úÎUCKݍ      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefg h i j k l m n o p q r s t u v w x y z { | }~€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’“”•–—˜™š›œžŸ Ą˘Ł¤ĽŚ§Safe=Parse nucleotide sequence. Allowed letters according to IUPACeParse nucleotide alignment entry. Allowed letters according to IUPAC and commonly used gap charactersJParse protein amino acid code sequence. Allowed letters according to IUPACrParse protein amino acid code alignment entry. Allowed letters according to IUPAC and commonly used gap charactersSafeIDatatype contains all elements for the consenus result of input alignment XDatatype contains all result elements for each member of the input alignment ;All elements of RNAz output are contained in this datatype #  !"#$%&'(#  !"#$%&'(# !"#$%&'(     !"#$%&'(Safe /MRun external RNAz command and read the output into the corresponding datatype¨ Parse the input as RNAz datatypeŠ'Parse a RNAz field containing a Double Ş/Parse a RNAz field containing a String Ť-Parse a RNAz field containing a Int ŹParse a RNAz result ­+Parse the consenus of RNAz results 0parse RNAz from input string1/parse from input filePath /¨ŠŞŤŹ­01&  !"#$%&'(/01/01 /¨ŠŞŤŹ­01Safe25Data structure for (sub-) optimal interaction region @ƒData structure for individual interaction between a target and query nucleic acid seqence, contains all (sub)-optimal interactions 23456789:;<=>?@ABCD23456789:;<=>?@ABCD@ABCD23456789:;<=>?2 3456789:;<=>?@ABCDSafeŽ4Parse the input as list of RNAupInteraction datatypeŻ,Parse the consenus of RNAup results °Parse a RNAupInteractionRegionąParse a RNAupFileNameI#parse RNAupOutput from input stringJ/parse from input filePath ŽŻ°ąIJ23456789:;<=>?@ABCDIJIJŽŻ°ąIJSafeKYData structure for individual interaction between a target and query nucleic acid seqenceKLMNOPQRSTUVWXYZKLNMOPQRSTUVWXYZKLMNOPQRSTUVWXYZKLMNOPQRSTUVWXYZSafe˛6Parse the input as list of RNAplexInteraction datatypeł.Parse the consenus of RNAplex results ]%parse RNAplexOutput from input string^/parse from input filePath ˛ł]^KLNMOPQRSTUVWXYZ]^]^˛ł]^Safe_Data structure for RNAfold_`abcd_`abcd_`abcd_`abcd SafegPRun external RNAfold command and read the output into the corresponding datatype´+Parse the consenus of RNAz results h&parse RNAfold output from input stringi>parse RNAfold output from input filePath g´hi _`abcdghighig´hi SafejData structurejkljkljkljkl Safeľ+Parse the consenus of RNAz results o*parse RNAdistance output from input stringpBparse RNAdistance output from input filePath ľopjklopopľop Safeq8Data structure for cofolding of 2 nucleic acid sequencesqrstuvwqrstuvwqrstuvwqrstuvw SafezRun external RNAcofold command ś0Parse the consenus of RNAcofold results {(parse RNAcofold output from input string|@parse RNAcofold output from input filePath zś{| qrstuvwz{|z{|zś{|Safe} RNAcode Hit‰>All elements of RNAcode output are contained in this datatype }~€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’}~‚ƒ†„€…‡ˆ‰Š‹ŒŽ‘’‰Š‹ŒŽ‘’}~€‚ƒ„…†‡ˆ} ~€‚ƒ„…†‡ˆ‰ Š‹ŒŽ‘’Safe —PRun external RNAcode command and read the output into the corresponding datatypeˇ+Parse the tabular input as RNAcode datatype¸Parse the input as RNAcodeHitš#Parse the input as RNAcode datatypeşParse the input as RNAcodeHit˜parse RNAcode from input string™7parse RNAcode from input filePath šparse RNAcode from input string›7parse RNAcode from input filePath —ˇ¸šş˜™š›}~‚ƒ†„€…‡ˆ‰Š‹ŒŽ‘’—˜™š›—˜™š› —ˇ¸šş˜™š›SafeœŞData structure corrsponds with alifoldoutput redirected to file. Output written directly to commandline also contains number of sequences and length of consensus sequenceœžŸ Ą˘œžŸ Ą˘œžŸ Ą˘œžŸ Ą˘Safeť+Parse the consenus of RNAz results Ś)parse RNAalifold output from input string§Aparse RNAalifold output from input filePath ĽťŚ§ œžŸ Ą˘ĽŚ§ĽŚ§ĽťŚ§SafeŠ  !"#$%&'(/0123456789:;<=>?@ABCDIJKLNMOPQRSTUVWXYZ]^_`abcdghijklopqrstuvwz{|}~‚ƒ†„€…‡ˆ‰Š‹ŒŽ‘’—˜™š›œžŸ Ą˘ĽŚ§ź !"##$%&'()*+,-./0123456789:;<=>?@ABBCDEFGHIJKLMNOOPQRSTUVWXYYZ[\]^_`abcdefghijkllmnopqr s t u v v w x y z { | | } ~  €  ‚ ƒ „ … †‡‡ˆ‰Š‹ŒŽ‘’’“”•–—˜™š›œžŸ Ą˘Ł¤¤ĽŚ§¨ŠŞŤŹ­ŽŻ°ą˛ł´ľśˇ¸šş ť ź ˝žżŔÁÂĂ,ViennaRNAParser-1.3.0-1v9bhA94LVO1rvCXgPKzmbBio.ViennaRNAParserLibrary Bio.RNAzDataBio.RNAzParser Bio.RNAupDataBio.RNAupParserBio.RNAplexDataBio.RNAplexParserBio.RNAfoldDataBio.RNAfoldParserBio.RNAdistanceDataBio.RNAdistanceParserBio.RNAcofoldDataBio.RNAcofoldParserBio.RNAcodeDataBio.RNAcodeParserBio.RNAalifoldDataBio.RNAalifoldParserBio.ViennaRNAParser readDoublereadIntparseNucleotideSequenceparseNucleotideAlignmentEntryparseProteinSequenceparseProteinAlignmentEntry RNAzConsensusconsensusSequenceconsensusDotBracket RNAzResultheaderresultSequence dotBracketminimumFreeEnergyzScorezscoreCalculationApproachRNAzversionsequenceNumber columnNumberreadingDirectionmeanPairwiseIdentityshannonEntropy gcContent#meanSingleSequenceMinimumFreeEnergyconsensusMinimumFreeEnergyenergyContributioncovarianceContributioncombinationsPair meanZScorestructureConservationIndexbackgroundModel decisionModelsvmDecisionValuesvmRNAClassProbability prediction rnazResults rnazConsensus$fShowRNAzResult$fEqRNAzResult$fShowRNAzConsensus$fEqRNAzConsensus $fShowRNAz$fEqRNAz systemRNAz parseRNAzreadRNAzRNAupInteractionRegionupSecondaryStructureupQueryDuplexBeginupQueryDuplexEndupTargetDuplexBeginupTargetDuplexEndupDuplexEnergy!upDuplexEnergyWithoutAccessiblityupQueryAccessiblityupTargetAccessibilityupQuerySequenceupTargetSequenceupOutputFileNameRNAupInteractionupQueryIdentifierupTargetIdentifierupInteractions$fShowRNAupInteractionRegion$fEqRNAupInteractionRegion$fShowRNAupInteraction$fEqRNAupInteraction parseRNAup readRNAupRNAplexInteractiontargetIdentifierqueryIdentifierplexSecondaryStructuretargetDuplexBegintargetDuplexEndqueryDuplexBeginqueryDuplexEnd duplexEnergyduplexEnergyWithoutAccessiblityqueryAccessiblitytargetAccessibilityprefilterStart prefilterStopprefilterEnergy$fShowRNAplexInteraction$fEqRNAplexInteraction parseRNAplex readRNAplexRNAfoldsequenceIdentifier foldSequencefoldSecondaryStructure foldingEnergy $fShowRNAfold $fEqRNAfold systemRNAfold parseRNAfold readRNAfold RNAdistancesecondaryStructureDistance$fShowRNAdistance$fEqRNAdistanceparseRNAdistancereadRNAdistance RNAcofoldcoFoldSequence1coFoldSequence2coFoldSecondaryStructure1coFoldSecondaryStructure2coFoldingEnergy$fShowRNAcofold $fEqRNAcofoldsystemRNAcofoldparseRNAcofold readRNAcofold RNAcodeHithssframelengthfromtonamestartendscorepvalueRNAcode rnacodeHitsrcAlignmentNumberrcTimercSampleNumberrcDelta rcBigOmega rcSmallOmega rcStopPenalty$fShowRNAcodeHit$fEqRNAcodeHit $fShowRNAcode $fEqRNAcode systemRNAcode parseRNAcode readRNAcodeparseRNAcodeTabularreadRNAcodeTabular RNAalifoldalignmentConsensusSequencealignmentConsensusDotBracket#alignmentConsensusMinimumFreeEnergy*alignmentConsensusInitialMinimumFreeEnergy/alignmentConsensusEnergyCovarianceContributions$fShowRNAalifold$fEqRNAalifoldsystemRNAalifoldparseRNAalifoldreadRNAalifold genParseRNAzparseRNAzDoubleFieldparseRNAzStringFieldparseRNAzIntFieldparseRNAzResultparseRNAzConsensusparseRNAupOutputparseRNAupInteractionparseRNAupInteractionRegionparseRNAupFileNameparseRNAplexOutputparseRNAplexInteractiongenParserRNAfoldgenParserRNAdistancegenParserRNAcofoldgenParseRNAcodeTabulargenParseRNAcodeTabularHitgenParseRNAcodegenParseRNAcodeHitgenParserRNAalifold