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Methods
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__del__
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__del__ ( self )
Deallocation of C sequence struct.
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__getitem__
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__getitem__ ( self, index )
Return an EmissionSequence object initialized with a reference to
sequence index.
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__init__
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__init__ (
self,
emissionDomain,
sequenceSetInput,
labelDomain=None,
labelInput=None,
)
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Exceptions
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IOError, 'File ' + str( sequenceSetInput ) + ' not found.'
NoValidCDataType, "C data type " + str( self.emissionDomain.CDataType ) + " invalid."
UnknownInputType, "inputType " + str(type( sequenceSetInput ) ) + " not recognized."
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__len__
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__len__ ( self )
Return the number of sequences in the SequenceSet.
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__str__
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__str__ ( self )
Defines string representation.
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getSeqLabel
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getSeqLabel ( self, index )
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getSequence
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getSequence ( self, index )
Returns the index-th sequence in internal representation
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Exceptions
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IndexOutOfBounds( str( index ) + " is out of bounds, only " + str( self.cseq.seq_number ) + "sequences" )
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getStateLabel
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getStateLabel ( self, index )
Returns the labeling of the index-th sequence in internal representation
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Exceptions
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IndexOutOfBounds( str( 0 ) + " is out of bounds, only " + str( self.cseq.seq_number ) + "labels" )
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getSubset
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getSubset ( self, seqIndixes )
Returns a SequenceSet containing (references to) the sequences with the indixes in
seqIndixes.
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getWeight
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getWeight ( self, i )
Return the weight of sequence i. Weights are used in Baum-Welch
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merge
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merge ( self, emissionSequences )
Merge emisisonSequences with self.
emisisonSequences can either be an EmissionSequence or SequenceSet object.
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Exceptions
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TypeError, "EmissionSequence or SequenceSet required, got " + str( emissionSequences.__class__.__name__ )
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sequenceLength
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sequenceLength ( self, i )
Return the lenght of sequence i in the SequenceSet
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setSeqLabel
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setSeqLabel (
self,
index,
value,
)
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setWeight
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setWeight (
self,
i,
w,
)
Return the weight of sequence i. Weights are used in Baum-Welch
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write
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write ( self, fileName )
Writes (appends) the SequenceSet into file fileName.
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