Enum gb_io::seq::Location

pub enum Location {
    Range((i64, Before), (i64, After)),
    Between(i64, i64),
    Complement(Box<Location>),
    Join(Vec<Location>),
    Order(Vec<Location>),
    Bond(Vec<Location>),
    OneOf(Vec<Location>),
    External(String, Option<Box<Location>>),
    Gap(GapLength),
}

Represents a Genbank “location”, used to specify the location of features and in the CONTIG line. See http://www.insdc.org/files/feature_table.html for a detailed description of what they mean.

Note that locations specified here must always refer to a nucleotide within the sequence. Ranges are inclusive in Genbank format, but represented as exclusive ranges, using 0-based indexing in this library. For example, 1..3 will be represented as Range((0, Before(false)), (4, After(false))).

To specify a range that wraps around on a circular sequence, Genbank files use join(x..last,1..y).

Variants

Range((i64, Before), (i64, After))

Represents a range of positions, indicated with [<]x..[>]y in the Genbank file. If < or > are present, then Before or After will be true, respectively. This means that the feature starts before/extends beyond the end point. Genbank files represent locations consisting of a single position with a single number. In this library this is represented using Range, i.e. 1 becomes Range((0, Before(false)), (1, After(false))).

Between(i64, i64)

Represented as n^n+1: This means that the location is between the two adjacent positions specified. On a circular sequence the last and first positions are also allowed.

Complement(Box<Location>)

INSDC: “Find the complement of the presented sequence in the span specified by “location” (i.e., read the complement of the presented strand in its 5’-to-3’ direction)“

Join(Vec<Location>)

INSDC: “The indicated elements should be joined (placed end-to-end) to form one contiguous sequence”

Order(Vec<Location>)

INSDC: “The elements can be found in the specified order (5’ to 3’ direction), but nothing is implied about the reasonableness about joining them”

Bond(Vec<Location>)

OneOf(Vec<Location>)

External(String, Option<Box<Location>>)

Gap(GapLength)

Implementations

impl Location

pub fn simple_range(a: i64, b: i64) -> Location

Convenience constructor for this commonly used variant

pub fn single(a: i64) -> Location

pub fn find_bounds(&self) -> Result<(i64, i64), LocationError>

Try to get the start and end of a location. Returns the starting and finishing locations, as an exclusive range.

pub fn truncate(&self, start: i64, end: i64) -> Option<Location>

Truncates this location, limiting it to the given bounds. Note: higher is exclusive. None is returned if no part of the location lies within the bounds.

pub fn to_gb_format(&self) -> String

pub fn from_gb_format(s: &str) -> Result<Location, GbParserError>

Trait Implementations

impl Clone for Location

fn clone(&self) -> Location

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for Location

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl<'de> Deserialize<'de> for Location

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error> where
    __D: Deserializer<'de>, 

Deserialize this value from the given Serde deserializer.

impl Display for Location

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl PartialEq<Location> for Location

fn eq(&self, other: &Location) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Location) -> bool

This method tests for !=.

impl Serialize for Location

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error> where
    __S: Serializer, 

Serialize this value into the given Serde serializer.

impl StructuralPartialEq for Location