forked from williamdlees/TRIgS
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RenderTree.py
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RenderTree.py
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# Copyright (c) 2015 William Lees
# Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated
# documentation files (the "Software"), to deal in the Software without restriction, including without limitation the
# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit
# persons to whom the Software is furnished to do so, subject to the following conditions:
# The above copyright notice and this permission notice shall be included in all copies or substantial portions of the
# Software.
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
# WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
# COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
# OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
# Various methods to render trees for the website
__author__ = 'William Lees'
__docformat__ = "restructuredtext en"
from ete2 import Tree, TreeStyle, TextFace, NodeStyle
class RenderTree():
def __init__(self):
pass
@staticmethod
def render_annotate(newick_path, output_path):
"""Render the annotated tree, showing internal node names.
The output_path should end in .PNG, .PDF or .SVG: this will determine the format.
To aid in testing, if output_path is None, the tree is shown rather than rendered.
"""
tree = Tree(newick_path, format=1)
ts = TreeStyle()
ts.show_leaf_name = True
ts.branch_vertical_margin = 15
ns = NodeStyle()
ns["size"] = 1
edge = 0
for node in tree.traverse():
node.name = node.name.replace("'", "")
node.name = node.name.replace("+", ",")
if not node.is_leaf() and node.name != 'NoName':
f = TextFace(node.name)
f.margin_top = 5
f.margin_bottom = 5
f.margin_right = 10
f.margin_left = 10
edge += 1
node.add_face(f, column=0, position="branch-top")
if output_path is None:
tree.show(tree_style=ts)
else:
tree.render(output_path)
if __name__ == '__main__':
RenderTree.render_annotate("C:\\Users\\william\\Dropbox (Personal)\\Research\\TreeAnnotateApp\\temp\\tmpviamgd\\annotated_treefile.new", None)