archaeopteryx 1.0.9 → 2.3.2

package/README.md

@@ -1,103 +1,206 @@
-# archaeopteryx-js
-Archaeopteryx.js is a software tool for the visualization and analysis of highly annotated phylogenetic trees.
-
-
-### Website
-https://sites.google.com/site/cmzmasek/home/software/archaeopteryx-js
-
-
-### Examples
-
-* http://www.phyloxml.org/archaeopteryx-js/euk_tol_collapsed_js.html
-
-* http://www.phyloxml.org/archaeopteryx-js/bcl2_js.html
-
-* http://www.phyloxml.org/archaeopteryx-js/influenza_ha_js.html
-
-
-### Detailed developer documentation
-https://docs.google.com/document/d/1COVe0iYbKtcBQxGTP4_zuimpk2FH9iusOVOgd5xCJ3A/edit
-
-
-### Dependencies
-Archaeopteryx.js has the following dependencies:
-* d3.js 
-* jQuery
-* jQuery UI
-* sax.js
-* phyloxml.js
-* forester.js
-
-For file (Newick/New Hampshire, phyloXML) and graphics (PNG, SVG) download/export, the following five libraries are required as well:
-* canvg
-* rgbcolor
-* Blob
-* canvas-toBlob (needed in some versions of Internet Explorer and Opera)
-* FileSaver
-
-Additionally, Archaeopteryx.js also requires the following CSS:
-* jquery-ui.css
-
-
-
-# forester
-forester is a general suite for dealing with phylogenetic trees.
-
-## forester Example
-
-This basic example shows how to parse a New Hampshire formatted String
-into to a object representing a phylogenetic tree.
-Followed by pre- and post-order traversal,
-and writing back to a New Hampshire formatted String.
-
-Change './forester' to 'forester' if you use this code outside of this package
-
-```
-var forester = require('./forester').forester;
-
-var newHampshireFormattedString = "(((a:1,b:1,c:1)N:2,(d:1,e:1)M:4)O:4,f:1)R:1;";
-var phylogeneticTree = forester.parseNewHampshire(newHampshireFormattedString);
-
-console.log('Pre-order traversal:');
-forester.preOrderTraversalAll(forester.getTreeRoot(phylogeneticTree), function (n) {
-    console.log(n.name + ':' + n.branch_length);
-});
-
-console.log('Post-order traversal:');
-forester.postOrderTraversalAll(forester.getTreeRoot(phylogeneticTree), function (n) {
-    console.log(n.name + ':' + n.branch_length);
-});
-
-console.log('In New Hampshire format:');
-var nh = forester.toNewHampshire(phylogeneticTree);
-console.log(nh);
-```
-
-Expected output:
-
-```
-Pre-order traversal:
-R:1
-f:1
-O:4
-M:4
-e:1
-d:1
-N:2
-c:1
-b:1
-a:1
-Post-order traversal:
-a:1
-b:1
-c:1
-N:2
-d:1
-e:1
-M:4
-O:4
-f:1
-R:1
-In New Hampshire format:
-(((a:1,b:1,c:1)N:2,(d:1,e:1)M:4)O:4,f:1)R:1;
-```
+# Archaeopteryx.js
+Archaeopteryx.js is a software tool for the visualization and analysis of highly annotated phylogenetic trees.
+
+
+### Website
+https://sites.google.com/view/archaeopteryxjs
+
+### npm
+https://www.npmjs.com/package/archaeopteryx
+
+### GitHub
+https://github.com/cmzmasek/archaeopteryx-js
+
+
+### Examples
+
+* [Bcl-2 gene family](http://www.phyloxml.org/archaeopteryx-js/bcl2_js.html)
+* Eukaryotic tree of life:
+  * [collapsed with initial depth = 5](http://www.phyloxml.org/archaeopteryx-js/euk_tol_collapsed_js.html)
+  * [uncollapsed](http://www.phyloxml.org/archaeopteryx-js/euk_tol_js.html)
+* [Influenza HA H3 collapsed by Country](http://www.phyloxml.org/archaeopteryx-js/influenza_collapsed.html)
+* [Amphibian phylogeny](http://www.phyloxml.org/archaeopteryx-js/amphi_frost_js.html)
+* Visualizations:
+  * [Herpesviridae DNA polymerases](http://www.phyloxml.org/archaeopteryx-js/hg1001_js.html)
+* RAxML examples:
+  * [bipartitions](http://www.phyloxml.org/archaeopteryx-js/raxml_bipartitions_bcl2_js.html)
+  * [bipartitionsBranchLabels](http://www.phyloxml.org/archaeopteryx-js/raxml_bipartitions_branchlabels_bcl2_js.html)
+* MSA Residue Visualization:
+  * [Bunyaviridae Glycoprotein](http://www.phyloxml.org/archaeopteryx-js/bunya_glycoprotein.html)
+  * [Bcl-2 protein](http://www.phyloxml.org/archaeopteryx-js/bcl2_msa.html)
+* Preset search fields:
+  * [H3N2](http://www.phyloxml.org/archaeopteryx-js/h3n2_search_js.html)
+* Grouping of species and years for visualization:
+  * [Viral Strains](http://www.phyloxml.org/archaeopteryx-js/many_species_js.html)
+* SARS-CoV-2 with mutations and PANGO lineages:
+  * [SARS-CoV-2](http://www.phyloxml.org/archaeopteryx-js/sars_cov_3.html)
+
+
+### Detailed developer documentation
+https://docs.google.com/document/d/1COVe0iYbKtcBQxGTP4_zuimpk2FH9iusOVOgd5xCJ3A/edit
+
+### Version History
+https://github.com/cmzmasek/archaeopteryx-js/wiki/Archaeopteryx.js-Version-History
+
+### Dependencies
+Archaeopteryx.js has the following dependencies:
+ * forester.js: https://www.npmjs.com/package/archaeopteryx
+ * phyloxml.js: https://www.npmjs.com/package/phyloxml
+ * d3.js (version 3): https://www.npmjs.com/package/d3/v/3.5.17
+ * jQuery (1.12.4): https://www.npmjs.com/package/jquery/v/1.12.4
+ * jQuery UI (1.12.1): https://www.npmjs.com/package/jquery-ui/v/1.12.1
+ * sax.js (1.2.4): https://www.npmjs.com/package/sax/v/1.2.4
+ 
+For file (Newick/New Hampshire, phyloXML) and graphics (PNG, SVG)
+download/export, the following five libraries are required as well:
+ * canvg: https://www.npmjs.com/package/canvg
+ * rgbcolor: https://www.npmjs.com/package/rgbcolor
+ * Blob.js: https://github.com/eligrey/Blob.js
+ * canvas-toBlob.js (needed in some versions of Internet Explorer and Opera): https://github.com/eligrey/canvas-toBlob.js
+ * FileSaver.js: https://github.com/eligrey/FileSaver.js
+ 
+Additionally, Archaeopteryx.js also requires the following CSS:
+ * jquery-ui.css: https://code.jquery.com/ui/1.12.0/themes/base/jquery-ui.css
+
+
+## Basic Example of HTML for launching Archaeopteryx.js
+
+Example of HTML page to launch a basic Archaeopteryx.js instance:
+```
+<!DOCTYPE html>
+<meta charset="utf-8">
+<head>
+   <title>Archaeopteryx.js Basic Demo</title>
+
+   <!-- For MS IE/Edge compatibility:-->
+   <meta http-equiv="X-UA-Compatible" content="IE=100">
+
+   <!-- D3.js, jQuery, and jQuery UI:-->
+   <script src="http://d3js.org/d3.v3.min.js"></script>
+   <script src="https://code.jquery.com/jquery-1.12.4.js"></script>
+   <script src="https://code.jquery.com/ui/1.12.0/jquery-ui.js"></script>
+
+   <!-- SAX XML parser:-->
+   <script src="http://www.phyloxml.org/js/dependencies/sax.js"></script>
+
+   <!-- Archaeopteryx.js requires forester.js and phyloxml.js:-->
+   <script src="http://path/to/phyloxml.js"></script>
+   <script src="http://path/to/forester.js"></script>
+   <script src="http://path/to/archaeopteryx.js"></script>
+
+   <!-- CSS for jQuery UI: -->
+   <link rel="stylesheet" href="https://code.jquery.com/ui/1.12.0/themes/base/jquery-ui.css">
+
+   <script>
+       function load() {
+           var options = {};
+           options.backgroundColorDefault = '#f0f0f0';
+           var settings = {};
+           var loc = 'https://raw.githubusercontent.com/cmzmasek/archaeopteryx-js/master/test/data/phyloxml_trees/apaf.xml';
+
+           jQuery.get(loc,
+                   function (data) {
+                       var tree = null;
+                       try {
+                           tree = archaeopteryx.parseTree(loc, data, true, false);
+                       }
+                       catch (e) {
+                           alert("error while parsing tree: " + e);
+                       }
+                       if (tree) {
+                           try {
+                               archaeopteryx.launch('#phylogram1', tree, options, settings);
+                           }
+                           catch (e) {
+                               alert("error while launching archaeopteryx: " + e);
+                           }
+                       }
+                   },
+                   "text")
+                   .fail(function () {
+                               alert("error: failed to read tree(s) from \"" + loc + "\"");
+                           }
+                   );
+       }
+   </script>
+</head>
+
+<body onload="load()">
+<div>
+   <h2>Archaeopteryx.js Basic Demo</h2>
+   <div id='phylogram1'></div>
+   <div id='controls0' class='ui-widget-content'></div>
+</div>
+</body>
+```
+
+
+
+
+# forester.js
+forester.js is a general suite for dealing with phylogenetic trees.
+
+## forester.js Example
+
+This basic example shows how to parse a New Hampshire formatted String
+into to a object representing a phylogenetic tree.
+Followed by pre- and post-order traversal,
+and writing back to a New Hampshire formatted String.
+
+Change './forester' to 'forester' if you use this code outside of this package
+
+```
+var forester = require('./forester').forester;
+
+var newHampshireFormattedString = "(((a:1,b:1,c:1)N:2,(d:1,e:1)M:4)O:4,f:1)R:1;";
+var phylogeneticTree = forester.parseNewHampshire(newHampshireFormattedString);
+
+console.log('Pre-order traversal:');
+forester.preOrderTraversalAll(forester.getTreeRoot(phylogeneticTree), function (n) {
+    console.log(n.name + ':' + n.branch_length);
+});
+
+console.log('Post-order traversal:');
+forester.postOrderTraversalAll(forester.getTreeRoot(phylogeneticTree), function (n) {
+    console.log(n.name + ':' + n.branch_length);
+});
+
+console.log('In New Hampshire format:');
+var nh = forester.toNewHampshire(phylogeneticTree);
+console.log(nh);
+```
+
+Expected output:
+
+```
+Pre-order traversal:
+R:1
+f:1
+O:4
+M:4
+e:1
+d:1
+N:2
+c:1
+b:1
+a:1
+Post-order traversal:
+a:1
+b:1
+c:1
+N:2
+d:1
+e:1
+M:4
+O:4
+f:1
+R:1
+In New Hampshire format:
+(((a:1,b:1,c:1)N:2,(d:1,e:1)M:4)O:4,f:1)R:1;
+```
+
+
+
+
+
+