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Python Node.treename方法代码示例

本文整理汇总了Python中tree.Node.treename方法的典型用法代码示例。如果您正苦于以下问题:Python Node.treename方法的具体用法?Python Node.treename怎么用?Python Node.treename使用的例子?那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在tree.Node的用法示例。


在下文中一共展示了Node.treename方法的1个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的Python代码示例。

示例1: parse

# 需要导入模块: from tree import Node [as 别名]
# 或者: from tree.Node import treename [as 别名]
def parse(data, ttable=None, treename=None):
    """
    Parse a newick string.

    *data* is any file-like object that can be coerced into shlex, or
    a string (converted to StringIO)

    *ttable* is a dictionary mapping node labels in the newick string
     to other values.

    Returns: the root node.
    """
    from tree import Node, Tree
    
    if type(data) in types.StringTypes:
        data = StringIO(data)
    
    start_pos = data.tell()
    tokens = Tokenizer(data)

    node = None; root = None
    lp=0; rp=0; rooted=1

    previous = None

    ni = 0 # node id counter (preorder) - zero-based indexing
    li = 0 # leaf index counter
    ii = 0 # internal node index counter
    pi = 0 # postorder sequence
    while 1:
        token = tokens.get_token()
        if token == ';' or token == tokens.eof:
            assert lp == rp, \
                   "unbalanced parentheses in tree description: (%s, %s)" \
                   % (lp, rp)
            break

        # internal node
        elif token == '(':
            lp = lp+1
            newnode = Node()
            newnode.ni = ni; ni += 1
            ## newnode.isleaf = False
            newnode.treename = treename
            if node:
                if node.children: newnode.left = node.children[-1].right+1
                else: newnode.left = node.left+1
                node.add_child(newnode)
            else:
                newnode.left = 1
            newnode.right = newnode.left+1
            node = newnode

        elif token == ')':
            rp = rp+1
            node = node.parent
            if node.children:
                node.right = node.children[-1].right + 1
            
        elif token == ',':
            node = node.parent
            if node.children:
                node.right = node.children[-1].right + 1
            
        # branch length
        elif token == ':':
            token = tokens.get_token()
            if token == '[':
                node.length_comment = tokens.parse_embedded_comment()
                token = tokens.get_token()

            if not (token == ''):
                try: brlen = float(token)
                except ValueError:
                    raise ValueError, ("invalid literal for branch length, "
                                       "'%s'" % token)
            else:
                raise 'NewickError', \
                      'unexpected end-of-file (expecting branch length)'

            node.length = brlen
        # comment
        elif token == '[':
            node.comment = tokens.parse_embedded_comment()
            if node.comment[0] == '&':
                # metadata
                meta = META.findall(node.comment[1:])
                if meta:
                    node.meta = {}
                    for k, v in meta:
                        v = eval(v.replace('{','(').replace('}',')'))
                        node.meta[k] = v

        # leaf node or internal node label
        else:
            if previous != ')': # leaf node
                if ttable:
                    try:
                        ttoken = (ttable.get(int(token)) or
                                  ttable.get(token))
#.........这里部分代码省略.........
开发者ID:ChriZiegler,项目名称:cython-experiments-1,代码行数:103,代码来源:newick.py


注:本文中的tree.Node.treename方法示例由纯净天空整理自Github/MSDocs等开源代码及文档管理平台,相关代码片段筛选自各路编程大神贡献的开源项目,源码版权归原作者所有,传播和使用请参考对应项目的License;未经允许,请勿转载。