archaeopteryx 1.8.1 → 2.3.2

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Files changed (6) hide show
  1. package/LICENSE +504 -0
  2. package/README.md +206 -203
  3. package/archaeopteryx.js +8596 -7248
  4. package/forester.js +1748 -1943
  5. package/package.json +17 -11
  6. package/forester_example.js +0 -25
package/README.md CHANGED
@@ -1,203 +1,206 @@
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- # Archaeopteryx.js
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- Archaeopteryx.js is a software tool for the visualization and analysis of highly annotated phylogenetic trees.
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-
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-
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- ### Website
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- https://sites.google.com/site/cmzmasek/home/software/archaeopteryx-js
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-
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- ### npm
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- https://www.npmjs.com/package/archaeopteryx
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-
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- ### GitHub
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- https://github.com/cmzmasek/archaeopteryx-js
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-
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-
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- ### Examples
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-
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- * [Bcl-2 gene family](http://www.phyloxml.org/archaeopteryx-js/bcl2_js.html)
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- * Eukaryotic tree of life:
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- * [collapsed with initial depth = 5](http://www.phyloxml.org/archaeopteryx-js/euk_tol_collapsed_js.html)
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- * [uncollapsed](http://www.phyloxml.org/archaeopteryx-js/euk_tol_js.html)
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- * [Influenza HA H3 collapsed by Country](http://www.phyloxml.org/archaeopteryx-js/influenza_collapsed.html)
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- * [Amphibian phylogeny](http://www.phyloxml.org/archaeopteryx-js/amphi_frost_js.html)
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- * Visualizations:
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- * [Herpesviridae DNA polymerases](http://www.phyloxml.org/archaeopteryx-js/hg1001_js.html)
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- * RAxML examples:
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- * [bipartitions](http://www.phyloxml.org/archaeopteryx-js/raxml_bipartitions_bcl2_js.html)
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- * [bipartitionsBranchLabels](http://www.phyloxml.org/archaeopteryx-js/raxml_bipartitions_branchlabels_bcl2_js.html)
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- * MSA Residue Visualization:
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- * [Bunyaviridae Glycoprotein](http://www.phyloxml.org/archaeopteryx-js/bunya_glycoprotein.html)
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- * [Bcl-2 protein](http://www.phyloxml.org/archaeopteryx-js/bcl2_msa.html)
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- * Preset search fields:
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- * [H3N2](http://www.phyloxml.org/archaeopteryx-js/h3n2_search_js.html)
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- * Grouping of species and years for visualization:
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- * [Viral Strains](http://www.phyloxml.org/archaeopteryx-js/many_species_js.html)
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-
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-
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-
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- ### Detailed developer documentation
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- https://docs.google.com/document/d/1COVe0iYbKtcBQxGTP4_zuimpk2FH9iusOVOgd5xCJ3A/edit
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-
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-
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- ### Dependencies
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- Archaeopteryx.js has the following dependencies:
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- * forester.js: https://www.npmjs.com/package/archaeopteryx
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- * phyloxml.js: https://www.npmjs.com/package/phyloxml
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- * d3.js (version 3): https://www.npmjs.com/package/d3/v/3.5.17
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- * jQuery (1.12.4): https://www.npmjs.com/package/jquery/v/1.12.4
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- * jQuery UI (1.12.1): https://www.npmjs.com/package/jquery-ui/v/1.12.1
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- * sax.js (1.2.4): https://www.npmjs.com/package/sax/v/1.2.4
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-
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- For file (Newick/New Hampshire, phyloXML) and graphics (PNG, SVG)
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- download/export, the following five libraries are required as well:
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- * canvg: https://www.npmjs.com/package/canvg
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- * rgbcolor: https://www.npmjs.com/package/rgbcolor
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- * Blob.js: https://github.com/eligrey/Blob.js
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- * canvas-toBlob.js (needed in some versions of Internet Explorer and Opera): https://github.com/eligrey/canvas-toBlob.js
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- * FileSaver.js: https://github.com/eligrey/FileSaver.js
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-
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- Additionally, Archaeopteryx.js also requires the following CSS:
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- * jquery-ui.css: https://code.jquery.com/ui/1.12.0/themes/base/jquery-ui.css
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-
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-
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- ## Basic Example of HTML for launching Archaeopteryx.js
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-
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- Example of HTML page to launch a basic Archaeopteryx.js instance:
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- ```
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- <!DOCTYPE html>
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- <meta charset="utf-8">
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- <head>
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- <title>Archaeopteryx.js Basic Demo</title>
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-
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- <!-- For MS IE/Edge compatibility:-->
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- <meta http-equiv="X-UA-Compatible" content="IE=100">
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-
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- <!-- D3.js, jQuery, and jQuery UI:-->
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- <script src="http://d3js.org/d3.v3.min.js"></script>
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- <script src="https://code.jquery.com/jquery-1.12.4.js"></script>
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- <script src="https://code.jquery.com/ui/1.12.0/jquery-ui.js"></script>
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-
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- <!-- SAX XML parser:-->
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- <script src="http://www.phyloxml.org/js/dependencies/sax.js"></script>
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-
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- <!-- Archaeopteryx.js requires forester.js and phyloxml.js:-->
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- <script src="http://path/to/phyloxml.js"></script>
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- <script src="http://path/to/forester.js"></script>
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- <script src="http://path/to/archaeopteryx.js"></script>
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-
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- <!-- CSS for jQuery UI: -->
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- <link rel="stylesheet" href="https://code.jquery.com/ui/1.12.0/themes/base/jquery-ui.css">
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-
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- <script>
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- function load() {
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- var options = {};
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- options.backgroundColorDefault = '#f0f0f0';
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- var settings = {};
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- var loc = 'https://raw.githubusercontent.com/cmzmasek/archaeopteryx-js/master/test/data/phyloxml_trees/apaf.xml';
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-
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- jQuery.get(loc,
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- function (data) {
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- var tree = null;
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- try {
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- tree = archaeopteryx.parseTree(loc, data, true, false);
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- }
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- catch (e) {
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- alert("error while parsing tree: " + e);
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- }
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- if (tree) {
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- try {
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- archaeopteryx.launch('#phylogram1', tree, options, settings);
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- }
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- catch (e) {
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- alert("error while launching archaeopteryx: " + e);
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- }
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- }
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- },
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- "text")
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- .fail(function () {
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- alert("error: failed to read tree(s) from \"" + loc + "\"");
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- }
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- );
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- }
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- </script>
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- </head>
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-
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- <body onload="load()">
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- <div>
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- <h2>Archaeopteryx.js Basic Demo</h2>
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- <div id='phylogram1'></div>
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- <div id='controls0' class='ui-widget-content'></div>
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- </div>
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- </body>
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- ```
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-
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-
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-
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-
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- # forester.js
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- forester.js is a general suite for dealing with phylogenetic trees.
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-
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- ## forester.js Example
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-
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- This basic example shows how to parse a New Hampshire formatted String
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- into to a object representing a phylogenetic tree.
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- Followed by pre- and post-order traversal,
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- and writing back to a New Hampshire formatted String.
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-
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- Change './forester' to 'forester' if you use this code outside of this package
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-
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- ```
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- var forester = require('./forester').forester;
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-
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- var newHampshireFormattedString = "(((a:1,b:1,c:1)N:2,(d:1,e:1)M:4)O:4,f:1)R:1;";
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- var phylogeneticTree = forester.parseNewHampshire(newHampshireFormattedString);
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-
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- console.log('Pre-order traversal:');
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- forester.preOrderTraversalAll(forester.getTreeRoot(phylogeneticTree), function (n) {
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- console.log(n.name + ':' + n.branch_length);
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- });
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-
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- console.log('Post-order traversal:');
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- forester.postOrderTraversalAll(forester.getTreeRoot(phylogeneticTree), function (n) {
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- console.log(n.name + ':' + n.branch_length);
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- });
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-
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- console.log('In New Hampshire format:');
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- var nh = forester.toNewHampshire(phylogeneticTree);
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- console.log(nh);
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- ```
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-
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- Expected output:
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-
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- ```
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- Pre-order traversal:
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- R:1
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- f:1
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- O:4
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- M:4
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- e:1
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- d:1
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- N:2
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- c:1
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- b:1
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- a:1
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- Post-order traversal:
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- a:1
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- b:1
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- c:1
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- N:2
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- d:1
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- e:1
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- M:4
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- O:4
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- f:1
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- R:1
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- In New Hampshire format:
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- (((a:1,b:1,c:1)N:2,(d:1,e:1)M:4)O:4,f:1)R:1;
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- ```
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-
199
-
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-
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-
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-
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-
1
+ # Archaeopteryx.js
2
+ Archaeopteryx.js is a software tool for the visualization and analysis of highly annotated phylogenetic trees.
3
+
4
+
5
+ ### Website
6
+ https://sites.google.com/view/archaeopteryxjs
7
+
8
+ ### npm
9
+ https://www.npmjs.com/package/archaeopteryx
10
+
11
+ ### GitHub
12
+ https://github.com/cmzmasek/archaeopteryx-js
13
+
14
+
15
+ ### Examples
16
+
17
+ * [Bcl-2 gene family](http://www.phyloxml.org/archaeopteryx-js/bcl2_js.html)
18
+ * Eukaryotic tree of life:
19
+ * [collapsed with initial depth = 5](http://www.phyloxml.org/archaeopteryx-js/euk_tol_collapsed_js.html)
20
+ * [uncollapsed](http://www.phyloxml.org/archaeopteryx-js/euk_tol_js.html)
21
+ * [Influenza HA H3 collapsed by Country](http://www.phyloxml.org/archaeopteryx-js/influenza_collapsed.html)
22
+ * [Amphibian phylogeny](http://www.phyloxml.org/archaeopteryx-js/amphi_frost_js.html)
23
+ * Visualizations:
24
+ * [Herpesviridae DNA polymerases](http://www.phyloxml.org/archaeopteryx-js/hg1001_js.html)
25
+ * RAxML examples:
26
+ * [bipartitions](http://www.phyloxml.org/archaeopteryx-js/raxml_bipartitions_bcl2_js.html)
27
+ * [bipartitionsBranchLabels](http://www.phyloxml.org/archaeopteryx-js/raxml_bipartitions_branchlabels_bcl2_js.html)
28
+ * MSA Residue Visualization:
29
+ * [Bunyaviridae Glycoprotein](http://www.phyloxml.org/archaeopteryx-js/bunya_glycoprotein.html)
30
+ * [Bcl-2 protein](http://www.phyloxml.org/archaeopteryx-js/bcl2_msa.html)
31
+ * Preset search fields:
32
+ * [H3N2](http://www.phyloxml.org/archaeopteryx-js/h3n2_search_js.html)
33
+ * Grouping of species and years for visualization:
34
+ * [Viral Strains](http://www.phyloxml.org/archaeopteryx-js/many_species_js.html)
35
+ * SARS-CoV-2 with mutations and PANGO lineages:
36
+ * [SARS-CoV-2](http://www.phyloxml.org/archaeopteryx-js/sars_cov_3.html)
37
+
38
+
39
+ ### Detailed developer documentation
40
+ https://docs.google.com/document/d/1COVe0iYbKtcBQxGTP4_zuimpk2FH9iusOVOgd5xCJ3A/edit
41
+
42
+ ### Version History
43
+ https://github.com/cmzmasek/archaeopteryx-js/wiki/Archaeopteryx.js-Version-History
44
+
45
+ ### Dependencies
46
+ Archaeopteryx.js has the following dependencies:
47
+ * forester.js: https://www.npmjs.com/package/archaeopteryx
48
+ * phyloxml.js: https://www.npmjs.com/package/phyloxml
49
+ * d3.js (version 3): https://www.npmjs.com/package/d3/v/3.5.17
50
+ * jQuery (1.12.4): https://www.npmjs.com/package/jquery/v/1.12.4
51
+ * jQuery UI (1.12.1): https://www.npmjs.com/package/jquery-ui/v/1.12.1
52
+ * sax.js (1.2.4): https://www.npmjs.com/package/sax/v/1.2.4
53
+
54
+ For file (Newick/New Hampshire, phyloXML) and graphics (PNG, SVG)
55
+ download/export, the following five libraries are required as well:
56
+ * canvg: https://www.npmjs.com/package/canvg
57
+ * rgbcolor: https://www.npmjs.com/package/rgbcolor
58
+ * Blob.js: https://github.com/eligrey/Blob.js
59
+ * canvas-toBlob.js (needed in some versions of Internet Explorer and Opera): https://github.com/eligrey/canvas-toBlob.js
60
+ * FileSaver.js: https://github.com/eligrey/FileSaver.js
61
+
62
+ Additionally, Archaeopteryx.js also requires the following CSS:
63
+ * jquery-ui.css: https://code.jquery.com/ui/1.12.0/themes/base/jquery-ui.css
64
+
65
+
66
+ ## Basic Example of HTML for launching Archaeopteryx.js
67
+
68
+ Example of HTML page to launch a basic Archaeopteryx.js instance:
69
+ ```
70
+ <!DOCTYPE html>
71
+ <meta charset="utf-8">
72
+ <head>
73
+ <title>Archaeopteryx.js Basic Demo</title>
74
+
75
+ <!-- For MS IE/Edge compatibility:-->
76
+ <meta http-equiv="X-UA-Compatible" content="IE=100">
77
+
78
+ <!-- D3.js, jQuery, and jQuery UI:-->
79
+ <script src="http://d3js.org/d3.v3.min.js"></script>
80
+ <script src="https://code.jquery.com/jquery-1.12.4.js"></script>
81
+ <script src="https://code.jquery.com/ui/1.12.0/jquery-ui.js"></script>
82
+
83
+ <!-- SAX XML parser:-->
84
+ <script src="http://www.phyloxml.org/js/dependencies/sax.js"></script>
85
+
86
+ <!-- Archaeopteryx.js requires forester.js and phyloxml.js:-->
87
+ <script src="http://path/to/phyloxml.js"></script>
88
+ <script src="http://path/to/forester.js"></script>
89
+ <script src="http://path/to/archaeopteryx.js"></script>
90
+
91
+ <!-- CSS for jQuery UI: -->
92
+ <link rel="stylesheet" href="https://code.jquery.com/ui/1.12.0/themes/base/jquery-ui.css">
93
+
94
+ <script>
95
+ function load() {
96
+ var options = {};
97
+ options.backgroundColorDefault = '#f0f0f0';
98
+ var settings = {};
99
+ var loc = 'https://raw.githubusercontent.com/cmzmasek/archaeopteryx-js/master/test/data/phyloxml_trees/apaf.xml';
100
+
101
+ jQuery.get(loc,
102
+ function (data) {
103
+ var tree = null;
104
+ try {
105
+ tree = archaeopteryx.parseTree(loc, data, true, false);
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+ }
107
+ catch (e) {
108
+ alert("error while parsing tree: " + e);
109
+ }
110
+ if (tree) {
111
+ try {
112
+ archaeopteryx.launch('#phylogram1', tree, options, settings);
113
+ }
114
+ catch (e) {
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+ alert("error while launching archaeopteryx: " + e);
116
+ }
117
+ }
118
+ },
119
+ "text")
120
+ .fail(function () {
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+ alert("error: failed to read tree(s) from \"" + loc + "\"");
122
+ }
123
+ );
124
+ }
125
+ </script>
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+ </head>
127
+
128
+ <body onload="load()">
129
+ <div>
130
+ <h2>Archaeopteryx.js Basic Demo</h2>
131
+ <div id='phylogram1'></div>
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+ <div id='controls0' class='ui-widget-content'></div>
133
+ </div>
134
+ </body>
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+ ```
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+
137
+
138
+
139
+
140
+ # forester.js
141
+ forester.js is a general suite for dealing with phylogenetic trees.
142
+
143
+ ## forester.js Example
144
+
145
+ This basic example shows how to parse a New Hampshire formatted String
146
+ into to a object representing a phylogenetic tree.
147
+ Followed by pre- and post-order traversal,
148
+ and writing back to a New Hampshire formatted String.
149
+
150
+ Change './forester' to 'forester' if you use this code outside of this package
151
+
152
+ ```
153
+ var forester = require('./forester').forester;
154
+
155
+ var newHampshireFormattedString = "(((a:1,b:1,c:1)N:2,(d:1,e:1)M:4)O:4,f:1)R:1;";
156
+ var phylogeneticTree = forester.parseNewHampshire(newHampshireFormattedString);
157
+
158
+ console.log('Pre-order traversal:');
159
+ forester.preOrderTraversalAll(forester.getTreeRoot(phylogeneticTree), function (n) {
160
+ console.log(n.name + ':' + n.branch_length);
161
+ });
162
+
163
+ console.log('Post-order traversal:');
164
+ forester.postOrderTraversalAll(forester.getTreeRoot(phylogeneticTree), function (n) {
165
+ console.log(n.name + ':' + n.branch_length);
166
+ });
167
+
168
+ console.log('In New Hampshire format:');
169
+ var nh = forester.toNewHampshire(phylogeneticTree);
170
+ console.log(nh);
171
+ ```
172
+
173
+ Expected output:
174
+
175
+ ```
176
+ Pre-order traversal:
177
+ R:1
178
+ f:1
179
+ O:4
180
+ M:4
181
+ e:1
182
+ d:1
183
+ N:2
184
+ c:1
185
+ b:1
186
+ a:1
187
+ Post-order traversal:
188
+ a:1
189
+ b:1
190
+ c:1
191
+ N:2
192
+ d:1
193
+ e:1
194
+ M:4
195
+ O:4
196
+ f:1
197
+ R:1
198
+ In New Hampshire format:
199
+ (((a:1,b:1,c:1)N:2,(d:1,e:1)M:4)O:4,f:1)R:1;
200
+ ```
201
+
202
+
203
+
204
+
205
+
206
+