Package csb :: Package bio :: Package hmm :: Class HHpredHit

Class HHpredHit

object --+
         |
        HHpredHit

Represents a single HHsearch hit.

Instance Methods

__init__(self, rank, id, start, end, qstart, qend, probability, qlength)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

__lt__(self, other)

source code

__repr__(self)
repr(x)

source code

__str__(self)
str(x)

source code

add_alignment(self, query, subject)
Add query/subject alignment to the hit.

source code

bool

equals(self, other)
Return True if self is completely identical to other (same id, same start and end positions). source code

bool

includes(self, other, tolerance=1)
Return True if other overlaps with self, that means other is fully or partially included in self when aligned over the query. source code

bool

surpasses(self, other)
Return True if self is a superior to other in terms of length and probability. source code

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__, __sizeof__, __subclasshook__

Properties
	alignment
	end
	evalue
	id
	identity
	length
	prob_sum
	probability
	pvalue
	qend
	qlength
	qstart
	rank
	score
	similarity
	slength
	ss_score
	start
Inherited from `object`: `__class__`

Method Details

init(self, rank, id, start, end, qstart, qend, probability, qlength)
(Constructor)

source code

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

rank (int) - rank of the hit
id (str) - id of the hit
start (int) - subject start
end (int) - subject end
qstart (int) - query start
qend (int) - query end
probability (float) - probability of the hit
qlength (int) - length of the query

Overrides: object.__init__

(inherited documentation)

repr(self)
(Representation operator)

source code

repr(x)

Overrides: object.__repr__: (inherited documentation)

str(self)
(Informal representation operator)

source code

str(x)

Overrides: object.__str__: (inherited documentation)

add_alignment(self, query, subject)

source code

Add query/subject alignment to the hit.

Parameters:

query (str) - the query sequence within the alignment region, with gaps
subject (str) - the subject sequence within the alignment region, with gaps

equals(self, other)

source code

Return True if self is completely identical to other (same id, same start and end positions).

Parameters:

other (HHpredHit) - right-hand-term

Returns: bool

includes(self, other, tolerance=1)

source code

Return True if other overlaps with self, that means other is fully or partially included in self when aligned over the query.

Parameters:

other (HHpredHit) - right-hand-term
tolerance (int) - allow partial overlaps for that number of residues at either end

Returns: bool

surpasses(self, other)

source code

Return True if self is a superior to other in terms of length and probability. These criteria are applied in the following order:

Length (the longer hit is better)
Probability (if they have the same length, the one with the higher probability is better)
Address (if they have the same length and probability, the one with higher memory ID wins; for purely practical reasons)

Parameters:

other (HHpredHit) - right-hand-term

Returns: bool

Property Details

alignment

Get Method:: unreachable.alignment(self)

end

Get Method:: unreachable.end(self)
Set Method:: unreachable.end(self, value)

evalue

Get Method:: unreachable.evalue(self)
Set Method:: unreachable.evalue(self, value)

id

Get Method:: unreachable.id(self)
Set Method:: unreachable.id(self, value)

identity

Get Method:: unreachable.identity(self)
Set Method:: unreachable.identity(self, value)

length

Get Method:: unreachable.length(self)

prob_sum

Get Method:: unreachable.prob_sum(self)
Set Method:: unreachable.prob_sum(self, value)

probability

Get Method:: unreachable.probability(self)
Set Method:: unreachable.probability(self, value)

pvalue

Get Method:: unreachable.pvalue(self)
Set Method:: unreachable.pvalue(self, value)

qend

Get Method:: unreachable.qend(self)
Set Method:: unreachable.qend(self, value)

qlength

Get Method:: unreachable.qlength(self)
Set Method:: unreachable.qlength(self, value)

qstart

Get Method:: unreachable.qstart(self)
Set Method:: unreachable.qstart(self, value)

rank

Get Method:: unreachable.rank(self)
Set Method:: unreachable.rank(self, value)

score

Get Method:: unreachable.score(self)
Set Method:: unreachable.score(self, value)

similarity

Get Method:: unreachable.similarity(self)
Set Method:: unreachable.similarity(self, value)

slength

Get Method:: unreachable.slength(self)
Set Method:: unreachable.slength(self, value)

ss_score

Get Method:: unreachable.ss_score(self)
Set Method:: unreachable.ss_score(self, value)

start

Get Method:: unreachable.start(self)
Set Method:: unreachable.start(self, value)

Class HHpredHit

__init__(self, rank, id, start, end, qstart, qend, probability, qlength) (Constructor)

__repr__(self) (Representation operator)

__str__(self) (Informal representation operator)

add_alignment(self, query, subject)

equals(self, other)

includes(self, other, tolerance=1)

surpasses(self, other)

alignment

end

evalue

id

identity

length

prob_sum

probability

pvalue

qend

qlength

qstart

rank

score

similarity

slength

ss_score

start

init(self, rank, id, start, end, qstart, qend, probability, qlength)
(Constructor)

repr(self)
(Representation operator)

str(self)
(Informal representation operator)