#include <iostream>
+#include "alg/alphabet.hpp"
+
// Sequence data class
//! Attach annotation information to a sequence track
//! functions need the serialization support to be in-class.
class seq_string : public std::string
{
+public:
+ typedef std::string::iterator iterator;
+ typedef std::string::reverse_iterator reverse_iterator;
+ typedef std::string::const_iterator const_iterator;
+ typedef std::string::const_reverse_iterator const_reverse_iterator;
private:
friend class boost::serialization::access;
template<class Archive>
//ar & BOOST_SERIALIZATION_BASE_OBJECT_NVP(std::string);
ar & boost::serialization::make_nvp("bases",
boost::serialization::base_object<std::string>(*this)
- );
+ );
}
};
class Sequence
{
public:
+ typedef std::string::value_type value_type;
typedef std::string::difference_type difference_type;
typedef std::string::iterator iterator;
+ typedef std::string::reverse_iterator reverse_iterator;
typedef std::string::const_iterator const_iterator;
+ typedef std::string::const_reverse_iterator const_reverse_iterator;
typedef std::string::reference reference;
typedef std::string::const_reference const_reference;
typedef std::string::size_type size_type;
static const size_type npos = std::string::npos;
enum strand_type { UnknownStrand, PlusStrand, MinusStrand, BothStrand };
-
- // some standard dna alphabets
- // Include nl (\012), and cr (\015) to make sequence parsing eol
- // convention independent.
-
- static const std::string dna_alphabet;
- static const std::string rna_alphabet;
- //! this is the general iupac alphabet for nucleotides
- static const std::string nucleic_iupac_alphabet;
- //! the protein alphabet
- static const std::string protein_alphabet;
-
- Sequence();
- ~Sequence();
- Sequence(const char* seq);
- Sequence(const std::string& seq);
+ enum alphabet_ref { reduced_dna_alphabet, reduced_rna_alphabet, reduced_nucleic_alphabet,
+ nucleic_alphabet, protein_alphabet };
+
+ Sequence(alphabet_ref a = reduced_nucleic_alphabet);
+ Sequence(const char* seq, alphabet_ref a = reduced_nucleic_alphabet);
+ Sequence(const std::string& seq, alphabet_ref a = reduced_nucleic_alphabet);
Sequence(const Sequence& seq);
+ ~Sequence();
//! assignment to constant sequences
Sequence &operator=(const Sequence&);
friend std::ostream& operator<<(std::ostream&, const Sequence&);
friend bool operator<(const Sequence&, const Sequence&);
friend bool operator==(const Sequence&, const Sequence&);
+ friend bool operator!=(const Sequence&, const Sequence&);
const_reference operator[](size_type) const;
//! set sequence to a (sub)string containing nothing but AGCTN
- void set_filtered_sequence(const std::string& seq,
- size_type start=0,
- size_type count=npos,
+ void set_filtered_sequence(const std::string& seq,
+ alphabet_ref a,
+ size_type start=0,
+ size_type count=npos,
strand_type strand=UnknownStrand);
//! retrive element at specific position
//! return a subsequence, copying over any appropriate annotation
Sequence subseq(int start=0, int count = std::string::npos);
+ //! reverse a character
+ std::string create_reverse_map() const;
//! return a reverse compliment (this needs to be improved?)
- std::string rev_comp() const;
+ Sequence rev_comp() const;
//! set sequence (filtered)
- void set_sequence(const std::string &);
+ void set_sequence(const std::string &, alphabet_ref);
//! get sequence
std::string get_sequence() const;
//! set species name
std::string get_fasta_header() const;
//! get name (will return the first non-empty, of fasta_header, species)
std::string get_name() const;
+ //! return a reference to whichever alphabet we're currently representing
+ const Alphabet& get_alphabet() const;
+ //! return a reference to whichever alphabet we're currently representing
+ const Alphabet& get_alphabet(alphabet_ref) const;
+ //! load sequence from fasta file using the sequences current alphabet
+ void load_fasta(const boost::filesystem::path file_path, int seq_num=1,
+ int start_index=0, int end_index=0);
//! load sequence AGCT from fasta file
//! \throw mussa_load_error
//! \throw sequence_empty_error
//! \throw sequence_empty_file_error
- void load_fasta(const boost::filesystem::path file_path, int seq_num=1,
- int start_index=0, int end_index=0);
+ void load_fasta(const boost::filesystem::path file_path,
+ alphabet_ref a,
+ int seq_num=1,
+ int start_index=0, int end_index=0);
+ void load_fasta(std::iostream& file,
+ int seq_num=1, int start_index=0, int end_index=0);
//! load sequence from stream
//! \throw mussa_load_error
//! \throw sequence_empty_error
//! \throw sequence_empty_file_error
- void load_fasta(std::iostream& file, int seq_num=1,
- int start_index=0, int end_index=0);
+ void load_fasta(std::iostream& file,
+ alphabet_ref a,
+ int seq_num=1,
+ int start_index=0, int end_index=0);
//! load sequence annotations
//! \throws mussa_load_error
void load_annot(const boost::filesystem::path file_path, int start_index, int end_index);
const std::list<motif>& motifs() const;
//! add a motif to our list of motifs
- //! \throws motif_normalize_error if there's something wrong with a_motif
void add_motif(const Sequence& a_motif);
//! clear our list of found motifs
void clear_motifs();
//! search a sequence for a_motif
//! \throws motif_normalize_error if there's something wrong with a_motif
- std::vector<int> find_motif(const std::string& a_motif) const;
- //! search a sequence for a_motif
- //! \throws motif_normalize_error if there's something wrong with a_motif
- std::vector<int> find_motif(const Sequence& a_motif) const;
- //! convert IUPAC symbols to upperase
- //! \throws motif_normalize_error if there is an invalid symbol
- static std::string motif_normalize(const std::string& a_motif);
-
+ std::vector<int> find_motif(const Sequence& a_motif) const;
//! annotate the current sequence with other sequences
void find_sequences(std::list<Sequence>::iterator start,
std::list<Sequence>::iterator end);
Sequence *parent;
//! hold a shared pointer to our sequence string
boost::shared_ptr<seq_string> seq;
+ //! which alphabet we're using
+ alphabet_ref alphabet;
//! start offset into the sequence
size_type seq_start;
//! number of basepairs of the shared sequence we represent
//! a seperate list for motifs since we're currently not saving them
std::list<motif> motif_list;
- void motif_scan(std::string a_motif, std::vector<int> * motif_match_starts) const;
+ void motif_scan(const Sequence& a_motif, std::vector<int> * motif_match_starts) const;
std::string rc_motif(std::string a_motif) const;
//! look for a string sequence type and and it to an annotation list
void add_string_annotation(std::string a_seq, std::string name);
void serialize(Archive& ar, const unsigned int /*version*/) {
ar & BOOST_SERIALIZATION_NVP(parent);
ar & BOOST_SERIALIZATION_NVP(seq);
+ ar & BOOST_SERIALIZATION_NVP(alphabet);
ar & BOOST_SERIALIZATION_NVP(seq_start);
ar & BOOST_SERIALIZATION_NVP(seq_count);
ar & BOOST_SERIALIZATION_NVP(strand);
projects / mussa.git / blobdiff