Struct Alignment

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pub struct Alignment<T> { /* private fields */ }

Expand description

An alignment of DNA or amino acids sequences

Aligned sequences should all have the same length. Each sequence is stored as one vector of chars. This allows an easy access to columns and rows of the alignment.

Implementations§

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impl<T> Alignment<T>

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pub const fn length(&self) -> &usize

Returns the fixed length of the Alignment self

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pub const fn n_sequences(&self) -> &usize

Returns the number of sequences contained in self

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pub fn iter_positions( &self, ) -> impl Iterator<Item = Vec<&T>> + ExactSizeIterator<Item = Vec<&T>>
where T: Clone,

Returns an Iterator over the positions of the alignment

§Examples

let align = Alignment::with_sequences(
    &[
        b"AVEQTPRK".to_vec(),
        b"SVEQTPRK".to_vec(),
        b"SVEQTPKK".to_vec(),
    ],
)
.unwrap();

for position in align.iter_positions() {
    assert_eq!(position.len(), 3)
}

Source

pub fn iter_sequences( &self, ) -> impl Iterator<Item = Vec<&T>> + ExactSizeIterator<Item = Vec<&T>>
where T: Clone,

Returns an Iterator over the sequences of the alignment

§Examples

let align = Alignment::with_sequences(
    &[
        b"AVEQTPRK".to_vec(),
        b"SVEQTPRK".to_vec(),
        b"SVEQTPKK".to_vec(),
    ],
)
.unwrap();

for sequence in align.iter_sequences() {
    assert_eq!(sequence.len(), 8)
}

Source

pub const fn new(length: usize) -> Self

Returns an empty Alignment of fixed length

§Examples

 let alignment = Alignment::<char>::new(42);

 assert_eq!(*alignment.length(), 42 as usize);
 assert_eq!(*alignment.n_sequences(), 0 as usize);

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pub const fn is_empty(&self) -> bool

Returns true if self doesn’t contains any sequence

§Examples

let alignment = Alignment::<char>::new(42);

assert!(alignment.is_empty())

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pub fn with_sequences(sequences: &[Vec<T>]) -> Result<Self, MultiSeqAlignError>
where T: Clone,

Create an Alignment from same length vectors of names, descriptions, sequences

§Examples

let align = Alignment::with_sequences(
    &[
        b"AVEQTPRK".to_vec(),
        b"SVEQTPRK".to_vec(),
        b"SVEQTPKK".to_vec(),
    ],
)
.unwrap();

assert_eq!(*align.length(), 8);
assert_eq!(*align.n_sequences(), 3);

§Errors

Will return an error if names, descriptions and sequences have different lengths, and also if the sequences have different lengths (based on the first sequence).

Source

pub fn add<'a>( &'a mut self, sequence: Vec<T>, ) -> Result<&'a mut Self, MultiSeqAlignError>

Add a sequence to self

The new sequence must have the same length than self.length.

§Examples

let mut align = Alignment::new(8);

 assert_eq!(*align.n_sequences(), 0);

align
    .add(b"AVEQTPRK".to_vec())
    .unwrap();

assert_eq!(*align.n_sequences(), 1);

align
    .add(b"SVEQTPRK".to_vec())
    .unwrap();

assert_eq!(*align.n_sequences(), 2);

§Errors

Will return an error if the length of sequence is different from the one of the alignment.

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pub fn nth_position(&self, n: usize) -> Option<Vec<&T>>

Returns all amino acids / bases at a position in the alignment self. The returned vector has a length equal of number of sequences in self.

§Examples

let align = Alignment::<u8>::with_sequences(
    &[b"ELK".to_vec(), b"ILK".to_vec()],
)
.unwrap();

assert_eq!(align.nth_position(0).unwrap(), &[&b'E', &b'I']);

§Panics

Panics if n is greater or equal to the length of the Alignment.

Source

pub fn nth_sequence(&self, index: usize) -> Option<Vec<&T>>

Returns all amino acids / bases of the sequence at the index of the Alignment self. The returned vector has a length equal to the length of the Alignment self.

§Examples

let align = Alignment::<u8>::with_sequences(
    &[b"ELK".to_vec(), b"ILK".to_vec()],
)
.unwrap();

assert_eq!(align.nth_sequence(1).unwrap(), &[&b'I', &b'L', &b'K']);