biu::Alphabet Class Reference
#include <Alphabet.hh>
Detailed Description
This class handels an alphabet for the sequence.Each member of the alphabet maps to an unique int index.
Definition at line 18 of file Alphabet.hh.
Public Types | |
| typedef size_t | AlphElem |
| typedef unsigned char | CAlphElem |
| typedef std::vector< CAlphElem > | CSequence |
| typedef std::vector< AlphElem > | Sequence |
Public Member Functions | |
| Alphabet (const std::vector< std::string > &alphabetStrings) | |
| Alphabet (const std::string &alphabetString, const size_t elementLength_) | |
| CSequence | compress (const Alphabet::Sequence &sequence) const |
| Sequence | decompress (const CSequence &sequence, const size_t seqLength) const |
| size_t | getAlphabetSize () const |
| AlphElem | getElement (const size_t index) const |
| AlphElem | getElement (const std::string &alphElemStr) const |
| size_t | getElementLength () const |
| size_t | getIndex (const std::string &elemStr) const |
| size_t | getIndex (const AlphElem &elem) const |
| Sequence | getSequence (const std::string &seqString) const |
| std::string | getString (const Alphabet::AlphElem &elem) const |
| std::string | getString (const Alphabet::Sequence &sequence) const |
| bool | isAlphabetSequence (const Sequence &seq) const |
| bool | isAlphabetString (const std::string &str) const |
| bool | operator!= (const Alphabet &alph2) const |
| bool | operator== (const Alphabet &alph2) const |
| virtual | ~Alphabet () |
Private Types | |
| typedef std::map< std::string, AlphElem > | STR2ALPH_TYPE |
Private Attributes | |
| std::vector< std::string > | alph2string |
| size_t | elementLength |
| STR2ALPH_TYPE | string2alph |
Member Typedef Documentation
| typedef size_t biu::Alphabet::AlphElem |
| typedef unsigned char biu::Alphabet::CAlphElem |
The internal representation of a compressed alphabet element.
Definition at line 24 of file Alphabet.hh.
| typedef std::vector<CAlphElem> biu::Alphabet::CSequence |
The internal representation of a compressed sequence of alphabet elements.
Definition at line 30 of file Alphabet.hh.
| typedef std::vector<AlphElem> biu::Alphabet::Sequence |
The internal representation of a sequence of alphabet elements.
Definition at line 27 of file Alphabet.hh.
typedef std::map<std::string, AlphElem> biu::Alphabet::STR2ALPH_TYPE [private] |
Constructor & Destructor Documentation
| biu::Alphabet::Alphabet | ( | const std::string & | alphabetString, | |
| const size_t | elementLength_ | |||
| ) |
Initialises an Alphabet object with the string representations given by the alphabetString. The string is members given in alphabetString.
The string it sliced into substrings of the length elementLength_ , therefor all alphabet elements have to have the same length.
Definition at line 9 of file Alphabet.cc.
| biu::Alphabet::Alphabet | ( | const std::vector< std::string > & | alphabetStrings | ) |
Construct an alphabet from a vector of strings
The indexing of elements in the vector has to be preserved by the alphabet
Definition at line 30 of file Alphabet.cc.
| biu::Alphabet::~Alphabet | ( | ) | [virtual] |
Definition at line 60 of file Alphabet.cc.
Member Function Documentation
| Alphabet::CSequence biu::Alphabet::compress | ( | const Alphabet::Sequence & | sequence | ) | const |
| Alphabet::Sequence biu::Alphabet::decompress | ( | const CSequence & | sequence, | |
| const size_t | seqLength | |||
| ) | const |
Decompresses a sequence.
- Parameters:
-
sequence the sequence to decompress seqLength the length of the uncompressed sequence encoded
Definition at line 171 of file Alphabet.cc.
| size_t biu::Alphabet::getAlphabetSize | ( | ) | const [inline] |
| Alphabet::AlphElem biu::Alphabet::getElement | ( | const size_t | index | ) | const |
Returns the corresponding AlphElem to the index.
- Parameters:
-
index has to be < getAlphabetSize()
Definition at line 144 of file Alphabet.cc.
| Alphabet::AlphElem biu::Alphabet::getElement | ( | const std::string & | alphElemStr | ) | const |
| size_t biu::Alphabet::getElementLength | ( | ) | const [inline] |
| size_t biu::Alphabet::getIndex | ( | const std::string & | elemStr | ) | const |
Returns the internal index of the AlphElem corresponding to the string. The index starts with 0 and is < getAlphabetSize()
Definition at line 139 of file Alphabet.cc.
| size_t biu::Alphabet::getIndex | ( | const AlphElem & | elem | ) | const |
Returns the internal index of the AlphElem. The index starts with 0 and is < getAlphabetSize()
Definition at line 134 of file Alphabet.cc.
| Alphabet::Sequence biu::Alphabet::getSequence | ( | const std::string & | seqString | ) | const |
Returns an internal sequence representation of the string.
Definition at line 80 of file Alphabet.cc.
| std::string biu::Alphabet::getString | ( | const Alphabet::AlphElem & | elem | ) | const |
Returns the string representation of the alphabet member.
Definition at line 107 of file Alphabet.cc.
| std::string biu::Alphabet::getString | ( | const Alphabet::Sequence & | sequence | ) | const |
Converts an internal sequence representation into a string.
Definition at line 94 of file Alphabet.cc.
| bool biu::Alphabet::isAlphabetSequence | ( | const Sequence & | seq | ) | const |
Returns whether or not a sequencec contains only elements compatible with the alphabet or not
Definition at line 199 of file Alphabet.cc.
| bool biu::Alphabet::isAlphabetString | ( | const std::string & | str | ) | const |
Returns whether or not a string contains only elements of the alphabet or not
Definition at line 122 of file Alphabet.cc.
| bool biu::Alphabet::operator!= | ( | const Alphabet & | alph2 | ) | const |
Definition at line 71 of file Alphabet.cc.
| bool biu::Alphabet::operator== | ( | const Alphabet & | alph2 | ) | const |
Definition at line 64 of file Alphabet.cc.
Field Documentation
std::vector<std::string> biu::Alphabet::alph2string [private] |
a mapping from alphabet elements to their string representation
Definition at line 42 of file Alphabet.hh.
size_t biu::Alphabet::elementLength [private] |
the length of a string representation of an alphabet element.
Definition at line 45 of file Alphabet.hh.
STR2ALPH_TYPE biu::Alphabet::string2alph [private] |
a mapping from a string representation to the corresponding alphabet element
Definition at line 39 of file Alphabet.hh.
The documentation for this class was generated from the following files:
- src/biu/Alphabet.hh
- src/biu/Alphabet.cc