Fixed unneccary gene annotation fetches

Author: y330

Eplant/views/ChromosomeViewer/utilities.ts

@@ -0,0 +1,91 @@
+//------------------
+// Helper Functions for Chromosome.tsx
+//------------------
+
+import {
+  ChromosomeItem,
+  GeneAnnotationItem,
+  GeneItem,
+  GeneRange,
+} from './types'
+
+/**
+ * formats a GeneItem into GeneAnnotationItem
+ */
+export const getGeneAnnotation = (gene: GeneItem): GeneAnnotationItem => {
+  const genePixelLoc: number = ((gene.start + gene.end) / 2) * 0.000015
+  const geneAnnotation: GeneAnnotationItem = {
+    id: gene.id,
+    chromosome: gene.chromosome,
+    location: genePixelLoc,
+    strand: gene.strand,
+  }
+  return geneAnnotation
+}
+/**
+ * Gets the Chromosome svg element.
+ */
+export const getChromosomeSvg = (
+  chrId: string
+): HTMLElement & SVGSVGElement => {
+  const svg = document.getElementById(chrId + '_svg') as HTMLElement &
+    SVGSVGElement
+  return svg
+}
+/**
+ * Gets the Chromosome top y-coordinate.
+ */
+export const getChromosomeYCoordinate = (id: string): number => {
+  return getChromosomeSvg(id).getBoundingClientRect().top
+}
+/**
+ * Gets the Chromosome right x-coordinate.
+ */
+export const getChromosomeXCoordinate = (id: string): number => {
+  return getChromosomeSvg(id).getBoundingClientRect().right
+}
+/**
+ * Gets the height of the Chromosome.
+ */
+export const getChromosomeHeight = (id: string): number => {
+  return getChromosomeSvg(id).getBoundingClientRect().height
+}
+/**
+ * Gets the number of base-pairs per pixel.
+ */
+export const getBpPerPixel = (chromosome: ChromosomeItem): number => {
+  return chromosome.size / (getChromosomeHeight(chromosome.id) - 1)
+}
+/**
+ * Converts a pixel value to the equivalent base-pair range.
+ */
+export const pixelToBp = (
+  range: GeneRange,
+  chromosome: ChromosomeItem,
+  pixel: number
+): GeneRange => {
+  const id = chromosome.id
+  if (
+    pixel > getChromosomeYCoordinate(id) &&
+    pixel < getChromosomeYCoordinate(id) + getChromosomeHeight(id)
+  ) {
+    const range = {
+      start: Math.floor(
+        (pixel - 1 - getChromosomeYCoordinate(id)) * getBpPerPixel(chromosome) +
+          1
+      ),
+      end: Math.floor(
+        (pixel - getChromosomeYCoordinate(id)) * getBpPerPixel(chromosome)
+      ),
+    }
+    if (range.end > chromosome.size) {
+      range.end = chromosome.size
+    }
+    return range
+  } else {
+    return {
+      start: 0,
+      end: 0,
+    }
+  }
+}