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Description | |||||||||||||||||||
Data types for sequence locations and sequence positions associated with specific, named sequences. | |||||||||||||||||||
Synopsis | |||||||||||||||||||
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Positions on named sequences | |||||||||||||||||||
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A position on a named sequence | |||||||||||||||||||
Contiguous location spans on named sequences | |||||||||||||||||||
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A location consisting of a contiguous span of positions on a named sequence. | |||||||||||||||||||
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Test whether a sequence position lies within a sequence location. This requires that the position lie within the location as per isWithin and have the same sequence name. | |||||||||||||||||||
Arbitrary location spans on named sequences | |||||||||||||||||||
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A general location, consisting of spans of sequence positions on a specific, named sequence. | |||||||||||||||||||
Testing for location intersection on named sequences | |||||||||||||||||||
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Test whether a sequence position lies within a sequence location. This requires that the position lie within the location as per isWithin and have the same sequence name. | |||||||||||||||||||
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Test whether two sequence locations overlap in any position. This requires that the locations overlap as per overlaps and have the same sequence name. | |||||||||||||||||||
Extracting subsequences | |||||||||||||||||||
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Extract the subsequence specified by a sequence location from a sequence database. The sequence name is used to retrieve the full sequence and the subsequence is extracted as by seqData | |||||||||||||||||||
Displaying locations on named sequences | |||||||||||||||||||
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Display a human-friendly representation of a SeqPos | |||||||||||||||||||
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Display a human-friendly representation of a ContigSeqLoc | |||||||||||||||||||
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Display a human-friendly representation of a SeqLoc | |||||||||||||||||||
Produced by Haddock version 2.4.2 |