[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

taxonium_component/src/utils/nexusToNewick.js

@@ -26,7 +26,6 @@ function nexusToNewick(nexusString) {
  // get the Newick string from the tree block
  const newickString = treeBlock[0].match(/\((.*?)\).+;/gims)[0];
 
-
  // translate the taxon labels in the Newick string
  const translatedNewickString = newickString.replace(
  /([^:\,\(\)]+)/gims,

taxonium_component/src/utils/processNewick.js

@@ -11,8 +11,6 @@ import reduceMaxOrMin from "./reduceMaxOrMin";
 import nexusToNewick from "../utils/nexusToNewick.js";
 const emptyList = [];
 
-
-
 async function do_fetch(url, sendStatusMessage, whatIsBeingDownloaded) {
  if (!sendStatusMessage) {
  sendStatusMessage = () => {};
@@ -86,15 +84,14 @@ function parseNewickKeyValue(newickKVString, obj_to_set) {
 
  const result = [];
  let match;
- 
+
  // Use the RegExp.exec() method to find all matches in the string
  while ((match = regex.exec(newickKVString)) !== null) {
-  // Remove the '&' character if it's present at the start of the key
-  const key = match[1].startsWith('&') ? match[1].slice(1) : match[1];
-  // Push the key-value pair to the result array
-  obj_to_set["meta_"+key] = match[2];
+ // Remove the '&' character if it's present at the start of the key
+ const key = match[1].startsWith("&") ? match[1].slice(1) : match[1];
+ // Push the key-value pair to the result array
+ obj_to_set["meta_" + key] = match[2];
  }
-
 }
 
 async function cleanup(tree) {
@@ -112,15 +109,13 @@ async function cleanup(tree) {
  num_tips: node.num_tips,
  is_tip: node.child.length === 0,
  node_id: node.node_id,
-
- }
+ };
  // if node.meta is not empty, parse it.
  // We need to parse things of the form "&name=blabla,mutations={T694A:1.0,C29870A:1.0},Ns={1-3,4-17,18-20,21-26,686-693,22029-22033,28248-28253,28271-28271}"
  if (node.meta) {
  parseNewickKeyValue(node.meta, to_return);
  }
  return to_return;
-
  });
 
  const scale_y = 2000;
@@ -147,7 +142,6 @@ export async function processNewick(data, sendStatusMessage) {
  if (data.filetype == "nexus") {
  const result = nexusToNewick(the_data);
  the_data = result.newick;
-
  }
 
  sendStatusMessage({
@@ -158,7 +152,6 @@ export async function processNewick(data, sendStatusMessage) {
  if (the_data[0] === "[") {
  the_data = the_data.slice(the_data.indexOf("]") + 1);
  }
-
 
  // remove newlines from the string
 
@@ -167,7 +160,6 @@ export async function processNewick(data, sendStatusMessage) {
 
  const tree = kn_parse(the_data);
  console.log("tree", tree);
-
 
  function assignNumTips(node) {
  if (node.child.length === 0) {
@@ -333,8 +325,7 @@ export async function processNewickAndMetadata(data, sendStatusMessage) {
  // add them to the set
  meta_keys.forEach((key) => {
  all_keys.add(key);
- }
- );
+ });
  });
  console.log("all_keys", all_keys);
  // update the blanks object to include all the keys
@@ -359,11 +350,9 @@ export async function processNewickAndMetadata(data, sendStatusMessage) {
  }
  });
 
-
  if (this_metadata) {
  Object.assign(node, this_metadata);
  }
-
  });
 
  return tree;