sequenceserver 3.1.3 → 3.2.0

data/public/js/visualisation_helpers.js

@@ -1,8 +1,7 @@
 import _ from 'underscore';
-import d3 from 'd3';
+import * as d3 from 'd3';
 export function get_colors_for_evalue(evalue, hits) {
-    var colors = d3.scale
-        .log()
+    var colors = d3.scaleLog()
         .domain([
             d3.min([1e-5, d3.min(hits.map(function (d) {
                 if (parseFloat(d.evalue) === 0.0) return undefined;
@@ -24,40 +23,38 @@ export function toLetters(num) {
     return pow ? toLetters(pow) + out : out;
 }
 
+export function getPrefix(str) {
+    if (str.length === 0) return '';
+
+    var lastChar = str.charAt(str.length - 1);
+    return /[a-zA-Z]/.test(lastChar) ? lastChar : '';
+}
+
 /**
- * Defines how ticks will be formatted.
+* Defines how ticks will be formatted.
  *
  * Examples: 200 aa, 2.4 kbp, 7.6 Mbp.
  *
  * Borrowed from Kablammo. Modified by Priyam based on https://github.com/mbostock/d3/issues/1722.
  */
 export function tick_formatter(scale, seq_type) {
-    var ticks = scale.ticks();
-    var prefix = d3.formatPrefix(ticks[ticks.length - 1]);
-    var suffixes = {amino_acid: 'aa', nucleic_acid: 'bp'};
+    const prefix = d3.format('~s')
+    const suffixes = {amino_acid: 'aa', nucleic_acid: 'bp'};
 
-    var digits = 0;
-    var format;
-    var _ticks;
+    return function (d) {
+        const formatted = prefix(d);
 
-    do {
-        format = d3.format('.' + digits + 'f');
-        _ticks = scale.ticks().map(function (d) {
-            return format(prefix.scale(d));
-        });
-        digits++;
+        return `${formatNumberUnits(formatted)}${suffixes[seq_type]}`;
+    };
+}
 
-    } while (_ticks.length !== _.uniq(_ticks).length);
+export function formatNumberUnits(number) {
+    const suffix = number.replace(/[0-9.]/g, '');
+    const numericPart = parseFloat(number).toFixed(2);
+    // Round to 1 decimal place
+    const rounded = Math.round(numericPart * 10) / 10;
 
-    return function (d) {
-        if (!prefix.symbol || d === scale.domain()[0]) {
-            return (d + ' ' + suffixes[seq_type]);
-        }
-        else {
-            return (format(prefix.scale(d)) +
-                  ' ' + prefix.symbol + suffixes[seq_type]);
-        }
-    };
+    return `${rounded % 1 === 0 ? rounded.toFixed(0) : rounded} ${suffix}`;
 }
 
 export function get_seq_type(algorithm) {
@@ -103,4 +100,4 @@ export function prettify_evalue(evalue) {
         else
             return base;
     }
-}
+}