bpp-seq
2.2.0
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#include <Bpp/Seq/Alphabet/RNY.h>
Public Member Functions | |
RNY (const NucleicAlphabet &) | |
RNY (const RNY &bia) | |
RNY & | operator= (const RNY &bia) |
RNY * | clone () const |
~RNY () | |
int | charToInt (const std::string &state) const throw (BadCharException) |
Give the int description of a state given its string description. More... | |
std::string | intToChar (int state) const throw (BadIntException) |
Give the string description of a state given its int description. More... | |
bool | containsGap (const std::string &state) const throw (BadCharException) |
unsigned int | getSize () const |
Get the number of resolved states in the alphabet (e.g. return 4 for DNA alphabet). This is the method you'll need in most cases. More... | |
unsigned int | getNumberOfTypes () const |
Get the number of distinct states in alphabet (e.g. return 15 for DNA alphabet). This is the number of integers used for state description. More... | |
int | getUnknownCharacterCode () const |
bool | isGap (int state) const |
std::vector< int > | getAlias (int state) const throw (BadIntException) |
Get all resolved states that match a generic state. More... | |
std::vector< std::string > | getAlias (const std::string &state) const throw (BadCharException) |
Get all resolved states that match a generic state. More... | |
bool | isUnresolved (int state) const |
bool | isUnresolved (const std::string &state) const |
std::string | getAlphabetType () const |
Identification method. More... | |
const NucleicAlphabet & | getLetterAlphabet () const |
std::string | getRNY (const std::string &, const std::string &, const std::string &) const throw (BadCharException) |
Get the char code for a triplet given the char code of the three underlying positions. More... | |
int | getRNY (int, int, int, const Alphabet &) const throw (BadCharException) |
Implement these methods from the Alphabet interface. | |
size_t | getNumberOfStates () const |
This is a convenient alias for getNumberOfChars(), returning a size_t instead of unsigned int. More... | |
unsigned int | getNumberOfChars () const |
Get the number of supported characters in this alphabet, including generic characters (e.g. return 20 for DNA alphabet). More... | |
std::string | getName (const std::string &state) const throw (BadCharException) |
Get the complete name of a state given its string description. More... | |
std::string | getName (int state) const throw (BadIntException) |
Get the complete name of a state given its int description. More... | |
bool | isIntInAlphabet (int state) const |
Tell if a state (specified by its int description) is allowed by the the alphabet. More... | |
bool | isCharInAlphabet (const std::string &state) const |
Tell if a state (specified by its string description) is allowed by the the alphabet. More... | |
int | getGeneric (const std::vector< int > &states) const throw (BadIntException) |
Get the generic state that match a set of states. More... | |
std::string | getGeneric (const std::vector< std::string > &states) const throw (AlphabetException) |
Get the generic state that match a set of states. More... | |
const std::vector< int > & | getSupportedInts () const |
const std::vector< std::string > & | getSupportedChars () const |
int | getGapCharacterCode () const |
bool | isGap (const std::string &state) const |
Specific methods to access AlphabetState | |
virtual AlphabetState & | getStateAt (size_t stateIndex) throw (IndexOutOfBoundsException) |
Get a state at a position in the alphabet_ vector. More... | |
virtual const AlphabetState & | getStateAt (size_t stateIndex) const throw (IndexOutOfBoundsException) |
Get a state at a position in the alphabet_ vector. More... | |
const AlphabetState & | getState (const std::string &letter) const throw (BadCharException) |
Get a state by its letter. More... | |
AlphabetState & | getState (const std::string &letter) throw (BadCharException) |
const AlphabetState & | getState (int num) const throw (BadIntException) |
Get a state by its num. More... | |
AlphabetState & | getState (int num) throw (BadIntException) |
int | getIntCodeAt (size_t stateIndex) const throw (IndexOutOfBoundsException) |
const std::string & | getCharCodeAt (size_t stateIndex) const throw (IndexOutOfBoundsException) |
size_t | getStateIndex (int state) const throw (BadIntException) |
size_t | getStateIndex (const std::string &state) const throw (BadCharException) |
Protected Member Functions | |
virtual void | registerState (AlphabetState *st) throw (Exception) |
Add a state to the Alphabet. More... | |
virtual void | setState (size_t pos, AlphabetState *st) throw (Exception, IndexOutOfBoundsException) |
Set a state in the Alphabet. More... | |
void | resize (size_t size) |
Resize the private alphabet_ vector. More... | |
void | remap () |
Re-update the maps using the alphabet_ vector content. More... | |
unsigned int | getStateCodingSize () const |
Get the size of the string coding a state. More... | |
bool | equals (const Alphabet &alphabet) const |
Comparison of alphabets. More... | |
Protected Attributes | |
Available codes | |
These vectors will be computed the first time you call the getAvailableInts or getAvailableChars method. | |
std::vector< std::string > | charList_ |
std::vector< int > | intList_ |
Private Attributes | |
const NucleicAlphabet & | nuclalph_ |
RNY::RNY | ( | const NucleicAlphabet & | na | ) |
Definition at line 52 of file RNY.cpp.
References bpp::AlphabetTools::isDNAAlphabet(), and bpp::AbstractAlphabet::registerState().
Referenced by clone().
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virtual |
Give the int description of a state given its string description.
state | The string description. |
BadCharException | When state is not a valid char description. |
Reimplemented from bpp::AbstractAlphabet.
Definition at line 433 of file RNY.cpp.
References bpp::AbstractAlphabet::charToInt().
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inlinevirtual |
bool RNY::containsGap | ( | const std::string & | state | ) | const |
throw | ( | BadCharException | |||
) |
Definition at line 416 of file RNY.cpp.
Referenced by isUnresolved().
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inlineprotectedvirtualinherited |
Comparison of alphabets.
Implements bpp::Alphabet.
Definition at line 268 of file AbstractAlphabet.h.
References bpp::Alphabet::getAlphabetType().
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virtual |
Get all resolved states that match a generic state.
If the given state is not a generic code then the output vector will contain this unique code.
state | The alias to resolve. |
BadIntException | When state is not a valid integer. |
Reimplemented from bpp::AbstractAlphabet.
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virtual |
Get all resolved states that match a generic state.
If the given state is not a generic code then the output vector will contain this unique code.
state | The alias to resolve. |
BadCharException | When state is not a valid char description. |
Reimplemented from bpp::AbstractAlphabet.
Definition at line 280 of file RNY.cpp.
References bpp::AbstractAlphabet::intToChar().
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inlinevirtual |
Identification method.
Used to tell if two alphabets describe the same type of sequences. For instance, this method is used by sequence containers to compare two alphabets and allow or deny addition of sequences.
Implements bpp::Alphabet.
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inlinevirtualinherited |
stateIndex | The index of the state to fetch. |
Implements bpp::Alphabet.
Definition at line 220 of file AbstractAlphabet.h.
References bpp::AlphabetState::getLetter(), and bpp::AbstractAlphabet::getStateAt().
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inlinevirtualinherited |
Implements bpp::Alphabet.
Definition at line 159 of file AbstractAlphabet.h.
Referenced by bpp::SequenceTools::replaceStopsWithGaps().
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virtualinherited |
Get the generic state that match a set of states.
If the given states contain generic code, each generic code is first resolved and then the new generic state is returned. If only a single resolved state is given the function return this state.
states | A vector of states to resolve. |
BadIntException | When a state is not a valid integer. |
Implements bpp::Alphabet.
Reimplemented in bpp::WordAlphabet, bpp::ProteicAlphabet, bpp::DNA, and bpp::RNA.
Definition at line 232 of file AbstractAlphabet.cpp.
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virtualinherited |
Get the generic state that match a set of states.
If the given states contain generic code, each generic code is first resolved and then the new generic state is returned. If only a single resolved state is given the function return this state.
states | A vector of states to resolve. |
BadCharException | when a state is not a valid char description. |
CharStateNotSupportedException | when the alphabet does not support Char state for unresolved state. |
Implements bpp::Alphabet.
Reimplemented in bpp::WordAlphabet, bpp::ProteicAlphabet, bpp::DNA, and bpp::RNA.
Definition at line 258 of file AbstractAlphabet.cpp.
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inlinevirtualinherited |
stateIndex | The index of the state to fetch. |
Implements bpp::Alphabet.
Definition at line 216 of file AbstractAlphabet.h.
References bpp::AlphabetState::getNum(), and bpp::AbstractAlphabet::getStateAt().
const NucleicAlphabet & RNY::getLetterAlphabet | ( | ) | const |
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virtualinherited |
Get the complete name of a state given its string description.
In case of several states with identical number (i.e. N and X for nucleic alphabets), this method will return the name of the first found in the vector.
state | The string description of the given state. |
BadCharException | When state is not a valid char description. |
Implements bpp::Alphabet.
Reimplemented in bpp::WordAlphabet.
Definition at line 164 of file AbstractAlphabet.cpp.
Referenced by bpp::WordAlphabet::getName().
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virtualinherited |
Get the complete name of a state given its int description.
In case of several states with identical number (i.e. N and X for nucleic alphabets), this method returns the name of the first found in the vector.
state | The int description of the given state. |
BadIntException | When state is not a valid integer. |
Implements bpp::Alphabet.
Definition at line 171 of file AbstractAlphabet.cpp.
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inlinevirtualinherited |
Get the number of supported characters in this alphabet, including generic characters (e.g. return 20 for DNA alphabet).
Implements bpp::Alphabet.
Definition at line 146 of file AbstractAlphabet.h.
References bpp::AbstractAlphabet::alphabet_.
Referenced by bpp::WordAlphabet::getNumberOfTypes(), bpp::WordAlphabet::getSize(), and bpp::NucleicAlphabet::registerState().
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inlinevirtualinherited |
This is a convenient alias for getNumberOfChars(), returning a size_t instead of unsigned int.
This funcion is typically used il loops over all states of an alphabet.
Implements bpp::Alphabet.
Definition at line 145 of file AbstractAlphabet.h.
References bpp::AbstractAlphabet::alphabet_.
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inlinevirtual |
Get the number of distinct states in alphabet (e.g. return 15 for DNA alphabet). This is the number of integers used for state description.
Implements bpp::Alphabet.
string RNY::getRNY | ( | const std::string & | pos1, |
const std::string & | pos2, | ||
const std::string & | pos3 | ||
) | const | ||
throw | ( | BadCharException | |
) |
Get the char code for a triplet given the char code of the three underlying positions.
The char code of each position must match the nucleic alphabet specified for this alphabet. NB: This performs pos1 + pos2 + pos3 after checking for each position validity.
pos1 | Char description for position 1. |
pos2 | Char description for position 2. |
pos3 | Char description for position 3. |
int RNY::getRNY | ( | int | i, |
int | j, | ||
int | k, | ||
const Alphabet & | alph | ||
) | const | ||
throw | ( | BadCharException | |
) |
Definition at line 321 of file RNY.cpp.
References bpp::AlphabetTools::isNucleicAlphabet().
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inlinevirtual |
Get the number of resolved states in the alphabet (e.g. return 4 for DNA alphabet). This is the method you'll need in most cases.
Implements bpp::Alphabet.
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virtualinherited |
Get a state by its letter.
This method must be overloaded in specialized classes to send back a reference of the corect type.
letter | The letter of the state to find. |
BadCharException | If the letter is not in the Alphabet. |
Implements bpp::Alphabet.
Reimplemented in bpp::NucleicAlphabet, and bpp::ProteicAlphabet.
Definition at line 94 of file AbstractAlphabet.cpp.
Referenced by bpp::CaseMaskedAlphabet::CaseMaskedAlphabet(), bpp::ProteicAlphabet::getState(), and bpp::NucleicAlphabet::getState().
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inherited |
Definition at line 130 of file AbstractAlphabet.cpp.
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virtualinherited |
Get a state by its num.
This method must be overloaded in specialized classes to send back a reference of the corect type.
num | The num of the state to find. |
BadIntException | If the num is not in the Alphabet. |
Implements bpp::Alphabet.
Reimplemented in bpp::NucleicAlphabet, and bpp::ProteicAlphabet.
Definition at line 112 of file AbstractAlphabet.cpp.
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inherited |
Definition at line 139 of file AbstractAlphabet.cpp.
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virtualinherited |
Get a state at a position in the alphabet_ vector.
This method must be overloaded in specialized classes to send back a reference of the corect type.
stateIndex | The index of the state in the alphabet_ vector. |
IndexOutOfBoundsException | If the index is invalid. |
Reimplemented in bpp::NucleicAlphabet, bpp::NumericAlphabet, and bpp::ProteicAlphabet.
Definition at line 148 of file AbstractAlphabet.cpp.
Referenced by bpp::AbstractAlphabet::getCharCodeAt(), bpp::AbstractAlphabet::getIntCodeAt(), bpp::ProteicAlphabet::getStateAt(), bpp::NumericAlphabet::getStateAt(), and bpp::NucleicAlphabet::getStateAt().
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virtualinherited |
Get a state at a position in the alphabet_ vector.
This method must be overloaded in specialized classes to send back a reference of the corect type.
stateIndex | The index of the state in the alphabet_ vector. |
IndexOutOfBoundsException | If the index is invalid. |
Implements bpp::Alphabet.
Reimplemented in bpp::NucleicAlphabet, bpp::NumericAlphabet, and bpp::ProteicAlphabet.
Definition at line 156 of file AbstractAlphabet.cpp.
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inlineprotectedvirtualinherited |
Get the size of the string coding a state.
Implements bpp::Alphabet.
Reimplemented in bpp::WordAlphabet.
Definition at line 266 of file AbstractAlphabet.h.
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virtualinherited |
Implements bpp::Alphabet.
Definition at line 121 of file AbstractAlphabet.cpp.
Referenced by bpp::AAIndex2Entry::getIndex().
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virtualinherited |
Implements bpp::Alphabet.
Definition at line 103 of file AbstractAlphabet.cpp.
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virtualinherited |
Note for developers of new alphabets: we return a const reference here since the list is supposed to be stored within the class and should not be modified outside the class.
Implements bpp::Alphabet.
Definition at line 301 of file AbstractAlphabet.cpp.
Referenced by bpp::CaseMaskedAlphabet::CaseMaskedAlphabet().
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virtualinherited |
Note for developers of new alphabets: we return a const reference here since the list is supposed to be stored within the class and should not be modified outside the class.
Implements bpp::Alphabet.
Definition at line 284 of file AbstractAlphabet.cpp.
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inlinevirtual |
Implements bpp::Alphabet.
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virtual |
Give the string description of a state given its int description.
state | The int description. |
BadIntException | When state is not a valid integer. |
Reimplemented from bpp::AbstractAlphabet.
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virtualinherited |
Tell if a state (specified by its string description) is allowed by the the alphabet.
state | The string description. |
Implements bpp::Alphabet.
Reimplemented in bpp::LetterAlphabet.
Definition at line 202 of file AbstractAlphabet.cpp.
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virtual |
state | The state to test. |
Reimplemented from bpp::AbstractAlphabet.
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inlinevirtualinherited |
state | The state to test. |
Implements bpp::Alphabet.
Definition at line 161 of file AbstractAlphabet.h.
References bpp::AbstractAlphabet::charToInt().
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virtualinherited |
Tell if a state (specified by its int description) is allowed by the the alphabet.
state | The int description. |
Implements bpp::Alphabet.
Definition at line 192 of file AbstractAlphabet.cpp.
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virtual |
state | The state to test. |
Implements bpp::Alphabet.
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virtual |
state | The state to test. |
Implements bpp::Alphabet.
Definition at line 421 of file RNY.cpp.
References containsGap().
Definition at line 75 of file RNY.h.
References bpp::AbstractAlphabet::operator=().
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protectedvirtualinherited |
Add a state to the Alphabet.
st | The state to add. |
Exception | If a wrong alphabet state is provided. |
Reimplemented in bpp::LetterAlphabet, bpp::NucleicAlphabet, bpp::NumericAlphabet, and bpp::DefaultAlphabet.
Definition at line 70 of file AbstractAlphabet.cpp.
Referenced by bpp::BinaryAlphabet::BinaryAlphabet(), bpp::WordAlphabet::build_(), bpp::IntegerAlphabet::IntegerAlphabet(), bpp::DefaultAlphabet::registerState(), bpp::NumericAlphabet::registerState(), bpp::LetterAlphabet::registerState(), and RNY().
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inlineprotectedinherited |
Re-update the maps using the alphabet_ vector content.
Definition at line 258 of file AbstractAlphabet.h.
References bpp::AbstractAlphabet::alphabet_, bpp::AbstractAlphabet::letters_, bpp::AbstractAlphabet::nums_, and bpp::AbstractAlphabet::updateMaps_().
Referenced by bpp::NumericAlphabet::remap().
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inlineprotectedinherited |
Resize the private alphabet_ vector.
size | The new size of the Alphabet. |
Definition at line 253 of file AbstractAlphabet.h.
References bpp::AbstractAlphabet::alphabet_.
Referenced by bpp::IntegerAlphabet::IntegerAlphabet().
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protectedvirtualinherited |
Set a state in the Alphabet.
pos | The index of the state in the alphabet_ vector. |
st | The new state to put in the Alphabet. |
Exception | If a wrong alphabet state is provided. |
IndexOutOfBoundsException | If an incorrect index is provided. |
Reimplemented in bpp::LetterAlphabet, bpp::NucleicAlphabet, and bpp::NumericAlphabet.
Definition at line 79 of file AbstractAlphabet.cpp.
Referenced by bpp::NumericAlphabet::setState(), and bpp::LetterAlphabet::setState().
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mutableprotectedinherited |
Definition at line 99 of file AbstractAlphabet.h.
Referenced by bpp::AbstractAlphabet::operator=().
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mutableprotectedinherited |
Definition at line 100 of file AbstractAlphabet.h.
Referenced by bpp::AbstractAlphabet::operator=().
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private |
Definition at line 68 of file RNY.h.
Referenced by getLetterAlphabet().