archaeopteryx 1.0.9 → 2.3.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/LICENSE +504 -0
- package/README.md +206 -103
- package/archaeopteryx.js +8596 -7224
- package/forester.js +1748 -1905
- package/package.json +17 -11
- package/forester_example.js +0 -25
package/package.json
CHANGED
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@@ -1,8 +1,14 @@
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{
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"name": "archaeopteryx",
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"version": "
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"version": "2.3.2",
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"description": "Archaeopteryx.js is a software tool for the visualization and analysis of highly annotated phylogenetic trees.",
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"main": "archaeopteryx.js",
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"files": [
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"archaeopteryx.js",
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"forester.js",
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"README.md",
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"LICENSE"
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],
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"scripts": {
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"test": "echo \"Error: no test specified\" && exit 1"
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},
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@@ -11,15 +17,15 @@
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"url": "git+https://github.com/cmzmasek/archaeopteryx-js.git"
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},
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"dependencies": {
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"phyloxml"
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"jquery-ui"
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"phyloxml": ">=0.9.16",
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"d3": "~3.5.17",
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"jquery": "~1.12.4",
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"jquery-ui": "~1.12.1",
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"canvg": "~1.5.3",
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"rgbcolor": "~1.0.1",
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"Blob.js": "git+https://github.com/eligrey/Blob.js.git",
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"canvas-toBlob.js": "git+https://github.com/eligrey/canvas-toBlob.js.git",
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"file-saver": "git+https://github.com/eligrey/FileSaver.js"
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},
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"keywords": [
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"archaeopteryx",
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"visualization"
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],
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"author": "Chris Zmasek",
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"license": "LGPL-2.1",
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"license": "LGPL-2.1-or-later",
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"bugs": {
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"url": "https://github.com/cmzmasek/archaeopteryx-js/issues"
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},
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package/forester_example.js
DELETED
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@@ -1,25 +0,0 @@
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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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var forester = require('./forester').forester;
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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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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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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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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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