Tree algorithms - #1
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akdel wants to merge 42 commits into
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added 30 commits
August 1, 2020 20:53
1. leaves property is a generator 2. added names to from_dict method 3. root property 4. find leaf by name
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August 5, 2020 01:38
holmrenser
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Aug 13, 2020
holmrenser
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holmrenser
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I have some comments on the clade and clades classes.
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| @dataclass | ||
| class Clade: | ||
| internode: Tree | ||
| clade: Set[str] | ||
| depth: int | ||
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| @classmethod | ||
| def from_internode(cls, internode: Tree, banned: [None, Set[str]] = None) -> 'Clade': | ||
| """ | ||
| Creates Clade from a given internode. | ||
| :param internode: A node which is not a leaf. | ||
| :param banned: banned node names. | ||
| :return: Clade instance | ||
| """ | ||
| assert internode.children is not None # makes sure that it's not a leaf | ||
| if banned is None: | ||
| banned = set() | ||
| clade: Set[str] = {x.name for x in internode.leaves if x.name not in banned} # removes any banned leaves. this is used in bootstrapping. | ||
| return cls(internode, clade, internode.depth) | ||
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| def compare_to(self, other: 'Clade') -> bool: | ||
| """ | ||
| Compares the clade leaves to another. | ||
| :param other: Clade instance to be compared | ||
| :return: returns True if clades are equal. | ||
| """ | ||
| if self.clade == other.clade: | ||
| return True | ||
| else: | ||
| return False |
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In my perspective a clade is a subtree. What is the use of making this a separate class?
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yes, you're right. I wasn't sure where I was going in the beginning, that's why I didn't want to touch the main class. I'll add them as a Tree method
added 4 commits
August 13, 2020 14:52
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Nj-tree with bootstrapping