!N      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMSafe      Safe     Safe !4Introduces all useful methods to create an alignmentN\Traceback starting point selector function, bool indicate if we have to add gaps to sequenceOA set of traceback conditionsPShould we stop?QShould we go daigonally?RShould we go vertically?SShould we go horizontally?TCondition, that gets matrix, i and j(Gap type)Substitution function for a values comparisonURepresents alignment matrix!"#$%&'NOVPQRST()U!%"#$&'NOVPQRST()U!"#$%&'NOVPQRST()U Safe*+W*+W*+W None,XYZ[\,XYZ[\,XYZ[\None -./012 /.-*+, *+/.-, /.-012 SafeL]^_`abcdefg9:;<hijklmnopqrstu]^_`abcdefg9:;<hijklmnopqrs]^_`abcdefg9:;<hijklmnopqrstuSafe!"=!%"#$&'()9:;<=)(!"#$%&'=9:;<= None>?@AB>?@AB>?@ABNone>?@AB>?@ABSafeCDEFGHIJCDEFGHIJCDEFGHIJSafevwvwSafeCDEFGHIJGHIJCDEFSafeKCDEFKKCDEFKSafe xyz{L|}~Lxyz{L|}~SafeMMMSafeLMLM !"#$%&'()*+,-./012 3 4 5 6 7 8 9 : ; < = >?@ABCDEFG H I J KL M N O P QRRSTUUVWXYZ [ \ ] ^ _ ` a b \ c d e f g h i i j k l m n o p q q r s t u v w x y z { | } ~ +bio-sequence-0.1.0.0-4BTgvzEtTSB5g66XozNpvJBio.Sequence.Alignment.MatrixBio.Sequence.AminoAcidBio.Sequence.AlignmentBio.Sequence.Alignment.Scoring Bio.Macro Bio.SequenceBio.Sequence.Parser.Fasta%Bio.Sequence.AminoAcid.Internal.Types$Bio.Sequence.Alignment.Internal.Type.Bio.Sequence.Alignment.Internal.Matrix.Scoring/Bio.Sequence.Alignment.Internal.Matrix.Template)Bio.Sequence.Alignment.Internal.Instances)Bio.Sequence.Alignment.Scoring.SimilarityBio.Macro.Internal.TypesBio.Macro.Internal.Instances)Bio.Sequence.Parser.Fasta.Internal.Parser-Bio.Sequence.Parser.Fasta.Internal.ConvertersBLOSUM62blosum62PAM250pam250NUC44nuc44 AminoAcidAlanineGlycineValine IsoleucineLeucine Methionine PhenylalanineTyrosine TryptophanSerine Threonine Asparagine GlutamineCysteineProlineArginine HistidineLysine AsparticAcid GlutamicAcid AcetylGroup MetilAmine shortName3 shortName fromShortCodefromChar Alignmentgap substitution conditionsinitsselector additionalGap Substitution ScoringMatrixscoringmatrix$fScoringMatrixNUC44$fScoringMatrixPAM250$fScoringMatrixBLOSUM62$fShowBLOSUM62 $fEqBLOSUM62 $fShowPAM250 $fEqPAM250 $fShowNUC44 $fEqNUC44mkGlobalmkLocal mkSemiglobalmkEditDistance alignment similarityhammingrelativeHammingalignmentScorealignmentSemiglobalScoreChain chainType chainResidues MacroMoleculemmNamemmChainsSequence fastaParser aminoParser StartSelector ConditionsisStopisDiagisVertisHoriz ConditionMatrix loadMatrix matrixDecinstDectypeDec functionDecmkClauseSimpleAlignmentaTypesubstaGap AlignmentTypeGlobalAlignmentLocalAlignmentSemiglobalAlignment EditDistancesubIJ localStartsemiglobalStart localConds defaultConds semiConds localStop defaultStop defaultDiag defaultVert defaultHorizlistKeyByValMax$fAlignmentSimpleAlignment$fAlignmentEditDistance$fFunctorChain$fFunctorMacroMolecule FastaSequencesNameresiduesfastaSequenceToSequence fastaSequencenamePnameP' sequencePlinePcharSeqToAminoSeq