s)      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^ _ ` 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 { | } ~  NoneB      Safe-Inferred24Length of sequence dataW the nucleotide at a specified sequence data offset, given in 0-based coordinates, or 0 if the offset is beyond the bounds of the data: the nucleotides in subsequence of the sequence data, or : if the region extends beyond the bounds of the sequence.@Nucleotides in a subsequence of the sequence data, padded with N; when the region extends beyond the bounds of the sequence.(Starting position in 0-based coordinatesLength Sequence data(Starting position in 0-based coordinatesLength Sequence data    None !"#$%&'!"#$%&'!"#$%&'!"#$%&'None24(tA nucleotide sequence or location on a nucleotide sequence that lies on a specific strand and has an orientation.*,Complement of a nucleotide character, swap AT and G<C preserving case and leave all other characters unchanged.+Convert the orientation of a ( thing based on a specified  ()*+()*+*()+ ()*+None3B,Stranded position in a sequence.0-based index of the position/Strand of the position0Returns a position resulting from sliding the original position along the sequence by a specified offset. A positive offset will move the position away from the 5' end of the forward stand of the sequence regardless of the strand of the position itself. Thus, 4slide (revCompl pos) off == revCompl (slide pos off)1Extract / the item at a specific sequence position, or 9 if the position lies outside the bounds of the sequence.,-./01 ,-./01 ,-./01,-./01None3=K2rContiguous sequence location defined by a span of sequence positions, lying on a specific strand of the sequence.3<The offset of the 5' end of the location, as a 0-based indexThe length of the locationThe strand of the location7The bounds of a sequence location. This is a pair consisting of the lowest and highest sequence offsets covered by the region. The bounds ignore the strand of the sequence location, and the first element of the pair will always be lower than the second.8Sequence position of the start of the location. This is the 5' end on the location strand, which will have a higher offset than 9 if the location is on the  strand.9?Sequence position of the end of the location, as described in 8.:kList of sequence positions in the location, in order from the 5' end to the 3' end of the location strand.;Extract  the nucleotide SeqLike for the sequence location, or H if f any part of the location lies outside the bounds of the sequence.<As ;, extract the nucleotide subsequence for the location, but any positions in the location lying outside the bounds of the sequence are returned as N.=Given a sequence position and a sequence location relative to the same sequence, compute a new position representing the original position relative to the subsequence defined by the location. If the sequence position lies outside of the sequence location, NothingP is returned; thus, the offset of the new position will always be in the range [0, length l - 1].>Given a sequence location and a sequence position within that location, compute a new position representing the original position relative to the outer sequence. If the sequence position lies outside the location, Nothing is returned.This function inverts =V when the sequence position lies within the position is actually within the location.?For an enclosing location and a sublocation in the same coordinate system, find the image of the sublocation relative to the enclosing location. For example, if the enclosing location spans (100, 150) and the sublocation is (110, 120) then ? will be (10, 20).@$Returns a sequence location produced by finding the inverse image of a sublocation, with coordinates given relative to an enclosing location, in the coordinate system of the enclosing location. For example, if the enclosing location spans (100, 150) and the sublocation is (10, 20) then @ will be (110, 120).AjReturns a sequence location produced by extending the original location on each end, based on a pair of ( 5' extension, /3' extension/). The 5' extension is applied to the 5' end of the location on the location strand; if the location is on the  strand, the 5' end will have a higher offset than the 3' end and this offset will increase by the amount of the 5' extension. Similarly, the 3' extension is applied to the 3' end of the location.BReturns TrueM when a sequence offset lies within a sequence location on the same sequenceCReturns Truen when a sequence position lies within a sequence location on the same sequence, and occupies the same strand.DReturns True6 when two sequence locations overlap at any position.E"Contigs that comprise the locationG_Create a sequence location between 0-based starting and ending bounds with a specified strand.HUCreate a sequence location lying between 0-based starting and ending offsets. When  start < enda, the location be on the forward strand, otherwise it will be on the reverse complement strand.ICreate a sequence location from the sequence position of the start of the location and the length of the position. The strand of the location, and the direction it extends from the starting position, are determined by the strand of the starting position.JReturns a location resulting from sliding the original location along the sequence by a specified offset. A positive offset will move the location away from the 5' end of the forward stand of the sequence regardless of the strand of the location itself. Thus, 6slide (revCompl cloc) off == revCompl (slide cloc off)&23456789:;<=>?@ABCDEFGHIJ23456789:;<=>?@ABCDEFGHIJ456789:;<=>?@ABCDEF233HIGJ23456789:;<=>?@ABCDEFGHIJNone3=KKgGeneral (disjoint) sequence region consisting of a concatenated set of one or more contiguous regions.P?Return the contiguous location spanned by the spliced location.KLMNOPQRKLMNOPQRKMLNOPQRKLMNOPQRNone234=BKS]A general location, consisting of spans of sequence positions on a specific, named sequence.TMA location consisting of a contiguous span of positions on a named sequence.UA position on a named sequenceSTUVWXYZ[\]STUVWXYZ[\][\WXYZVUTS] STUVWXYZ[\] None^Representation of a genomic transcript, with a gene and a transcript identifier, along with the genomic location of the processed transcript and an optional coding sequence on that transcript.`2Gene or locus name for a collection of transcriptsaSpecific transcript identifierb)Sequence location of processed transcriptc!Location of CDS on the transcriptdSplice junctions, which are isomorphic to the introns they span, but which support other biologically relevant constructors and accessors.gCreate a splice junction from a donor position (the last position in the 5' exon) and the acceptor position (the first position in the 3' exon).hJDonor position, i.e., the last position in the 5' exon around a junction.iNAcceptor position, i.e., the first position in the 3' exon around a junction.j;List of splice junctions from a spliced location, in order.k2 the location of the 5' UTR on the transcript, or  if there is no c on the transcript or if the cs location begins at the first nucleotide of the transcript--if a region is returned it will have positive length.l2 the location of the 3' UTR on the transcript, or  if there is no c on the transcript or if the cp location ends at the last nucleotide of the transcript--if a region is returned it will have positive length.m-Genomic location of CDS within the transcriptnR the input contigs sorted in stranded order, when all lie on the same strand, or ) if they are not all on the same strand.^_`abcdefghijklmn^_`abcdefghijklmndefghij^_`abcklmn ^_`abcdefghijklmn None24BoSimple representation of a s9 object as an arbitrary object adjoined with a location.s,Object with a genomic location expressed by S.u0Mapping objects to locations on named sequences v6Mapping objects to sequence locations in the sense of 4.w&Create an empty object / location map.Specify a characteristic size for efficient queries, which depends on the underlying genome. Smaller sizes yield fewer false candidates but greater memory usage and potentially slower queries.x>Insert a new object / location pair and reutrn the updated mapyNRetrieve a list of objects that could potentially overlap the query location.Some objects may not actually overlap the query location. Some objects may appear more than once in the list. However, no object whose location truly overlaps the query will be missing from the list.Overlap is defined by one or more nucleotides in common between the bounds of the two locations, regardless of the relative strands of the query and the object location.z%Create an empty object / location map%Specify a characteristic size as per w.{>Insert a new object / location pair and reutrn the updated map|NRetrieve a list of objects that could potentially overlap the query location.Some objects may not actually overlap the query location. Some objects may appear more than once in the list. However, no object whose location truly overlaps the query will be missing from the list.Overlap is defined by one or more nucleotides in common between the bounds of the two locations, regardless of the relative strands of the query and the object location, as well as the same name for the underlying reference sequence.8To retrieve objects and test for actual overlap see the s interface and  or .}@Construct a mapping from transcripts to their genomic locations.~#Construct a mapping from a general s object to its genomic locationRetrieve a list of s objects whose overall, contiguous genomic coordinates intersect at any position the genomic interval spanned by the specified 4n. This does not require that the spliced structure of the query is a subset of the spliced structure of the sS nor that the query location lie entirely within the hit location (contrast with ).When a strand argument is given, restrict matches to those lying on the same strand as the query location, for `Just Plus`, or the opposite strand, for `Just Minus`.Retrieve a list of sK objects whose spliced structure contains the query location specifically.opqrstuvwxyz{|}~opqrstuvwxyz{|}~vwxyuz{|}stopqr~opqrstuvwxyz{|}~         !"#$%&'()*+,-./01234566789:;<=8>?@ABCDEFGHIJKLMNOP9QRSTUVWXYZ[\\]^_`a b b c d e f g g h i j k l m n o p q q r s t u v w x y z { | } ~  ; v w seqloc-0.6.1Bio.SeqLoc.OnSeqBio.SeqLoc.PositionBio.SeqLoc.StrandBio.SeqLoc.ShiftedVectorBio.SeqLoc.SeqLikeBio.SeqLoc.LocReprBio.SeqLoc.LocationBio.SeqLoc.SpliceLocationBio.SeqLoc.TranscriptBio.SeqLoc.LocMap biocore-0.3.1Bio.Core.SequenceunSLSeqLabelunOffOffsetBio.Core.StrandPlusMinusStrand ShiftedVectorzeroisnullisvectoremptyemptyZ singleton replicatelengthnullstartend!?// modifySome ensureLow ensureHighSeqLikentAtsubseq subseqPadconcatLocReprreprunreprreprStr unreprMaybe unreprEither unreprErrStrandedrevComplcomplstrandedPosoffsetstrandslideatPos ContigLocoffset5LocationboundsstartPosendPosallPosseqData seqDataPadposIntoposOutofclocInto clocOutofextend offsetWithin posWithincontigOverlaps toContigsoverlapsfromBoundsStrand fromStartEnd fromPosLen SpliceLoc fromContigslocOutoflocInto contigSpan mergeContigsmergeAdjContigs SpliceSeqLoc ContigSeqLocSeqPos SeqOffsetOnSeq onSeqLabelunOnSeq toSeqLabel unSeqLabel andSameSeq TranscriptgeneIdtrxIdlocationcdsJunctionintronfromDonorAcceptordonoracceptor junctionsutr5utr3 cdsLocation sortContigs WithLocationwithoutLocation withLocate Locatablelocate SeqLocMapLocMapemptyLM insertLocqueryLocemptySLM insertSeqLoc querySeqLoctranscriptSeqLocMaplocatableSeqLocMapqueryLocatablequeryLocCompatiblebase Data.MaybeJustNothing listSubseq listSubseqPadbsSubseq bsSubseqPadlbsNtAt lbsSubseq lbsSubseqPad$fSeqLikeByteString$fSeqLikeByteString0 $fSeqLike[]$fLocReprOffset$fLocReprStrand$fStrandedByteString$fStrandedByteString0 $fStranded[]$fStrandedWord8$fStrandedChar$fStrandedStrand $fLocReprPos $fStrandedPos clocLength clocStrandto clocPosInto clocPosOutof clocExtend clocClocInto clocClocOutof clocOverlaps$fLocationContigLoc$fLocReprContigLoc$fStrandedContigLoc SpliceLocPrev_next SpliceLocLastcontig consContig goodJunctiontailscontigs firstContig lastContigcontigsAndOffsetsposIntoContigsposOutofContigs slocClocInto slocClocOutof regionOutof slocExtend$fLocationSpliceLoc$fLocReprSpliceLoc$fStrandedSpliceLocat $fBioSeqOnSeq$fLocReprOnSeq$fStrandedOnSeq$fHashableSeqLabelslash$fLocReprJunction slmBinSizelocmapsbinSizebinslocBins$fLocatableWithLocation$fLocatableTranscript$fLocatableOnSeq$fLocatableOnSeq0