Commit 10bc30f8 authored by Ivan Vanat's avatar Ivan Vanat
Browse files

documentation; added forgotten typing

parent a0f1ba8b

nested/core/executor.py

+5 −3
Original line number Diff line number Diff line
@@ -13,7 +13,7 @@ class Executor: 
        self.modules = modules

        self.sequence = sequence



    def run_main_loop(self):

    def run_main_loop(self) -> NoReturn:

        elements: List[BaseElement] = []



        for module in self.modules:
@@ -32,9 +32,11 @@ class Executor: 
            else:

                module.output_generator.generate_output(module.tool.output_object)



    def _crop_sequence(self, elements):

    def _crop_sequence(self, elements: List[BaseElement]) -> NoReturn:

        for element in elements:

            self.sequence = self.sequence[:element.location[0]] + self.sequence[element.location[1]:]

            lower_bound = min(element.location)

            upper_bound = max(element.location)

            self.sequence = self.sequence[:lower_bound] + self.sequence[upper_bound:]



    def _recalculate_coordinates(self, nested_list: List[BaseElement]) -> NoReturn:

        for i in reversed(range(len(nested_list) - 1)):

nested/entities/base_element.py

+7 −6
Original line number Diff line number Diff line
@@ -11,7 +11,7 @@ class BaseElement: 
    Class representing identified element in sequence.



        Attributes:

                location: coordinates of the element in format [lower, higher]

            location: coordinates of the element in format [from, to]

            score: score

            type: type of the element in string, should be used as a key in parent element features dictionary

            features: features of the element
@@ -44,6 +44,7 @@ class BaseElement: 
                        feature_type: Type = None) -> NoReturn:

        """

        Tries to create new feature and add it to features dictionary.



        Args:

            name: key in features dictionary and type in created feature

            location: location

nested/entities/te.py

+11 −12
Original line number Diff line number Diff line
@@ -8,18 +8,19 @@ from nested.entities.domain_dante import DomainDante 
class TE(BaseElement):

    possible_domains: List[str] = ["GAG", "PROT", "INT", "RT", "RH", "aRH", "CHD", "CHDCR"]



    """Class representing TE. Every location is in format [from, to].

    """

    Class representing TE. Every location is in format [from, to].



    Attributes:

        ppt (list): location of ppt

        pbs (list): location of pbs

        location (list): position of TE in gene

        ltr_left_location (list): location of left ltr

        ltr_right_location (list): location of right ltr

        tsr_left (list): location of left tsr

        tsr_right (list): location of right tsr

        features (dict): dictionary of features assigned to TE (i.e. list of domains on the optimal path in graph)

        score (float): evaluated score of TE

        ppt: location of ppt

        pbs: location of pbs

        location: position of TE in gene

        ltr_left_location: location of left ltr

        ltr_right_location: location of right ltr

        tsr_left: location of left tsr

        tsr_right: location of right tsr

        features: dictionary of features assigned to TE (i.e. list of domains on the optimal path in graph)

        score: evaluated score of TE

    """



    def __init__(self, ppt: List[int], pbs: List[int], location: List[int],
@@ -35,10 +36,8 @@ class TE(BaseElement): 
        self.try_add_feature("tsr_left", tsr_left)

        self.try_add_feature("tsr_right", tsr_right)



        # remove or turn into properties

        self.ppt = ppt

        self.pbs = pbs

        self.location = location

        self.ltr_left_location = ltr_left_location

        self.ltr_right_location = ltr_right_location

        self.tsr_left = tsr_left