úÎ2ç/DB      !"#$%&'()*+,-./ 0 1 2 3 4 5 6 7 8 9 : ; < = > ? @ A &State for import and export functions JSimple RfamClan data wrapper. Could Easily be just a list of bytestrings,  which it is using strings       #Import the complete data strictly. .Given a list of bytestrings, create one Clan. #TODO return Maybe, make crash-safe    HFor each species, we store the name and a classification list from most J general (head) to most specific (last). The database comes with the NCBI  taxon identifier (taxid). Given a name such as Drosophila Melanogaster , returns d.melanogaster. =Provide name-based lookup as the most-common usage scenario. -TODO there are 9 duplicates in the names, let's find them and see what is  going on And a map based on taxon id Imports taxonomy data. Given a B, create a species entry. MNOTE The taxonomy format is, for each species, a line consisting of: taxid - M tab - species name - tab - semicolon separated list of classification names  - dot - end of line. NConvenience function: given a taxonomy file, produce both maps simultanously. Captures a complete alignment .part of target sequence (start counting at 1) which part of the CM/stk do we align to the CM for this alignment should be either C or D  bit score !&number of hits we expect to find with score or higher for targetSequence length "? #? $Mscaffold, chromosome, ... (the name of the sequence, not the sequence data!) %9fancy secondary structure annotation using wuss notation &+query consensus (upper: highly, lower: weak/no) '8represents where positive and negative scores come from (.the target sequence which aligns to the model )*any annotations that could be associated (# lines)  !"#$%&'() !"#$%&'() !"#$%&'() !"#$%&'()*FTransforms a stream into verbose hits. We need to keep a state in the C accumulator to keep track of the current CM, scaffold and strand. EParses one CM query result. +$Parses multiple four-line elements. ;Convenience function: read all results into a single list. *+*+*+,-7This transformer keeps a 1-1 relationship between each  and E bytestring representation. Useful for merging different streams, if  individual s are to be annotated. .Given the current state a and verbose hit h, determine if any state  switches have to be emitted.  Convert a 1 to a string, ready for printing as in the input  file. ,-F.,-.,-. /0123456789 /0123456789 /0123456789 / 01234567890123456789 :&Transform a stream into tabular hits. ;HConvenience function to load from file and return a big list of tabular  hits. :;:;:; >?.  !"#$%&'()*/0123456789:<=>?@A./0123456789<: !"#$%&'()=*>?@ A>?G    !""#$%&'()*+,-./01234 5 5 6 7 8 9 : ; < = > ?  @ A B C D EFGHIJKIJLMNOBiobaseInfernal-0.5.4.0$Biobase.Infernal.VerboseHit.InternalBiobase.Infernal.ClanBiobase.Infernal.Clan.ImportBiobase.Infernal.Taxonomy Biobase.Infernal.Taxonomy.ImportBiobase.Infernal.VerboseHit"Biobase.Infernal.VerboseHit.Import"Biobase.Infernal.VerboseHit.ExportBiobase.Infernal.TabularHit"Biobase.Infernal.TabularHit.ImportBiobase.InfernalAliGoaliCM aliScaffold aliStrand aliAnnotationClan accession identifiermembersstringsfromFilemkClanSpeciesnameclassificationtaxid shortenName iSpeciesMap iTaxIdMap eneeSpecies mkSpeciesStrand VerboseHitvhTargetvhQueryvhCMvhStrandvhScorevhEvaluevhPvaluevhGC vhScaffoldvhWuss vhConsensus vhScoring vhSequence vhAnnotationeneeVerboseHiteneeByteStringeneeByteStringsshowVerboseHit TabularHitthModelthTargetthScaffoldStartthScaffoldStop thQueryStart thQueryStop thBitScorethEvalue thGCpercenteneeTabularHit thFromFile vhFromFilevhEneeByteStringvhEneeByteStrings tFromFile cFromFilebytestring-0.9.1.10Data.ByteString.Internal ByteStringbaseGHC.Num+-qsnewAcc