sbol3.location
Module Contents
Classes
The Cut class has been introduced to enable the specification of a |
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The EntireSequence class does not have any additional |
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The Location class is used to represent the location of Features |
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A Range object specifies a region via discrete, inclusive start and |
Functions
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Used by Document to construct a Cut when reading an SBOL file. |
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Used by Document to construct an EntireSequence when reading an SBOL file. |
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Used by Document to construct a Range when reading an SBOL file. |
Attributes
- class Cut(sequence: Sequence | str, at: int, *, orientation: str = None, order: int = None, identity: str = None, type_uri: str = SBOL_CUT)
Bases:
Location
The Cut class has been introduced to enable the specification of a region between two discrete positions. This specification is accomplished using the at property, which specifies a discrete position that corresponds to the index of a character in the elements String of a Sequence (except in the case when at is equal to zero).
- accept(visitor: Any) Any
Invokes visit_cut on visitor with self as the only argument.
- Parameters:
visitor (Any) – The visitor instance
- Raises:
AttributeError – If visitor lacks a visit_cut method
- Returns:
Whatever visitor.visit_cut returns
- Return type:
Any
- validate(report: ValidationReport = None) ValidationReport
- class EntireSequence(sequence: Sequence | str, *, orientation: str = None, order: int = None, identity: str = None, type_uri: str = SBOL_ENTIRE_SEQUENCE)
Bases:
Location
The EntireSequence class does not have any additional properties. Use of this class indicates that the linked Sequence describes the entirety of the Component or Feature parent of this Location object.
- accept(visitor: Any) Any
Invokes visit_entire_sequence on visitor with self as the only argument.
- Parameters:
visitor (Any) – The visitor instance
- Raises:
AttributeError – If visitor lacks a visit_entire_sequence method
- Returns:
Whatever visitor.visit_entire_sequence returns
- Return type:
Any
- class Location(sequence: Sequence | str, identity: str, type_uri: str, *, orientation: str | None = None, order: int = None)
Bases:
Identified
,abc.ABC
The Location class is used to represent the location of Features within Sequences. This class is extended by the Range, Cut, and EntireSequence classes
- validate(report: ValidationReport = None) ValidationReport
- class Range(sequence: Sequence | str, start: int, end: int, *, orientation: str = None, order: int = None, identity: str = None, type_uri: str = SBOL_RANGE)
Bases:
Location
A Range object specifies a region via discrete, inclusive start and end positions that correspond to indices for characters in the elements String of a Sequence.
Note that the index of the first location is 1, as is typical practice in biology, rather than 0, as is typical practice in computer science.
- accept(visitor: Any) Any
Invokes visit_range on visitor with self as the only argument.
- Parameters:
visitor (Any) – The visitor instance
- Raises:
AttributeError – If visitor lacks a visit_range method
- Returns:
Whatever visitor.visit_range returns
- Return type:
Any
- validate(report: ValidationReport = None) ValidationReport
- build_cut(identity: str, type_uri: str = SBOL_CUT)
Used by Document to construct a Cut when reading an SBOL file.
- build_entire_sequence(identity: str, type_uri: str = SBOL_ENTIRE_SEQUENCE)
Used by Document to construct an EntireSequence when reading an SBOL file.
- build_range(identity: str, type_uri: str = SBOL_RANGE)
Used by Document to construct a Range when reading an SBOL file.
- int_property