úÎx»jÖÌ      !"#$%&'()*+,-./0123456789:;<= > ? @ A B C D E F G H I J K L M N O P Q R S T U V W X Y Z [ \ ] ^ _ ` a b c d e f ghijklmnopqrstuvwxyz{|}~€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’“”•–—˜™š›œžŸ ¡¢£¤¥¦§¨©ª«¬­®¯°±²³´µ¶·¸¹º»¼½¾¿ÀÁÂÃÄÅÆÇÈÉÊË 'Define the basic operations on a ring. '==zero does not work well for min-plus    BSome default instances. Left out the Num one, so that you have to E explicitly instanciate if you want to go around the Ring structure. Ì$Ring operations over Energy values.      BSome default instances. Left out the Num one, so that you have to E explicitly instanciate if you want to go around the Ring structure. Í#Ring operations over Score values.       BSome default instances. Left out the Num one, so that you have to E explicitly instanciate if you want to go around the Ring structure. Î'Ring operations over Partition values. 7From (Gibbs free) energy to partition function values. GTODO temperature is running around here: move to some library later on )How to convert between different values. ÏBA data structure describing all fields as used by the Turner 2004 I parameter set. Some fields are commented out until they are being used.  !"#$%&'()*+,-./012345 !"#$%&'()*+,-./012345ÐÑÒ !"#$%&'()*+,-./012345 !"#$%&'()*+,-./012345 !"#$%&'()*+,-./0123456HStockholm format data. We have a set of sequences with sequence data, a L set of column annotations and unknown data (actually: known, but we do not  care). 789:;6789:;6789:;6789:;789:;<<Ó<< =>?@ABCDEFGHIJKL)=>?@ABCDÔÕÖ×ØEFGHÙÚÛÜÝÞßàIJáâãäåæçèKLéêëìCDEFGHB?@A=>IJKL=>>?@A@ABCDDEFGHIJKL MIsecondary structure representation using an explicit tree, SSExt encodes I the length of the underlying sequence. Each node can contain additional  information under a. NOPFA secondary structure. It is explicit that we store the length of the 0 sequence. (length n, last index (n-1) problem) QRST:A complex of one or more primary and secondary structures UVWX.generate an SSTree from a secondary structure MNOPQRSTUVWX TUVWPQRSMONX MONNOPQRSQRSTUVWUVWX YIGiven the secondary structure notation, generate the dot-bracket string. Z?transforms a pseudoknot-free dotbracket string into a pairlist YZYZYZ [1given an SSTree, return the shape representation \]^_`[\]^_í`[\]^_`[\]^_` abcdefJData structure containing all necessary tables for the Turner 2004 model. G Note the temperature, using an additional function, rescaling becomes H possible. A Show and a Read instance are automatically derived but one  should use the Turner andor Vienna import!export facilities. All data uses H complete tables, where any base can pair with any other. Missing data (î  in tables) is given by ï, otherwise we have 'Just Int'. In general, have a look here:  url{http:rna.urmc.rochester.eduNNDBturner04/index.html} where  parameters are explained. HConversion from Turner to Vienna is only possible in one direction as a : number of parameters are not used in Vienna RNA Folding. abcdeffedcbaabcdefggOhthe different state types ijklmnopqrthe different node types stuvwxyz{[branches are transition without attached probability becaue both branches are always taken |}~€)can emit either one nucleotide or a pair ‚ƒ„…†‡1CMType is important if we want to set localBegin / localEnd! ˆ‰Š One state ‹ŒŽ‘’“Describes one node ”•–—˜™š›IA complete covariance model. Each node and each state can be tagged with D additional data. Typically, say after parsing, the tag will be (). œžŸ ¡¢£¤@generate a local model with local begin prob and local end prob ¥¦§8given a CM in score mode, change it to probability mode ¨.Given a CM in prob mode, change to score mode ©$normalize all PROBabilities in a CM ª«¬­®¯°Aextract the main state for each node (eg MP state for MATP node) ±<Checks for each node, if it can be target of a local begin. ²4Checks for each node if it can lead to a local end. ³=transform scores into probabilities, given a nullmodel for x back into scores HTransform a state, setting probabilities instead of scores. Requires CM ! knowledge for background model. ´<Transform a state, setting scores instead of probabilities. µ¶Qhijklmnopqrstuvwxyz{|}~€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’“”•–—˜™š›œžŸ ¡¢£¤¥¦§¨©ª«¬­®¯°±²ðñ³´µ¶Q›œžŸ ¡¢£“”•–—˜™šŠ‹ŒŽ‘’‡‰ˆ€„…†‚ƒ†{~|}rzyxwvutshqponmlkji¤¥¦§¨©ª«¬­®¯°±²³´µ¶Oh qponmlkjiijklmnopqrzyxwvutsstuvwxyz{~|}|}~€„…†‚ƒ†‚ƒ„…†‡‰ˆˆ‰Š‹ŒŽ‘’‹ŒŽ‘’“”•–—˜™š”•–—˜™š›œžŸ ¡¢£œžŸ ¡¢£¤¥¦§¨©ª«¬­®¯°±²³´µ¶ò·¸·¸¹CMain export function for CMs. Creates a string that is accepted by  Infernal º export a specific node, used by ¹ »"export a specific states, used by º ¹º»ó¹º»¹º»¼DmaxBound on Int is problematic, if we try something like maxBound + $ maxBound which happens very often. ¼" is used for settings like lookup + tables, etc while comparisons are against ½. L Both values need to be small enough not to overflow in typical situations. ½¾¼½¾ôõ¼½¾¼½¾¿ÀÁÂÃJAn empty Turner2004 set, with Vienna-style keys for tables. Unused fields I are commented out. Activate them in BiobaseTurner before doing the same  here! ¿ÀÁÂÃö÷ÂÁÀ¿Ã¿ÀÁÂÃøùúûüýÄ+Imports Vienna tables from a given string. þ3Apply all parsed blocks to a Turner2004 structure. ÿÄÄÄÅÅ ÆDExport the files required for default values in the ViennaRNA 2.0 C  package. Export the main C file Export iloops 1x1  Export iloops 2x1  Export iloops 2x2    ÆÆÆ>Transform from tuple-based keys to a pair of list-based keys. Ç6Show the key of the line, minus the changing last key ÇÇÇÈJConvert from Turner keys to Vienna keys and all values from Double to Int Vienna values are Int's that have 2-digit precision. ÈÈÈÉDThe max operation applied to all relevant tables. (This serves as a ' pointer, which tables to manipulate). ÉÉÉÊECreate partition tables out of normal energy tables. Note that these 0 values are not normalized. An additional term 1Z(1kt) would be required H which is missing until we are done calculating the partition function. @All energy contributions are rescaled from dekacals back to kcal/mol. DWe explicitly set all probabilities =0 where the energy is >= eMax. ÊÊÊËËËË !"#$%%&''()*++,-./001234456789:;<=>?@ABCDEFGHIJKLMMNOPQR S S T U V W X X Y Z [ \ ] ^ _ ` a b a c c d e f f g h i j k l m n o p q r s t u v wxyz{|}~€‚ƒ„…†‡ˆ‰Š‹ŒŒŽ‘’“”•–—˜™šš›œžŸ ¡¢¢£¤¥¦§¨©©ª«¬­®¯°±²³´µ¶·¸¹º»¼½¾¿ÀÁÂÃRÄÅÆÇÈÉÊtËÌÍÎÏÐÑÑÒÓÔÕÖ×ØÙÚÛÜÝ Þ ß à á â ã ä å æ ç è é ê ë ì í î ï ð ñ ò ó ô õ ö ÷øùúøûüýþÿ     ¬Biobase-0.1.0.0Biobase.Types.RingBiobase.Types.EnergyBiobase.Types.ScoreBiobase.Types.PartitionBiobase.Types.ConvertBiobase.Turner.TablesBiobase.Infernal.Stockholm!Biobase.Infernal.Stockholm.Import Biobase.RNABiobase.StructureBiobase.Structure.DotBracketBiobase.Structure.ShapesBiobase.TurnerBiobase.Turner.ImportBiobase.Infernal.CMBiobase.Infernal.CM.ImportBiobase.Infernal.CM.ExportBiobase.ConstantsBiobase.ViennaBiobase.Vienna.Import.ViennaParBiobase.Vienna.DefaultBiobase.Vienna.Export.ViennaCBiobase.Vienna.Export.ViennaParBiobase.Vienna.Import.Turner'Biobase.Vienna.Modification.NonStandard%Biobase.Vienna.Modification.Partition'Biobase.Vienna.Modification.TemperatureRing.+..*..^..^^.negonezeroisZeroEnergyunEnergyScoreunScoreexpm1log1p Partition unPartition' mkPartition unPartitionlogSumKelvinunKelvinConvertconvert Turner2004stackdangle3dangle5hairpinL hairpinMM hairpinLookupbulgeLiloop1x1iloop1x2iloop2x2iloopMM iloop2x3MM iloop1xnMMiloopLmultiMMniniomaxNinio multiOffsetmultiNuc multiHelixextMM largeLooptermAUintermolecularInit Stockholm sequencescolAnnotations exAnnotationsunknownfromFile ViennaPair MkPrimary mkPrimary unPrimaryPrimary Nucleotide nucCharList charNucListcharToNucleotidenucleotideToChar vpStrList strVpListtoPairpairsSSTreeSSExt SecondarylenpairingsComplexcomments structurestoSSTree dotbracketdotbracketToPairlisttoShape5toShape4toShape3toShape2toShape1toShapeBasepair TurnerSet TemperatureTurnerEnthalpy TurnerEntropy TurnerTables parseTurner StateTypeESBMRMLDIRILMPNodeTypeENDBEGRBEGLROOTBIFMATRMATLMATP TransitiontscoreBranchtchildEmissionEmitPeNucLeNucREmitSeNucescoreCMTypeCMScoreCMProbStatesidstypesnodesparents schildren semissionstagNodenidntypenparents nchildrennstatesntagCMnodesstatesheader localBeginlocalEndcmType nullModel cmMakeLocalcmMakeLocalBegincmMakeLocalEnd cmScore2Prob cmProb2ScorecmNormalizeProbabilitiesstatesScore2ProblocalBeginScore2ProblocalEndScore2ProbstatesProb2ScorelocalBeginProb2ScorelocalEndProb2Score nodeMainStatelocalBeginPossiblelocalEndPossiblestateScore2ProbstateProb2ScoretransitionTargetsnodeMainStateAssocs fromStringtoString nodeToString stateToStringeInfeMaxfInfViennaPartitionTablesViennaEnergyTablesViennaIntTables emptyTables importPar turner2004GHexport fromTurnernonStandardMaxpartitionTablesadjustTemperature $fRingEnergy $fRingScore$fRingPartitionconstRdmapdZipWith zipWithPAmkPairnucEnucAnucCnucGnucUvpNPvpCGvpGCvpGUvpUGvpAUvpUAvpNSacguacguStr acguPairseacgunpnsPcguaPcgnsP pairTable vienna2Tuplevienna2RevTuple tuple2Viennatuple2RevViennamkDashesbaseGHC.Base. Data.MaybeNothing score2Prob prob2Score addneginfstringSkelvinC0gasconstemptyIVemptyVBlockABlockascsbhdrints updateTableisHblockblocksblock assocBlockcomment defaultPars DirectoryexportCexport11export21export22pdpiprintNumLKeyshowKeyf2i