localStorage.setItem('lgv-trackLabels', trackLabels);
                     localStorage.setItem('lgv-showCytobands', s(showCytobandsSetting));
                     localStorage.setItem('lgv-showCenterLine', s(showCenterLine));
                 }
@@ -1235,22 +1250,18 @@ export function stateModelFactory(pluginManager) {
                 if (session.focusedViewId === self.id && (e.ctrlKey || e.metaKey)) {
                     if (e.code === 'ArrowLeft') {
                         e.preventDefault();
-                        // pan left
                         self.slide(-0.9);
                     }
-                    if (e.code === 'ArrowRight') {
+                    else if (e.code === 'ArrowRight') {
                         e.preventDefault();
-                        // pan right
                         self.slide(0.9);
                     }
-                    if (e.code === 'ArrowUp' && self.scaleFactor === 1) {
+                    else if (e.code === 'ArrowUp' && self.scaleFactor === 1) {
                         e.preventDefault();
-                        // zoom in
                         self.zoom(self.bpPerPx / 2);
                     }
-                    if (e.code === 'ArrowDown' && self.scaleFactor === 1) {
+                    else if (e.code === 'ArrowDown' && self.scaleFactor === 1) {
                         e.preventDefault();
-                        // zoom out
                         self.zoom(self.bpPerPx * 2);
                     }
                 }

package/esm/LinearGenomeView/svgcomponents/SVGTrackLabel.js

@@ -1,9 +1,11 @@
 import React from 'react';
 import { useTheme } from '@mui/material';
+import { coarseStripHTML } from '@jbrowse/core/util';
 export default function SVGTrackLabel({ trackLabels, trackName, fontSize, trackLabelOffset, x, }) {
     const theme = useTheme();
     const fill = theme.palette.text.primary;
     const xoff = trackLabels === 'overlay' ? 5 : 0;
     const yoff = trackLabels === 'offset' ? 5 : 0;
-    return trackLabels !== 'none' ? (React.createElement("g", null, trackLabels === 'left' ? (React.createElement("text", { x: trackLabelOffset - 40, y: 20, fill: fill, fontSize: fontSize, dominantBaseline: "hanging", textAnchor: "end" }, trackName)) : (React.createElement("text", { x: x + xoff, y: yoff, fill: fill, fontSize: fontSize, dominantBaseline: "hanging" }, trackName)))) : null;
+    const name = coarseStripHTML(trackName);
+    return trackLabels !== 'none' ? (React.createElement("g", null, trackLabels === 'left' ? (React.createElement("text", { x: trackLabelOffset - 40, y: 20, fill: fill, fontSize: fontSize, dominantBaseline: "hanging", textAnchor: "end" }, name)) : (React.createElement("text", { x: x + xoff, y: yoff, fill: fill, fontSize: fontSize, dominantBaseline: "hanging" }, name)))) : null;
 }

package/esm/index.d.ts

@@ -198,7 +198,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 resizeHeight(distance: number): number;
             } & {
                 featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
-                featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
+                featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined; /**
+                 * #slot configuration.LinearGenomeViewPlugin.trackLabels
+                 */
                 currStatsBpPerPx: number;
             } & {
                 readonly currentBytesRequested: number;
@@ -401,7 +403,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 resizeHeight(distance: number): number;
             } & {
                 featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
-                featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
+                featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined; /**
+                 * #slot configuration.LinearGenomeViewPlugin.trackLabels
+                 */
                 currStatsBpPerPx: number;
             } & {
                 readonly currentBytesRequested: number;
@@ -694,7 +698,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
             resizeHeight(distance: number): number;
         } & {
             featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
-            featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
+            featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined; /**
+             * #slot configuration.LinearGenomeViewPlugin.trackLabels
+             */
             currStatsBpPerPx: number;
         } & {
             readonly currentBytesRequested: number;
@@ -894,9 +900,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 hideHeaderOverview: boolean;
                 hideNoTracksActive: boolean;
                 trackSelectorType: string;
-                trackLabels: string;
                 showCenterLine: boolean;
                 showCytobandsSetting: boolean;
+                trackLabels: string;
                 showGridlines: boolean;
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
                 width: number;
@@ -905,7 +911,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 setDisplayName(name: string): void;
                 setWidth(newWidth: number): void;
-                setMinimized(flag: boolean): void;
+                setMinimized(flag: boolean): void; /**
+                 * #slot configuration.LinearGenomeViewPlugin.trackLabels
+                 */
             } & {
                 volatileWidth: number | undefined;
                 minimumBlockWidth: number;
@@ -919,6 +927,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 leftOffset: import("./LinearGenomeView").BpOffset | undefined;
                 rightOffset: import("./LinearGenomeView").BpOffset | undefined;
             } & {
+                readonly trackLabelsSetting: any;
                 readonly width: number;
                 readonly interRegionPaddingWidth: number;
                 readonly assemblyNames: string[];
@@ -1082,9 +1091,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
                 hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
                 trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-                trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
                 showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
                 showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+                trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
                 showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
             }, {
                 width: number;
@@ -1093,7 +1102,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 setDisplayName(name: string): void;
                 setWidth(newWidth: number): void;
-                setMinimized(flag: boolean): void;
+                setMinimized(flag: boolean): void; /**
+                 * #slot configuration.LinearGenomeViewPlugin.trackLabels
+                 */
             } & {
                 volatileWidth: number | undefined;
                 minimumBlockWidth: number;
@@ -1107,6 +1118,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 leftOffset: import("./LinearGenomeView").BpOffset | undefined;
                 rightOffset: import("./LinearGenomeView").BpOffset | undefined;
             } & {
+                readonly trackLabelsSetting: any;
                 readonly width: number;
                 readonly interRegionPaddingWidth: number;
                 readonly assemblyNames: string[];
@@ -1280,9 +1292,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 hideHeaderOverview: boolean;
                 hideNoTracksActive: boolean;
                 trackSelectorType: string;
-                trackLabels: string;
                 showCenterLine: boolean;
                 showCytobandsSetting: boolean;
+                trackLabels: string;
                 showGridlines: boolean;
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
                 width: number;
@@ -1291,7 +1303,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 setDisplayName(name: string): void;
                 setWidth(newWidth: number): void;
-                setMinimized(flag: boolean): void;
+                setMinimized(flag: boolean): void; /**
+                 * #slot configuration.LinearGenomeViewPlugin.trackLabels
+                 */
             } & {
                 volatileWidth: number | undefined;
                 minimumBlockWidth: number;
@@ -1305,6 +1319,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 leftOffset: import("./LinearGenomeView").BpOffset | undefined;
                 rightOffset: import("./LinearGenomeView").BpOffset | undefined;
             } & {
+                readonly trackLabelsSetting: any;
                 readonly width: number;
                 readonly interRegionPaddingWidth: number;
                 readonly assemblyNames: string[];
@@ -1468,9 +1483,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
                 hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
                 trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-                trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
                 showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
                 showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+                trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
                 showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
             }, {
                 width: number;
@@ -1479,7 +1494,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 setDisplayName(name: string): void;
                 setWidth(newWidth: number): void;
-                setMinimized(flag: boolean): void;
+                setMinimized(flag: boolean): void; /**
+                 * #slot configuration.LinearGenomeViewPlugin.trackLabels
+                 */
             } & {
                 volatileWidth: number | undefined;
                 minimumBlockWidth: number;
@@ -1493,6 +1510,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 leftOffset: import("./LinearGenomeView").BpOffset | undefined;
                 rightOffset: import("./LinearGenomeView").BpOffset | undefined;
             } & {
+                readonly trackLabelsSetting: any;
                 readonly width: number;
                 readonly interRegionPaddingWidth: number;
                 readonly assemblyNames: string[];
@@ -1666,9 +1684,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 hideHeaderOverview: boolean;
                 hideNoTracksActive: boolean;
                 trackSelectorType: string;
-                trackLabels: string;
                 showCenterLine: boolean;
                 showCytobandsSetting: boolean;
+                trackLabels: string;
                 showGridlines: boolean;
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
                 width: number;
@@ -1677,7 +1695,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 setDisplayName(name: string): void;
                 setWidth(newWidth: number): void;
-                setMinimized(flag: boolean): void;
+                setMinimized(flag: boolean): void; /**
+                 * #slot configuration.LinearGenomeViewPlugin.trackLabels
+                 */
             } & {
                 volatileWidth: number | undefined;
                 minimumBlockWidth: number;
@@ -1691,6 +1711,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 leftOffset: import("./LinearGenomeView").BpOffset | undefined;
                 rightOffset: import("./LinearGenomeView").BpOffset | undefined;
             } & {
+                readonly trackLabelsSetting: any;
                 readonly width: number;
                 readonly interRegionPaddingWidth: number;
                 readonly assemblyNames: string[];
@@ -1854,9 +1875,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
                 hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
                 trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-                trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
                 showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
                 showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+                trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
                 showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
             }, {
                 width: number;
@@ -1865,7 +1886,9 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 setDisplayName(name: string): void;
                 setWidth(newWidth: number): void;
-                setMinimized(flag: boolean): void;
+                setMinimized(flag: boolean): void; /**
+                 * #slot configuration.LinearGenomeViewPlugin.trackLabels
+                 */
             } & {
                 volatileWidth: number | undefined;
                 minimumBlockWidth: number;
@@ -1879,6 +1902,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 leftOffset: import("./LinearGenomeView").BpOffset | undefined;
                 rightOffset: import("./LinearGenomeView").BpOffset | undefined;
             } & {
+                readonly trackLabelsSetting: any;
                 readonly width: number;
                 readonly interRegionPaddingWidth: number;
                 readonly assemblyNames: string[];
@@ -2021,6 +2045,19 @@ export default class LinearGenomeViewPlugin extends Plugin {
             }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
         }) => import("react").JSX.Element;
     };
+    /**
+     * #config LinearGenomeViewConfigSchema
+     */
+    configurationSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        /**
+         * #slot configuration.LinearGenomeViewPlugin.trackLabels
+         */
+        trackLabels: {
+            type: string;
+            defaultValue: string;
+            model: import("mobx-state-tree").ISimpleType<string>;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
     install(pluginManager: PluginManager): void;
     configure(pluginManager: PluginManager): void;
 }

package/esm/index.js

@@ -10,6 +10,8 @@ import LinearBasicDisplayF from './LinearBasicDisplay';
 import FeatureTrackF from './FeatureTrack';
 import BasicTrackF from './BasicTrack';
 import LaunchLinearGenomeViewF from './LaunchLinearGenomeView';
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { types } from 'mobx-state-tree';
 export default class LinearGenomeViewPlugin extends Plugin {
     constructor() {
         super(...arguments);
@@ -22,6 +24,23 @@ export default class LinearGenomeViewPlugin extends Plugin {
             ZoomControls,
             LinearGenomeView,
         };
+        /**
+         * #config LinearGenomeViewConfigSchema
+         */
+        this.configurationSchema = ConfigurationSchema('LinearGenomeViewConfigSchema', {
+            /**
+             * #slot configuration.LinearGenomeViewPlugin.trackLabels
+             */
+            trackLabels: {
+                type: 'string',
+                defaultValue: 'overlapping',
+                model: types.enumeration('trackLabelOptions', [
+                    'offset',
+                    'overlapping',
+                    'hidden',
+                ]),
+            },
+        });
     }
     install(pluginManager) {
         FeatureTrackF(pluginManager);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-genome-view",
-  "version": "2.7.0",
+  "version": "2.7.2",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -65,5 +65,5 @@
     "access": "public"
   },
   "module": "esm/index.js",
-  "gitHead": "dbe7fb1af01fc89f833d2744635eb44a17365b41"
+  "gitHead": "9052b295f2d322e729254457ed9fe2231fb22cce"
 }