Struct ScoringMatrix

pub struct ScoringMatrix { /* private fields */ }

A matrix storing position-specific odds-ratio for a motif.

Implementations

impl ScoringMatrix

pub fn __init__<'py>( values: Bound<'py, PyDict>, background: Option<PyObject>, protein: bool, ) -> PyResult<PyClassInitializer<Self>>

Create a new scoring matrix.

pub fn __eq__(&self, object: Bound<'_, PyAny>) -> PyResult<bool>

pub fn __len__(&self) -> usize

pub fn __getitem__<'py>( slf: PyRef<'py, Self>, index: isize, ) -> PyResult<Bound<'py, PyAny>>

pub fn score_distribution<'py>( slf: Bound<'py, Self>, ) -> PyResult<Py<ScoreDistribution>>

pub fn protein(&self) -> bool

bool: True if the scoring matrix stores protein scores.

pub fn calculate( slf: Bound<'_, Self>, sequence: &mut StripedSequence, ) -> PyResult<StripedScores>

Calculate the PSSM score for all positions of the given sequence.

Returns: ~lightmotif.StripedScores: The PSSM scores for every position of the input sequence, stored into a striped matrix for fast vectorized operations.

Note: This method uses the best implementation for the local platform, prefering AVX2 if available.

pub fn pvalue(slf: Bound<'_, Self>, score: f64, method: &str) -> PyResult<f64>

Translate an absolute score to a P-value for this PSSM.

pub fn max_score(slf: PyRef<'_, Self>) -> f32

pub fn score(slf: Bound<'_, Self>, pvalue: f64, method: &str) -> PyResult<f64>

Translate a P-value to an absolute score for this PSSM.

pub fn reverse_complement(slf: PyRef<'_, Self>) -> PyResult<ScoringMatrix>

Compute the reverse complement of this scoring matrix.

Trait Implementations

impl Debug for ScoringMatrix

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

Formats the value using the given formatter.

impl IntoPy<Py<PyAny>> for ScoringMatrix

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 ScoringMatrix

type Target = ScoringMatrix

The Python output type

type Output = Bound<'py, <ScoringMatrix 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 ScoringMatrix

type Frozen = False

Whether the pyclass is frozen.

impl PyClassImpl for ScoringMatrix

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<ScoringMatrix>

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<ScoringMatrix> for PyClassImplCollector<ScoringMatrix>

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

impl PyClass__eq__SlotFragment<ScoringMatrix> for PyClassImplCollector<ScoringMatrix>

unsafe fn __eq__( self, py: Python<'_>, _raw_slf: *mut PyObject, arg0: *mut PyObject, ) -> PyResult<*mut PyObject>

Safety: _slf and _other must be valid non-null Python objects

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

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

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

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

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

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

impl PyMethods<ScoringMatrix> for PyClassImplCollector<ScoringMatrix>

fn py_methods(self) -> &'static PyClassItems

impl PyTypeInfo for ScoringMatrix

const NAME: &'static str = "ScoringMatrix"

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 ScoringMatrix

impl HasCustomRichCmp for ScoringMatrix