úÎGÿ'      !"#$%& ('()*+ ,-./0123 456789:;<=>    Isecondary structure representation using an explicit tree, SSExt encodes I the length of the underlying sequence. Each node can contain additional  information under a. FA secondary structure. It is explicit that we store the length of the 0 sequence. (length n, last index (n-1) problem) :A complex of one or more primary and secondary structures .generate an SSTree from a secondary structure   IGiven the secondary structure notation, generate the dot-bracket string. ?transforms a pseudoknot-free dotbracket string into a pairlist 1given an SSTree, return the shape representation  !"# !"?# !"# !"#$DmaxBound on Int is problematic, if we try something like maxBound + $ maxBound which happens very often. $" is used for settings like lookup + tables, etc while comparisons are against %. L Both values need to be small enough not to overflow in typical situations. %&$%&$%&$%&@       !"#$%&'()*+,-./0123456789:;<=>?@ABiobase-0.0.2.0 Biobase.RNABiobase.StructureBiobase.Structure.DotBracketBiobase.Structure.ShapesBiobase.Constants ViennaPair MkPrimary mkPrimary unPrimaryPrimary Nucleotide nucCharList charNucListcharToNucleotidenucleotideToChar vpStrList strVpListtoPairpairsSSTreeSSExt SecondarylenpairingsComplexcomments structurestoSSTree dotbracketdotbracketToPairlisttoShape5toShape4toShape3toShape2toShape1toShapeeInfeMaxfInfnucEnucAnucCnucGnucUvpNPvpCGvpGCvpGUvpUGvpAUvpUAvpNSacguacguStr acguPairseacgunpnsPcguaPcgnsP vienna2Tuplevienna2RevTuple tuple2Viennatuple2RevViennamkDashes