ó "ˆIc@s=dZddlZddlmZddlmZddlmZddlm Z ddl m Z ddl m Z d efd „ƒYZ d „Zd dd „ƒYZdejefd„ƒYZdejefd„ƒYZddd„ƒYZdejfd„ƒYZedkr9ejddƒZejdeƒndS(s4Tests for Genetic Algorithm mutation functionality. iÿÿÿÿN(t MutableSeq(tSingleLetterAlphabet(tOrganism(tSafeFitnessMutation(tConversionMutation(tSinglePositionMutationt TestAlphabetcBseZdZdddgZRS(sSimple test alphabet. t1t2t3(t__name__t __module__t__doc__tletters(((stest_GAMutation.pyRscCs|jƒ}t|jƒS(s,Simple class for calculating fitnesses. (ttoseqtinttdata(tgenomet seq_genome((stest_GAMutation.pyt test_fitnesss tMutationHelpercBs&eZdZdZd„Zd„ZRS(sGMixin class which provides useful functions for testing mutations. iôcCsƒd}xEt|jƒD]4}|j|jƒ}||jkr|d7}qqWt|ƒt|jƒ}||kstdƒ‚dS(sFTest the ability of a mutator to always mutate. Arguments: o mutator - The mutation class we're testing. o expected_percent - The minimum percent of mutations we expect to see under 'always mutate.' This will depend on how many letters are in the alphabet and other factors. iis2Did not recieve an acceptable number of mutations.N(tranget num_trialstmutatetorganismtfloattAssertionError(tselftmutatortexpected_percentt num_mutationsttrialtnew_orgtpercent_mutants((stest_GAMutation.pyt_always_mutate"s cCsKxDt|jƒD]3}|j|jƒ}||jkstdƒ‚qWdS(sATest that a mutator does not cause unexpected mutations. sUnexpected mutation foundN(RRRRR(RRRR ((stest_GAMutation.pyt _never_mutate9s(R R R RR"R#(((stest_GAMutation.pyRs tConversionTestcBs)eZdZd„Zd„Zd„ZRS(sBTest mutation which just converts one gene in the chromosome. cCs(tdtƒƒ}t|tƒ|_dS(Nt1111(RRRRR(RR((stest_GAMutation.pytsetUpCscCs)tddƒ}d}|j||ƒdS(s)Test ability to cause mutations. t mutation_rategð?gÍÌÌÌÌÌì?N(RR"(RRR((stest_GAMutation.pyttest_always_mutateGscCs tddƒ}|j|ƒdS(s8Make sure we do not mutate at unexpected times. R'gN(RR#(RR((stest_GAMutation.pyttest_never_mutateVs(R R R R&R(R)(((stest_GAMutation.pyR$@s  tSinglePositionTestcBs)eZdZd„Zd„Zd„ZRS(s5Test mutations at a single position in a genome. cCs(tdtƒƒ}t|tƒ|_dS(NR%(RRRRR(RR((stest_GAMutation.pyR&_scCs)tddƒ}d}|j||ƒdS(s)Test ability to cause mutations. R'gð?g333333ã?N(RR"(RRR((stest_GAMutation.pyR(cscCs tddƒ}|j|ƒdS(s8Make sure we do not mutate at unexpected times. R'gN(RR#(RR((stest_GAMutation.pyR)os(R R R R&R(R)(((stest_GAMutation.pyR*\s  t TestMutatorcBs eZdZd„Zd„ZRS(s#Provide basic mutator ability. cCs d|_dS(Ntlower(ttype(R((stest_GAMutation.pyt__init__xscCs¾|jjƒ}|j}|jƒ}|jdkr7|S|jdkrottt|ƒdƒ|jƒ|_|S|jdkr§ttt|ƒdƒ|jƒ|_|St d|jƒ‚dS(NtsameR,ithighers Got type %s( RRRtcopyR-RtstrRtalphabett ValueError(Rtorgtorg_genome_seqtold_org_genomeR ((stest_GAMutation.pyR{s  (R R R R.R(((stest_GAMutation.pyR+us tSafeFitnessTestcBs)eZdZd„Zd„Zd„ZRS(s=Test mutation which does not allow decreases in fitness. cCs@tƒ|_td|jƒ}t|tƒ|_tƒ|_dS(NR(RR3RRRR5R+t test_mutator(RR((stest_GAMutation.pyR&‘s cCsÄt|jƒ}d|j_|j|jƒ}||jksHtdƒ‚d|j_|j|jƒ}||jkstdƒ‚d|j_|j|jƒ}|j|jjksÀtdƒ‚dS(s5Make sure we always keep the higher fitness. R/s)Did not retain organism for same fitness.R,s9Did not retain organism when crossover had lower fitness.R0s4Did not get new organism when it had higher fitness.N(RR9R-RR5Rtfitness(RRR ((stest_GAMutation.pyttest_keep_higher˜s     cCsÍt|jdƒ}d|j_|j|jƒ}||jksKtdƒ‚d|j_|j|jƒ}|j|jjksŠtdƒ‚d|j_|j|jƒ}|j|jjksÉtdƒ‚dS( sBMake sure we always keep the new organism when specified. gð?R/s)Did not retain organism for same fitness.R,s3Did not get new organism when it had lower fitness.R0s9Did not get new organism under higher fitness conditions.N(RR9R-RR5RR:(RRR ((stest_GAMutation.pyt test_keep_new¬s     (R R R R&R;R<(((stest_GAMutation.pyR8Žs  t__main__t verbosityit testRunner(((R tunittesttBio.SeqRt Bio.AlphabetRtBio.GA.OrganismRtBio.GA.Mutation.GeneralRtBio.GA.Mutation.SimpleRRRRRtTestCaseR$R*R+R8R tTextTestRunnertrunnertmain(((stest_GAMutation.pyts"  #2