*ë
.ÖÒ9c       so     d  k  Z   d k l Z l Z  d k l Z  d f  d „  ƒ  YZ S h  Z T x5 e i i ƒ  d T r \ Z	 Z
 U e e
 ƒ e e	 <qi WV h  Z W x5 e i i ƒ  d W r \ Z	 Z
 X e e
 ƒ e e	 <q­ WZ h  Z [ x5 e i i ƒ  d [ r \ Z	 Z
 \ e e
 ƒ e e	 <qñ W] h  Z ^ x5 e i i ƒ  d ^ r \ Z	 Z
 _ e e
 ƒ e e	 <q5Wb h  Z c x5 e i i ƒ  d c r \ Z	 Z
 d e e
 ƒ e e	 <qyWe h  Z f x5 e i i ƒ  d f r \ Z	 Z
 g e e
 ƒ e e	 <q½Wi h  Z j x5 e i i ƒ  d j r \ Z	 Z
 k e e
 ƒ e e	 <qWl h  Z m x5 e i i ƒ  d m r \ Z	 Z
 n e e
 ƒ e e	 <qEWd  S(   N(   s   Alphabets   Seq(   s
   CodonTables
   Translatorc      sD     d „  Z  
 d d „ Z  d „  Z 1 d „  Z E d „  Z RS(   Nc    s     | |  _   h  |  _ d  S(   N(   s   tables   selfs   _encoded(   s   selfs   table(    (    s,   /mit/seven/lib/python/Bio/Tools/Translate.pys   __init__ s   s   *c    sE  
  t  o' | i |  i i j p t d | i ‚  | i }  g  }
  |
 i
 }  |  i }  | i i }	  t | ƒ }  xH t d | | d d ƒ d  r' }  | |	 | | | d !| ƒ ƒ qŸ W y  |  i | } Wn;  t j
 o,  t i | i ƒ }  | |  i | <n X t i t i |
 d ƒ | ƒ Sd  S(   Ns-   cannot translate from the given alphabet (%s)i    i   s    (   s	   __debug__s   seqs   alphabets   selfs   tables   nucleotide_alphabets   AssertionErrors   datas   ss   letterss   appends   forward_tables   gets   lens   ns   ranges   is   stop_symbols   _encodeds   KeyErrors   Alphabets   HasStopCodons   protein_alphabets   Seqs   strings   join(   s   selfs   seqs   stop_symbols   appends   tables   ss   ns   alphabets   is   gets   letters(    (    s,   /mit/seven/lib/python/Bio/Tools/Translate.pys	   translate
 s    1	  	%c    s   ! t  o3 | i |  i i j p t d | i |  i i f ‚ $ | i } % g  } & | i
 } ' |  i i } ( t | ƒ } ) yM * xC t d | | d d ƒ d * r" } + | | | | | d !ƒ q¥ WWn , t j
 o
 . n X/ t i t i | d ƒ |  i i ƒ Sd  S(   Ns7   cannot translate from given alphabet (have %s, need %s)i    i   s    (   s	   __debug__s   seqs   alphabets   selfs   tables   nucleotide_alphabets   AssertionErrors   datas   ss   letterss   appends   forward_tables   lens   ns   ranges   is   KeyErrors   Seqs   strings   joins   protein_alphabet(   s   selfs   seqs   appends   ss   tables   ns   is   letters(    (    s,   /mit/seven/lib/python/Bio/Tools/Translate.pys   translate_to_stop s   =	  	$c    s%  1 3 t  | i t i ƒ o 4 |  i | ƒ Sn 5 t o- | i i |  i i	 j p t
 d | i i ‚ 8 | i } 9 | i i } : g  } ; | i } < |  i i } = xL | i d = r< } > | | j o ? | | t ƒ n A | | | ƒ q¶ WB t i t i | d ƒ C |  i i ƒ Sd  S(   Ns2   cannot back translate from the given alphabet (%s)i    s    (   s
   isinstances   seqs   alphabets   Alphabets   HasStopCodons   selfs   _back_translate_no_stops	   __debug__s   tables   protein_alphabets   AssertionErrors   datas   ss   stop_symbols   letters   letterss   appends
   back_tables   cs   Nones   Seqs   strings   joins   nucleotide_alphabet(   s   selfs   seqs   appends   tables   letters   ss   cs   letters(    (    s,   /mit/seven/lib/python/Bio/Tools/Translate.pys   back_translate1 s   7	 	c    s½   E G t  o' | i |  i i j p t d | i ‚ J | i } K g  } L | i
 } M |  i i } N x' | i d N r } O | | | ƒ qs WP t i t i | d ƒ Q |  i i ƒ Sd  S(   Ns2   cannot back translate from the given alphabet (%s)i    s    (   s	   __debug__s   seqs   alphabets   selfs   tables   protein_alphabets   AssertionErrors   datas   ss   letterss   appends
   back_tables   cs   Seqs   strings   joins   nucleotide_alphabet(   s   selfs   seqs   appends   tables   letterss   cs   s(    (    s,   /mit/seven/lib/python/Bio/Tools/Translate.pys   _back_translate_no_stopE s   1	 	(   s   __init__s	   translates   translate_to_stops   back_translates   _back_translate_no_stop(    (    (    s,   /mit/seven/lib/python/Bio/Tools/Translate.pys
   Translator s
   i    (   s   strings   Bios   Alphabets   Seqs   Bio.Datas
   CodonTables
   Translators   unambiguous_dna_by_names   itemss   keys   values   unambiguous_dna_by_ids   unambiguous_rna_by_names   unambiguous_rna_by_ids   ambiguous_dna_by_names   ambiguous_dna_by_ids   ambiguous_rna_by_names   ambiguous_rna_by_id(   s   ambiguous_dna_by_ids   ambiguous_dna_by_names   unambiguous_dna_by_names   ambiguous_rna_by_ids   keys
   CodonTables   unambiguous_rna_by_ids
   Translators   values   unambiguous_rna_by_names   Alphabets   Seqs   strings   unambiguous_dna_by_ids   ambiguous_rna_by_name(    (    s,   /mit/seven/lib/python/Bio/Tools/Translate.pys   ? sF   N	 	 	 	 	 	 	 	 