Struct Strand

pub struct Strand<Label, DomainLabel> {
    pub domains: Vec<Domain<DomainLabel>>,
    pub sequence: Option<Cow<'static, str>>,
    pub cyclic: bool,
    pub color: Option<Color>,
    pub label: Option<Label>,
}

A DNA strand.

Fields

domains: Vec<Domain<DomainLabel>>

The (ordered) vector of domains, where each domain is a directed interval of a helix.

sequence: Option<Cow<'static, str>>

The sequence of this strand, if any. If the sequence is longer than specified by the domains, a prefix is assumed. Can be skipped in the serialisation.

cyclic: bool

Is this sequence cyclic? Can be skipped (and defaults to false) in the serialization.

color: Option<Color>

Colour of this strand. If skipped, a default colour will be chosen automatically.

label: Option<Label>

An optional label for the strand. Can be serde_json::Value::Null, and skipped in the serialisation.

Implementations

impl<Label, DomainLabel> Strand<Label, DomainLabel>

pub fn find_nucl(&self, nucl: isize) -> (isize, isize, bool)

Find the nucl-th nucleotide of the strand. Output is (h, x, b) so that the nucl-th nucleotide of the strand is on helix h at position x with orientation b.

impl<StrandLabel, DomainLabel> Strand<StrandLabel, DomainLabel>

pub fn default_color(&self) -> Color

Provide a default color to the strand.

pub fn set_kelly_color(&mut self, color: usize)

Choose a color for this strand.

pub fn is_empty(&self) -> bool

Return true iff the strand is empty

pub fn len(&self) -> usize

Total length of the strand

pub fn from_domain(domain: Domain<DomainLabel>) -> Self

Create a strand made of one domain

pub fn first_nucl(&self) -> Option<(isize, isize, bool)>

Return the first Nucleotide of the strand if the length is at least 1. Return None otherwise

pub fn last_nucl(&self) -> Option<(isize, isize, bool)>

Return the last Nucleotide of the strand if the length is at least 1. Return None otherwise

pub fn nth_nucl(&self, n: usize) -> Option<(isize, isize, bool)>

Return the n-th nucleotide of the strand, or None if the length of the strand is less than n.

pub fn set_sequence(&mut self, seq: String)

Set the sequence of the strand, if the strand is longer than the provided sequence, the 3’ end of the strand will not have a sequence. If the sequence is longer than the strand, the last chars of the sequence will be ignored

Trait Implementations

impl<Label: Clone, DomainLabel: Clone> Clone for Strand<Label, DomainLabel>

fn clone(&self) -> Strand<Label, DomainLabel>

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl<Label: Debug, DomainLabel: Debug> Debug for Strand<Label, DomainLabel>

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

Formats the value using the given formatter.

impl<Label: Default, DomainLabel: Default> Default for Strand<Label, DomainLabel>

fn default() -> Strand<Label, DomainLabel>

Returns the “default value” for a type.

impl<'de, Label, DomainLabel> Deserialize<'de> for Strand<Label, DomainLabel>

where Label: Deserialize<'de>, DomainLabel: Deserialize<'de>,

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl<Label, DomainLabel> Serialize for Strand<Label, DomainLabel>

where Label: Serialize, DomainLabel: Serialize,

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

where __S: Serializer,

Serialize this value into the given Serde serializer.