ó
gbc           @   s    d  Z  d e f d „  ƒ  YZ d S(   sH   
    implement fastn/fastp sililarity search algorithm for BioSequence.
t   Fastc           B   s&   e  Z d  d „ Z d „  Z d „  Z RS(   i   c            s˜   i  } t  ˆ ƒ ‰ xd ‡  ‡ f d †  t t ˆ ƒ ˆ  ƒ Dƒ D]9 \ } } | | k rh | | j | ƒ q< | g | | <q< Wˆ  |  _ | |  _ ˆ |  _ d S(   s›   
        @param seq: sequence to hash
        @type seq: BioSequence
        @param kup: word size used for hashing process
        @type kup: int
        c         3   s,   |  ]" } ˆ | | ˆ  !j  ƒ  | f Vq d  S(   N(   t   upper(   t   .0t   i(   t   kupt   seq(    s,   lib/python2.7/site-packages/obitools/fast.pys	   <genexpr>   s    N(   t   strt   xranget   lent   appendt   _kupt   _hasht   _seq(   t   selfR   R   t   hasht   wordt   pos(    (   R   R   s,   lib/python2.7/site-packages/obitools/fast.pyt   __init__   s    6		c            sð   i  } t  ˆ ƒ j ƒ  ‰ |  j } |  j ‰  x~ ‡  ‡ f d †  t t ˆ ƒ ˆ  ƒ Dƒ D]S \ } } | j | g  ƒ } x2 | D]* } | | } | j | d ƒ d | | <qy WqT Wt | j ƒ  ƒ }	 g  | D] }
 | |
 |	 k rÄ |
 ^ qÄ } |	 | f S(   sC  
        Align one sequence with the fast hash table.
        
        @param seq: the sequence to align
        @type seq: BioSequence
        
        @return: where smax is the
                 score of the largest diagonal and pmax the
                 associated shift 
        @rtype: a int tuple (smax,pmax)
        c         3   s&   |  ] } ˆ | | ˆ  !| f Vq d  S(   N(    (   R   R   (   R   R   (    s,   lib/python2.7/site-packages/obitools/fast.pys	   <genexpr>+   s    i    i   (	   R   R   R   R
   R   R   t   gett   maxt   values(   R   R   t   histoR   R   R   t
   matchedpost   pt   deltat   smaxt   xt   pmax(    (   R   R   s,   lib/python2.7/site-packages/obitools/fast.pyt   __call__   s    		6
")c         C   s   t  |  j ƒ S(   N(   R   R   (   R   (    (    s,   lib/python2.7/site-packages/obitools/fast.pyt   __len__4   s    (   t   __name__t
   __module__R   R   R   (    (    (    s,   lib/python2.7/site-packages/obitools/fast.pyR       s   	N(   t   __doc__t   objectR    (    (    (    s,   lib/python2.7/site-packages/obitools/fast.pyt   <module>   s   