*ë
ŠĆ9c       sÚ      d  k  Z   d  k Z  d k l Z  e d  Z  e d  Z  e d  Z  d   Z # d   Z	 ' d   Z
 0 d   Z ; d	   Z B d
 d  Z I d
 d
 f d  Z Q e d  Z W e d  Z d  S(   N(   s   default_managerc    sY     | t j o  d } n 
 d | }  t i |  i |  }  | i |   Sd  S(   Ns
   translators   translator.id.%d(	   s   ids   Nones   ss   default_managers   resolves   seqs   alphabets
   translators	   translate(   s   seqs   ids   ss
   translator(    (    s"   /mit/seven/lib/python/Bio/utils.pys	   translate s
   c    sY     | t j o  d } n  d | }  t i |  i |  }  | i |   Sd  S(   Ns
   translators   translator.id.%d(	   s   ids   Nones   ss   default_managers   resolves   seqs   alphabets
   translators   translate_to_stop(   s   seqs   ids   ss
   translator(    (    s"   /mit/seven/lib/python/Bio/utils.pys   translate_to_stop s
   c    sY     | t j o  d } n  d | }  t i |  i |  }  | i |   Sd  S(   Ns
   translators   translator.id.%d(	   s   ids   Nones   ss   default_managers   resolves   seqs   alphabets
   translators   back_translate(   s   seqs   ids   ss
   translator(    (    s"   /mit/seven/lib/python/Bio/utils.pys   back_translate s
   c    s/      t  i |  i d  } ! | i |   Sd  S(   Ns   transcriber(   s   default_managers   resolves   seqs   alphabets   transcribers
   transcribe(   s   seqs   transcriber(    (    s"   /mit/seven/lib/python/Bio/utils.pys
   transcribe s   c    s/   # $ t  i |  i d  } % | i |   Sd  S(   Ns   transcriber(   s   default_managers   resolves   seqs   alphabets   transcribers   back_transcribe(   s   seqs   transcriber(    (    s"   /mit/seven/lib/python/Bio/utils.pys   back_transcribe# s   c    s   ' ( ) |  i } * g  } + x: |  i d + r* } , | | j o - | i |  n q* W. t i t i	 | d  |  i
 i
  Sd S(   s@   given a sequence with gap encoding, return the ungapped sequencei    s    N(   s   seqs   gap_chars   gaps   letterss   datas   cs   appends   Seqs   strings   joins   alphabet(   s   seqs   gaps   letterss   c(    (    s"   /mit/seven/lib/python/Bio/utils.pys   ungap' s   	 	c    s   0 1 h  } 2 x& |  i i  d 2 r } 3 d | | <q W4 y+ 5 x! |  i d 5 r } 6 | | qM WWn 7 t j
 o 8 d Sn X9 d Sd  S(   Ni    i   (   s   letterss   seqs   alphabets   cs   datas   KeyError(   s   seqs   letterss   c(    (    s"   /mit/seven/lib/python/Bio/utils.pys   verify_alphabet0 s   	 	 	c    sa   ; < h  } = t |  i  } > x2 |  i i d > r } ? t i	 | |  | | <q0 W@ | Sd  S(   Ni    (
   s   dicts   buffers   seqs   datas   ss   alphabets   letterss   cs   strings   count(   s   seqs   ss   dicts   c(    (    s"   /mit/seven/lib/python/Bio/utils.pys   count_monomers; s   	 	f0.0c    sD   B C | } D x' |  i d D r } E | | | } q WF | Sd  S(   Ni    (   s   zeros   totals   seqs   datas   cs   table(   s   seqs   tables   zeros   cs   total(    (    s"   /mit/seven/lib/python/Bio/utils.pys   sumB s
   	 	c    sl   I J | \ } } K xC |  i d K r3 } L | | \ } } M | | } N | | } q! WO | | f Sd  S(   Ni    (	   s   zeros   xs   ys   seqs   datas   cs   tables   x2s   y2(   s   seqs   tables   zeros   y2s   xs   ys   x2s   c(    (    s"   /mit/seven/lib/python/Bio/utils.pys   sum_2pleI s    	c    s6   Q R | t j o T d d n U t |  |  Sd  S(   Ni   i    (   s   weight_tables   Nones   sums   seq(   s   seqs   weight_table(    (    s"   /mit/seven/lib/python/Bio/utils.pys   total_weightQ s   c    s6   W X | t j o Y d d n Z t |  |  Sd  S(   Ni   i    (   s   weight_tables   Nones   sum_2ples   seq(   s   seqs   weight_table(    (    s"   /mit/seven/lib/python/Bio/utils.pys   total_weight_rangeW s   (   s   strings   Seqs   PropertyManagers   default_managers   Nones	   translates   translate_to_stops   back_translates
   transcribes   back_transcribes   ungaps   verify_alphabets   count_monomerss   sums   sum_2ples   total_weights   total_weight_range(   s   sum_2ples	   translates   verify_alphabets   total_weights   translate_to_stops
   transcribes   sums   back_transcribes   total_weight_ranges   back_translates   Seqs   strings   count_monomerss   default_managers   ungap(    (    s"   /mit/seven/lib/python/Bio/utils.pys   ? s   		