Merge branch 'main' of https://github.com/chromoskein/chromoskein (0fe23f04) · Commits · Visitlab / Chromatin / chromoskein

app/src/App.tsx

+1 −0

Original line number	Diff line number	Diff line
		@@ -206,6 +206,7 @@ function App(): JSX.Element {
		{
		type: "bin-coordinates-single",
		dataId: undefined,
		mappingIds: [],
		visible: false,
		from: 0,
		to: 0

app/src/components/RightPanel/ChromatinViewportConfigurationPanel.tsx

+43 −0

Original line number	Diff line number	Diff line
		@@ -47,6 +47,18 @@ export function ChromatinViewportConfigurationPanel(props: {
		} as IComboBoxOption;
		});

		const otherData1DOptions = data.data
		.filter(d => d.type == "sparse-1d-data-text" \|\| d.type == "sparse-1d-data-numerical")
		.map(d => {
		return {
		key: isoDataID.unwrap(d.id),
		id: isoDataID.unwrap(d.id).toString(),
		text: d.name,
		}
		})



		const [isCalloutVisible, setIsCalloutVisible] = useState<boolean>(false);

		const selections = useSelections(0, [configuration, updateConfiguration], props.dataReducer, props.selectionsReducer);
		@@ -129,6 +141,19 @@ export function ChromatinViewportConfigurationPanel(props: {
		}
		};

		const setOtherData1D = (event: React.FormEvent<IComboBox>, option?: IComboBoxOption) => {

		const selected = option?.selected;
		if (option) {
		updateConfiguration({
		...configuration,
		otherMapValues: selected
		? [...configuration.otherMapValues, isoDataID.wrap(Number(option!.key))]
		: configuration.otherMapValues.filter(id => id != isoDataID.wrap(Number(option!.key)))
		});
		}
		}

		const setRadius = (radius: number) => {
		if (!configuration.data) return;

		@@ -309,6 +334,24 @@ export function ChromatinViewportConfigurationPanel(props: {
		}
		/>)
		}
		<Text nowrap block variant='large'>The other map 1D data</Text>
		{otherData1DOptions.length <= 0 && ("No more data available.")}
		{
		otherData1DOptions.length > 0 && (<ComboBox
		label=""
		allowFreeform={false}
		autoComplete={'on'}
		multiSelect
		options={otherData1DOptions}
		onChange={setOtherData1D}
		// onItemClick={setData1D}
		style={{ marginTop: '8px', padding: '4px' }}
		shouldRestoreFocus={false}
		selectedKey={
		configuration.otherMapValues.map(k => isoDataID.unwrap(k))
		}
		/>)
		}

		{/* SELECTIONS */}
		<div style={{ display: 'block', width: '100%', marginTop: '16px' }}></div>

app/src/components/Tools/CoordinatePreview.tsx

+30 −3

Original line number	Diff line number	Diff line
		import { Dispatch } from "react";
		import { binToGenomicCoordinate } from "../../modules/coordniatesUtils";
		import { CoordinatePreviewAction, CoordinatePreviewState } from "../../modules/storage/models/coordinatePreview";
		import { BinPositionsData, DataAction, DataState } from "../../modules/storage/models/data";
		import { BinPositionsData, DataAction, DataState, Sparse1DTextData, Sparse1DNumericData } from "../../modules/storage/models/data";
		import { ConfigurationAction, ConfigurationState } from "../../modules/storage/models/viewports";
		import { useConfigurationTypeless } from "../hooks";

		@@ -13,7 +13,7 @@ export function CoordinatePreview(props: {
		}) {
		const [coordinatePreview, dispatchCoordinatePreview] = props.coordinatePreviewReducer;
		const [data, dispatchData] = props.dataReducer;
		if (!coordinatePreview.visible) {
		if (!coordinatePreview.visible \|\| coordinatePreview.dataId == null) {
		return <></>
		}

		@@ -22,10 +22,37 @@ export function CoordinatePreview(props: {
		return <></>
		}

		const renderMapped = (genomicFrom: number, genomicTo: number) => {
		const mappedPairs = [];
		for (const mappedId of coordinatePreview.mappingIds) {
		const mappedData = data.data.find(d => d.id == mappedId);
		if (!mappedData) {
		continue
		}
		if (mappedData.type != 'sparse-1d-data-text' && mappedData.type != 'sparse-1d-data-numerical') {
		throw `No representation for data type ${mappedData.type}`
		}


		if (mappedData.type == 'sparse-1d-data-text') {
		const data1d = mappedData.values as Sparse1DTextData
		for (const txtValue of data1d.filter(v => v.from <= genomicTo && v.to >= genomicFrom)) {
		mappedPairs.push(<><span>{mappedData.name}: {txtValue.name} </span> \| </>)
		}
		}
		if (mappedData.type == 'sparse-1d-data-numerical') {
		const data1d = mappedData.values as Sparse1DNumericData
		for (const txtValue of data1d.filter(v => v.from <= genomicTo && v.to >= genomicFrom)) {
		mappedPairs.push(<><span>{mappedData.name}: {txtValue.value} </span> \| </>)
		}
		}
		}
		return mappedPairs;
		}
		if (dataModel.type == '3d-positions') {
		const dataModel3d = dataModel as BinPositionsData;
		const [genomicFrom, genomicTo] = binToGenomicCoordinate(coordinatePreview.from, dataModel3d.basePairsResolution)
		return <div style={props.style}>Bin: {coordinatePreview.from} (Genomic: {genomicFrom} - {genomicTo})</div>
		return <div style={props.style}>Bin: {coordinatePreview.from} (Genomic: {genomicFrom} - {genomicTo}) \| {renderMapped(genomicFrom, genomicTo)}</div>

		}

app/src/components/dialogs/NewGenomicDataDialog.tsx

+0 −1

Original line number	Diff line number	Diff line
		@@ -50,7 +50,6 @@ export function NewGenomicDataDialog(props: {


		if (file != null) {
		debugger;
		parsedFile = parseBED(file.content, delimiter)
		if (parsedFile.length == 0) {
		parsedFileColumns = [];

app/src/components/viewports/ChromatinViewport.tsx

+1 −1

Original line number	Diff line number	Diff line
		@@ -184,6 +184,7 @@ export function ChromatinViewport(props: {
		visible: true,
		type: "bin-coordinates-single",
		dataId: iso<DataID>().wrap(closestIntersection.chromatinPart.dataId),
		mappingIds: configuration.otherMapValues,
		from: closestIntersection.binIndex
		})
		}, [viewport, closestIntersection])
		@@ -544,7 +545,6 @@ export function ChromatinViewport(props: {
		const sphereRadius = tool.radius;
		const value = isAltPressed ? 0 : 1;


		for (let chromosomeIndex = 0; chromosomeIndex < configuration.chromosomes.length; chromosomeIndex++) {
		const chromatinPart = viewport.getChromatinPartByChromosomeIndex(chromosomeIndex);
		if (!chromatinPart \|\| !configuration.chromosomes[chromosomeIndex]) return;