Struct classeq_core::domain::dtos::tree::Tree

pub struct Tree {
    pub id: Uuid,
    pub name: String,
    pub min_branch_support: f64,
    pub root: Clade,
    pub annotations: Option<Vec<Annotation>>,
    pub kmers_map: Option<KmersMap>,
    /* private fields */
}

Fields

id: Uuid

The unique identifier for the tree.

The id is a unique identifier for the tree. The id is a Universally Unique Identifier (UUID) that is generated when the tree is created.

name: String

The human-readable name for the tree.

When the tree is created using the from_file function, the name is set from the file name where the tree is parsed from.

min_branch_support: f64

The minimum branch support value.

The minimum branch support value is the minimum support value for a branch to be included in the tree. Branches with support values below this value are removed from the tree and children are reconnected to the parent node.

root: Clade

The root Clade of the tree.

The root is the root Clade of the tree. The root Clade is the starting point of the tree and contains the children nodes.

annotations: Option<Vec<Annotation>>

The annotations associated with the tree.

The annotations are the taxonomic annotations associated with nodes in the tree. The annotations are stored as a vector of Annotation objects.

kmers_map: Option<KmersMap>

Implementations

impl Tree

pub fn new(id: Uuid, name: String, min_branch_support: f64, root: Clade) -> Tree

Create a new Tree object.

The function creates a new Tree object with an id, name, and root Clade. The id is a unique identifier for the tree. The name is a human-readable name for the tree. The root is the root Clade of the tree.

pub fn get_in_memory_size(&self) -> Option<String>

pub fn update_in_memory_size(&mut self)

pub fn pretty_print(&self)

Pretty print the tree.

The function prints the tree in a human-readable format. The function prints the root node and recursively prints each child node.

pub fn from_yaml_file(file_path: &Path) -> Result<Tree, MappedErrors>

pub fn init_from_file( tree_path: &Path, min_branch_support: f64, ) -> Result<Tree, MappedErrors>

Create a new Tree from a .newick file.

The phylotre::tree::Tree is parsed from the file and converted to a Tree object with a root Clade.

Trait Implementations

impl Debug for Tree

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

Formats the value using the given formatter.

impl<'de> Deserialize<'de> for Tree

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

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl Serialize for Tree

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

where __S: Serializer,

Serialize this value into the given Serde serializer.