@jbrowse/plugin-linear-genome-view 3.6.4 → 3.7.0

package/esm/LinearBasicDisplay/model.d.ts

@@ -179,6 +179,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
+    mouseoverExtraInformation: string | undefined;
     featureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
 } & {
@@ -193,9 +194,22 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
+    readonly layoutFeatures: import("@jbrowse/core/util/compositeMap").default<string, [number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]>;
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
-    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
-    searchFeatureByID(id: string): [number, number, number, number] | undefined;
+    getFeatureByID(blockKey: string, id: string): ([number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]) | undefined;
+    searchFeatureByID(id: string): ([number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]) | undefined;
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
@@ -204,6 +218,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature): void;
+    setMouseoverExtraInformation(extra?: string): void;
 } & {
     reload(): Promise<void>;
 } & {

package/esm/LinearGenomeView/components/Cytobands.js

@@ -26,7 +26,9 @@ function rightTriangle(x, _y, width, height) {
 const colorMap = {
     gneg: 'rgb(227,227,227)',
     gpos25: 'rgb(142,142,142)',
+    gpos33: 'rgb(142,142,142)',
     gpos50: 'rgb(85,85,85)',
+    gpos66: 'rgb(85,85,85)',
     gpos100: 'rgb(0,0,0)',
     gpos75: 'rgb(57,57,57)',
     gvar: 'rgb(0,0,0)',

package/esm/LinearGenomeView/components/RegionWidthEditorDialog.js

@@ -4,7 +4,7 @@ import { Dialog } from '@jbrowse/core/ui';
 import { toLocale } from '@jbrowse/core/util';
 import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
 import { observer } from 'mobx-react';
-const toP = (s = 0) => +(+s).toFixed(1);
+const toP = (s = 0) => +s.toFixed(1);
 const RegionWidthEditorDialog = observer(function ({ model, handleClose, }) {
     const { bpPerPx, width } = model;
     const [val, setVal] = useState(toLocale(toP(bpPerPx * width)));

package/esm/LinearGenomeView/components/SequenceSearchDialog.js

@@ -35,7 +35,7 @@ const SequenceSearchDialog = observer(function ({ model, handleClose, }) {
                                     } }), label: "Case insensitive" })] }), error ? _jsx(Typography, { color: "error", children: `${error}` }) : null] }), _jsxs(DialogActions, { children: [_jsx(Button, { onClick: () => {
                             var _a;
                             if (value) {
-                                const trackId = `sequence_search_${+Date.now()}`;
+                                const trackId = `sequence_search_${Date.now()}`;
                                 const session = getSession(model);
                                 const { assemblyManager } = session;
                                 const assemblyName = model.assemblyNames[0];

package/esm/LinearGenomeView/components/TrackContainer.js

@@ -9,7 +9,7 @@ import { makeStyles } from 'tss-react/mui';
 import Gridlines from './Gridlines';
 import TrackLabelContainer from './TrackLabelContainer';
 import TrackRenderingContainer from './TrackRenderingContainer';
-const useStyles = makeStyles()({
+const useStyles = makeStyles()(theme => ({
     root: {
         marginTop: 2,
         overflow: 'hidden',
@@ -19,11 +19,15 @@ const useStyles = makeStyles()({
         background: 'none',
     },
     resizeHandle: {
-        height: 3,
+        height: 4,
         boxSizing: 'border-box',
         position: 'relative',
+        background: 'transparent',
+        '&:hover': {
+            background: theme.palette.divider,
+        },
     },
-});
+}));
 const TrackContainer = observer(function ({ model, track, }) {
     const { classes, cx } = useStyles();
     const display = track.displays[0];

package/esm/LinearGenomeView/components/TrackLabelMenu.js

@@ -19,7 +19,7 @@ const TrackLabelMenu = observer(function ({ track, }) {
     const pinned = track.pinned;
     const { isTopLevelView } = view;
     const items = [
-        ...(isTopLevelView
+        ...(!isTopLevelView
             ? []
             : [
                 {

package/esm/LinearGenomeView/components/useRangeSelect.js

@@ -1,4 +1,4 @@
-import { useEffect, useState } from 'react';
+import { useCallback, useEffect, useState } from 'react';
 import { getRelativeX } from './util';
 export function useRangeSelect(ref, model, shiftOnly) {
     const [startX, setStartX] = useState();
@@ -6,6 +6,11 @@ export function useRangeSelect(ref, model, shiftOnly) {
     const [anchorPosition, setAnchorPosition] = useState();
     const [guideX, setGuideX] = useState();
     const mouseDragging = startX !== undefined && anchorPosition === undefined;
+    const handleClose = useCallback(() => {
+        setAnchorPosition(undefined);
+        setStartX(undefined);
+        setCurrentX(undefined);
+    }, []);
     useEffect(() => {
         function computeOffsets(offsetX) {
             if (startX === undefined) {
@@ -28,6 +33,10 @@ export function useRangeSelect(ref, model, shiftOnly) {
             if (startX !== undefined && ref.current) {
                 const { clientX, clientY } = event;
                 const offsetX = getRelativeX(event, ref.current);
+                if (Math.abs(offsetX - startX) <= 3) {
+                    handleClose();
+                    return;
+                }
                 setAnchorPosition({
                     offsetX,
                     clientX,
@@ -49,15 +58,7 @@ export function useRangeSelect(ref, model, shiftOnly) {
             };
         }
         return () => { };
-    }, [startX, mouseDragging, model, ref]);
-    useEffect(() => {
-        if (!mouseDragging &&
-            currentX !== undefined &&
-            startX !== undefined &&
-            Math.abs(currentX - startX) <= 3) {
-            handleClose();
-        }
-    }, [mouseDragging, currentX, startX]);
+    }, [startX, mouseDragging, model, ref, handleClose]);
     function mouseDown(event) {
         if (shiftOnly && !event.shiftKey) {
             return;
@@ -84,11 +85,6 @@ export function useRangeSelect(ref, model, shiftOnly) {
     function mouseOut() {
         setGuideX(undefined);
     }
-    function handleClose() {
-        setAnchorPosition(undefined);
-        setStartX(undefined);
-        setCurrentX(undefined);
-    }
     function handleMenuItemClick(_, callback) {
         callback();
         handleClose();

package/esm/LinearGenomeView/model.d.ts

@@ -59,8 +59,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     readonly interRegionPaddingWidth: number;
     readonly assemblyNames: string[];
     readonly assemblyDisplayNames: string[];
-    readonly isTopLevelView: import("@jbrowse/core/util").AbstractViewModel | undefined;
-    readonly stickyViewHeaders: boolean | undefined;
+    readonly isTopLevelView: boolean;
+    readonly stickyViewHeaders: boolean;
     readonly rubberbandTop: number;
     readonly pinnedTracksTop: number;
 } & {

package/esm/LinearGenomeView/model.js

@@ -106,7 +106,7 @@ export function stateModelFactory(pluginManager) {
         },
         get isTopLevelView() {
             const session = getSession(self);
-            return session.views.find(r => r.id === self.id);
+            return session.views.some(r => r.id === self.id);
         },
         get stickyViewHeaders() {
             const session = getSession(self);
@@ -647,7 +647,7 @@ export function stateModelFactory(pluginManager) {
                     onClick: self.horizontallyFlip,
                 },
                 {
-                    label: 'Color by CDS',
+                    label: 'Color by CDS and draw amino acids',
                     type: 'checkbox',
                     checked: self.colorByCDS,
                     icon: PaletteIcon,

package/esm/LinearGenomeView/util.js

@@ -2,7 +2,7 @@ import { assembleLocString, parseLocString } from '@jbrowse/core/util';
 export function chooseGridPitch(scale, minMajorPitchPx, minMinorPitchPx) {
     scale = Math.abs(scale);
     const minMajorPitchBp = minMajorPitchPx * scale;
-    const majorMagnitude = Number.parseInt(Number(minMajorPitchBp).toExponential().split(/e/i)[1], 10);
+    const majorMagnitude = +minMajorPitchBp.toExponential().split(/e/i)[1];
     let majorPitch = 10 ** majorMagnitude;
     while (majorPitch < minMajorPitchBp) {
         majorPitch *= 2;

package/esm/index.d.ts

@@ -176,6 +176,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
             regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
         } & {
+            mouseoverExtraInformation: string | undefined;
             featureIdUnderMouse: undefined | string;
             contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
         } & {
@@ -190,9 +191,22 @@ export default class LinearGenomeViewPlugin extends Plugin {
         } & {
             readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
             readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
+            readonly layoutFeatures: import("@jbrowse/core/util/compositeMap").default<string, [number, number, number, number] | [number, number, number, number, {
+                label?: string;
+                description?: string;
+                refName: string;
+            }]>;
             getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
-            getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
-            searchFeatureByID(id: string): [number, number, number, number] | undefined;
+            getFeatureByID(blockKey: string, id: string): ([number, number, number, number] | [number, number, number, number, {
+                label?: string;
+                description?: string;
+                refName: string;
+            }]) | undefined;
+            searchFeatureByID(id: string): ([number, number, number, number] | [number, number, number, number, {
+                label?: string;
+                description?: string;
+                refName: string;
+            }]) | undefined;
         } & {
             addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
             deleteBlock(key: string): void;
@@ -201,6 +215,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             clearFeatureSelection(): void;
             setFeatureIdUnderMouse(feature?: string): void;
             setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature): void;
+            setMouseoverExtraInformation(extra?: string): void;
         } & {
             reload(): Promise<void>;
         } & {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-genome-view",
-  "version": "3.6.4",
+  "version": "3.7.0",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -38,7 +38,7 @@
     "useSrc": "node ../../scripts/useSrc.js"
   },
   "dependencies": {
-    "@jbrowse/core": "^3.6.4",
+    "@jbrowse/core": "^3.7.0",
     "@mui/icons-material": "^7.0.0",
     "@mui/material": "^7.0.0",
     "@types/file-saver": "^2.0.1",
@@ -57,5 +57,5 @@
     "access": "public"
   },
   "module": "esm/index.js",
-  "gitHead": "3db8e50ce2bd9c081efbf6c2e7ae5f342380a25a"
+  "gitHead": "85bdd0d58286b7adbfd408146b15847676317635"
 }