eXpress “1.5”
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The SequenceFwd class implements the Sequence abstract class for storing the forward sequence. More...
#include <sequence.h>
Public Member Functions | |
SequenceFwd () | |
Dummy SequenceFwd constructor. | |
SequenceFwd (const std::string &seq, bool rev, bool prob=false) | |
SequenceFwd constructor encodes and stores the given nucleotide sequence. | |
SequenceFwd (const SequenceFwd &other) | |
SequenceFwd copy constructor. | |
SequenceFwd & | operator= (const SequenceFwd &other) |
SequenceFwd assignment constructor, copies the given SequenceFwd object. | |
void | set (const std::string &seq, bool rev) |
A member function that encodes the given sequence and overwrites the current stored sequence with it. | |
size_t | operator[] (const size_t index) const |
An accessor for the encoded character at the given index. | |
size_t | get_ref (const size_t index) const |
An accessor for the encoded reference character at the given index. | |
float | get_exp (const size_t index, const size_t nuc) const |
An accessor for the expected nucleotide frequency (logged). | |
float | get_obs (const size_t index, const size_t nuc) const |
An accessor for the observed nucleotide frequency (logged). | |
void | update_est (const size_t index, const size_t nuc, float mass) |
A member function that updates the posterior nucleotide distribution if probabilistic. | |
void | update_obs (const size_t index, const size_t nuc, float mass) |
A member function that updates the observed frequency distribution if probabilistic. | |
void | update_exp (const size_t index, const size_t nuc, float mass) |
A member function that updates the expected frequency distribution if probabilistic. | |
float | get_prob (const size_t index, const size_t nuc) const |
An accessor for the posterior nucleotide distribution (logged). | |
bool | prob () const |
Accessor to determine if the sequence is probabilistic. | |
bool | empty () const |
Accessor to determine if the sequence has 0 length. | |
size_t | length () const |
An accessor for the length of the encoded sequence. | |
void | calc_p_vals (std::vector< double > &p_vals) const |
A member function that calculates p-values based on the observed and expected nucleotide frequences for the sequence. |
The SequenceFwd class implements the Sequence abstract class for storing the forward sequence.
Documentation is only provided for methods not documented in the abstract Sequence class.
Definition at line 177 of file sequence.h.
SequenceFwd::SequenceFwd | ( | const std::string & | seq, |
bool | rev, | ||
bool | prob = false |
||
) |
SequenceFwd constructor encodes and stores the given nucleotide sequence.
seq | the nucleotide sequence string to encode and store. |
rev | a boolean if the sequence should be reverse complemented before encoding. |
Definition at line 30 of file sequence.cpp.
SequenceFwd::SequenceFwd | ( | const SequenceFwd & | other | ) |
SequenceFwd copy constructor.
other | the SequenceFwd object to copy. |
Definition at line 40 of file sequence.cpp.
void SequenceFwd::calc_p_vals | ( | std::vector< double > & | p_vals | ) | const [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. |
Implements Sequence.
bool SequenceFwd::empty | ( | ) | const [inline, virtual] |
Accessor to determine if the sequence has 0 length.
Implements Sequence.
Definition at line 242 of file sequence.h.
float SequenceFwd::get_exp | ( | const size_t | index, |
const size_t | nuc | ||
) | const [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. |
Implements Sequence.
Definition at line 99 of file sequence.cpp.
float SequenceFwd::get_obs | ( | const size_t | index, |
const size_t | nuc | ||
) | const [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. |
Implements Sequence.
Definition at line 94 of file sequence.cpp.
float SequenceFwd::get_prob | ( | const size_t | index, |
const size_t | nuc | ||
) | const [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. |
Implements Sequence.
Definition at line 89 of file sequence.cpp.
size_t SequenceFwd::get_ref | ( | const size_t | index | ) | const [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) |
Implements Sequence.
Definition at line 83 of file sequence.cpp.
size_t SequenceFwd::length | ( | ) | const [inline, virtual] |
An accessor for the length of the encoded sequence.
Implements Sequence.
Definition at line 243 of file sequence.h.
SequenceFwd & SequenceFwd::operator= | ( | const SequenceFwd & | other | ) |
SequenceFwd assignment constructor, copies the given SequenceFwd object.
other | the Sequence object to copy. |
Definition at line 50 of file sequence.cpp.
size_t SequenceFwd::operator[] | ( | const size_t | index | ) | const [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) |
Implements Sequence.
Definition at line 75 of file sequence.cpp.
bool SequenceFwd::prob | ( | ) | const [inline, virtual] |
Accessor to determine if the sequence is probabilistic.
Implements Sequence.
Definition at line 241 of file sequence.h.
void SequenceFwd::set | ( | const std::string & | seq, |
bool | rev | ||
) | [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. |
Implements Sequence.
Definition at line 63 of file sequence.cpp.
void SequenceFwd::update_est | ( | const size_t | index, |
const size_t | nuc, | ||
float | mass | ||
) | [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. |
Implements Sequence.
Definition at line 104 of file sequence.cpp.
void SequenceFwd::update_exp | ( | const size_t | index, |
const size_t | nuc, | ||
float | mass | ||
) | [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. |
Implements Sequence.
Definition at line 114 of file sequence.cpp.
void SequenceFwd::update_obs | ( | const size_t | index, |
const size_t | nuc, | ||
float | mass | ||
) | [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. |
Implements Sequence.
Definition at line 109 of file sequence.cpp.