ó BªVCc@sUdZddlZdd d„ƒYZdefd„ƒYZdefd„ƒYZdS( s Generalized N-Point Crossover. For even values of N, perform N point crossover (select N/2 points each in the two genomes, and alternate) For odd values of N, perform symmetric N+1 point crossover (select N/2 points for both genomes) N-Point introduction (my notation): genome 1: A-----B-----C-----D-----E-----F-----G genome 2: a=====b=====c=====d=====e=====f=====g 2-point, symmetric (points=1): A-----B-----C- 1 -D-----E-----F-----G a=====b=====c= 2 =d=====e=====f=====g returns: (ABCdefg, abcDEFG) 2-point, asymmetric (points=2): A-----B- 1 -C-----D-----E-----F-----G a=====b=====c=====d=====e= 2 =f=====g returns: (ABfg, abcdeCDEFG) and for the drastic (n can be arbitrary to the length of the genome!): 12-point, symmetric (points=11): A- 1 -B- 2 -C- 3 -D- 4 -E- 5 -F- 6 -G a= 7 =b= 8 =c= 9 =d= 10 e= 11 f= 12 g returns: (AbCdEfG, aBcDeFg) (note that points=12 will yield the same result, but 11 may be somewhat faster) iÿÿÿÿNtGeneralPointCrossovercBs5eZdZdd„Zd„Zd„Zd„ZRS(sPerform n-point crossover between genomes at some defined rates. Ideas on how to use this class: - Call it directly ( construct, do_crossover ) - Use one of the provided subclasses - Inherit from it: * replace _generate_locs with a more domain specific technique * replace _crossover with a more efficient technique for your point-count gš™™™™™¹?cCs.||_|d|_||jd|_dS(sBInitialize to do crossovers at the specified probability. iN(t_crossover_probt_symt_npoints(tselftpointstcrossover_prob((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/GA/Crossover/GeneralPoint.pyt__init__/s  c CsT|jƒ|jƒf}tjƒ}||jkrPt|djƒt|djƒf}t|ƒ}|jdks‡|j|dkr—|d|_ng}|j|ƒ}|jdkrÄ|}n?||dkrê|j|dƒ}n|}|j|dƒ} |j d|||fƒ} |j d|||fƒ|d_| |d_n|S(s7Potentially do a crossover between the two organisms. iii( tcopytrandomRtlentgenometminRt_generate_locsRt _crossover( Rtorg_1torg_2tnew_orgtcrossover_chancetboundtmboundty_locstx_locstxlocsttmp((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/GA/Crossover/GeneralPoint.pyt do_crossover7s& & " "cCsˆg}xct|jƒD]R}tjd|dƒ}x&||krZtjd|dƒ}q5W|j|ƒqW|jƒdg||gS(sÏGeneralized Location Generator: arguments: bound (int) - upper bound returns: [0]+x_0...x_n+[bound] where n=self._npoints-1 and 0 < x_0 < x_1 ... < bound ii(trangeRR trandinttappendtsort(RRtresultst incrementtx((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/GA/Crossover/GeneralPoint.pyR ^s  cCs‰||j||d }xitd|jƒD]U}||d}||j||||||d!}|r{||}q,|}q,W|S(soGeneralized Crossover Function: arguments: x (int) - genome number [0|1] no (organism,organism) - new organisms locs (int list, int list) - lists of locations, [0, +n points+, bound] for each genome (sync'd with x) return type: sequence (to replace no[x]) ii(R RR(RR tnotlocststntmodett((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/GA/Crossover/GeneralPoint.pyRqs(  (t__name__t __module__t__doc__RRR R(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/GA/Crossover/GeneralPoint.pyR#s    ' t TwoCrossovercBs eZdZd„Zd„ZRS(s”Helper class for Two Point crossovers Offers more efficient replacements to the GeneralPoint framework for single pivot crossovers cCsdtjd|dƒ|gS(sYReplacement generation see GeneralPoint._generate_locs documentation for details ii(R R(RR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/GA/Crossover/GeneralPoint.pyR ‘scCs<|dd}||j||d ||j||dS(sTReplacement crossover see GeneralPoint._crossover documentation for details ii(R (RR R!R"ty((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/GA/Crossover/GeneralPoint.pyR™s(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/GA/Crossover/GeneralPoint.pyR*‹s tInterleaveCrossovercBs,eZdZdd„Zd„Zd„ZRS(s\Demonstration class for Interleaving crossover Interleaving: AbCdEfG, aBcDeFg gš™™™™™¹?cCstj|d|ƒdS(Ni(RR(RR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/GA/Crossover/GeneralPoint.pyR¦scCstd|dƒS(Niÿÿÿÿi(R(RR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/GA/Crossover/GeneralPoint.pyR ©scCsy||jdd!}xHtd|jdƒD]0}||d}|||j||d!}q+W|||j|jdS(Niiii(R RR(RR 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/GA/Crossover/GeneralPoint.pyR¬s  (R'R(R)RR R(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/GA/Crossover/GeneralPoint.pyR,¡s  ((R)R RR*R,(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/GA/Crossover/GeneralPoint.pyts h