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| Bio.Location.ContigLocation |
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| Description |
Data type for a sequence location consiting of a contiguous range
of positions on the sequence.
Throughout, sequence position refers to a Pos which includes a
strand. An index into a sequence is referred to as an offset, and
is generally of type Offset.
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| Synopsis |
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| Sequence locations
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| Contiguous sequence location defined by a span of sequence
positions, lying on a specific strand of the sequence.
| | Constructors | | ContigLoc | | | offset5 :: !Offset | The offset of the 5' end of the location, as a 0-based index
| | length :: !Offset | The length of the location
| | strand :: !Strand | The strand of the location
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|  Instances | |
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| Create a sequence location lying between 0-based starting and
ending offsets. When start < end, the location
be on the forward strand, otherwise it will be on the
reverse complement strand.
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| Create 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.
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| Locations and positions
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| The 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.
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| Sequence position of the start of the location. This is the 5'
end on the location strand, which will have a higher offset than
endPos if the location is on the RevCompl strand.
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| Sequence position of the end of the location, as described in startPos.
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| 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,
Nothing is returned; thus, the offset of the new position will
always be in the range [0, length cloc - 1].
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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 posInto when the sequence position lies
within the position is actually within the location.
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| Returns True when a sequence position lies within a sequence
location on the same sequence, and occupies the same strand.
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| Returns True when two sequence locations overlap at any
position.
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| Extracting subsequences
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| Extract the nucleotide SeqData for the sequence location. If
any part of the location lies outside the bounds of the sequence,
an error results.
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| As seqData, extract the nucleotide subsequence for the
location. Any positions in the location lying outside the bounds
of the sequence are returned as N rather than producing an error.
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| Transforming locations
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Returns 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,
slide (revCompl cloc) off == revCompl (slide cloc off)
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| Returns 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
RevCompl 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.
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| Displaying locations
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| Display a human-friendly, zero-based representation of a sequence location.
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| Produced by Haddock version 2.6.1 |
