Struct SequenceCollection 

pub struct SequenceCollection {
    pub metadata: SequenceCollectionMetadata,
    pub sequences: Vec<SequenceRecord>,
}

A single Sequence Collection, which may or may not hold data.

Fields

metadata: SequenceCollectionMetadata

Collection metadata (digest, level 1 digests, n_sequences, file_path)

sequences: Vec<SequenceRecord>

Vector of SequenceRecords, which contain metadata (name, length, digests, alphabet) and optionally the actual sequence data.

Implementations

impl SequenceCollection

pub fn from_records(records: Vec<SequenceRecord>) -> Self

Create a SequenceCollection from a vector of SequenceRecords.

pub fn to_level2(&self) -> CollectionLevel2

Return level 2 representation (full arrays, spec format). Transposes Vec into parallel arrays.

pub fn build_sorted_sequences(&self) -> Vec<String>

Build the sorted_sequences array as SQ.-prefixed digest strings, sorted lexicographically.

pub fn build_name_length_pairs(&self) -> Vec<Value>

Build the name_length_pairs array as JSON value objects {“length”: N, “name”: “X”}. Keys are in alphabetical order per canonical JSON.

pub fn build_sorted_name_length_pairs(&self) -> Vec<Value>

Build the sorted_name_length_pairs array as JSON value objects, sorted by their canonical JSON digest.

pub fn compare(&self, other: &SequenceCollection) -> SeqColComparison

Compare this collection with another, following the seqcol spec comparison algorithm.

Dynamically includes ancillary attributes (name_length_pairs, sorted_name_length_pairs, sorted_sequences) when present in each collection’s metadata.

Trait Implementations

impl Clone for SequenceCollection

fn clone(&self) -> SequenceCollection

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for SequenceCollection

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

Formats the value using the given formatter.

impl Display for SequenceCollection

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

Formats the value using the given formatter.

impl From<SequenceCollection> for SequenceCollectionRecord

fn from(collection: SequenceCollection) -> Self

Converts to this type from the input type.

impl<'a> IntoIterator for &'a SequenceCollection

type Item = &'a SequenceRecord

The type of the elements being iterated over.

type IntoIter = Iter<'a, SequenceRecord>

Which kind of iterator are we turning this into?

fn into_iter(self) -> Self::IntoIter

Creates an iterator from a value.

impl IntoIterator for SequenceCollection

type Item = SequenceRecord

The type of the elements being iterated over.

type IntoIter = IntoIter<SequenceRecord>

Which kind of iterator are we turning this into?

fn into_iter(self) -> Self::IntoIter

Creates an iterator from a value.

impl SequenceCollectionExt for SequenceCollection

fn from_fasta<P: AsRef<Path>>(file_path: P) -> Result<SequenceCollection>

Default behavior: read and write cache

fn from_path_no_cache<P: AsRef<Path>>( file_path: P, ) -> Result<SequenceCollection>

No caching at all

fn write_collection_rgsi<P: AsRef<Path>>(&self, file_path: P) -> Result<()>

Write the SequenceCollection to an RGSI file.

fn write_rgsi(&self) -> Result<()>

Write the SequenceCollection to an RGSI file using the stored file path.

fn to_record(&self) -> SequenceCollectionRecord

Convert to a SequenceCollectionRecord for storage.

fn write_fasta<P: AsRef<Path>>( &self, file_path: P, line_width: Option<usize>, ) -> Result<()>

Write the SequenceCollection to a FASTA file.

fn from_rgsi<P: AsRef<Path>>(file_path: P) -> Result<SequenceCollection>

fn from_path_with_cache<P: AsRef<Path>>( file_path: P, read_cache: bool, write_cache: bool, ) -> Result<SequenceCollection>