@jbrowse/plugin-linear-genome-view 5.0.0-beta.13 → 5.0.0-beta.16

package/esm/LinearGenomeView/components/useRangeSelect.js

@@ -1,5 +1,6 @@
 import { useCallback, useState } from 'react';
 import { getRelativeX } from '@jbrowse/core/util/getRelativeX';
+import { isFromPortal } from '@jbrowse/core/util/pressOwner';
 import { useWindowDrag } from '../../shared/useWindowDrag.js';
 import { isOnScalebarRefLabel } from './util.js';
 export function useRangeSelect(ref, model, shiftOnly) {
@@ -44,7 +45,7 @@ export function useRangeSelect(ref, model, shiftOnly) {
         },
     });
     function mouseDown(event) {
-        if (shiftOnly && !event.shiftKey) {
+        if (isFromPortal(event) || (shiftOnly && !event.shiftKey)) {
             return;
         }
         // a press with the refName menu already open reopens it on the label under
@@ -65,7 +66,7 @@ export function useRangeSelect(ref, model, shiftOnly) {
     }
     function mouseMove(event) {
         // Keep the rubberband visible while a drag-selection menu is open
-        if (anchorPosition?.isClick === false) {
+        if (anchorPosition?.isClick === false || isFromPortal(event)) {
             return;
         }
         const wantsGuide = !mouseDragging && (!shiftOnly || event.shiftKey);

package/esm/LinearGenomeView/components/useSearchBoxPrefs.d.ts

@@ -22,5 +22,7 @@ export type SearchBoxPrefs = ReturnType<typeof useSearchBoxPrefs>;
 /**
  * The menu rows that drive those prefs. "Stacked" rather than "Vertical": the
  * two headers name the same state and had drifted apart on it once already.
+ * A caller spreading the rows into a "Show..." submenu passes `'Search boxes'`
+ * as the toggle's label.
  */
-export declare function searchBoxMenuItems({ showSearchBoxes, setShowSearchBoxes, sideBySide, setSideBySide, }: SearchBoxPrefs): MenuItem[];
+export declare function searchBoxMenuItems({ showSearchBoxes, setShowSearchBoxes, sideBySide, setSideBySide, }: SearchBoxPrefs, toggleLabel?: string): MenuItem[];

package/esm/LinearGenomeView/components/useSearchBoxPrefs.js

@@ -22,11 +22,13 @@ export function useSearchBoxPrefs(prefix, numViews) {
 /**
  * The menu rows that drive those prefs. "Stacked" rather than "Vertical": the
  * two headers name the same state and had drifted apart on it once already.
+ * A caller spreading the rows into a "Show..." submenu passes `'Search boxes'`
+ * as the toggle's label.
  */
-export function searchBoxMenuItems({ showSearchBoxes, setShowSearchBoxes, sideBySide, setSideBySide, }) {
+export function searchBoxMenuItems({ showSearchBoxes, setShowSearchBoxes, sideBySide, setSideBySide, }, toggleLabel = 'Show search boxes') {
     return [
         {
-            label: 'Show search boxes',
+            label: toggleLabel,
             type: 'checkbox',
             checked: showSearchBoxes,
             onClick: () => {

package/esm/LinearGenomeView/components/useSideScroll.js

@@ -1,4 +1,5 @@
 import { useEffect, useRef } from 'react';
+import { isClaimedPress } from '@jbrowse/core/util/pressOwner';
 import { transaction } from 'mobx';
 // A press that travels further than this is a pan, and the click that ends it
 // is not a click. A hand that wobbles two pixels can still select something.
@@ -13,9 +14,6 @@ const PAN_CLICK_THRESHOLD_PX = 4;
 // before any track sees it.
 const PAN_DRAGGING_ATTR = 'data-pan-dragging';
 const PAN_MOVED_ATTR = 'data-pan-moved';
-function preventDefault(event) {
-    event.preventDefault();
-}
 function pointOf(event) {
     return { x: event.clientX, y: event.clientY };
 }
@@ -51,13 +49,7 @@ export function useSideScroll(model) {
         if (event.shiftKey || event.button !== 0 || !event.isPrimary) {
             return;
         }
-        // a draggable element, a control that claimed the press (resize handles,
-        // the scalebar, a legend), or a button: `closest`, since the press usually
-        // lands on a child of the control
-        const target = event.target;
-        if (target.draggable ||
-            target.closest('[data-gesture-owner]') ||
-            target.closest('button')) {
+        if (isClaimedPress(event)) {
             return;
         }
         const left = host.getBoundingClientRect().left;
@@ -66,6 +58,13 @@ export function useSideScroll(model) {
         const pointers = new Map([[event.pointerId, pointOf(event)]]);
         let applied = new Map(pointers);
         let frame;
+        // only a selection that starts in the tracks, so a press that leaks here
+        // cannot block selection in the rest of the app
+        function blockSelection(e) {
+            if (e.target instanceof Node && host.contains(e.target)) {
+                e.preventDefault();
+            }
+        }
         function flush() {
             frame = undefined;
             const [a, b] = [...pointers.keys()];
@@ -124,7 +123,7 @@ export function useSideScroll(model) {
             window.removeEventListener('pointermove', move, true);
             window.removeEventListener('pointerup', release, true);
             window.removeEventListener('pointercancel', release, true);
-            window.removeEventListener('selectstart', preventDefault, true);
+            window.removeEventListener('selectstart', blockSelection, true);
             gestureRef.current = undefined;
         }
         // pointercancel as well as pointerup: the browser cancels a touch it takes
@@ -146,7 +145,7 @@ export function useSideScroll(model) {
         window.addEventListener('pointermove', move, true);
         window.addEventListener('pointerup', release, true);
         window.addEventListener('pointercancel', release, true);
-        window.addEventListener('selectstart', preventDefault, true);
+        window.addEventListener('selectstart', blockSelection, true);
         gestureRef.current = {
             join(e) {
                 if (e.pointerType !== 'touch' || pointers.size > 1) {

package/esm/LinearGenomeView/lazyDialogs.d.ts

@@ -8,10 +8,25 @@ export declare const SequenceSearchDialog: import("react").LazyExoticComponent<(
     model: import("./components/searchModes.ts").SequenceSearchModel;
     handleClose: () => void;
 }) => import("react").JSX.Element>;
-export declare const ExportSvgDialog: import("react").LazyExoticComponent<typeof import("./components/ExportSvgDialog.tsx").default>;
+export declare const ExportSvgDialog: import("react").LazyExoticComponent<({ model, handleClose, chooseWidth, }: {
+    model: {
+        width?: number;
+        effectiveTrackLabels?: import("@jbrowse/display-kit/types").ViewTrackLabelMode;
+        exportSvg(opts: import("@jbrowse/core/ui").BaseExportSvgOptions & {
+            trackLabels: import("@jbrowse/display-kit/types").TrackLabelMode;
+            showGridlines: boolean;
+            viewWidth?: number;
+        }): Promise<unknown>;
+    };
+    handleClose: () => void;
+    chooseWidth?: boolean;
+}) => import("react").JSX.Element>;
 export declare const GetSequenceDialog: import("react").LazyExoticComponent<({ model, regions, handleClose, }: {
     model: import("@jbrowse/mobx-state-tree").IAnyStateTreeNode;
     regions: import("@jbrowse/core/util").Region[];
     handleClose: () => void;
 }) => import("react").JSX.Element>;
-export declare const RegionWidthEditorDialog: import("react").LazyExoticComponent<typeof import("./components/RegionWidthEditorDialog.tsx").default>;
+export declare const RegionWidthEditorDialog: import("react").LazyExoticComponent<({ model, handleClose, }: {
+    model: import("./model.ts").LinearGenomeViewModel;
+    handleClose: () => void;
+}) => import("react").JSX.Element>;

package/esm/LinearGenomeView/menuItems.js

@@ -1,5 +1,5 @@
 import { Highlighter, TrackSelector as TrackSelectorIcon, } from '@jbrowse/core/ui/Icons';
-import { radioItems } from '@jbrowse/core/ui/menuItems';
+import { radioItems, subMenuIfAny } from '@jbrowse/core/ui/menuItems';
 import { makeShowSubMenu } from '@jbrowse/core/ui/showSubMenu';
 import { assembleLocStrings, getDialogHost, getSession, isSessionWithAddSessionTrack, toLocale, } from '@jbrowse/core/util';
 import { basePaintedAt, computeMoveToLayout, } from '@jbrowse/core/util/Base1DUtils';
@@ -7,6 +7,7 @@ import { copyText } from '@jbrowse/core/util/copyText';
 import { renameIds } from '@jbrowse/core/util/types/mst';
 import { getSnapshot } from '@jbrowse/mobx-state-tree';
 import CenterFocusStrongIcon from '@mui/icons-material/CenterFocusStrong';
+import CodeIcon from '@mui/icons-material/Code';
 import ContentCopyIcon from '@mui/icons-material/ContentCopy';
 import FitScreenIcon from '@mui/icons-material/FitScreen';
 import FolderOpenIcon from '@mui/icons-material/FolderOpen';
@@ -97,7 +98,7 @@ export function buildMenuItems(self) {
             icon: TrackSelectorIcon,
         },
         {
-            label: 'Export SVG',
+            label: 'Export SVG...',
             icon: PhotoCameraIcon,
             onClick: () => {
                 session.queueDialog(handleClose => [
@@ -105,10 +106,22 @@ export function buildMenuItems(self) {
                     {
                         model: self,
                         handleClose,
+                        chooseWidth: true,
                     },
                 ]);
             },
         },
+        {
+            label: 'Export R script',
+            icon: CodeIcon,
+            onClick: () => {
+                import('./rExport/exportLinearView.js')
+                    .then(({ downloadRScript }) => downloadRScript(self))
+                    .catch((e) => {
+                    session.notifyError(`${e}`, e);
+                });
+            },
+        },
         ...(isSessionWithAddSessionTrack(session)
             ? [
                 {
@@ -165,7 +178,7 @@ export function buildMenuItems(self) {
         ...makeShowSubMenu([
             showAllRegionsMenuItem(self),
             {
-                label: 'Show ruler only',
+                label: 'Ruler only',
                 type: 'checkbox',
                 checked: self.scalebarOnly,
                 onClick: () => {
@@ -173,7 +186,7 @@ export function buildMenuItems(self) {
                 },
             },
             {
-                label: 'Show header',
+                label: 'Header',
                 type: 'checkbox',
                 checked: !self.hideHeader,
                 // opts out of the checkbox "stay open" default: with the header
@@ -185,7 +198,7 @@ export function buildMenuItems(self) {
                 },
             },
             {
-                label: 'Show header overview',
+                label: 'Header overview',
                 type: 'checkbox',
                 checked: !self.hideHeaderOverview,
                 onClick: () => {
@@ -196,7 +209,7 @@ export function buildMenuItems(self) {
             ...(self.canShowCytobands
                 ? [
                     {
-                        label: 'Show ideogram',
+                        label: 'Ideogram',
                         type: 'checkbox',
                         checked: self.showCytobands,
                         onClick: () => {
@@ -206,7 +219,7 @@ export function buildMenuItems(self) {
                 ]
                 : []),
             {
-                label: 'Show center line',
+                label: 'Center line',
                 type: 'checkbox',
                 checked: self.showCenterLine,
                 onClick: () => {
@@ -214,7 +227,7 @@ export function buildMenuItems(self) {
                 },
             },
             {
-                label: 'Show guidelines',
+                label: 'Guidelines',
                 type: 'checkbox',
                 checked: self.showGridlines,
                 onClick: () => {
@@ -222,7 +235,7 @@ export function buildMenuItems(self) {
                 },
             },
             {
-                label: 'Show track outlines',
+                label: 'Track outlines',
                 type: 'checkbox',
                 checked: self.showTrackOutlines,
                 onClick: () => {
@@ -230,7 +243,7 @@ export function buildMenuItems(self) {
                 },
             },
             {
-                label: 'Show no tracks active button',
+                label: 'No tracks active button',
                 type: 'checkbox',
                 checked: !self.hideNoTracksActive,
                 onClick: () => {
@@ -239,7 +252,7 @@ export function buildMenuItems(self) {
             },
             { type: 'subHeader', label: 'Sequence' },
             {
-                label: 'Show CDS reading frame colors',
+                label: 'CDS reading frame colors',
                 type: 'checkbox',
                 checked: self.colorByCDS,
                 onClick: () => {
@@ -247,7 +260,7 @@ export function buildMenuItems(self) {
                 },
             },
             {
-                label: 'Show amino acids when zoomed in',
+                label: 'Amino acids when zoomed in',
                 type: 'checkbox',
                 checked: self.showAminoAcids,
                 onClick: () => {
@@ -331,7 +344,7 @@ export function buildRubberBandMenuItems(self, launchItems) {
             },
         },
         {
-            label: 'Get sequence',
+            label: 'Get sequence...',
             icon: MenuOpenIcon,
             onClick: () => {
                 const regions = self.getSelectedRegions(leftOffset, rightOffset);
@@ -365,17 +378,12 @@ export function buildRubberBandMenuItems(self, launchItems) {
                 }
             },
         },
-        ...(launch.length
-            ? [
-                {
-                    label: 'Launch',
-                    icon: LaunchIcon,
-                    type: 'subMenu',
-                    priority: -1000,
-                    subMenu: launch,
-                },
-            ]
-            : []),
+        ...subMenuIfAny({
+            label: 'Launch',
+            icon: LaunchIcon,
+            priority: -1000,
+            subMenu: launch,
+        }),
     ];
 }
 /**