clj-hgvs.coordinate
Data structures and functions to handle HGVS coordinates.
->region-keyword
(->region-keyword s)
->region-str
(->region-str k)
Calculable
protocol
members
minus
(minus this n)
Subtracts n from the given coordinate and returns the new coordinate.
plus
(plus this n)
Adds n to the given coordinate and returns the new coordinate.
circular-dna-coordinate
(circular-dna-coordinate position)
Returns CircularDNACoordinate instance having position. Throws an exception
if position is illegal.
coding-dna-coordinate
(coding-dna-coordinate position)(coding-dna-coordinate position offset region)
Returns CodingDNACoordinate instance having position, offset, and region.
Throws an exception if any input is illegal.
comparable-coordinates?
(comparable-coordinates? coord1 coord2)
Returns true if the two coordinates are comparable, else false.
Coordinate
protocol
members
plain
(plain this)
Returns a plain map representing the given coordinate.
genomic-coordinate
(genomic-coordinate position)
Returns GenomicCoordinate instance having position. Throws an exception if
position is illegal.
ICodingDNACoordinate
protocol
members
in-exon?
(in-exon? this)
Returns true if the coordinate is located in exon, else false.
mitochondrial-coordinate
(mitochondrial-coordinate position)
Returns MitochondrialCoordinate instance having position. Throws an exception
if position is illegal.
non-coding-dna-coordinate
(non-coding-dna-coordinate position)
Returns NonCodingDNACoordinate instance having position. Throws an exception
if position is illegal.
parse-circular-dna-coordinate
(parse-circular-dna-coordinate s)
Parses a coordinate string used in circular-dna mutations, returning a
CircularDNACoordinate or UnknownCoordinate.
parse-coding-dna-coordinate
(parse-coding-dna-coordinate s)
Parses a coordinate string used in coding DNA mutations, returning a
CodingDNACoordinate or UnknownCoordinate.
parse-coordinate
(parse-coordinate s t)
parse-genomic-coordinate
(parse-genomic-coordinate s)
Parses a coordinate string used in genomic mutations, returning a
GenomicCoordinate or UnknownCoordinate.
parse-mitochondrial-coordinate
(parse-mitochondrial-coordinate s)
Parses a coordinate string used in mitochondrial mutations, returning a
MitochondrialCoordinate or UnknownCoordinate.
parse-non-coding-dna-coordinate
(parse-non-coding-dna-coordinate s)
Parses a coordinate string used in non-coding DNA mutations, returning a
NonCodingDNACoordinate or UnknownCoordinate.
parse-protein-coordinate
(parse-protein-coordinate s)
Parses a coordinate string used in protein mutations, returning a
ProteinCoordinate or UnknownCoordinate.
parse-rna-coordinate
(parse-rna-coordinate s)
Parses a coordinate string used in RNA mutations, returning a RNACoordinate
or UnknownCoordinate.
parse-uncertain-coordinate
(parse-uncertain-coordinate s t)
protein-coordinate
(protein-coordinate position)
Returns ProteinCoordinate instance having position. Throws an exception if
position is illegal.
restore
multimethod
(restore m)
Restores a plain map to a suitable coordinate record.
rna-coordinate
(rna-coordinate position offset region)
Returns RNACoordinate instance having position, offset, and region. Throws an
exception if any input is illegal.
uncertain-coordinate
(uncertain-coordinate start end)
Returns UncertainCoordinate instance having start and end. Throws an
exception if any input is illegal.
unknown-coordinate
(unknown-coordinate)
Returns UnknownCoordinate instance.