Package obitools :: Package location :: Class SimpleLocation
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Class SimpleLocation

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A simple location is describe a continuous region of a sequence define by a begin and a end position.

Instance Methods [hide private]
 
__init__(self, begin, end)
Build a new SimpleLocation instance.
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_extractSequence(self, sequence) source code
 
isDirect(self) source code
bool
isSimple(self)
Indicate if a location is composed of a single continuous region or is composed by the junction of several locations by the join operator.
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isFullLength(self) source code
 
simplify(self) source code
bool
needNucleic(self)
If a location contains a complement operator, it can be use only on nucleic sequence.
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__str__(self)
str(x)
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shift(self, s) source code
 
_getglocpos(self) source code
 
getGloc(self) source code
 
getBegin(self) source code
 
getEnd(self) source code

Inherited from Location: __abs__, __cmp__, extractSequence, getFivePrime, getThreePrime

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

Properties [hide private]
  begin
beginning position of the location
  end
ending position of the location

Inherited from Location: fivePrime, threePrime

Inherited from object: __class__

Method Details [hide private]

__init__(self, begin, end)
(Constructor)

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Build a new SimpleLocation instance. Valid position are define on [1,N] with N the length of the sequence.

Parameters:
  • begin (int) - start position of the location
  • end (int) - end position of the location
Overrides: object.__init__

isDirect(self)

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Overrides: Location.isDirect

isSimple(self)

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Indicate if a location is composed of a single continuous region or is composed by the junction of several locations by the join operator.

Returns: bool
True if the location is composed of a single continuous region.
Overrides: Location.isSimple
(inherited documentation)

isFullLength(self)

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Overrides: Location.isFullLength

needNucleic(self)

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If a location contains a complement operator, it can be use only on nucleic sequence.

Returns: bool
True if location contains a complement operator
Overrides: Location.needNucleic
(inherited documentation)

__str__(self)
(Informal representation operator)

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str(x)

Overrides: object.__str__
(inherited documentation)

shift(self, s)

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Overrides: Location.shift

getGloc(self)

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Overrides: Location.getGloc

getBegin(self)

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Overrides: Location.getBegin

getEnd(self)

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Overrides: Location.getEnd

Property Details [hide private]

begin

beginning position of the location

Get Method:
getBegin(self)

end

ending position of the location

Get Method:
getEnd(self)