clj-hgvs.coordinate — clj-hgvs 0.4.6

Data structures and functions to handle HGVS coordinates.

->region-keyword clj/s

(->region-keyword s)

->region-str clj/s

(->region-str k)

Calculable clj/s protocol

minus clj/s

(minus this n)

Subtracts n from the given coordinate and returns the new coordinate.

plus clj/s

(plus this n)

Adds n to the given coordinate and returns the new coordinate.

circular-dna-coordinate clj/s

(circular-dna-coordinate position)

Returns CircularDNACoordinate instance having position. Throws an exception if position is illegal.

CircularDNACoordinate clj/s

coding-dna-coordinate clj/s

(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.

CodingDNACoordinate clj/s

comparable-coordinates? clj/s

(comparable-coordinates? coord1 coord2)

Returns true if the two coordinates are comparable, else false.

Coordinate clj/s protocol

format clj/s

(format this)

Returns a string representing the given coordinate.

plain clj/s

(plain this)

Returns a plain map representing the given coordinate.

genomic-coordinate clj/s

(genomic-coordinate position)

Returns GenomicCoordinate instance having position. Throws an exception if position is illegal.

GenomicCoordinate clj/s

ICodingDNACoordinate clj/s protocol

in-exon? clj/s

(in-exon? this)

Returns true if the coordinate is located in exon, else false.

mitochondrial-coordinate clj/s

(mitochondrial-coordinate position)

Returns MitochondrialCoordinate instance having position. Throws an exception if position is illegal.

MitochondrialCoordinate clj/s

non-coding-dna-coordinate clj/s

(non-coding-dna-coordinate position)

Returns NonCodingDNACoordinate instance having position. Throws an exception if position is illegal.

NonCodingDNACoordinate clj/s

parse-circular-dna-coordinate clj/s

(parse-circular-dna-coordinate s)

Parses a coordinate string used in circular-dna mutations, returning a CircularDNACoordinate or UnknownCoordinate.

parse-coding-dna-coordinate clj/s

(parse-coding-dna-coordinate s)

Parses a coordinate string used in coding DNA mutations, returning a CodingDNACoordinate or UnknownCoordinate.

parse-coordinate clj/s

(parse-coordinate s t)

parse-genomic-coordinate clj/s

(parse-genomic-coordinate s)

Parses a coordinate string used in genomic mutations, returning a GenomicCoordinate or UnknownCoordinate.

parse-mitochondrial-coordinate clj/s

(parse-mitochondrial-coordinate s)

Parses a coordinate string used in mitochondrial mutations, returning a MitochondrialCoordinate or UnknownCoordinate.

parse-non-coding-dna-coordinate clj/s

(parse-non-coding-dna-coordinate s)

Parses a coordinate string used in non-coding DNA mutations, returning a NonCodingDNACoordinate or UnknownCoordinate.

parse-protein-coordinate clj/s

(parse-protein-coordinate s)

Parses a coordinate string used in protein mutations, returning a ProteinCoordinate or UnknownCoordinate.

parse-rna-coordinate clj/s

(parse-rna-coordinate s)

Parses a coordinate string used in RNA mutations, returning a RNACoordinate or UnknownCoordinate.

parse-uncertain-coordinate clj/s

(parse-uncertain-coordinate s t)

protein-coordinate clj/s

(protein-coordinate position)

Returns ProteinCoordinate instance having position. Throws an exception if position is illegal.

ProteinCoordinate clj/s

restore clj/s multimethod

(restore m)

Restores a plain map to a suitable coordinate record.

rna-coordinate clj/s

(rna-coordinate position offset region)

Returns RNACoordinate instance having position, offset, and region. Throws an exception if any input is illegal.

RNACoordinate clj/s

uncertain-coordinate clj/s

(uncertain-coordinate start end)

Returns UncertainCoordinate instance having start and end. Throws an exception if any input is illegal.

UncertainCoordinate clj/s

unknown-coordinate clj/s

(unknown-coordinate)

Returns UnknownCoordinate instance.

UnknownCoordinate clj/s