Trait SummaryData 

pub trait SummaryData<DI>:
    Clone
    + Debug
    + Send
    + Sync
    + PartialEq
    + Serialize
    + DeserializeOwned {
    // Required methods
    fn print(
        &self,
        translator: &Translator,
        config: &SummaryConfig,
        id_group_translator: Option<&HashMap<ID, ID>>,
    ) -> String;
    fn print_ol(
        &self,
        translator: &Translator,
        config: &SummaryConfig,
        id_group_translator: Option<&HashMap<ID, ID>>,
    ) -> String;
    fn print_json(
        &self,
        translator: &Translator,
        config: &SummaryConfig,
        id_group_translator: Option<&HashMap<ID, ID>>,
    ) -> String;
    fn mem(&self) -> usize;
    fn summarize<K: Kmer, F: Iterator<Item = KmerDataItem<K, DI>>>(
        items: F,
        config: &SummaryConfig,
    ) -> (bool, Exts, Self);
    fn summarizer() -> Summarizers;

    // Provided methods
    fn tags(&self) -> Option<Tags> { ... }
    fn sum(&self) -> Option<u32> { ... }
    fn ids(&self) -> Option<&[ID]> { ... }
    fn p_value(&self, _config: &SummaryConfig) -> Option<f32> { ... }
    fn fold_change(&self, _config: &SummaryConfig) -> Option<f32> { ... }
    fn sample_count(&self) -> Option<usize> { ... }
    fn edge_mults(&self) -> Option<&EdgeMult> { ... }
    fn quality(&self) -> Option<BaseQuality> { ... }
    fn fix_edge_data(&mut self, _exts: Exts) { ... }
    fn set_edge_mults(&mut self, _edge_mults: Option<EdgeMult>) { ... }
    fn mapped_ids(&self) -> Option<&[ID]> { ... }
    fn set_mapped_ids(&mut self, _mapped_ids: Box<[ID]>) { ... }
    fn mapped_edge_ids(&self) -> Option<&EdgeMap> { ... }
    fn set_mapped_edge_ids(&mut self, _mapped_edge_ids: Option<EdgeMap>) { ... }
    fn join_test(&self, other: &Self) -> bool { ... }
    fn valid(&self, _config: &SummaryConfig) -> bool { ... }
}

Trait for summarizing k-mers, determines the data saved in the graph nodes

Required Methods

fn print( &self, translator: &Translator, config: &SummaryConfig, id_group_translator: Option<&HashMap<ID, ID>>, ) -> String

format the node data

fn print_ol( &self, translator: &Translator, config: &SummaryConfig, id_group_translator: Option<&HashMap<ID, ID>>, ) -> String

format the node data in for json

fn print_json( &self, translator: &Translator, config: &SummaryConfig, id_group_translator: Option<&HashMap<ID, ID>>, ) -> String

format the node data in one line

fn mem(&self) -> usize

get the size of the structure, including contents of boxed slices

fn summarize<K: Kmer, F: Iterator<Item = KmerDataItem<K, DI>>>( items: F, config: &SummaryConfig, ) -> (bool, Exts, Self)

summarize k-mers

fn summarizer() -> Summarizers

check summerizer kind

Provided Methods

fn tags(&self) -> Option<Tags>

get Tags and the overall count, returns None if data is insufficient

fn sum(&self) -> Option<u32>

get the number of observations, returns None if data is insufficient

fn ids(&self) -> Option<&[ID]>

get the IDs, returns None if data is insufficient

fn p_value(&self, _config: &SummaryConfig) -> Option<f32>

get the p-value, returns None if data is insufficient

fn fold_change(&self, _config: &SummaryConfig) -> Option<f32>

get the log2(fold change), returns None if data is insufficient

fn sample_count(&self) -> Option<usize>

get the number of samples the sequence was observed in, returns None if data is insufficient

fn edge_mults(&self) -> Option<&EdgeMult>

get the coverage of the node edges

fn quality(&self) -> Option<BaseQuality>

get the quality of the node k-mer

fn fix_edge_data(&mut self, _exts: Exts)

fix the EdgeMult by removing hanging edges

fn set_edge_mults(&mut self, _edge_mults: Option<EdgeMult>)

set the edge mults

fn mapped_ids(&self) -> Option<&[ID]>

get a reference to the mapped ids, returns None if data is insufficient

fn set_mapped_ids(&mut self, _mapped_ids: Box<[ID]>)

add mapped ids to the node data

fn mapped_edge_ids(&self) -> Option<&EdgeMap>

get a reference to the IDs mapped to the node edges, returns None id data is insuffivient

fn set_mapped_edge_ids(&mut self, _mapped_edge_ids: Option<EdgeMap>)

add mapped IDs to the node’s edges

fn join_test(&self, other: &Self) -> bool

check if the data can be joined into one

fn valid(&self, _config: &SummaryConfig) -> bool

check if node is valid according to: min kmer obs, group fraction, p-value

Dyn Compatibility

This trait is not dyn compatible.

In older versions of Rust, dyn compatibility was called "object safety".

Implementations on Foreign Types

impl SummaryData<u8> for u32

Number of observations for the k-mer

fn print( &self, _: &Translator, _: &SummaryConfig, _: Option<&HashMap<ID, ID>>, ) -> String

fn print_ol( &self, _: &Translator, _: &SummaryConfig, _: Option<&HashMap<ID, ID>>, ) -> String

fn print_json( &self, _: &Translator, _: &SummaryConfig, _: Option<&HashMap<ID, ID>>, ) -> String

fn mem(&self) -> usize

fn sum(&self) -> Option<u32>

fn valid(&self, config: &SummaryConfig) -> bool

fn summarize<K: Kmer, F: Iterator<Item = KmerDataItem<K, Tag>>>( items: F, config: &SummaryConfig, ) -> (bool, Exts, Self)

fn summarizer() -> Summarizers

Implementors

impl SummaryData<IDTag> for IDData

impl SummaryData<IDTag> for IDEMData

impl SummaryData<IDTag> for IDMapEMData

impl SummaryData<IDTag> for IDMapEMQualityData

impl SummaryData<IDTag> for IDSumData

impl SummaryData<IDTag> for IDTagsCountsData

impl SummaryData<IDTag> for IDTagsCountsPEMData

impl SummaryData<u8> for GroupCountData

impl SummaryData<u8> for MapEMEmapQualityData

impl SummaryData<u8> for RelCountData

impl SummaryData<u8> for SumMapEMQualityData

impl SummaryData<u8> for TagVecData

impl SummaryData<u8> for TagsCountsData

impl SummaryData<u8> for TagsCountsEMData

impl SummaryData<u8> for TagsCountsPData

impl SummaryData<u8> for TagsCountsPEMData

impl SummaryData<u8> for TagsCountsPEMQualityData

impl SummaryData<u8> for TagsCountsSumData

impl SummaryData<u8> for TagsData

impl SummaryData<u8> for TagsSumData