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 |
| CSequence | compressS (const std::string &sequence) const |
| Sequence | decompress (const CSequence &sequence, const size_t seqLength) const |
| std::string | decompressS (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 __gnu_cxx::hash_map< std::string, AlphElem, hash_string > | STR2ALPH_MAP |
Private Attributes | |
| std::vector< std::string > | alph2string |
| std::vector< int > | compressBase |
| size_t | elementLength |
| STR2ALPH_MAP | string2alph |
Data Structures | |
| class | hash_string |
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 __gnu_cxx::hash_map< std::string, AlphElem, hash_string > biu::Alphabet::STR2ALPH_MAP [private] |
Definition at line 55 of file Alphabet.hh.
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.
| 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
| virtual biu::Alphabet::~Alphabet | ( | ) | [virtual] |
Member Function Documentation
| CSequence biu::Alphabet::compress | ( | const Alphabet::Sequence & | sequence | ) | const |
Compresses a sequence.
- Parameters:
-
sequence the sequence to compress
- Returns:
- the compressed sequence representation
| CSequence biu::Alphabet::compressS | ( | const std::string & | sequence | ) | const |
Compresses a string.
- Parameters:
-
sequence the string to compress
- Returns:
- the compressed sequence representation
Decompresses a sequence.
- Parameters:
-
sequence the sequence to decompress seqLength the length of the uncompressed sequence encoded
- Returns:
- the sequence that was compressed
| std::string biu::Alphabet::decompressS | ( | const CSequence & | sequence, | |
| const size_t | seqLength | |||
| ) | const |
Decompresses a sequence and generates directely a string.
- Parameters:
-
sequence the sequence to decompress seqLength the length of the uncompressed sequence encoded
- Returns:
- the string that was compressed
| size_t biu::Alphabet::getAlphabetSize | ( | ) | const |
Returns the size of the alphabet.
- Returns:
- the number of elements in the alphabet
| AlphElem biu::Alphabet::getElement | ( | const size_t | index | ) | const |
Returns the corresponding AlphElem to the index.
- Parameters:
-
index alphabet element index (has to be < getAlphabetSize())
- Returns:
- the indexed element
| AlphElem biu::Alphabet::getElement | ( | const std::string & | alphElemStr | ) | const |
Returns the index the alphabet member maps to.
- Parameters:
-
alphElemStr the string to encode
- Returns:
- internal representation of the alphabet element string
| size_t biu::Alphabet::getElementLength | ( | ) | const |
Returns the length of a alphabet element.
- Returns:
- the string length of one alphabet element
| 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()
- Parameters:
-
elemStr the alphabet element string to get the index for
- Returns:
- the index of this element
| size_t biu::Alphabet::getIndex | ( | const AlphElem & | elem | ) | const |
Returns the internal index of the AlphElem. The index starts with 0 and is < getAlphabetSize()
- Parameters:
-
elem the alphabet element to get the index for
- Returns:
- the index of this element
| Sequence biu::Alphabet::getSequence | ( | const std::string & | seqString | ) | const |
Returns an internal sequence representation of the string.
- Parameters:
-
seqString the string to encode
- Returns:
- the encoded sequence
| std::string biu::Alphabet::getString | ( | const Alphabet::AlphElem & | elem | ) | const |
Returns the string representation of the alphabet member.
- Parameters:
-
elem the internal alphabet element representation
- Returns:
- the string encoded by the element
| std::string biu::Alphabet::getString | ( | const Alphabet::Sequence & | sequence | ) | const |
Converts an internal sequence representation into a string.
- Parameters:
-
sequence the sequence to decode
- Returns:
- the string encoded by the sequence
| bool biu::Alphabet::isAlphabetSequence | ( | const Sequence & | seq | ) | const |
Returns whether or not a sequencec contains only elements compatible with the alphabet or not
- Parameters:
-
seq the sequence to check
- Returns:
- true if the sequence is valid for this alphabet, false otherwise
| bool biu::Alphabet::isAlphabetString | ( | const std::string & | str | ) | const |
Returns whether or not a string contains only elements of the alphabet or not
- Parameters:
-
str the string to check
- Returns:
- true if the string is valid for this alphabet, false otherwise
| bool biu::Alphabet::operator!= | ( | const Alphabet & | alph2 | ) | const |
| bool biu::Alphabet::operator== | ( | const Alphabet & | alph2 | ) | const |
Field Documentation
std::vector<std::string> biu::Alphabet::alph2string [private] |
a mapping from alphabet elements to their string representation
Definition at line 65 of file Alphabet.hh.
std::vector<int> biu::Alphabet::compressBase [private] |
Holds the multiplyer for the ith position of a sequence when compressed into a CSequence. Each CAlphElem can encode compressBase.size() many AlphElem elements.
Definition at line 73 of file Alphabet.hh.
size_t biu::Alphabet::elementLength [private] |
the length of a string representation of an alphabet element.
Definition at line 68 of file Alphabet.hh.
STR2ALPH_MAP biu::Alphabet::string2alph [private] |
a mapping from a string representation to the corresponding alphabet element
Definition at line 62 of file Alphabet.hh.
The documentation for this class was generated from the following file:
- src/biu/Alphabet.hh