Package csb :: Package bio :: Package sequence :: Module alignment :: Class AlignmentResult |
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# Class AlignmentResult

source code

    object --+
             |
            AlignmentResult

Represents a pairwise sequence alignment result.

Instance Methods
__init__(self, score, query, subject, qstart, qend, start, end) x.__init__(...) initializes x; see help(type(x)) for signature | source code
__str__(self) str(x) | source code
SequenceAlignment |
alignment(self) Returns: as a sequence alignment object | source code
Inherited from `object`: `__delattr__`, `__format__`, `__getattribute__`, `__hash__`, `__new__`, `__reduce__`, `__reduce_ex__`, `__repr__`, `__setattr__`, `__sizeof__`, `__subclasshook__`

Properties
int | end Subject end position
int | gaps Total number of gaps (query + subject)
int | identicals Number of identical residues
int | identity Percentage of identical residues
bool | is_empty Return True if this is an empty alignment (i.e.
int | length Alignment length (query + subject + gaps / 2)
int | qend Query end position
int | qstart Query start position
AbstractSequence | query Aligned query sequence (with gaps)
float | score Raw alignment score
int | start Subject start position
AbstractSequence | subject Aligned subject sequence (with gaps)
Inherited from `object`: `__class__`

Method Details

### __init__(self, score, query, subject, qstart, qend, start, end) (Constructor) | source code
x.__init__(...) initializes x; see help(type(x)) for signature Parameters: `score` (float) - raw alignment score `query` (AbstractSequence) - aligned query sequence (with gaps) `subject` (AbstractSequence) - aligned subject sequence (with gaps) `qstart` (int) - query start position `qend` (int) - query end position `start` (int) - subject start position `end` (int) - subject end position Overrides: object.__init__ (inherited documentation)

### __str__(self) (Informal representation operator) | source code
str(x) Overrides: object.__str__ (inherited documentation)

### alignment(self) | source code
Returns: SequenceAlignment as a sequence alignment object

Property Details

### end Subject end position Get Method: unreachable.end(self) - Subject end position Type: int

### gaps Total number of gaps (query + subject) Get Method: unreachable.gaps(self) - Total number of gaps (query + subject) Type: int

### identicals Number of identical residues Get Method: unreachable.identicals(self) - Number of identical residues Type: int

### identity Percentage of identical residues Get Method: unreachable.identity(self) - Percentage of identical residues Type: int

### is_empty Return True if this is an empty alignment (i.e. no matches) Get Method: unreachable.is_empty(self) - Return True if this is an empty alignment (i.e. Type: bool

### length Alignment length (query + subject + gaps / 2) Get Method: unreachable.length(self) - Alignment length (query + subject + gaps / 2) Type: int

### qend Query end position Get Method: unreachable.qend(self) - Query end position Type: int

### qstart Query start position Get Method: unreachable.qstart(self) - Query start position Type: int

### query Aligned query sequence (with gaps) Get Method: unreachable.query(self) - Aligned query sequence (with gaps) Type: AbstractSequence

### score Raw alignment score Get Method: unreachable.score(self) - Raw alignment score Type: float

### start Subject start position Get Method: unreachable.start(self) - Subject start position Type: int

### subject Aligned subject sequence (with gaps) Get Method: unreachable.subject(self) - Aligned subject sequence (with gaps) Type: AbstractSequence