ó
r/Ic           @   s¬   d  Z  d d l Z d d l Z d „  Z d f  d „  ƒ  YZ d f  d „  ƒ  YZ d e f d	 „  ƒ  YZ d
 f  d „  ƒ  YZ d f  d „  ƒ  YZ d e f d „  ƒ  YZ	 d „  Z
 d S(   s   SPARK-0.6.1iÿÿÿÿNc         C   s   g  i  |  j  g } } } xl | D]d } x | j D] } | j | ƒ q1 Wx: t | ƒ D], } | | k rU | j | ƒ d | | <qU qU Wq! W| S(   Ni   (   t	   __class__t	   __bases__t   appendt   dir(   t   instancet   namelistt   namedictt	   classlistt   ct   bt   name(    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyt	   _namelist   s    t   GenericScannerc           B   s>   e  Z d  „  Z d „  Z d „  Z d „  Z d „  Z d „  Z RS(   c         C   sr   |  j  ƒ  } t j | t j ƒ |  _ i  |  _ x> |  j j j ƒ  D]* \ } } t |  d | ƒ |  j | d <q@ Wd  S(   Nt   t_i   (   t   reflectt   ret   compilet   VERBOSEt
   index2funct
   groupindext   itemst   getattr(   t   selft   patternR
   t   number(    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyt   __init__'   s
    	c         C   s*   t  |  | ƒ j } d | d | f } | S(   Ns
   (?P<%s>%s)i   (   R   t   __doc__(   R   R
   t   doct   rv(    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyt   makeRE/   s    c         C   su   g  } xI t  |  ƒ D]; } | d  d k r | d k r | j |  j | ƒ ƒ q q W| j |  j d ƒ ƒ d j | ƒ S(   Ni   R   t	   t_defaultt   |(   R   R   R   t   join(   R   R   R
   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyR   4   s    c         C   s   d | GHt  ‚ d  S(   Ns   Lexical error at position %s(   t
   SystemExit(   R   t   st   pos(    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyt   error=   s    	c         C   sÃ   d } t  | ƒ } xª | | k  r¾ |  j j | | ƒ } | d  k rU |  j | | ƒ n  | j ƒ  } xK t t  | ƒ ƒ D]7 } | | rt | |  j k rt |  j | | | ƒ qt qt W| j ƒ  } q Wd  S(   Ni    (	   t   lenR   t   matcht   NoneR$   t   groupst   rangeR   t   end(   R   R"   R#   t   nt   mR(   t   i(    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyt   tokenizeA   s    c         C   s   d S(   s   ( . | \n )+N(    (   R   R"   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyR   O   s    (   t   __name__t
   __module__R   R   R   R$   R.   R   (    (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyR   &   s   						t   GenericParserc           B   s’   e  Z d  „  Z d Z d Z d „  Z d „  Z d „  Z d „  Z d „  Z	 d „  Z
 d	 „  Z d
 „  Z d „  Z d „  Z d „  Z d „  Z d „  Z RS(   c         C   sD   i  |  _  i  |  _ i  |  _ |  j ƒ  |  j | ƒ |  _ d |  _ d  S(   Ni   (   t   rulest	   rule2funct	   rule2namet   collectRulest   augmentt	   startRulet   ruleschanged(   R   t   start(    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyR   T   s    			
t   STARTt   EOFc         C   s
   | | f S(   N(    (   R   t   rulet   func(    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyt
   preprocessb   s    c   
      C   s@  | j  ƒ  } g  } x> t t | ƒ ƒ D]* } | | d k r% | j | d ƒ q% q% W| j t | ƒ ƒ xÊ t t | ƒ d ƒ D]² } | | | } | | | d | | d !} | t | ƒ f } |  j | | ƒ \ } }	 | |  j k rþ |  j | j | ƒ n | g |  j | <|	 |  j | <| j d |  j	 | <q} Wd |  _
 d  S(   Ns   ::=i   i   (   t   splitR)   R%   R   t   tupleR>   R2   R3   R/   R4   R8   (
   R   R   R=   R2   t   indexR-   t   lhst   rhsR<   t   fn(    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyt   addRuled   s"    c         C   sV   xO t  |  ƒ D]A } | d  d k r t |  | ƒ } | j } |  j | | ƒ q q Wd  S(   Ni   t   p_(   R   R   R   RE   (   R   R
   R=   R   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyR5   |   s
    	c         C   sL   |  j  | |  j f f } d „  |  j | <| g |  j |  j  <d |  j | <| S(   Nc         S   s   |  d S(   Ni    (    (   t   args(    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyt   <lambda>Š   s    t    (   t   _STARTt   _EOFR3   R2   R4   (   R   R9   R7   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyR6   ƒ   s
    c   
      C   sO  i  } i  |  _  x³ |  j j ƒ  D]¢ } x™ | D]‘ \ } } | |  j  k rW i  |  j  | <n  t | ƒ d k r€ d |  j  | d  <q, n  | d } | |  j k r­ d |  j  | | <q, d | | | f <q, Wq Wd } x} | rJd } xj | j ƒ  D]\ \ } } t |  j  | ƒ }	 |  j  | j |  j  | ƒ t |  j  | ƒ |	 k rç d } qç qç WqÎ Wd  S(   Ni    i   (   t   firstR2   t   valuesR%   R'   t   keyst   update(
   R   t   uniont   rulelistRB   RC   t   symt   changest   srct   destt   destlen(    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyt	   makeFIRST   s*    	
	c         C   s   d  S(   N(   R'   (   R   t   token(    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyt
   typestring±   s    c         C   s   d | GHt  ‚ d  S(   Ns"   Syntax error at or near `%s' token(   R!   (   R   RX   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyR$   ´   s    	c         C   s/  i  } | j  |  j ƒ i |  j d d f g d 6} |  j rH |  j ƒ  n  xV t t | ƒ ƒ D]B } g  | | d <| | g  k rƒ Pn  |  j | | | | | ƒ q[ W| t | ƒ d k  sÚ | | d |  j d d f g k rù | d =|  j | | d ƒ n  |  j	 | | |  j d d f | d f ƒ } | d =| S(   Ni    i   i   iÿÿÿÿ(
   R   RK   R7   R8   RW   t   xrangeR%   t
   buildStateR$   t	   buildTree(   R   t   tokenst   treet   statesR-   R   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyt   parse¸   s     	9+c         C   s•  i  } | | } i  } xx| D]p} | \ }	 }
 } |	 \ } } |
 t  | ƒ k r=t  | ƒ d k ru | | f | | <n  x¿ | | D]³ } | | k r– Pn  | \ } } } | \ } } | | | d !| f k r€ | | d | f } | | k r| j | ƒ | | f g | | | f <q3| | | f j | | f ƒ q€ q€ Wq n  | |
 } | |  j k r\| | k rÈ|	 |
 d | f } | | } | | k r®| j | ƒ | g | | | f <qÈ| | | f j | ƒ n  | | k rÚq n  d | | <| |  j k	 r|  j | ƒ pd  } | d  k	 ræxÉ |  j | D]º } | d | f } | d } t  | ƒ d k rf| j | ƒ q"n  | d } | |  j k r¤| | k r‘q"q¤| j | ƒ q"n  |  j | } d  | k rÏ| | k rÏq"n  | j | ƒ q"Wq n  x¤ |  j | D]a } | d } t  | ƒ d k r?| d |  j k r?| | d k r?qôn  | j | d | f ƒ qôWq | | k r | | d j |	 |
 d | f ƒ q q Wd  S(   Ni    i   (   R%   R   R2   RK   RY   R'   RL   (   R   RX   R_   R-   R^   t   needsCompletiont   statet	   predictedt   itemR<   R#   t   parentRB   RC   t   pitemt   prulet   ppost   pparentt   plhst   prhst   newt   nextSymt	   olditem_it   ttypet   prhs0RL   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyR[   Ð   s„    
	$






c         C   s'   g  } |  j  | | d | | ƒ | d S(   Niÿÿÿÿi    (   t   buildTree_r(   R   R]   R^   t   roott   stack(    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyR\   D  s    c         C   s6  | \ \ } } } }	 xÞ | d k rõ | | | f |	 f }
 |
 | k rz | d } |	 d }	 | j  d | | ƒ | d } q | |
 } t | ƒ d k r¨ |  j | ƒ } n
 | d } |  j | | | | | ƒ } | d } | \ \ } } } } | }	 q W| \ } } |  j | | t | ƒ  ƒ } | g | t | ƒ *| S(   Ni    i   (   t   insertR%   t	   ambiguityRq   R3   (   R   Rs   R]   t   tokposR^   Rr   R<   R#   Re   Rb   t   wantt   childrent   childt   crulet   cpost   cparentt   cstateRB   RC   t   result(    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyRq   I  s,    



	

c         C   s¯   g  } i  } xo t  t | ƒ ƒ D][ } | | \ \ } } } } | \ }	 }
 |  j | } | j t |
 ƒ | f ƒ | | | <q W| j ƒ  t d „  | ƒ } | | |  j | ƒ S(   Nc         S   s   |  \ } } | S(   N(    (   t   .0t   aR	   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyRH   †  s    (   R)   R%   R4   R   t   sortt   mapt   resolve(   R   Rx   t   sortlistt
   name2indexR-   R<   R#   Re   RA   RB   RC   R
   t   list(    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyRu   u  s    
c         C   s   | d S(   Ni    (    (   R   R†   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyRƒ   ‰  s    (   R/   R0   R   RJ   RK   R>   RE   R5   R6   RW   RY   R$   R`   R[   R\   Rq   Ru   Rƒ   (    (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyR1   S   s    						"				t		,	t   GenericASTBuilderc           B   s5   e  Z d  „  Z d „  Z d „  Z d „  Z d „  Z RS(   c         C   s   t  j |  | ƒ | |  _ d  S(   N(   R1   R   t   AST(   R   Rˆ   R9   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyR   š  s    c         C   s(   |  d „ } | \ } } | | | ƒ f S(   Nc         S   s   |  | d „ S(   Nc         S   s   | j  |  | ƒ S(   N(   t   buildASTNode(   RG   RB   R   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyRH      s    (    (   RB   R   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyRH   Ÿ  s    (    (   R   R<   R=   t   rebindRB   RC   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyR>   ž  s    c         C   s_   g  } xF | D]> } t  | |  j ƒ r5 | j | ƒ q | j |  j | ƒ ƒ q W|  j | | ƒ S(   N(   t
   isinstanceRˆ   R   t   terminalt   nonterminal(   R   RG   RB   Rx   t   arg(    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyR‰   ¥  s    c         C   s   | S(   N(    (   R   RX   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyRŒ   ®  s    c         C   s#   |  j  | ƒ } | | t | ƒ *| S(   N(   Rˆ   R%   (   R   t   typeRG   R   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyR   °  s    (   R/   R0   R   R>   R‰   RŒ   R   (    (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyR‡   ™  s
   					t#   GenericASTTraversalPruningExceptionc           B   s   e  Z RS(    (   R/   R0   (    (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyR   ¿  s   t   GenericASTTraversalc           B   sD   e  Z d  „  Z d „  Z d „  Z d d „ Z d d „ Z d „  Z RS(   c         C   s   | |  _  d  S(   N(   t   ast(   R   R’   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyR   Ã  s    c         C   s   | j  S(   N(   R   (   R   t   node(    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyRY   Æ  s    c         C   s
   t  ‚ d  S(   N(   R   (   R   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyt   pruneÉ  s    c         C   sÓ   | d  k r |  j } n  yO d |  j | ƒ } t |  | ƒ rY t |  | ƒ } | | ƒ n |  j | ƒ Wn t k
 r{ d  SXx | D] } |  j | ƒ qƒ W| d } t |  | ƒ rÏ t |  | ƒ } | | ƒ n  d  S(   Nt   n_t   _exit(   R'   R’   RY   t   hasattrR   t   defaultR   t   preorder(   R   R“   R
   R=   t   kid(    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyR™   Ì  s     
c         C   s…   | d  k r |  j } n  x | D] } |  j | ƒ q Wd |  j | ƒ } t |  | ƒ rt t |  | ƒ } | | ƒ n |  j | ƒ d  S(   NR•   (   R'   R’   t	   postorderRY   R—   R   R˜   (   R   R“   Rš   R
   R=   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyR›   â  s    c         C   s   d  S(   N(    (   R   R“   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyR˜   ñ  s    N(	   R/   R0   R   RY   R”   R'   R™   R›   R˜   (    (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyR‘   Â  s   			t   GenericASTMatcherc           B   sA   e  Z d  „  Z d „  Z d „  Z d „  Z d d „ Z d „  Z RS(   c         C   s   t  j |  | ƒ | |  _ d  S(   N(   R1   R   R’   (   R   R9   R’   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyR   ü  s    c         C   sJ   |  d „ } | \ } } t  | ƒ } | j ƒ  | t | ƒ f | | ƒ f S(   Nc         S   s   |  | d „ S(   Nc         S   s   | j  |  | ƒ S(   N(   t
   foundMatch(   RG   R=   R   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyRH     s    (    (   R=   R   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyRH     s    (   R†   t   reverseR@   (   R   R<   R=   RŠ   RB   RC   t   rhslist(    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyR>      s
    
c         C   s   | | d ƒ | d S(   Niÿÿÿÿ(    (   R   RG   R=   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyR   
  s    c         C   s‰   |  j  j d | ƒ d } xG | D]? } | d k rH |  j  j d d ƒ n  | d } |  j | ƒ q  W| d k r… |  j  j d d ƒ n  d  S(   Ni    t   (i   t   )(   t   inputRt   t   match_r(   R   R“   Rx   Ry   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyR£     s    
c         C   sB   | d  k r |  j } n  g  |  _ |  j | ƒ |  j |  j ƒ d  S(   N(   R'   R’   R¢   R£   R`   (   R   R’   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyR&     s
    	c         C   s   | d S(   Niÿÿÿÿ(    (   R   R†   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyRƒ   #  s    N(	   R/   R0   R   R>   R   R£   R'   R&   Rƒ   (    (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyRœ   û  s   		
		c         C   s³   x¬ t  t | ƒ ƒ D]˜ } d G| GHx\ | | D]P \ \ } } } } d G| Gd Gd j | |  ƒ Gd Gd j | | ƒ Gd G| GHq- W| t |  ƒ k  r Hd Gt |  | ƒ GHHq q Wd  S(   NRb   s   	s   ::=t    t   .t   ,RX   (   R)   R%   R    t   str(   R]   R_   R-   RB   RC   R#   Re   (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyt   _dump)  s    	 (   t   __version__R   t   sysR   R   R1   R‡   R   R‘   Rœ   R¨   (    (    (    s„   /oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Parsers/spark.pyt   <module>   s   	-ÿ G&9.