eXpress “1.5”
|
The Sequence class is an abstract class whose implmentations are used to store and access encoded nucleotide sequences. More...
#include <sequence.h>
Public Member Functions | |
Sequence () | |
Dummy Sequence constructor. | |
virtual | ~Sequence () |
Dummy Sequence destructor. | |
virtual void | set (const std::string &seq, bool rev)=0 |
A member function that encodes the given sequence and overwrites the current stored sequence with it. | |
virtual size_t | operator[] (const size_t index) const =0 |
An accessor for the encoded character at the given index. | |
virtual size_t | get_ref (const size_t index) const =0 |
An accessor for the encoded reference character at the given index. | |
virtual void | update_est (const size_t index, const size_t nuc, float mass)=0 |
A member function that updates the posterior nucleotide distribution if probabilistic. | |
virtual void | update_obs (const size_t index, const size_t nuc, float mass)=0 |
A member function that updates the observed frequency distribution if probabilistic. | |
virtual void | update_exp (const size_t index, const size_t nuc, float mass)=0 |
A member function that updates the expected frequency distribution if probabilistic. | |
virtual float | get_prob (const size_t index, const size_t nuc) const =0 |
An accessor for the posterior nucleotide distribution (logged). | |
virtual float | get_obs (const size_t index, const size_t nuc) const =0 |
An accessor for the observed nucleotide frequency (logged). | |
virtual float | get_exp (const size_t index, const size_t nuc) const =0 |
An accessor for the expected nucleotide frequency (logged). | |
virtual bool | prob () const =0 |
Accessor to determine if the sequence is probabilistic. | |
virtual size_t | length () const =0 |
An accessor for the length of the encoded sequence. | |
virtual bool | empty () const =0 |
Accessor to determine if the sequence has 0 length. | |
virtual void | calc_p_vals (std::vector< double > &p_vals) const =0 |
A member function that calculates p-values based on the observed and expected nucleotide frequences for the sequence. | |
std::string | serialize () |
A member function to serialize a string into an array of bytes, with each nucleotide represented by 2 bits. |
The Sequence class is an abstract class whose implmentations are used to store and access encoded nucleotide sequences.
They also supports probabilistic sequences, meaning that each position stores a distribution over nucleotides.
Definition at line 58 of file sequence.h.
virtual void Sequence::calc_p_vals | ( | std::vector< double > & | p_vals | ) | const [pure virtual] |
A member function that calculates p-values based on the observed and expected nucleotide frequences for the sequence.
Experimental.
p_vals | a reference to an empty vector of doubles to fill with p-values at each position. |
Implemented in SequenceFwd, and SequenceRev.
virtual bool Sequence::empty | ( | ) | const [pure virtual] |
Accessor to determine if the sequence has 0 length.
Implemented in SequenceFwd, and SequenceRev.
virtual float Sequence::get_exp | ( | const size_t | index, |
const size_t | nuc | ||
) | const [pure virtual] |
An accessor for the expected nucleotide frequency (logged).
index | the index of the position to access. |
nuc | the nucleotide to return the frequency of. |
Implemented in SequenceFwd, and SequenceRev.
virtual float Sequence::get_obs | ( | const size_t | index, |
const size_t | nuc | ||
) | const [pure virtual] |
An accessor for the observed nucleotide frequency (logged).
index | the index of the position to access. |
nuc | the nucleotide to return the frequency of. |
Implemented in SequenceFwd, and SequenceRev.
virtual float Sequence::get_prob | ( | const size_t | index, |
const size_t | nuc | ||
) | const [pure virtual] |
An accessor for the posterior nucleotide distribution (logged).
index | the index of the position to access. |
nuc | the nucleotide to return the probability of. |
Implemented in SequenceFwd, and SequenceRev.
virtual size_t Sequence::get_ref | ( | const size_t | index | ) | const [pure virtual] |
An accessor for the encoded reference character at the given index.
May differ from the operator[] if the sequence is probabilistic.
index | the index of the encoded reference character to return (assumed to be < _len) |
Implemented in SequenceFwd, and SequenceRev.
virtual size_t Sequence::length | ( | ) | const [pure virtual] |
An accessor for the length of the encoded sequence.
Implemented in SequenceFwd, and SequenceRev.
virtual size_t Sequence::operator[] | ( | const size_t | index | ) | const [pure virtual] |
An accessor for the encoded character at the given index.
If the sequence is probabilistic, returns the mode. Otherwise, returns the reference.
index | the index of the encoded character to return (assumed to be < _len) |
Implemented in SequenceFwd, and SequenceRev.
virtual bool Sequence::prob | ( | ) | const [pure virtual] |
Accessor to determine if the sequence is probabilistic.
Implemented in SequenceFwd, and SequenceRev.
virtual void Sequence::set | ( | const std::string & | seq, |
bool | rev | ||
) | [pure virtual] |
A member function that encodes the given sequence and overwrites the current stored sequence with it.
seq | the nucleotide sequence to encode and store. |
rev | a boolean if the sequence should be reverse complemented before encoding. |
Implemented in SequenceFwd, and SequenceRev.
virtual void Sequence::update_est | ( | const size_t | index, |
const size_t | nuc, | ||
float | mass | ||
) | [pure virtual] |
A member function that updates the posterior nucleotide distribution if probabilistic.
index | the index of the position to update. |
nuc | the nucleotide to increment the mass of. |
mass | the amount to increment the nucleotide's mass by. |
Implemented in SequenceFwd, and SequenceRev.
virtual void Sequence::update_exp | ( | const size_t | index, |
const size_t | nuc, | ||
float | mass | ||
) | [pure virtual] |
A member function that updates the expected frequency distribution if probabilistic.
index | the index of the position to update. |
nuc | the nucleotide to increment the mass of. |
mass | the amount to increment the nucleotide's mass by. |
Implemented in SequenceFwd, and SequenceRev.
virtual void Sequence::update_obs | ( | const size_t | index, |
const size_t | nuc, | ||
float | mass | ||
) | [pure virtual] |
A member function that updates the observed frequency distribution if probabilistic.
index | the index of the position to update. |
nuc | the nucleotide to increment the mass of. |
mass | the amount to increment the nucleotide's mass by. |
Implemented in SequenceFwd, and SequenceRev.