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", so this trait is not object safe.

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<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

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