úÎ,.)'6      !"#$%&'()*+,-./012 3 4 5 &State for import and export functions HFor each species, we store the name and a classification list from most J general (head) to most specific (last). The database comes with the NCBI  taxon identifier (taxid).  Given a name such as Drosophila Melanogaster , returns d.melanogaster.      =Provide name-based lookup as the most-common usage scenario. -TODO there are 9 duplicates in the names, let's find them and see what is  going on And a map based on taxon id Imports taxonomy data. Given a 6, create a species entry. MNOTE The taxonomy format is, for each species, a line consisting of: taxid - M tab - species name - tab - semicolon separated list of classification names  - dot - end of line. NConvenience function: given a taxonomy file, produce both maps simultanously.    Captures a complete alignment .part of target sequence (start counting at 1) which part of the CM/stk do we align to the CM for this alignment should be either 7 or 8  bit score &number of hits we expect to find with score or higher for targetSequence length ? ? Mscaffold, chromosome, ... (the name of the sequence, not the sequence data!) 9fancy secondary structure annotation using wuss notation +query consensus (upper: highly, lower: weak/no) 8represents where positive and negative scores come from .the target sequence which aligns to the model  FTransforms a stream into verbose hits. We need to keep a state in the C accumulator to keep track of the current CM, scaffold and strand. 9Parses one CM query result. !$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. $Given the current state a and verbose hit h, determine if any state  switches have to be emitted.  Convert a 1 to a string, ready for printing as in the input  file. "#:$"#$"#$ %&'()*+,-./ %&'()*+,-./ %&'()*+,-./ % &'()*+,-./&'()*+,-./0&Transform a stream into tabular hits. 1HConvenience function to load from file and return a big list of tabular  hits. 010101 45%  %&'()*+,-./02345%%&'()*+,-./203 45 45;      !"#$%&'()*++,-./012345 6 7 8 9:;<=>?=>@ABCBiobaseInfernal-0.5.2.0$Biobase.Infernal.VerboseHit.InternalBiobase.Infernal.Taxonomy Biobase.Infernal.Taxonomy.ImportBiobase.Infernal.VerboseHit"Biobase.Infernal.VerboseHit.Import"Biobase.Infernal.VerboseHit.ExportBiobase.Infernal.TabularHit"Biobase.Infernal.TabularHit.ImportBiobase.InfernalAliGoaliCM aliScaffold aliStrandSpeciesnameclassificationtaxid shortenName iSpeciesMap iTaxIdMap eneeSpecies mkSpeciesfromFileStrand VerboseHitvhTargetvhQueryvhCMvhStrandvhScorevhEvaluevhPvaluevhGC vhScaffoldvhWuss vhConsensus vhScoring vhSequenceeneeVerboseHiteneeByteStringeneeByteStringsshowVerboseHit TabularHitthModelthTargetthScaffoldStartthScaffoldStop thQueryStart thQueryStop thBitScorethEvalue thGCpercenteneeTabularHit thFromFile vhFromFilevhEneeByteStringvhEneeByteStringsbytestring-0.9.1.10Data.ByteString.Internal ByteStringbaseGHC.Num+-qsnewAcc