ó "ˆIc@sŸdZddlZddlmZddlmZddlmZddlm Z ddl m Z ddl m Z dd l mZdd lmZdd lmZd efd „ƒYZd„Zdejfd„ƒYZdejfd„ƒYZdejfd„ƒYZdejfd„ƒYZdejfd„ƒYZdd!d„ƒYZdejfd„ƒYZedkr›ejddƒZej d eƒndS("s5Tests different Genetic Algorithm crossover classes. iÿÿÿÿN(t MutableSeq(tSingleLetterAlphabet(tOrganism(tSafeFitnessCrossover(tGeneralPointCrossover(tInterleaveCrossover(tTwoPointCrossover(tSinglePointCrossover(tUniformCrossovert TestAlphabetcBs&eZdZdddgZd„ZRS(sSimple test alphabet. t1t2t3cCsdS(Ni((tselftoalpha((stest_GACrossover.pytcontainss(t__name__t __module__t__doc__tlettersR(((stest_GACrossover.pyR scCs|jƒ}t|jƒS(s,Simple class for calculating fitnesses. (ttoseqtinttdata(tgenomet seq_genome((stest_GACrossover.pyt test_fitnesss tSinglePointTestcBs eZdZd„Zd„ZRS(s"Test simple point crossovers. cCsgtƒ|_td|jƒ}t|tƒ|_td|jƒ}t|tƒ|_tdƒ|_dS(Nt11111t22222gð?( R talphabetRRRtorg_1torg_2Rt crossover(R tgenome_1tgenome_2((stest_GACrossover.pytsetUp%s  cCs“|jj}|jj}|jj|j|jƒ\}}|j|krY|j|ksetdƒ‚||jkrƒ||jkstdƒ‚dS(s2Test basic point crossover functionality. s*Did not perform a crossover when expected.s0Returned an exact copy of the original organism.N(RRRR t do_crossovertAssertionError(R tstart_genome_1tstart_genome_2t new_org_1t new_org_2((stest_GACrossover.pyttest_basic_crossover/s   !(RRRR#R*(((stest_GACrossover.pyR"s t UniformTestcBs2eZdZd„Zd„Zd„Zd„ZRS(s"Test simple point crossovers. cCsŽtƒ|_td|jƒ}t|tƒ|_td|jƒ}t|tƒ|_td|jƒ}t|tƒ|_tddƒ|_ dS(Nt11111111t22222222t333gð?gš™™™™™é?( R RRRRRRtorg_3RR (R R!R"tgenome_3((stest_GACrossover.pyR#Bs cCs“|jj}|jj}|jj|j|jƒ\}}|j|krY|j|ksetdƒ‚||jkrƒ||jkstdƒ‚dS(s4Test basic uniform crossover functionality. s*Did not perform a crossover when expected.s0Returned an exact copy of the original organism.N(RRRR R$R%(R R&R'R(R)((stest_GACrossover.pyR*Os   ! cCsÆ|jj|j|jƒ\}}t|jƒt|jƒksKtdƒ‚|jjƒjdƒ|jjƒjdƒks‡tdƒ‚|jjt|jƒ|jt|jƒksÂtdƒ‚dS(sATest properties of differing genome length, uniform crossovers. s3Strings are of wrong sizes after uniform crossover.R R s9There should be equal distributions of the smaller strings;Uniform should not touch non-overlapping elements of genomeN( R R$RR/tlenRR%ttostringtcount(R R(R)((stest_GACrossover.pyttest_ds_prop_uniform_crossover`s!   cCs»|jj|j|jƒ\}}t|jƒt|jƒksKtdƒ‚|jjƒjdƒ|jjƒjdƒkr«|jjƒjdƒ|jjƒjdƒks·tdƒ‚dS(s=Test properties of equal genome length, uniform crossovers. s9Strings are of different sizes after symmetric crossover.R R s,There should be equal, inverse distributionsN( R R$RRR1RR%R2R3(R R(R)((stest_GACrossover.pyttest_ss_prop_uniform_crossoverrs!  (RRRR#R*R4R5(((stest_GACrossover.pyR+?s   tInterleaveTestcBs2eZdZd„Zd„Zd„Zd„ZRS(s&Test 'simple' 4-point crossovers. cCs‹tƒ|_td|jƒ}t|tƒ|_td|jƒ}t|tƒ|_td|jƒ}t|tƒ|_tdƒ|_ dS(NRRt 333333333gð?( R RRRRRRR/Rt _crossover(R R!R"R0((stest_GACrossover.pyR#†s cCs“|jj}|jj}|jj|j|jƒ\}}|j|krY|j|ksetdƒ‚||jkrƒ||jkstdƒ‚dS(s7Test basic interleave crossover functionality. s*Did not perform a crossover when expected.s0Returned an exact copy of the original organism.N(RRRR8R$R%(R R&R'R(R)((stest_GACrossover.pyR*“s   ! cCsñ|jj|j|jƒ\}}t|jƒt|jƒksKtdƒ‚|jjƒjdƒ|jjƒjdƒkr«|jjƒjdƒ|jjƒjdƒks·tdƒ‚|jjƒdkrá|jjƒdksítdƒ‚dS( s0Test properties of interleave point crossover. s9Strings are of different sizes after symmetric crossover.R R s,There should be equal, inverse distributionst12121t21212sDid not interleave.N( R8R$RRR1RR%R2R3(R R(R)((stest_GACrossover.pyttest_prop_sym_crossover¤s!   cCsÉ|jj}|jj}|jj|j|jƒ\}}|j|krY|j|ksetdƒ‚||jkrƒ||jkstdƒ‚|jjƒdkr¹|jjƒdksÅtdƒ‚dS(s:Test basic interleave crossover with asymmetric genomes. s*Did not perform a crossover when expected.s0Returned an exact copy of the original organism.t13131t31313333sDid not interleave with growth.N(RRR/R8R$R%R2(R R&tstart_genome_3R(t new_org_3((stest_GACrossover.pyttest_prop_asym_crossover¹s   !  (RRRR#R*R;R@(((stest_GACrossover.pyR6ƒs   t FourPointTestcBs2eZdZd„Zd„Zd„Zd„ZRS(s&Test 'simple' 4-point crossovers. cCs|tƒ|_td|jƒ}t|tƒ|_td|jƒ}t|tƒ|_tddƒ|_tddƒ|_ dS(NRRigð?i( R RRRRRRRt sym_crossovertasym_crossover(R R!R"((stest_GACrossover.pyR#Ñs cCs“|jj}|jj}|jj|j|jƒ\}}|j|krY|j|ksetdƒ‚||jkrƒ||jkstdƒ‚dS(s4Test basic 4-point crossover functionality. s*Did not perform a crossover when expected.s0Returned an exact copy of the original organism.N(RRRRBR$R%(R R&R'R(R)((stest_GACrossover.pyR*Üs   ! cCs»|jj|j|jƒ\}}t|jƒt|jƒksKtdƒ‚|jjƒjdƒ|jjƒjdƒkr«|jjƒjdƒ|jjƒjdƒks·tdƒ‚dS(s1Test properties of symmetric 4-point crossover. s9Strings are of different sizes after symmetric crossover.R R s,There should be equal, inverse distributionsN( RBR$RRR1RR%R2R3(R R(R)((stest_GACrossover.pyR;ís!  cCs“|jj}|jj}|jj|j|jƒ\}}|j|krY|j|ksetdƒ‚||jkrƒ||jkstdƒ‚dS(s?Test basic asymmetric 2-point crossover functionality. s*Did not perform a crossover when expected.s0Returned an exact copy of the original organism.N(RRRRCR$R%(R R&R'R(R)((stest_GACrossover.pyttest_basic_asym_crossoverÿs   ! (RRRR#R*R;RD(((stest_GACrossover.pyRAÎs   t TwoPointTestcBs eZdZd„Zd„ZRS(s$Test simple 2-point crossovers. cCsgtƒ|_td|jƒ}t|tƒ|_td|jƒ}t|tƒ|_tdƒ|_dS(NR,R-gð?( R RRRRRRRRC(R R!R"((stest_GACrossover.pyR#s  cCs“|jj}|jj}|jj|j|jƒ\}}|j|krY|j|ksetdƒ‚||jkrƒ||jkstdƒ‚dS(s?Test basic asymmetric 2-point crossover functionality. s*Did not perform a crossover when expected.s0Returned an exact copy of the original organism.N(RRRRCR$R%(R R&R'R(R)((stest_GACrossover.pyRDs   ! (RRRR#RD(((stest_GACrossover.pyREs t TestCrossovercBs eZdZd„Zd„ZRS(sCProvide basic crossover functionality for testing SafeFitness. cCs d|_dS(Ntlower(ttype(R ((stest_GACrossover.pyt__init__4sc CsZ|jjƒ}|jjƒ}|j}|j}|jƒ}|jƒ}|jdkra||fS|jdkrÏtt|ƒdƒ} tt|ƒdƒ} t| |jjƒ|_t| |jjƒ|_nQ|jdkr tt|ƒdƒ} tt|ƒdƒ} nt d|jƒ‚t| |jjƒ|_t| |jjƒ|_||fS(NtsameRGithighers Got type %s( RRRtcopyRHtstrRRRt ValueError( R RRtseq_org1tseq_org2t org1_genomet org2_genomeR(R)tnew_org1_genometnew_org2_genome((stest_GACrossover.pyR$9s0     (RRRRIR$(((stest_GACrossover.pyRF1s tSafeFitnessTestcBs)eZdZd„Zd„Zd„ZRS(s6Tests for crossovers which do not reduce fitness. cCsdtƒ|_td|jƒ}t|tƒ|_td|jƒ}t|tƒ|_tƒ|_dS(NR ( R RRRRRRRFttest_crossover(R R!R"((stest_GACrossover.pyR#\s  cCst|jƒ}d|j_|j|j|jƒ\}}||jkrW||jksctdƒ‚d|j_|j|j|jƒ\}}||jkr«||jks·tdƒ‚d|j_|j|j|jƒ\}}|j|jjkr |j|jjkstdƒ‚dS(s@Make sure we always keep higher fitness when specified. RJs)Did not retain organism for same fitness.RGs9Did not retain organism when crossover had lower fitness.RKs4Did not get new organism when it had higher fitness.N(RRVRHR$RRR%tfitness(R R R(R)((stest_GACrossover.pyttest_keep_higherfs !  !  cCst|jdƒ}d|j_|j|j|jƒ\}}||jkrZ||jksftdƒ‚d|j_|j|j|jƒ\}}||jkr®||jksºtdƒ‚d|j_|j|j|jƒ\}}|j|jjkr|j|jjkstdƒ‚dS( sGMake sure we do normal crossover functionality when specified. gð?RJs)Did not retain organism for same fitness.RGs3Did not retain lower fitness organism in crossover.RKs9Did not get new organism under higher fitness conditions.N(RRVRHR$RRR%RW(R R R(R)((stest_GACrossover.pyttest_keep_lower~s !  !  (RRRR#RXRY(((stest_GACrossover.pyRUYs t__main__t verbosityit testRunner((!RtunittesttBio.SeqRt Bio.AlphabetRtBio.GA.OrganismRtBio.GA.Crossover.GeneralRtBio.GA.Crossover.GeneralPointRRtBio.GA.Crossover.TwoPointRtBio.GA.Crossover.PointRtBio.GA.Crossover.UniformRR RtTestCaseRR+R6RARERFRURtTextTestRunnertrunnertmain(((stest_GACrossover.pyts,  DKD(=