feat(api): subscription for genomic axis changes

editor/Editor.tsx

@@ -332,12 +332,17 @@ function Editor(props: RouteComponentProps) {
  // gosRef.current.api.subscribe('trackClick', (type, eventData) => {
  // console.warn(type, eventData.id, eventData.spec, eventData.shape);
  // });
+ // Location API
+ // gosRef.current.api.subscribe('location', (type, eventData) => {
+ // console.warn(type, eventData.id, eventData.genomicRange);
+ // });
  }
  return () => {
  // gosRef.current?.api.unsubscribe('mouseOver');
  // gosRef.current?.api.unsubscribe('click');
  // gosRef.current?.api.unsubscribe('rangeSelect');
  // gosRef.current?.api.unsubscribe('trackClick');
+ // gosRef.current?.api.unsubscribe('location');
  };
  }, [gosRef.current]);
 

src/core/gosling.schema.ts

@@ -253,6 +253,13 @@ interface RangeMouseEventData extends CommonEventData {
  genomicRange: [GenomicPosition, GenomicPosition] | null;
 }
 
+/**
+ * Data about the genomic range of a track
+ */
+interface LocationEventData extends Omit<CommonEventData, 'data'> {
+ genomicRange: [GenomicPosition, GenomicPosition];
+}
+
 /**
  * The visual parameters that determine the shape of a linear track.
  * Origin is the left top corner.
@@ -295,6 +302,7 @@ export type _EventMap = {
  rawData: CommonEventData;
  trackMouseOver: TrackMouseEventData;
  trackClick: TrackMouseEventData; // TODO (Jul-25-2022): with https:/higlass/higlass/pull/1098, we can support circular layouts
+ location: LocationEventData;
 };
 
 /** Options for determining mouse events in detail, e.g., turning on specific events only */

src/core/utils/assembly.ts

@@ -18,19 +18,48 @@ export interface ChromSize {
 
 /**
  * Get relative chromosome position (e.g., `100` => `{ chromosome: 'chr1', position: 100 }`)
+ * @param absPos number which is the absolute chromosome position
+ * @param assembly the assembly used to calculate which chromosome position
+ * @param returnWithinAssembly If true, then if the absolute position is before the first chromosome, it returns the
+ * first position of the first chromosome. If the absolute position is after the last chromosome, it returns the last
+ * position of the last chromosome
+ * @returns the genomic position of the absPos
  */
-export function getRelativeGenomicPosition(absPos: number, assembly?: Assembly): GenomicPosition {
- const [chromosome, absInterval] = Object.entries(computeChromSizes(assembly).interval).find(d => {
- const [start, end] = d[1];
- return start <= absPos && absPos < end;
- }) ?? [null, null];
-
- if (!chromosome || !absInterval) {
- // The number is out of range
+export function getRelativeGenomicPosition(
+ absPos: number,
+ assembly?: Assembly,
+ returnWithinAssembly = false
+): GenomicPosition {
+ const chrSizes = Object.entries(computeChromSizes(assembly).interval);
+ const minPosChr = { chromosome: 'unknown', position: Infinity } as GenomicPosition;
+ const maxPosChr = { chromosome: 'unknown', position: 0 } as GenomicPosition;
+ for (const chrSize of chrSizes) {
+ const [chromosome, absInterval] = chrSize;
+ const [start, end] = absInterval;
+ // absPos was found within this chromosome
+ if (start <= absPos && absPos < end) {
+ return { chromosome, position: absPos - start } as GenomicPosition;
+ }
+ // Update the min and max chromosomes found
+ if (start < minPosChr.position) {
+ minPosChr.chromosome = chromosome;
+ minPosChr.position = start;
+ }
+ if (end > maxPosChr.position) {
+ maxPosChr.chromosome = chromosome;
+ maxPosChr.position = end;
+ }
+ }
+ if (returnWithinAssembly) {
+ // Return either the min or max chromosome position
+ if (absPos < minPosChr.position) {
+ return minPosChr;
+ } else {
+ return maxPosChr;
+ }
+ } else {
  return { chromosome: 'unknown', position: absPos };
  }
-
- return { chromosome, position: absPos - absInterval[0] };
 }
 
 /**

src/gosling-track/gosling-track.ts

@@ -449,6 +449,18 @@ const factory: PluginTrackFactory<Tile, GoslingTrackOptions> = (HGC, context, op
  this.refreshTiles();
  this.draw();
  this.forceDraw();
+
+ // Publish the new genomic axis domain
+ const genomicRange = newXScale
+ .domain()
+ .map(absPos => getRelativeGenomicPosition(absPos, this.#assembly, true)) as [
+ GenomicPosition,
+ GenomicPosition
+ ];
+ publish('location', {
+ id: context.viewUid,
+ genomicRange: genomicRange
+ });
  }
 
  /* *