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| DNASequence (const std::string &seq_name, const std::string &comment_, const std::string &seq, size_t seq_id=0) |
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| DNASequence (const std::string &seq_name, const std::string &comment_, unsigned int seq_length=0, size_t seq_id=0) |
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| DNASequence (const Sequence &seq) |
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char & | operator[] (unsigned int index) |
| Access operator. More...
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const char & | operator[] (unsigned int index) const |
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const std::string & | name () const |
| Returns the name of the sequence. More...
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void | name (const std::string &na) |
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const std::string & | sequence () const |
| Returns the sequence as a string. More...
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void | sequence (const std::string &seq) |
| Sets the sequence. More...
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const std::string & | comment () const |
| Returns the comment of a string. More...
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void | comment (const std::string &com) |
| Sets the comment. More...
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size_t | size () const |
| The length of the sequence. More...
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size_t | length () const |
| The length of the sequence. More...
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size_t | ungapped_size () const |
| The size of the sequence without gaps. More...
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size_t | id () const |
| Returns the sequence id of the sequence. More...
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void | id (size_t val) |
| Sets the id of the sequence. More...
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template<class T > |
void | append (const T &seq) |
| Appends a string to the sequence.
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void | append (const Sequence &seq) |
| Appends a string to the sequence.
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void | append (char c) |
| Appends a char to the sequence.
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void | resize (unsigned int new_length) |
| Resizes the sequence. More...
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void | to_upper () |
| Turns all charachters of the sequence to uppercase.
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void | to_lower () |
| Turns all characters of the sequence to lowercase.
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void | reverse () |
| Reverses the order of characters in the sequence.
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void | insert_gaps (const std::vector< std::pair< unsigned int, unsigned int > > vec) |
| Inserts gaps into the sequence. More...
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void | insert_gaps (const std::string &edit_string) |
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(Note that these are not member functions.)
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template<typename SequenceType > |
SequenceType | substr (const SequenceType &seq, size_t start, size_t length) |
| returns a new Sequence that is a substring of an existing one. More...
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template<typename SequenceType > |
SequenceType | substr_no_renaming (const SequenceType &seq, size_t start, size_t length) |
| returns a new Sequence that is a substring of an existing one. More...
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template<typename SequenceType > |
SequenceType * | substr_end (const SequenceType &seq, size_t start, size_t end) |
| returns a new Sequence that is a substring of an existing one. More...
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template<typename SequenceType > |
void | reverse_complement (SequenceType &seq) |
| Computes the reverse complement of a DNA sequence. More...
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template<typename SequenceTypeIn , typename SequenceTypeOut > |
SequenceTypeOut | dna2prot (const SequenceTypeIn &seq) |
| Turns a DNA sequence into a ProteinSequence. More...
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A special class for DNA sequences.