@sjcrh/proteinpaint-shared 2.111.0 → 2.112.1-0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-shared",
-  "version": "2.111.0",
+  "version": "2.112.1-0",
   "description": "ProteinPaint code that is shared between server and client-side workspaces",
   "type": "module",
   "main": "src/index.js",

package/src/descriptive.stats.js

@@ -2,7 +2,7 @@ import { roundValueAuto } from './roundValue.js'
 
 /* This file generates summary statistics on any given array of numbers*/
 
-export default function summaryStats(array) {
+export function summaryStats(array) {
 	//console.log("array:",array)
 	let arr = array
 	if (typeof array[0] == 'string') {
@@ -14,18 +14,12 @@ export default function summaryStats(array) {
 	const sorted_arr = arr.sort((a, b) => a - b)
 	const n = arr.length
 
-	//compute mean
-	function mean(arr) {
-		if (arr.length === 0) throw new Error('No data provided')
-		return arr.reduce((a, b) => a + b) / n
-	}
-
 	//compute median
 	const median = computePercentile(sorted_arr, 50)
-	const mean_arr = mean(sorted_arr)
-	const squareDiffs = arr.map(x => (x - mean_arr) ** 2).reduce((a, b) => a + b, 0)
+	//compute mean
+	const mean = getMean(arr)
 	// compute variance
-	const variance = squareDiffs / (n - 1)
+	const variance = getVariance(sorted_arr)
 	// compute standard deviation
 	const stdDev = Math.sqrt(variance)
 
@@ -45,7 +39,7 @@ export default function summaryStats(array) {
 			{ id: 'min', label: 'Minimum', value: roundValueAuto(min, true) },
 			{ id: 'p25', label: '1st quartile', value: roundValueAuto(p25, true) },
 			{ id: 'median', label: 'Median', value: roundValueAuto(median, true) },
-			{ id: 'mean', label: 'Mean', value: roundValueAuto(mean(arr), true) },
+			{ id: 'mean', label: 'Mean', value: roundValueAuto(mean, true) },
 			{ id: 'p75', label: '3rd quartile', value: roundValueAuto(p75, true) },
 			{ id: 'max', label: 'Maximum', value: roundValueAuto(max, true) },
 			{ id: 'SD', label: 'Standard deviation', value: roundValueAuto(stdDev, true) },
@@ -60,3 +54,18 @@ function computePercentile(values, percentile) {
 	const value = Number.isInteger(index) ? (values[index] + values[index + 1]) / 2 : values[Math.ceil(index)]
 	return value
 }
+
+export function getMean(data) {
+	return data.reduce((sum, value) => sum + value, 0) / data.length
+}
+
+export function getVariance(data) {
+	const meanValue = getMean(data)
+	const squaredDifferences = data.map(value => Math.pow(value - meanValue, 2))
+	return squaredDifferences.reduce((sum, value) => sum + value, 0) / data.length
+}
+
+export function getStdDev(data) {
+	const variance = getVariance(data)
+	return Math.sqrt(variance)
+}

package/src/roundValue.js

@@ -22,10 +22,10 @@ export function roundValue(value, digits) {
  * TODO: Review digit logic.
  */
 
-export function roundValueAuto(value, format = false) {
+export function roundValueAuto(value, format = false, defaultDigits = 2) {
 	if (!value && value != 0) return value
 	const dp = decimalPlacesUntilFirstNonZero(value)
-	const digits = Math.abs(value) > 1 ? 2 : dp > 0 ? dp + 1 : 2
+	const digits = Math.abs(value) > 1 ? defaultDigits : dp > 0 ? dp + 1 : defaultDigits
 	if (format) return formatValue(value, digits)
 	return roundValue(value, digits)
 }

package/src/termdb.usecase.js

@@ -111,9 +111,10 @@ export function isUsableTerm(term, _usecase, termdbConfig, ds) {
 		case 'profileForms':
 			if (!term.isleaf) {
 				const ancestors = term.id.split('__').length //depends on using the __ naming convension!
-				if (ancestors == 2) {
+				if (ancestors == 3) {
+					// 3rd level term is a domain, we show the templates associated to this domain
 					uses.add('plot')
-				} else if (ancestors < 2) uses.add('branch')
+				} else if (ancestors < 3) uses.add('branch')
 			}
 			return uses