npm - @jbrowse/plugin-wiggle - Versions diffs - 2.1.4 → 2.1.6 - Mend

@jbrowse/plugin-wiggle 2.1.4 → 2.1.6

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (46) hide show

package/dist/BigWigAdapter/BigWigAdapter.js CHANGED Viewed

@@ -25,17 +25,17 @@ class BigWigAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         return this.setupP;
     }
     async getRefNames(opts) {
-        const { header: { refsByName }, } = await this.setup(opts);
-        return Object.keys(refsByName);
+        const { header } = await this.setup(opts);
+        return Object.keys(header.refsByName);
     }
     async refIdToName(refId) {
         var _a;
-        const { header: { refsByNumber }, } = await this.setup();
-        return (_a = refsByNumber[refId]) === null || _a === void 0 ? void 0 : _a.name;
+        const { header } = await this.setup();
+        return (_a = header.refsByNumber[refId]) === null || _a === void 0 ? void 0 : _a.name;
     }
     async getGlobalStats(opts) {
-        const { header: { totalSummary }, } = await this.setup(opts);
-        return (0, stats_1.rectifyStats)(totalSummary);
+        const { header } = await this.setup(opts);
+        return (0, stats_1.rectifyStats)(header.totalSummary);
     }
     getFeatures(region, opts = {}) {
         const { refName, start, end } = region;

package/dist/BigWigAdapter/BigWigAdapter.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/CreateMultiWiggleExtension/index.js CHANGED Viewed

@@ -28,48 +28,56 @@ const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
 const ConfirmDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./ConfirmDialog'))));
 function default_1(pm) {
-    pm.addToExtensionPoint('TrackSelector-multiTrackMenuItems', () => {
+    pm.addToExtensionPoint('TrackSelector-multiTrackMenuItems', (items, props) => {
+        const { session } = props;
         return [
-            {
-                label: 'Create multi-wiggle track',
-                onClick: (model) => {
-                    const tracks = model.selection;
-                    const trackIds = tracks.map(c => (0, configuration_1.readConfObject)(c, 'name'));
-                    function makeTrack(arg) {
-                        const subadapters = tracks
-                            .map(c => (0, configuration_1.readConfObject)(c, 'adapter'))
-                            .map((c, idx) => ({ ...c, source: trackIds[idx] }));
-                        const assemblyNames = [
-                            ...new Set(tracks.map(c => (0, configuration_1.readConfObject)(c, 'assemblyNames')).flat()),
-                        ];
-                        const now = +Date.now();
-                        const trackId = `multitrack-${now}-sessionTrack`;
-                        (0, util_1.getSession)(model).addTrackConf({
-                            type: 'MultiQuantitativeTrack',
-                            trackId,
-                            name: arg.name,
-                            assemblyNames,
-                            adapter: {
-                                type: 'MultiWiggleAdapter',
-                                subadapters,
-                            },
-                        });
-                        model.view.showTrack(trackId);
-                    }
-                    (0, util_1.getSession)(model).queueDialog(handleClose => [
-                        ConfirmDialog,
-                        {
-                            tracks,
-                            onClose: (arg, arg1) => {
-                                if (arg) {
-                                    makeTrack(arg1);
-                                }
-                                handleClose();
-                            },
+            ...items,
+            ...((0, util_1.isSessionWithAddTracks)(session)
+                ? [
+                    {
+                        label: 'Create multi-wiggle track',
+                        onClick: (model) => {
+                            const tracks = model.selection;
+                            const trackIds = tracks.map(c => (0, configuration_1.readConfObject)(c, 'name'));
+                            function makeTrack(arg) {
+                                const subadapters = tracks
+                                    .map(c => (0, configuration_1.readConfObject)(c, 'adapter'))
+                                    .map((c, idx) => ({ ...c, source: trackIds[idx] }));
+                                const assemblyNames = [
+                                    ...new Set(tracks
+                                        .map(c => (0, configuration_1.readConfObject)(c, 'assemblyNames'))
+                                        .flat()),
+                                ];
+                                const now = +Date.now();
+                                const trackId = `multitrack-${now}-sessionTrack`;
+                                (0, util_1.getSession)(model).addTrackConf({
+                                    type: 'MultiQuantitativeTrack',
+                                    trackId,
+                                    name: arg.name,
+                                    assemblyNames,
+                                    adapter: {
+                                        type: 'MultiWiggleAdapter',
+                                        subadapters,
+                                    },
+                                });
+                                model.view.showTrack(trackId);
+                            }
+                            (0, util_1.getSession)(model).queueDialog(handleClose => [
+                                ConfirmDialog,
+                                {
+                                    tracks,
+                                    onClose: (arg, arg1) => {
+                                        if (arg && arg1) {
+                                            makeTrack(arg1);
+                                        }
+                                        handleClose();
+                                    },
+                                },
+                            ]);
                         },
-                    ]);
-                },
-            },
+                    },
+                ]
+                : []),
         ];
     });
 }

package/dist/CreateMultiWiggleExtension/index.js.map CHANGED Viewed

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package/dist/LinearWiggleDisplay/models/model.d.ts CHANGED Viewed

@@ -119,7 +119,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     readonly adapterConfig: any;
     readonly parentTrack: any;
     renderProps(): any;
-    readonly rendererType: any;
+    readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
     readonly DisplayMessageComponent: React.FC<any> | undefined;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -186,7 +186,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     afterAttach(): void;
 } & {
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | undefined;
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     contextMenuItems(): {
         label: string;
@@ -213,9 +213,9 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
         scoreMin: number;
         scoreMax: number;
     }): void;
-    setColor(color: string): void;
-    setPosColor(color: string): void;
-    setNegColor(color: string): void;
+    setColor(color?: string): void;
+    setPosColor(color?: string): void;
+    setNegColor(color?: string): void;
     setLoading(aborter: AbortController): void;
     selectFeature(feature: Feature): void;
     setResolution(res: number): void;
@@ -239,7 +239,11 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     readonly maxScore: any;
     readonly minScore: any;
 } & {
-    readonly rendererConfig: any;
+    readonly rendererConfig: {
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: unknown): any;
+    } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
 } & {
     readonly filled: any;
     readonly summaryScoreModeSetting: any;

package/dist/LinearWiggleDisplay/models/model.js CHANGED Viewed

@@ -206,7 +206,7 @@ const stateModelFactory = (pluginManager, configSchema) => mobx_state_tree_1.typ
             ...(negColor !== undefined ? { negColor } : {}),
             ...(posColor !== undefined ? { posColor } : {}),
             ...(minSize !== undefined ? { minSize } : {}),
-        }, (0, mobx_state_tree_1.getEnv)(self));
+        }, (0, util_1.getEnv)(self));
     },
 }))
     .views(self => {

package/dist/LinearWiggleDisplay/models/model.js.map CHANGED Viewed

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package/dist/MultiLinearWiggleDisplay/components/SetColorDialog.d.ts CHANGED Viewed

@@ -2,7 +2,7 @@
 import { Source } from '../../util';
 export default function SetColorDialog({ model, handleClose, }: {
     model: {
-        sources: Source[];
+        sources?: Source[];
         setLayout: (s: Source[]) => void;
         clearLayout: () => void;
     };

package/dist/MultiLinearWiggleDisplay/components/SetColorDialog.js CHANGED Viewed

@@ -63,8 +63,7 @@ function SetColorDialog({ model, handleClose, }) {
     const { classes } = useStyles();
     const { sources } = model;
     const [currLayout, setCurrLayout] = (0, react_1.useState)((0, clone_1.default)(sources || []));
-    const [showTipsTmp, setShowTips] = (0, util_1.useLocalStorage)('multiwiggle-showTips', 'true');
-    const showTips = showTipsTmp === 'true';
+    const [showTips, setShowTips] = (0, util_1.useLocalStorage)('multiwiggle-showTips', true);
     return (react_1.default.createElement(material_1.Dialog, { PaperComponent: PaperComponent, open: true, onClose: handleClose, maxWidth: "xl", "aria-labelledby": "draggable-dialog-title" // this area is important for the draggable functionality
      },
         react_1.default.createElement(material_1.DialogTitle, { style: { cursor: 'move' }, id: "draggable-dialog-title" },
@@ -73,7 +72,7 @@ function SetColorDialog({ model, handleClose, }) {
             react_1.default.createElement(material_1.IconButton, { className: classes.closeButton, onClick: handleClose },
                 react_1.default.createElement(Close_1.default, null))),
         react_1.default.createElement(material_1.DialogContent, { className: classes.content },
-            react_1.default.createElement(material_1.Button, { variant: "contained", style: { float: 'right' }, onClick: () => setShowTips(showTips ? 'false' : 'true') }, showTips ? 'Hide tips' : 'Show tips'),
+            react_1.default.createElement(material_1.Button, { variant: "contained", style: { float: 'right' }, onClick: () => setShowTips(!showTips) }, showTips ? 'Hide tips' : 'Show tips'),
             react_1.default.createElement("br", null),
             showTips ? (react_1.default.createElement(react_1.default.Fragment, null,
                 "Helpful tips",
@@ -89,11 +88,11 @@ function SetColorDialog({ model, handleClose, }) {
         react_1.default.createElement(material_1.DialogActions, null,
             react_1.default.createElement(material_1.Button, { variant: "contained", type: "submit", color: "inherit", onClick: () => {
                     model.clearLayout();
-                    setCurrLayout(model.sources);
+                    setCurrLayout(model.sources || []);
                 } }, "Clear custom settings"),
             react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
                     handleClose();
-                    setCurrLayout([...model.sources]);
+                    setCurrLayout([...(model.sources || [])]);
                 } }, "Cancel"),
             react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", type: "submit", onClick: () => {
                     model.setLayout(currLayout);

package/dist/MultiLinearWiggleDisplay/components/SetColorDialog.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.js CHANGED Viewed

@@ -33,7 +33,7 @@ const Wrapper = (0, mobx_react_1.observer)(({ children, model, exportSVG, }) =>
                 left: 0,
                 pointerEvents: 'none',
                 height,
-                width: 1800,
+                width: (0, util_1.getContainingView)(model).width,
             } }, children));
     }
 });

package/dist/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/MultiLinearWiggleDisplay/models/model.d.ts CHANGED Viewed

@@ -126,7 +126,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     readonly adapterConfig: any;
     readonly parentTrack: any;
     renderProps(): any;
-    readonly rendererType: any;
+    readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
     readonly DisplayMessageComponent: React.FC<any> | undefined;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -193,7 +193,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     afterAttach(): void;
 } & {
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | undefined;
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     contextMenuItems(): {
         label: string;
@@ -254,7 +254,11 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     readonly maxScore: number;
     readonly minScore: number;
 } & {
-    readonly rendererConfig: any;
+    readonly rendererConfig: {
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: unknown): any;
+    } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
 } & {
     readonly needsScalebar: boolean;
     readonly needsFullHeightScalebar: boolean;

package/dist/MultiLinearWiggleDisplay/models/model.js CHANGED Viewed

@@ -238,7 +238,7 @@ const stateModelFactory = (pluginManager, configSchema) => mobx_state_tree_1.typ
             ...(negColor !== undefined ? { negColor } : {}),
             ...(posColor !== undefined ? { posColor } : {}),
             ...(minSize !== undefined ? { minSize } : {}),
-        }, (0, mobx_state_tree_1.getEnv)(self));
+        }, (0, util_1.getEnv)(self));
     },
 }))
     .views(self => ({

package/dist/MultiLinearWiggleDisplay/models/model.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/MultiWiggleAddTrackWidget/AddTrackWorkflow.js CHANGED Viewed

@@ -80,7 +80,7 @@ function MultiWiggleWidget({ model }) {
                     bigWigs = JSON.parse(val);
                 }
                 catch (e) {
-                    bigWigs = val.split('\n');
+                    bigWigs = val.split(/\n|\r\n|\r/);
                 }
                 const obj = typeof bigWigs[0] === 'string'
                     ? { bigWigs }

package/dist/MultiWiggleAddTrackWidget/AddTrackWorkflow.js.map CHANGED Viewed

	@@ -1 +1 @@
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