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bpp::DefaultAlphabet Class Reference

The DefaultAlphabet class. More...

#include <Bpp/Seq/Alphabet/DefaultAlphabet.h>

+ Inheritance diagram for bpp::DefaultAlphabet:
+ Collaboration diagram for bpp::DefaultAlphabet:

Public Member Functions

 DefaultAlphabet ()
 
 DefaultAlphabet (const DefaultAlphabet &bia)
 
DefaultAlphabetoperator= (const DefaultAlphabet &bia)
 
DefaultAlphabetclone () const
 
virtual ~DefaultAlphabet ()
 
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...
 
std::string getAlphabetType () const
 Identification method. More...
 
int getUnknownCharacterCode () const
 
bool isUnresolved (int state) const
 
bool isUnresolved (const std::string &state) const
 
bool isCharInAlphabet (char state) const
 
bool isCharInAlphabet (const std::string &state) const
 Tell if a state (specified by its string description) is allowed by the the alphabet. More...
 
int charToInt (const std::string &state) const throw (BadCharException)
 Give the int description of a state given its string description. More...
 
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...
 
std::string intToChar (int state) const throw (BadIntException)
 Give the string description 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...
 
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...
 
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 (int state) const
 
bool isGap (const std::string &state) const
 
Specific methods to access AlphabetState
virtual AlphabetStategetStateAt (size_t stateIndex) throw (IndexOutOfBoundsException)
 Get a state at a position in the alphabet_ vector. More...
 
virtual const AlphabetStategetStateAt (size_t stateIndex) const throw (IndexOutOfBoundsException)
 Get a state at a position in the alphabet_ vector. More...
 
const AlphabetStategetState (const std::string &letter) const throw (BadCharException)
 Get a state by its letter. More...
 
AlphabetStategetState (const std::string &letter) throw (BadCharException)
 
const AlphabetStategetState (int num) const throw (BadIntException)
 Get a state by its num. More...
 
AlphabetStategetState (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

void registerState (AlphabetState *st) throw (Exception)
 Add a state to the Alphabet. More...
 
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

std::string chars_
 
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_
 

Detailed Description

The DefaultAlphabet class.

This alphabet should match virtually any type of sequences. This should be used by who does not care of the sequence type.

Definition at line 54 of file DefaultAlphabet.h.

Constructor & Destructor Documentation

DefaultAlphabet::DefaultAlphabet ( )

Definition at line 48 of file DefaultAlphabet.cpp.

References chars_, registerState(), and bpp::TextTools::toString().

Referenced by clone().

bpp::DefaultAlphabet::DefaultAlphabet ( const DefaultAlphabet bia)
inline

Definition at line 67 of file DefaultAlphabet.h.

virtual bpp::DefaultAlphabet::~DefaultAlphabet ( )
inlinevirtual

Definition at line 84 of file DefaultAlphabet.h.

Member Function Documentation

DefaultAlphabet* bpp::DefaultAlphabet::clone ( ) const
inlinevirtual

Implements bpp::LetterAlphabet.

Definition at line 76 of file DefaultAlphabet.h.

References DefaultAlphabet().

bool bpp::AbstractAlphabet::equals ( const Alphabet alphabet) const
inlineprotectedvirtualinherited

Comparison of alphabets.

Returns
true If the two instances are of the same class.

Implements bpp::Alphabet.

Definition at line 268 of file AbstractAlphabet.h.

References bpp::Alphabet::getAlphabetType().

std::vector< int > AbstractAlphabet::getAlias ( int  state) const
throw (BadIntException
)
virtualinherited

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.

Parameters
stateThe alias to resolve.
Returns
A vector of resolved states.
Exceptions
BadIntExceptionWhen state is not a valid integer.

Implements bpp::Alphabet.

Reimplemented in bpp::WordAlphabet, bpp::ProteicAlphabet, bpp::RNY, bpp::NumericAlphabet, bpp::DNA, and bpp::RNA.

Definition at line 212 of file AbstractAlphabet.cpp.

std::vector< std::string > AbstractAlphabet::getAlias ( const std::string &  state) const
throw (BadCharException
)
virtualinherited

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.

Parameters
stateThe alias to resolve.
Returns
A vector of resolved states.
Exceptions
BadCharExceptionWhen state is not a valid char description.

Implements bpp::Alphabet.

Reimplemented in bpp::WordAlphabet, bpp::ProteicAlphabet, bpp::RNY, bpp::NumericAlphabet, bpp::DNA, and bpp::RNA.

Definition at line 222 of file AbstractAlphabet.cpp.

std::string bpp::DefaultAlphabet::getAlphabetType ( ) const
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.

Returns
A text describing the alphabet.

Implements bpp::Alphabet.

Definition at line 89 of file DefaultAlphabet.h.

const std::string& bpp::AbstractAlphabet::getCharCodeAt ( size_t  stateIndex) const
throw (IndexOutOfBoundsException
)
inlinevirtualinherited
Returns
The char code of a given state.
Parameters
stateIndexThe 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().

int bpp::AbstractAlphabet::getGapCharacterCode ( ) const
inlinevirtualinherited
Returns
The int code for gap characters.

Implements bpp::Alphabet.

Definition at line 159 of file AbstractAlphabet.h.

Referenced by bpp::SequenceTools::replaceStopsWithGaps().

int AbstractAlphabet::getGeneric ( const std::vector< int > &  states) const
throw (BadIntException
)
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.

Parameters
statesA vector of states to resolve.
Returns
A int code for the computed state.
Exceptions
BadIntExceptionWhen 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.

References bpp::MapTools::getKeys(), and bpp::TextTools::toString().

std::string AbstractAlphabet::getGeneric ( const std::vector< std::string > &  states) const
throw (AlphabetException
)
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.

Parameters
statesA vector of states to resolve.
Returns
A string code for the computed state.
Exceptions
BadCharExceptionwhen a state is not a valid char description.
CharStateNotSupportedExceptionwhen 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.

References bpp::MapTools::getKeys(), and bpp::TextTools::toString().

int bpp::AbstractAlphabet::getIntCodeAt ( size_t  stateIndex) const
throw (IndexOutOfBoundsException
)
inlinevirtualinherited
Returns
The int code of a given state.
Parameters
stateIndexThe 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().

std::string AbstractAlphabet::getName ( const std::string &  state) const
throw (BadCharException
)
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.

Parameters
stateThe string description of the given state.
Returns
The name of the state.
Exceptions
BadCharExceptionWhen 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().

std::string AbstractAlphabet::getName ( int  state) const
throw (BadIntException
)
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.

Parameters
stateThe int description of the given state.
Returns
The name of the state.
Exceptions
BadIntExceptionWhen state is not a valid integer.

Implements bpp::Alphabet.

Definition at line 171 of file AbstractAlphabet.cpp.

unsigned int bpp::AbstractAlphabet::getNumberOfChars ( ) const
inlinevirtualinherited

Get the number of supported characters in this alphabet, including generic characters (e.g. return 20 for DNA alphabet).

Returns
The total number of supported character descriptions.

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().

size_t bpp::AbstractAlphabet::getNumberOfStates ( ) const
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_.

unsigned int bpp::DefaultAlphabet::getNumberOfTypes ( ) const
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.

Returns
The number of distinct states.

Implements bpp::Alphabet.

Definition at line 88 of file DefaultAlphabet.h.

unsigned int bpp::DefaultAlphabet::getSize ( ) const
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.

Returns
The number of resolved states.

Implements bpp::Alphabet.

Definition at line 87 of file DefaultAlphabet.h.

const AlphabetState & AbstractAlphabet::getState ( const std::string &  letter) const
throw (BadCharException
)
virtualinherited

Get a state by its letter.

This method must be overloaded in specialized classes to send back a reference of the corect type.

Parameters
letterThe letter of the state to find.
Exceptions
BadCharExceptionIf 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().

AlphabetState & AbstractAlphabet::getState ( const std::string &  letter)
throw (BadCharException
)
inherited

Definition at line 130 of file AbstractAlphabet.cpp.

const AlphabetState & AbstractAlphabet::getState ( int  num) const
throw (BadIntException
)
virtualinherited

Get a state by its num.

This method must be overloaded in specialized classes to send back a reference of the corect type.

Parameters
numThe num of the state to find.
Exceptions
BadIntExceptionIf 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.

AlphabetState & AbstractAlphabet::getState ( int  num)
throw (BadIntException
)
inherited

Definition at line 139 of file AbstractAlphabet.cpp.

AlphabetState & AbstractAlphabet::getStateAt ( size_t  stateIndex)
throw (IndexOutOfBoundsException
)
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.

Parameters
stateIndexThe index of the state in the alphabet_ vector.
Exceptions
IndexOutOfBoundsExceptionIf 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().

const AlphabetState & AbstractAlphabet::getStateAt ( size_t  stateIndex) const
throw (IndexOutOfBoundsException
)
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.

Parameters
stateIndexThe index of the state in the alphabet_ vector.
Exceptions
IndexOutOfBoundsExceptionIf the index is invalid.

Implements bpp::Alphabet.

Reimplemented in bpp::NucleicAlphabet, bpp::NumericAlphabet, and bpp::ProteicAlphabet.

Definition at line 156 of file AbstractAlphabet.cpp.

unsigned int bpp::AbstractAlphabet::getStateCodingSize ( ) const
inlineprotectedvirtualinherited

Get the size of the string coding a state.

Returns
The size of the tring coding each states in the Alphabet.
Author
Sylvain Gaillard

Implements bpp::Alphabet.

Reimplemented in bpp::WordAlphabet.

Definition at line 266 of file AbstractAlphabet.h.

size_t AbstractAlphabet::getStateIndex ( int  state) const
throw (BadIntException
)
virtualinherited
Returns
The indices of the states with corresponding int code.

Implements bpp::Alphabet.

Definition at line 121 of file AbstractAlphabet.cpp.

Referenced by bpp::AAIndex2Entry::getIndex().

size_t AbstractAlphabet::getStateIndex ( const std::string &  state) const
throw (BadCharException
)
virtualinherited
Returns
The index of the state with corresponding char code.

Implements bpp::Alphabet.

Definition at line 103 of file AbstractAlphabet.cpp.

const std::vector< std::string > & AbstractAlphabet::getSupportedChars ( ) const
virtualinherited
Returns
A list of all supported character codes.

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().

const std::vector< int > & AbstractAlphabet::getSupportedInts ( ) const
virtualinherited
Returns
A list of all supported int codes.

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.

int bpp::DefaultAlphabet::getUnknownCharacterCode ( ) const
inlinevirtual
Returns
The int code for unknown characters.

Implements bpp::Alphabet.

Definition at line 90 of file DefaultAlphabet.h.

bool bpp::LetterAlphabet::isCharInAlphabet ( char  state) const
inlineinherited
bool bpp::LetterAlphabet::isCharInAlphabet ( const std::string &  state) const
inlinevirtualinherited

Tell if a state (specified by its string description) is allowed by the the alphabet.

Parameters
stateThe string description.
Returns
'true' if the state in known.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 90 of file LetterAlphabet.h.

References bpp::LetterAlphabet::isCharInAlphabet().

bool bpp::AbstractAlphabet::isGap ( int  state) const
inlinevirtualinherited
Parameters
stateThe state to test.
Returns
'True' if the state is a gap.

Implements bpp::Alphabet.

Reimplemented in bpp::RNY, and bpp::NumericAlphabet.

Definition at line 160 of file AbstractAlphabet.h.

bool bpp::AbstractAlphabet::isGap ( const std::string &  state) const
inlinevirtualinherited
Parameters
stateThe state to test.
Returns
'True' if the state is a gap.

Implements bpp::Alphabet.

Definition at line 161 of file AbstractAlphabet.h.

References bpp::AbstractAlphabet::charToInt().

bool AbstractAlphabet::isIntInAlphabet ( int  state) const
virtualinherited

Tell if a state (specified by its int description) is allowed by the the alphabet.

Parameters
stateThe int description.
Returns
'true' if the state in known.

Implements bpp::Alphabet.

Definition at line 192 of file AbstractAlphabet.cpp.

bool bpp::DefaultAlphabet::isUnresolved ( int  state) const
inlinevirtual
Parameters
stateThe state to test.
Returns
'True' if the state is unresolved.

Implements bpp::Alphabet.

Definition at line 91 of file DefaultAlphabet.h.

bool bpp::DefaultAlphabet::isUnresolved ( const std::string &  state) const
inlinevirtual
Parameters
stateThe state to test.
Returns
'True' if the state is unresolved.

Implements bpp::Alphabet.

Definition at line 92 of file DefaultAlphabet.h.

DefaultAlphabet& bpp::DefaultAlphabet::operator= ( const DefaultAlphabet bia)
inline

Definition at line 69 of file DefaultAlphabet.h.

References chars_, and bpp::LetterAlphabet::operator=().

void bpp::DefaultAlphabet::registerState ( AlphabetState st)
throw (Exception
)
inlineprotectedvirtual

Add a state to the Alphabet.

Parameters
stThe state to add.
Exceptions
ExceptionIf a wrong alphabet state is provided.

Reimplemented from bpp::AbstractAlphabet.

Definition at line 58 of file DefaultAlphabet.h.

References bpp::AbstractAlphabet::registerState().

Referenced by DefaultAlphabet().

void bpp::AbstractAlphabet::remap ( )
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().

void bpp::AbstractAlphabet::resize ( size_t  size)
inlineprotectedinherited

Resize the private alphabet_ vector.

Parameters
sizeThe new size of the Alphabet.

Definition at line 253 of file AbstractAlphabet.h.

References bpp::AbstractAlphabet::alphabet_.

Referenced by bpp::IntegerAlphabet::IntegerAlphabet().

void bpp::LetterAlphabet::setState ( size_t  pos,
AlphabetState st 
)
throw (Exception,
IndexOutOfBoundsException
)
inlineprotectedvirtualinherited

Set a state in the Alphabet.

Parameters
posThe index of the state in the alphabet_ vector.
stThe new state to put in the Alphabet.
Exceptions
ExceptionIf a wrong alphabet state is provided.
IndexOutOfBoundsExceptionIf an incorrect index is provided.

Reimplemented from bpp::AbstractAlphabet.

Reimplemented in bpp::NucleicAlphabet.

Definition at line 110 of file LetterAlphabet.h.

References bpp::LetterAlphabet::caseSensitive_, bpp::LetterAlphabet::letters_, and bpp::AbstractAlphabet::setState().

Referenced by bpp::NucleicAlphabet::setState().

Member Data Documentation

std::vector<std::string> bpp::AbstractAlphabet::charList_
mutableprotectedinherited

Definition at line 99 of file AbstractAlphabet.h.

Referenced by bpp::AbstractAlphabet::operator=().

std::string bpp::DefaultAlphabet::chars_
protected

Definition at line 61 of file DefaultAlphabet.h.

Referenced by DefaultAlphabet(), and operator=().

std::vector<int> bpp::AbstractAlphabet::intList_
mutableprotectedinherited

Definition at line 100 of file AbstractAlphabet.h.

Referenced by bpp::AbstractAlphabet::operator=().


The documentation for this class was generated from the following files: