úÎ&š!²[      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZHStockholm format data. We have a set of sequences with sequence data, a L set of column annotations and unknown data (actually: known, but we do not  care). [Othe different state types  the different node types [branches are transition without attached probability becaue both branches are always taken )can emit either one nucleotide or a pair !"#$%&1CMType is important if we want to set localBegin / localEnd! '() One state *+,-./012Describes one node 3456789:IA complete covariance model. Each node and each state can be tagged with D additional data. Typically, say after parsing, the tag will be (). ;<=>?@ABC@generate a local model with local begin prob and local end prob DEF8given a CM in score mode, change it to probability mode G.Given a CM in prob mode, change to score mode H$normalize all PROBabilities in a CM IJKLMNOAextract the main state for each node (eg MP state for MATP node) P<Checks for each node, if it can be target of a local begin. Q4Checks for each node if it can lead to a local end. R=transform scores into probabilities, given a nullmodel for x back into scores HTransform a state, setting probabilities instead of scores. Requires CM ! knowledge for background model. S<Transform a state, setting scores instead of probabilities. TUQ  !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQ\]RSTUQ:;<=>?@AB23456789)*+,-./01&('# $%!"% CDEFGHIJKLMNOPQRSTUO   # $%!"% !"#$%&(''()*+,-./01*+,-./01234567893456789:;<=>?@AB;<=>?@ABCDEFGHIJKLMNOPQRSTU^VWVWXCMain export function for CMs. Creates a string that is accepted by  Infernal Y export a specific node, used by X Z"export a specific states, used by Y XYZ_XYZXYZ`      !"#$%&'()*+,--./01234556789:;<<=>?@ABCDEFGHIJKLMNOPQRSTUV WXYZ[\]^_`BiobaseInfernal-0.0.2.0Biobase.Infernal.Stockholm!Biobase.Infernal.Stockholm.ImportBiobase.Infernal.CMBiobase.Infernal.CM.ImportBiobase.Infernal.CM.Export Stockholm sequencescolAnnotations exAnnotationsunknownfromFile StateTypeESBMRMLDIRILMPNodeTypeENDBEGRBEGLROOTBIFMATRMATLMATP TransitiontscoreBranchtchildEmissionEmitPeNucLeNucREmitSeNucescoreCMTypeCMScoreCMProbStatesidstypesnodesparents schildren semissionstagNodenidntypenparents nchildrennstatesntagCMnodesstatesheader localBeginlocalEndcmType nullModel cmMakeLocalcmMakeLocalBegincmMakeLocalEnd cmScore2Prob cmProb2ScorecmNormalizeProbabilitiesstatesScore2ProblocalBeginScore2ProblocalEndScore2ProbstatesProb2ScorelocalBeginProb2ScorelocalEndProb2Score nodeMainStatelocalBeginPossiblelocalEndPossiblestateScore2ProbstateProb2ScoretransitionTargetsnodeMainStateAssocs fromStringtoString nodeToString stateToStringmkPair score2Prob prob2Score addneginfstringS