ó
gbc           @   sŤ   d  d l  Z  d  d l Z d  d l m Z d  d l m Z d   Z e  j d  Z d   Z	 e  j d  Z
 d d d  Z e  j d	  Z d
   Z d d  Z d d  Z d S(   i˙˙˙˙N(   t   universalOpen(   t   PhylogenicTreec         c   sź   d } d } |  d d k rł x t  d t |    D]n } |  | } | d k r[ | d 7} n | d k rt | d 8} n  | d k r2 | r2 |  | | !V| d } q2 q2 W|  | | !Vn |  Vd  S(   Ni    i   t   (t   )t   ,(   t   xranget   len(   t   datat   levelt   startt   it   c(    (    s8   lib/python2.7/site-packages/obitools/phylogeny/newick.pyt   subNodeIterator   s    
s]   \s*(?P<subnodes>\(.*\))?(?P<name>[^ :]+)? *(?P<bootstrap>[0-9.]+)?(:(?P<distance>-?[0-9.]+))?c         C   s    t  j |   j d  } | d s/ d  | d <n  | d sF d  | d <n t | d  | d <| d sq d  | d <n t | d  | d <| d s d  | d <n  | S(   Ni    t   namet	   bootstrapt   distancet   subnodes(   t   _nodeParsert   matcht	   groupdictt   Nonet   float(   R   t
   parsedNode(    (    s8   lib/python2.7/site-packages/obitools/phylogeny/newick.pyt
   nodeParser   s    



s   \s+c      
   C   sÜ   | d  k r0 t   } t j d |   j   }  n  t |   } | d  k	 r | j d | d d | d | d d | d  \ } } n | j d | d  } | | _ | d rŘ x+ t	 | d  D] } t
 | | |  qť Wn  | S(   Nt    t   node1R   t   index2R   R   R   (   R   R   t   _cleanTreeDatat   subt   stripR   t   addEdget   addNodet   rootR   t
   treeParser(   R   t   treet   parentR   t   sont   subnode(    (    s8   lib/python2.7/site-packages/obitools/phylogeny/newick.pyR!   1   s    	
	
s   \[.*\]c         c   s   t  |   }  |  j   } t j |  } t j d |  j   } | rR | d } n d  } x: | j d  D]) } t |  } | r | | _	 n  | Vqh Wd  S(   Nt    i    t   ;(
   R    t   readt   _treecommentt   findallR   R   R   t   splitR!   t   comment(   t   fileR   R,   R"   t   t(    (    s8   lib/python2.7/site-packages/obitools/phylogeny/newick.pyt   treeIteratorK   s    i    c   	      C   s  | j  } | d  k r d } n  | j } | d  k r< d } n
 d | } | j } | d  k rd d } n d t |  } d d | d } | j g  |  j |  D] } t |  | | d  ^ q  } | rđ d d | d | d d | d	 } n  d
 | | | | f S(   NR&   s   :%6.5fs    %ds   ,
R   i   s   (
s   
R   s   %s%s%s%s(   t   _nameR   t   _distt
   _bootstrapt   intt   joint   childNodeIteratort
   nodeWriter(	   R"   t   nodet   deepR   R   R   t   nodeseparatort   xR   (    (    s8   lib/python2.7/site-packages/obitools/phylogeny/newick.pyR6   \   s"    				
			2)c         C   s2   | d  k	 r | } n |  j   } t |  |  d S(   NR'   (   R   t   getRootR6   (   R"   t	   startnodeR    (    (    s8   lib/python2.7/site-packages/obitools/phylogeny/newick.pyt
   treeWriterv   s    	(   t   ret   syst   obitools.utilsR    t   obitools.phylogenyR   R   t   compileR   R   R   R   R!   R)   R/   R6   R=   (    (    (    s8   lib/python2.7/site-packages/obitools/phylogeny/newick.pyt   <module>   s   			