@jbrowse/plugin-linear-genome-view/esm/LinearGenomeView/menuItems.js

JBrowse 2 linear genome view

import { TrackSelector as TrackSelectorIcon } from '@jbrowse/core/ui/Icons';
import { getSession, isSessionWithAddTracks, toLocale, } from '@jbrowse/core/util';
import CenterFocusStrongIcon from '@mui/icons-material/CenterFocusStrong';
import ContentCopyIcon from '@mui/icons-material/ContentCopy';
import FolderOpenIcon from '@mui/icons-material/FolderOpen';
import LabelIcon from '@mui/icons-material/Label';
import MenuOpenIcon from '@mui/icons-material/MenuOpen';
import PaletteIcon from '@mui/icons-material/Palette';
import PhotoCameraIcon from '@mui/icons-material/PhotoCamera';
import SearchIcon from '@mui/icons-material/Search';
import SyncAltIcon from '@mui/icons-material/SyncAlt';
import VisibilityIcon from '@mui/icons-material/Visibility';
import ZoomInIcon from '@mui/icons-material/ZoomIn';
import { ExportSvgDialog, GetSequenceDialog, ReturnToImportFormDialog, SequenceSearchDialog, } from "./lazyDialogs.js";
function toLocaleRounded(n) {
    return toLocale(Math.round(n));
}
export function rewriteOnClicks(self, trackType, viewMenuActions) {
    for (const action of viewMenuActions) {
        if ('subMenu' in action) {
            rewriteOnClicks(self, trackType, action.subMenu);
        }
        if ('onClick' in action) {
            const holdOnClick = action.onClick;
            action.onClick = (...args) => {
                for (const track of self.tracks) {
                    if (track.type === trackType) {
                        holdOnClick.apply(track, [track, ...args]);
                    }
                }
            };
        }
    }
}
export function buildMenuItems(self) {
    if (!self.hasDisplayedRegions) {
        return [];
    }
    const { canShowCytobands, showCytobands } = self;
    const session = getSession(self);
    const menuItems = [
        {
            label: 'Return to import form',
            onClick: () => {
                session.queueDialog(handleClose => [
                    ReturnToImportFormDialog,
                    {
                        model: self,
                        handleClose,
                    },
                ]);
            },
            icon: FolderOpenIcon,
        },
        ...(isSessionWithAddTracks(session)
            ? [
                {
                    label: 'Sequence search',
                    icon: SearchIcon,
                    onClick: () => {
                        session.queueDialog(handleClose => [
                            SequenceSearchDialog,
                            {
                                model: self,
                                handleClose,
                            },
                        ]);
                    },
                },
            ]
            : []),
        {
            label: 'Export SVG',
            icon: PhotoCameraIcon,
            onClick: () => {
                session.queueDialog(handleClose => [
                    ExportSvgDialog,
                    {
                        model: self,
                        handleClose,
                    },
                ]);
            },
        },
        {
            label: 'Open track selector',
            onClick: self.activateTrackSelector,
            icon: TrackSelectorIcon,
        },
        {
            label: 'Horizontally flip',
            icon: SyncAltIcon,
            onClick: self.horizontallyFlip,
        },
        {
            label: 'Color by CDS and draw amino acids',
            type: 'checkbox',
            checked: self.colorByCDS,
            icon: PaletteIcon,
            onClick: () => {
                self.setColorByCDS(!self.colorByCDS);
            },
        },
        {
            label: 'Show...',
            icon: VisibilityIcon,
            subMenu: [
                {
                    label: 'Show all regions in assembly',
                    onClick: self.showAllRegionsInAssembly,
                },
                {
                    label: 'Show center line',
                    type: 'checkbox',
                    checked: self.showCenterLine,
                    onClick: () => {
                        self.setShowCenterLine(!self.showCenterLine);
                    },
                },
                {
                    label: 'Show header',
                    type: 'checkbox',
                    checked: !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);
                    },
                    disabled: self.hideHeader,
                },
                {
                    label: 'Show no tracks active button',
                    type: 'checkbox',
                    checked: !self.hideNoTracksActive,
                    onClick: () => {
                        self.setHideNoTracksActive(!self.hideNoTracksActive);
                    },
                },
                {
                    label: 'Show guidelines',
                    type: 'checkbox',
                    checked: self.showGridlines,
                    onClick: () => {
                        self.setShowGridlines(!self.showGridlines);
                    },
                },
                ...(canShowCytobands
                    ? [
                        {
                            label: 'Show ideogram',
                            type: 'checkbox',
                            checked: self.showCytobands,
                            onClick: () => {
                                self.setShowCytobands(!showCytobands);
                            },
                        },
                    ]
                    : []),
            ],
        },
        {
            label: 'Track labels',
            icon: LabelIcon,
            subMenu: [
                {
                    label: 'Overlapping',
                    icon: VisibilityIcon,
                    type: 'radio',
                    checked: self.trackLabelsSetting === 'overlapping',
                    onClick: () => {
                        self.setTrackLabels('overlapping');
                    },
                },
                {
                    label: 'Offset',
                    icon: VisibilityIcon,
                    type: 'radio',
                    checked: self.trackLabelsSetting === 'offset',
                    onClick: () => {
                        self.setTrackLabels('offset');
                    },
                },
                {
                    label: 'Hidden',
                    icon: VisibilityIcon,
                    type: 'radio',
                    checked: self.trackLabelsSetting === 'hidden',
                    onClick: () => {
                        self.setTrackLabels('hidden');
                    },
                },
            ],
        },
    ];
    for (const [key, value] of self.trackTypeActions.entries()) {
        if (value.length) {
            menuItems.push({
                type: 'divider',
            }, {
                type: 'subHeader',
                label: key,
            });
            for (const action of value) {
                menuItems.push(action);
            }
        }
    }
    return menuItems;
}
export function buildRubberBandMenuItems(self) {
    const { leftOffset, rightOffset } = self;
    const leftRef = leftOffset?.refName ?? '';
    const rightRef = rightOffset?.refName ?? '';
    const leftCoord = toLocaleRounded((leftOffset?.coord ?? 0) + 1);
    const rightCoord = toLocaleRounded(rightOffset?.coord ?? 0);
    const rangeString = leftRef === rightRef
        ? `${leftRef}:${leftCoord}-${rightCoord}`
        : `${leftRef}:${leftCoord}..${rightRef}:${rightCoord}`;
    return [
        {
            label: 'Zoom to region',
            icon: ZoomInIcon,
            onClick: () => {
                self.moveTo(self.leftOffset, self.rightOffset);
            },
        },
        {
            label: 'Get sequence',
            icon: MenuOpenIcon,
            onClick: () => {
                getSession(self).queueDialog(handleClose => [
                    GetSequenceDialog,
                    {
                        model: self,
                        handleClose,
                    },
                ]);
            },
        },
        {
            label: 'Copy range',
            icon: ContentCopyIcon,
            onClick: async () => {
                const { default: copy } = await import('copy-to-clipboard');
                copy(rangeString);
            },
        },
    ];
}
export function buildRubberbandClickMenuItems(self, clickOffset) {
    const { coord, refName } = clickOffset;
    if (coord === undefined || refName === undefined) {
        return [];
    }
    const locString = `${refName}:${toLocaleRounded(coord + 1)}`;
    return [
        {
            label: 'Center view here',
            icon: CenterFocusStrongIcon,
            onClick: () => {
                self.centerAt(coord, refName);
            },
        },
        {
            label: 'Zoom to base level',
            icon: ZoomInIcon,
            onClick: () => {
                self.centerAt(coord, refName);
                self.zoomTo(self.minBpPerPx);
            },
        },
        {
            label: `Copy coordinate (${locString})`,
            icon: ContentCopyIcon,
            onClick: async () => {
                const { default: copy } = await import('copy-to-clipboard');
                copy(locString);
            },
        },
    ];
}