Merge pull request #40 from clockor2/documentation

📝 add fetch example

docs/examples/fetch.md

@@ -0,0 +1,15 @@
+Here, we demonstrate how to read in a tree from a url using a `fetch()` request from the fetch API. In this case, we are reading in a list of trees used for testing.
+
+```typescript
+    let url = 'https://raw.githubusercontent.com/clockor2/phylojs/main/test/data/egTree.nwk'
+    let newick;
+
+    fetch(url)
+      .then(res => res.text())
+      .then(txt => {newick = txt})
+
+    // log first 99 characters to show newick is defined
+    console.log(newick.slice(0,99))
+    // Returns:
+    // (Jeddah-1_KF917527_camel_2013-11-08:0.0000013865,Jeddah-1_KF958702_human_2013-11-05:0.0000013652,((
+```

docs/examples/test/examples.spec.ts

@@ -2,7 +2,7 @@
 //////// Testing examples for documentation /////////
 /////////////////////////////////////////////////////
 
-import { readNewick, readTreesFromPhyloXML, writeNewick, Tree } from '@phylojs';
+import { readNewick, readTreesFromPhyloXML, readTreesFromNewick, writeNewick, Tree } from '@phylojs';
 
 describe('Examples', () => {
   test('RTTR', () => {
@@ -192,6 +192,43 @@ describe('Examples', () => {
     expect(inNewick).not.toEqual(outNewick)
   })
 
+  test('multiple trees with newick', () => {
+    // Using two small trees here
+
+    const inNewick = '((A:1,B:1):1,C:1);\n((A:1,B:1):1,C:1);'
+    let trees = readTreesFromNewick(inNewick);
+
+    // Operate on trees using array methods. E.g. Reroot, ladderise, and scale branch lengths randomly
+
+    trees.forEach(t => t.reroot(t.nodeList[4])) // arbitrarily to 4th node
+    trees.forEach(t => t.ladderise())
+    trees.forEach(t => t.nodeList.forEach(
+      n => n.branchLength ? n.branchLength *= Math.floor(10*Math.random() + 1) : 0
+    ))
+
+    // write output
+    let outNewick = trees.map(t => writeNewick(t)).join('\n')
+
+    expect(inNewick).not.toEqual(outNewick)
+  })
+
+  // COMMENTED OUT BC JEST DOESN'T LIKE FETCH API
+  // test('multiple trees with fetch', () => {
+  //   // Using two small trees here
+
+  //   let url = 'https://raw.githubusercontent.com/clockor2/phylojs/main/test/data/egTree.nwk'
+  //   let newick;
+
+  //   fetch(url)
+  //     .then(res => res.text())
+  //     .then(txt => {newick = txt})
+
+  //   // log first 99 characters to show newick is defined
+  //   console.log(newick.slice(0,99))
+  //   // Returns:
+  //   // (Jeddah-1_KF917527_camel_2013-11-08:0.0000013865,Jeddah-1_KF958702_human_2013-11-05:0.0000013652,((
+  // })
+
   test('getBranchLengthRatio()', () => {
     function getBranchLengthRatio(tree: Tree): number {
 

docs/examples/treeArray.md

@@ -44,9 +44,12 @@ In the below example, we parse two trees from phyloXML format, reroot them, resc
     </phylogeny>
     </phyloxml>`;
 
+    let in = fetch('https://raw.githubusercontent.com/clockor2/phylojs/main/test/data/egTree.nwk')
+        .then(res => res.text())
+        .then(nwk => console.log(nwk))
     // Read trees
-    let trees = readTreesFromPhyloXML(inPhyloXML);
-
+    //let trees = readTreesFromPhyloXML(inPhyloXML);
+    
     // Operate on trees using array methods. E.g. reroot, ladderise, and scale branch lengths randomly
     trees.forEach(t => t.reroot(t.nodeList[4])) // arbitrarily on branch to 4th node
     trees.forEach(t => t.ladderise())

mkdocs.yml

@@ -54,6 +54,7 @@ nav:
     - examples/index.md
     - Overview of the Tree Class: examples/tree.md
     - Visualise: examples/visualise.md
+    - Fetching Trees fron a URL: examples/fetch.md
     - Finding the MRCA: examples/mrca.md
     - Root-to-tip regression: examples/rttr.md
     - Rerooting: examples/reroot.md