@jbrowse/plugin-wiggle
Version:
JBrowse 2 wiggle adapters, tracks, etc.
260 lines (259 loc) • 9.86 kB
JavaScript
import { lazy } from 'react';
import { getConf } from '@jbrowse/core/configuration';
import { getContainingView, getSession } from '@jbrowse/core/util';
import { types } from '@jbrowse/mobx-state-tree';
import EqualizerIcon from '@mui/icons-material/Equalizer';
import PaletteIcon from '@mui/icons-material/Palette';
import VisibilityIcon from '@mui/icons-material/Visibility';
import SharedWiggleMixin from "../shared/SharedWiggleMixin.js";
import axisPropsFromTickScale from "../shared/axisPropsFromTickScale.js";
import { YSCALEBAR_LABEL_OFFSET, getScale } from "../util.js";
const Tooltip = lazy(() => import("./components/Tooltip.js"));
const SetColorDialog = lazy(() => import("./components/SetColorDialog.js"));
const rendererTypes = new Map([
['xyplot', 'XYPlotRenderer'],
['density', 'DensityRenderer'],
['line', 'LinePlotRenderer'],
]);
function stateModelFactory(pluginManager, configSchema) {
return types
.compose('LinearWiggleDisplay', SharedWiggleMixin(configSchema), types.model({
type: types.literal('LinearWiggleDisplay'),
invertedSetting: types.maybe(types.boolean),
}))
.actions(self => ({
setInverted(arg) {
self.invertedSetting = arg;
},
}))
.views(self => ({
get TooltipComponent() {
return Tooltip;
},
get rendererTypeName() {
const name = self.rendererTypeNameSimple;
const rendererType = rendererTypes.get(name);
if (!rendererType) {
throw new Error(`unknown renderer ${name}`);
}
return rendererType;
},
get quantitativeStatsRelevantToCurrentZoom() {
const view = getContainingView(self);
return self.stats?.currStatsBpPerPx === view.bpPerPx;
},
get graphType() {
return (self.rendererTypeName === 'XYPlotRenderer' ||
self.rendererTypeName === 'LinePlotRenderer');
},
get inverted() {
return self.invertedSetting ?? getConf(self, 'inverted');
},
}))
.views(self => {
const { renderProps: superRenderProps } = self;
return {
adapterProps() {
const superProps = superRenderProps();
const { filters, resolution, scaleOpts } = self;
return {
...superProps,
rpcDriverName: self.effectiveRpcDriverName,
config: self.rendererConfig,
displayCrossHatches: self.displayCrossHatchesSetting,
scaleOpts,
resolution,
filters,
};
},
get ticks() {
const { inverted, scaleType, domain, height } = self;
const minimalTicks = getConf(self, 'minimalTicks');
if (domain) {
const ticks = axisPropsFromTickScale(getScale({
scaleType,
domain,
range: [
height - YSCALEBAR_LABEL_OFFSET,
YSCALEBAR_LABEL_OFFSET,
],
inverted,
}), 4);
return height < 100 || minimalTicks
? { ...ticks, values: domain }
: ticks;
}
else {
return undefined;
}
},
};
})
.views(self => ({
renderProps() {
const { inverted, ticks, height, domain } = self;
const superProps = self.adapterProps();
const view = getContainingView(self);
const statsRegion = JSON.stringify(view.dynamicBlocks);
return {
...self.adapterProps(),
notReady: superProps.notReady ||
!domain ||
self.stats?.statsRegion !== statsRegion,
height,
ticks,
inverted,
offset: YSCALEBAR_LABEL_OFFSET,
};
},
get fillSetting() {
if (self.filled) {
return 0;
}
else if (self.minSize === 1) {
return 1;
}
else {
return 2;
}
},
get quantitativeStatsReady() {
const view = getContainingView(self);
return (view.initialized &&
self.featureDensityStatsReadyAndRegionNotTooLarge &&
!self.error);
},
}))
.views(self => {
const { trackMenuItems: superTrackMenuItems } = self;
const hasRenderings = getConf(self, 'defaultRendering');
return {
wiggleBaseTrackMenuItems() {
return [
...superTrackMenuItems(),
{
label: 'Score',
icon: EqualizerIcon,
subMenu: self.scoreTrackMenuItems(),
},
];
},
wiggleOnlyTrackMenuItems() {
return [
...(self.canHaveFill
? [
{
label: 'Fill mode',
subMenu: ['filled', 'no fill', 'no fill w/ emphasis'].map((elt, idx) => ({
label: elt,
type: 'radio',
checked: self.fillSetting === idx,
onClick: () => {
self.setFill(idx);
},
})),
},
]
: []),
...(hasRenderings
? [
{
label: 'Renderer type',
subMenu: ['xyplot', 'density', 'line'].map(key => ({
label: key,
type: 'radio',
checked: self.rendererTypeNameSimple === key,
onClick: () => {
self.setRendererType(key);
},
})),
},
]
: []),
{
label: 'Color',
icon: PaletteIcon,
onClick: () => {
getSession(self).queueDialog(handleClose => [
SetColorDialog,
{
model: self,
handleClose,
},
]);
},
},
];
},
};
})
.views(self => ({
trackMenuItems() {
return [
...self.wiggleBaseTrackMenuItems(),
{
label: 'Show...',
icon: VisibilityIcon,
subMenu: [
{
label: 'Show tooltips',
type: 'checkbox',
checked: self.showTooltipsEnabled,
onClick: () => {
self.setShowTooltips(!self.showTooltipsEnabled);
},
},
...(self.graphType
? [
{
label: 'Show inverted',
type: 'checkbox',
checked: self.inverted,
onClick: () => {
self.setInverted(!self.inverted);
},
},
{
label: 'Show cross hatches',
type: 'checkbox',
checked: self.displayCrossHatchesSetting,
onClick: () => {
self.toggleCrossHatches();
},
},
]
: []),
],
},
...self.wiggleOnlyTrackMenuItems(),
];
},
}))
.actions(self => {
const { renderSvg: superRenderSvg } = self;
return {
afterAttach() {
;
(async () => {
const { getQuantitativeStatsAutorun } = await import("../getQuantitativeStatsAutorun.js");
getQuantitativeStatsAutorun(self);
})();
},
async renderSvg(opts) {
const { renderSvg } = await import("./renderSvg.js");
return renderSvg(self, opts, superRenderSvg);
},
};
})
.postProcessSnapshot(snap => {
if (!snap) {
return snap;
}
const { invertedSetting, ...rest } = snap;
return {
...rest,
...(invertedSetting !== undefined ? { invertedSetting } : {}),
};
});
}
export default stateModelFactory;