Struct ReadfishSummary

pub struct ReadfishSummary { /* private fields */ }

Organise the data and methods for analysing a readfish PAF file.

Implementations

impl ReadfishSummary

pub fn new() -> Self

Creates a new instance of ReadfishSummary with default values.

This function initializes a new ReadfishSummary struct with default values for all fields. The summary field will be initialized with an empty Summary instance. The _conf, _sequencing_summary, and _paf_file fields will be set to None, indicating that they have not been initialized with specific values yet.

Returns

A new ReadfishSummary instance with default values.

Examples

use readfish_tools::ReadfishSummary;

let summary = ReadfishSummary::new();
assert_eq!(summary.has_conf(), false); // _conf field is not set yet
assert_eq!(summary.has_sequencing_summary(), false); // _sequencing_summary field is not set yet
assert_eq!(summary.has_paf_file(), false); // _paf_file field is not set yet

pub fn conf(&self) -> Option<&Conf>

Update a condition on the summary Get the config TOML file for the readfish run.

pub fn set_conf(&mut self, conf: Conf)

Set the config TOML file for the readfish run.

pub fn parse_conf_file(&mut self, conf_path: PathBuf)

Parse a path to a config file and add it to the ReadfishSummary

pub fn sequencing_summary(&self) -> Option<&SeqSum>

Get the sequencing summary file.

pub fn set_sequencing_summary(&mut self, sequencing_summary: SeqSum)

Set the sequencing summary file.

pub fn parse_sequencing_summary(&mut self, seq_sum_path: PathBuf)

Parse a provided sequencing summary file path and set it on the summary

pub fn paf_file(&self) -> Option<&Paf>

Get the PAF file.

pub fn set_paf_file(&mut self, paf_file: Paf)

Set the PAF file.

pub fn has_conf(&self) -> bool

Check if the config TOML file is set.

pub fn has_sequencing_summary(&self) -> bool

Check if the sequencing summary file is set.

pub fn has_paf_file(&self) -> bool

Check if the PAF file is set.

impl ReadfishSummary

Implements methods for interacting with a ReadfishSummary instance from Python.

pub fn print_summary(&self) -> PyResult<()>

Prints the summary of the ReadfishSummary to the standard output.

This method borrows the ReadfishSummary immutably and prints its summary to the standard output. The summary is obtained by calling the borrow method on the RefCell<Summary> field of the ReadfishSummary.

Returns

This function returns a PyResult<()> to indicate success or failure. If the summary is successfully printed, Ok(()) is returned. If an error occurs during printing, an appropriate PyErr will be set, and Err will be returned.

Examples

/// Method to print the summary of ReadfishSummary.
pub fn print_summary(&self) -> PyResult<()> {
    println!("{}", self.summary.borrow());
    Ok(())
}

The method can be called on an instance of ReadfishSummary to print its summary.

Trait Implementations

impl Default for ReadfishSummary

fn default() -> Self

Returns the “default value” for a type.

impl IntoPy<Py<PyAny>> for ReadfishSummary

fn into_py(self, py: Python<'_>) -> PyObject

Performs the conversion.

impl PyClass for ReadfishSummary

type Frozen = False

Whether the pyclass is frozen.

impl PyClassImpl for ReadfishSummary

const IS_BASETYPE: bool = false

#[pyclass(subclass)]

const IS_SUBCLASS: bool = false

#[pyclass(extends=…)]

const IS_MAPPING: bool = false

#[pyclass(mapping)]

const IS_SEQUENCE: bool = false

#[pyclass(sequence)]

type Layout = PyCell<ReadfishSummary>

Layout

type BaseType = PyAny

Base class

type ThreadChecker = ThreadCheckerStub<ReadfishSummary>

This handles following two situations:

type PyClassMutability = <<PyAny as PyClassBaseType>::PyClassMutability as PyClassMutability>::MutableChild

Immutable or mutable

type Dict = PyClassDummySlot

Specify this class has #[pyclass(dict)] or not.

type WeakRef = PyClassDummySlot

Specify this class has #[pyclass(weakref)] or not.

type BaseNativeType = PyAny

The closest native ancestor. This is PyAny by default, and when you declare #[pyclass(extends=PyDict)], it’s PyDict.

fn items_iter() -> PyClassItemsIter

fn doc(py: Python<'_>) -> PyResult<&'static CStr>

Rendered class doc

fn lazy_type_object() -> &'static LazyTypeObject<Self>

fn dict_offset() -> Option<isize>

fn weaklist_offset() -> Option<isize>

impl PyClassNewTextSignature<ReadfishSummary> for PyClassImplCollector<ReadfishSummary>

fn new_text_signature(self) -> Option<&'static str>

impl<'a, 'py> PyFunctionArgument<'a, 'py> for &'a ReadfishSummary

type Holder = Option<PyRef<'py, ReadfishSummary>>

fn extract(obj: &'py PyAny, holder: &'a mut Self::Holder) -> PyResult<Self>

impl<'a, 'py> PyFunctionArgument<'a, 'py> for &'a mut ReadfishSummary

type Holder = Option<PyRefMut<'py, ReadfishSummary>>

fn extract(obj: &'py PyAny, holder: &'a mut Self::Holder) -> PyResult<Self>

impl PyMethods<ReadfishSummary> for PyClassImplCollector<ReadfishSummary>

fn py_methods(self) -> &'static PyClassItems

impl PyTypeInfo for ReadfishSummary

const NAME: &'static str = "ReadfishSummary"

Class name.

const MODULE: Option<&'static str> = ::core::option::Option::None

Module name, if any.

type AsRefTarget = PyCell<ReadfishSummary>

Utility type to make Py::as_ref work.

fn type_object_raw(py: Python<'_>) -> *mut PyTypeObject

Returns the PyTypeObject instance for this type.

fn type_object(py: Python<'_>) -> &PyType

Returns the safe abstraction over the type object.

fn is_type_of(object: &PyAny) -> bool

Checks if object is an instance of this type or a subclass of this type.

fn is_exact_type_of(object: &PyAny) -> bool

Checks if object is an instance of this type.