Struct EncodedSequence

pub struct EncodedSequence { /* private fields */ }

A biological sequence encoded as digits.

Implementations

impl EncodedSequence

pub fn __init__<'py>( sequence: Bound<'py, PyString>, protein: bool, ) -> PyResult<PyClassInitializer<Self>>

Encode a sequence.

pub fn __str__(&self) -> String

Convert the encoded sequence to a string.

pub fn __len__(&self) -> usize

Get the length of the encoded sequence.

pub fn __copy__(&self) -> Self

Get a copy of the encoded sequence.

pub fn __getitem__(&self, index: Py_ssize_t) -> PyResult<u8>

Get an element of the encoded sequence.

pub fn protein(&self) -> bool

bool: True if the encoded sequence is a protein sequence.

pub fn copy(&self) -> Self

Create a copy of this sequence.

pub fn stripe(&self) -> StripedSequence

Convert this sequence into a striped matrix.

Returns: ~lightmotif.StripedSequence: The input sequence, stored in a column-major matrix.

Trait Implementations

impl Clone for EncodedSequence

fn clone(&self) -> EncodedSequence

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for EncodedSequence

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

Formats the value using the given formatter.

impl IntoPy<Py<PyAny>> for EncodedSequence

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

👎Deprecated since 0.23.0: IntoPy is going to be replaced by IntoPyObject. See the migration guide (https://pyo3.rs/v0.23.0/migration) for more information.

Performs the conversion.

impl<'py> IntoPyObject<'py> for EncodedSequence

type Target = EncodedSequence

The Python output type

type Output = Bound<'py, <EncodedSequence as IntoPyObject<'py>>::Target>

The smart pointer type to use.

type Error = PyErr

The type returned in the event of a conversion error.

fn into_pyobject( self, py: Python<'py>, ) -> Result<<Self as IntoPyObject<'_>>::Output, <Self as IntoPyObject<'_>>::Error>

Performs the conversion.

impl PyClass for EncodedSequence

type Frozen = False

Whether the pyclass is frozen.

impl PyClassImpl for EncodedSequence

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 BaseType = PyAny

Base class

type ThreadChecker = SendablePyClass<EncodedSequence>

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<EncodedSequence> for PyClassImplCollector<EncodedSequence>

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

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

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

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

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

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

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

impl PyMethods<EncodedSequence> for PyClassImplCollector<EncodedSequence>

fn py_methods(self) -> &'static PyClassItems

impl PyTypeInfo for EncodedSequence

const NAME: &'static str = "EncodedSequence"

Class name.

const MODULE: Option<&'static str>

Module name, if any.

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

Returns the PyTypeObject instance for this type.

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

Returns the safe abstraction over the type object.

fn type_object_bound(py: Python<'_>) -> Bound<'_, PyType>

👎Deprecated since 0.23.0: renamed to PyTypeInfo::type_object

Deprecated name for PyTypeInfo::type_object.

fn is_type_of(object: &Bound<'_, PyAny>) -> bool

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

fn is_type_of_bound(object: &Bound<'_, PyAny>) -> bool

👎Deprecated since 0.23.0: renamed to PyTypeInfo::is_type_of

Deprecated name for PyTypeInfo::is_type_of.

fn is_exact_type_of(object: &Bound<'_, PyAny>) -> bool

Checks if object is an instance of this type.

fn is_exact_type_of_bound(object: &Bound<'_, PyAny>) -> bool

👎Deprecated since 0.23.0: renamed to PyTypeInfo::is_exact_type_of

Deprecated name for PyTypeInfo::is_exact_type_of.

impl DerefToPyAny for EncodedSequence